Daily Papers

Graph Neural Networks (GNNs) with numerical node features and graph structure as inputs have demonstrated superior performance on various supervised learning tasks with graph data. However the numerical node features utilized by GNNs are commonly extracted from raw data which is of text or tabular (numeric/categorical) type in most real-world applications. The best models for such data types in most standard supervised learning settings with IID (non-graph) data are not simple neural network layers and thus are not easily incorporated into a GNN. Here we propose a robust stacking framework that fuses graph-aware propagation with arbitrary models intended for IID data, which are ensembled and stacked in multiple layers. Our layer-wise framework leverages bagging and stacking strategies to enjoy strong generalization, in a manner which effectively mitigates label leakage and overfitting. Across a variety of graph datasets with tabular/text node features, our method achieves comparable or superior performance relative to both tabular/text and graph neural network models, as well as existing state-of-the-art hybrid strategies that combine the two.

Foundation Models (FMs) serve as a general class for the development of artificial intelligence systems, offering broad potential for generalization across a spectrum of downstream tasks. Despite extensive research into self-supervised learning as the cornerstone of FMs, several outstanding issues persist in Graph Foundation Models that rely on graph self-supervised learning, namely: 1) Homogenization. The extent of generalization capability on downstream tasks remains unclear. 2) Scalability. It is unknown how effectively these models can scale to large datasets. 3) Efficiency. The training time and memory usage of these models require evaluation. 4) Training Stop Criteria. Determining the optimal stopping strategy for pre-training across multiple tasks to maximize performance on downstream tasks. To address these questions, we have constructed a rigorous benchmark that thoroughly analyzes and studies the generalization and scalability of self-supervised Graph Neural Network (GNN) models. Regarding generalization, we have implemented and compared the performance of various self-supervised GNN models, trained to generate node representations, across tasks such as node classification, link prediction, and node clustering. For scalability, we have compared the performance of various models after training using full-batch and mini-batch strategies. Additionally, we have assessed the training efficiency of these models by conducting experiments to test their GPU memory usage and throughput. Through these experiments, we aim to provide insights to motivate future research. The code for this benchmark is publicly available at https://github.com/NYUSHCS/GraphFM.

We introduce a new molecular dataset, named Alchemy, for developing machine learning models useful in chemistry and material science. As of June 20th 2019, the dataset comprises of 12 quantum mechanical properties of 119,487 organic molecules with up to 14 heavy atoms, sampled from the GDB MedChem database. The Alchemy dataset expands the volume and diversity of existing molecular datasets. Our extensive benchmarks of the state-of-the-art graph neural network models on Alchemy clearly manifest the usefulness of new data in validating and developing machine learning models for chemistry and material science. We further launch a contest to attract attentions from researchers in the related fields. More details can be found on the contest website https://alchemy.tencent.com. At the time of benchamrking experiment, we have generated 119,487 molecules in our Alchemy dataset. More molecular samples are generated since then. Hence, we provide a list of molecules used in the reported benchmarks.

For supervised learning with tabular data, decision tree ensembles produced via boosting techniques generally dominate real-world applications involving iid training/test sets. However for graph data where the iid assumption is violated due to structured relations between samples, it remains unclear how to best incorporate this structure within existing boosting pipelines. To this end, we propose a generalized framework for iterating boosting with graph propagation steps that share node/sample information across edges connecting related samples. Unlike previous efforts to integrate graph-based models with boosting, our approach is anchored in a principled meta loss function such that provable convergence can be guaranteed under relatively mild assumptions. Across a variety of non-iid graph datasets with tabular node features, our method achieves comparable or superior performance than both tabular and graph neural network models, as well as existing hybrid strategies that combine the two. Beyond producing better predictive performance than recently proposed graph models, our proposed techniques are easy to implement, computationally more efficient, and enjoy stronger theoretical guarantees (which make our results more reproducible).

Most graph neural network models learn embeddings of nodes in static attributed graphs for predictive analysis. Recent attempts have been made to learn temporal proximity of the nodes. We find that real dynamic attributed graphs exhibit complex co-evolution of node attributes and graph structure. Learning node embeddings for forecasting change of node attributes and birth and death of links over time remains an open problem. In this work, we present a novel framework called CoEvoGNN for modeling dynamic attributed graph sequence. It preserves the impact of earlier graphs on the current graph by embedding generation through the sequence. It has a temporal self-attention mechanism to model long-range dependencies in the evolution. Moreover, CoEvoGNN optimizes model parameters jointly on two dynamic tasks, attribute inference and link prediction over time. So the model can capture the co-evolutionary patterns of attribute change and link formation. This framework can adapt to any graph neural algorithms so we implemented and investigated three methods based on it: CoEvoGCN, CoEvoGAT, and CoEvoSAGE. Experiments demonstrate the framework (and its methods) outperform strong baselines on predicting an entire unseen graph snapshot of personal attributes and interpersonal links in dynamic social graphs and financial graphs.

It is now possible to reconstruct dynamic human motion and shape from a sparse set of cameras using Neural Radiance Fields (NeRF) driven by an underlying skeleton. However, a challenge remains to model the deformation of cloth and skin in relation to skeleton pose. Unlike existing avatar models that are learned implicitly or rely on a proxy surface, our approach is motivated by the observation that different poses necessitate unique frequency assignments. Neglecting this distinction yields noisy artifacts in smooth areas or blurs fine-grained texture and shape details in sharp regions. We develop a two-branch neural network that is adaptive and explicit in the frequency domain. The first branch is a graph neural network that models correlations among body parts locally, taking skeleton pose as input. The second branch combines these correlation features to a set of global frequencies and then modulates the feature encoding. Our experiments demonstrate that our network outperforms state-of-the-art methods in terms of preserving details and generalization capabilities.

Catalyst discovery and optimization is key to solving many societal and energy challenges including solar fuels synthesis, long-term energy storage, and renewable fertilizer production. Despite considerable effort by the catalysis community to apply machine learning models to the computational catalyst discovery process, it remains an open challenge to build models that can generalize across both elemental compositions of surfaces and adsorbate identity/configurations, perhaps because datasets have been smaller in catalysis than related fields. To address this we developed the OC20 dataset, consisting of 1,281,040 Density Functional Theory (DFT) relaxations (~264,890,000 single point evaluations) across a wide swath of materials, surfaces, and adsorbates (nitrogen, carbon, and oxygen chemistries). We supplemented this dataset with randomly perturbed structures, short timescale molecular dynamics, and electronic structure analyses. The dataset comprises three central tasks indicative of day-to-day catalyst modeling and comes with pre-defined train/validation/test splits to facilitate direct comparisons with future model development efforts. We applied three state-of-the-art graph neural network models (CGCNN, SchNet, Dimenet++) to each of these tasks as baseline demonstrations for the community to build on. In almost every task, no upper limit on model size was identified, suggesting that even larger models are likely to improve on initial results. The dataset and baseline models are both provided as open resources, as well as a public leader board to encourage community contributions to solve these important tasks.

As Chile's electric power sector advances toward a future powered by renewable energy, accurate forecasting of renewable generation is essential for managing grid operations. The integration of renewable energy sources is particularly challenging due to the operational difficulties of managing their power generation, which is highly variable compared to fossil fuel sources, delaying the availability of clean energy. To mitigate this, we quantify the impact of increasing intermittent generation from wind and solar on thermal power plants in Chile and introduce a hybrid wind speed forecasting methodology which combines two custom ML models for Chile. The first model is based on TiDE, an MLP-based ML model for short-term forecasts, and the second is based on a graph neural network, GraphCast, for medium-term forecasts up to 10 days. Our hybrid approach outperforms the most accurate operational deterministic systems by 4-21% for short-term forecasts and 5-23% for medium-term forecasts and can directly lower the impact of wind generation on thermal ramping, curtailment, and system-level emissions in Chile.

Large language models (LLMs) such as generative pretrained transformers (GPTs) have shown potential for various commercial applications, but their applicability for materials design remains underexplored. In this article, we introduce AtomGPT, a model specifically developed for materials design based on transformer architectures, to demonstrate the capability for both atomistic property prediction and structure generation. We show that a combination of chemical and structural text descriptions can efficiently predict material properties with accuracy comparable to graph neural network models, including formation energies, electronic bandgaps from two different methods and superconducting transition temperatures. Furthermore, we demonstrate that AtomGPT can generate atomic structures for tasks such as designing new superconductors, with the predictions validated through density functional theory calculations. This work paves the way for leveraging LLMs in forward and inverse materials design, offering an efficient approach to the discovery and optimization of materials.

The Machine Learning for Combinatorial Optimization (ML4CO) NeurIPS 2021 competition aims to improve state-of-the-art combinatorial optimization solvers by replacing key heuristic components with machine learning models. On the dual task, we design models to make branching decisions to promote the dual bound increase faster. We propose a knowledge inheritance method to generalize knowledge of different models from the dataset aggregation process, named KIDA. Our improvement overcomes some defects of the baseline graph-neural-networks-based methods. Further, we won the 1st Place on the dual task. We hope this report can provide useful experience for developers and researchers. The code is available at https://github.com/megvii-research/NeurIPS2021-ML4CO-KIDA.

In this work, we present the ChemNLP library that can be used for 1) curating open access datasets for materials and chemistry literature, developing and comparing traditional machine learning, transformers and graph neural network models for 2) classifying and clustering texts, 3) named entity recognition for large-scale text-mining, 4) abstractive summarization for generating titles of articles from abstracts, 5) text generation for suggesting abstracts from titles, 6) integration with density functional theory dataset for identifying potential candidate materials such as superconductors, and 7) web-interface development for text and reference query. We primarily use the publicly available arXiv and Pubchem datasets but the tools can be used for other datasets as well. Moreover, as new models are developed, they can be easily integrated in the library. ChemNLP is available at the websites: https://github.com/usnistgov/chemnlp and https://jarvis.nist.gov/jarvischemnlp.

Non-Fungible Tokens (NFTs) represent deeds of ownership, based on blockchain technologies and smart contracts, of unique crypto assets on digital art forms (e.g., artworks or collectibles). In the spotlight after skyrocketing in 2021, NFTs have attracted the attention of crypto enthusiasts and investors intent on placing promising investments in this profitable market. However, the NFT financial performance prediction has not been widely explored to date. In this work, we address the above problem based on the hypothesis that NFT images and their textual descriptions are essential proxies to predict the NFT selling prices. To this purpose, we propose MERLIN, a novel multimodal deep learning framework designed to train Transformer-based language and visual models, along with graph neural network models, on collections of NFTs' images and texts. A key aspect in MERLIN is its independence on financial features, as it exploits only the primary data a user interested in NFT trading would like to deal with, i.e., NFT images and textual descriptions. By learning dense representations of such data, a price-category classification task is performed by MERLIN models, which can also be tuned according to user preferences in the inference phase to mimic different risk-return investment profiles. Experimental evaluation on a publicly available dataset has shown that MERLIN models achieve significant performances according to several financial assessment criteria, fostering profitable investments, and also beating baseline machine-learning classifiers based on financial features.

Node features and structural information of a graph are both crucial for semi-supervised node classification problems. A variety of graph neural network (GNN) based approaches have been proposed to tackle these problems, which typically determine output labels through feature aggregation. This can be problematic, as it implies conditional independence of output nodes given hidden representations, despite their direct connections in the graph. To learn the direct influence among output nodes in a graph, we propose the Explicit Pairwise Factorized Graph Neural Network (EPFGNN), which models the whole graph as a partially observed Markov Random Field. It contains explicit pairwise factors to model output-output relations and uses a GNN backbone to model input-output relations. To balance model complexity and expressivity, the pairwise factors have a shared component and a separate scaling coefficient for each edge. We apply the EM algorithm to train our model, and utilize a star-shaped piecewise likelihood for the tractable surrogate objective. We conduct experiments on various datasets, which shows that our model can effectively improve the performance for semi-supervised node classification on graphs.

The advent of the "pre-train, prompt" paradigm has recently extended its generalization ability and data efficiency to graph representation learning, following its achievements in Natural Language Processing (NLP). Initial graph prompt tuning approaches tailored specialized prompting functions for Graph Neural Network (GNN) models pre-trained with specific strategies, such as edge prediction, thus limiting their applicability. In contrast, another pioneering line of research has explored universal prompting via adding prompts to the input graph's feature space, thereby removing the reliance on specific pre-training strategies. However, the necessity to add feature prompts to all nodes remains an open question. Motivated by findings from prompt tuning research in the NLP domain, which suggest that highly capable pre-trained models need less conditioning signal to achieve desired behaviors, we advocate for strategically incorporating necessary and lightweight feature prompts to certain graph nodes to enhance downstream task performance. This introduces a combinatorial optimization problem, requiring a policy to decide 1) which nodes to prompt and 2) what specific feature prompts to attach. We then address the problem by framing the prompt incorporation process as a sequential decision-making problem and propose our method, RELIEF, which employs Reinforcement Learning (RL) to optimize it. At each step, the RL agent selects a node (discrete action) and determines the prompt content (continuous action), aiming to maximize cumulative performance gain. Extensive experiments on graph and node-level tasks with various pre-training strategies in few-shot scenarios demonstrate that our RELIEF outperforms fine-tuning and other prompt-based approaches in classification performance and data efficiency.

We present Simplified Text-Attributed Graph Embeddings (STAGE), a straightforward yet effective method for enhancing node features in Graph Neural Network (GNN) models that encode Text-Attributed Graphs (TAGs). Our approach leverages Large-Language Models (LLMs) to generate embeddings for textual attributes. STAGE achieves competitive results on various node classification benchmarks while also maintaining a simplicity in implementation relative to current state-of-the-art (SoTA) techniques. We show that utilizing pre-trained LLMs as embedding generators provides robust features for ensemble GNN training, enabling pipelines that are simpler than current SoTA approaches which require multiple expensive training and prompting stages. We also implement diffusion-pattern GNNs in an effort to make this pipeline scalable to graphs beyond academic benchmarks.

Understanding political polarization on social platforms is important as public opinions may become increasingly extreme when they are circulated in homogeneous communities, thus potentially causing damage in the real world. Automatically detecting the political ideology of social media users can help better understand political polarization. However, it is challenging due to the scarcity of ideology labels, complexity of multimodal contents, and cost of time-consuming data collection process. In this study, we adopt a heterogeneous graph neural network to jointly model user characteristics, multimodal post contents as well as user-item relations in a bipartite graph to learn a comprehensive and effective user embedding without requiring ideology labels. We apply our framework to online discussions about economy and public health topics. The learned embeddings are then used to detect political ideology and understand political polarization. Our framework outperforms the unimodal, early/late fusion baselines, and homogeneous GNN frameworks by a margin of at least 9% absolute gain in the area under the receiver operating characteristic on two social media datasets. More importantly, our work does not require a time-consuming data collection process, which allows faster detection and in turn allows the policy makers to conduct analysis and design policies in time to respond to crises. We also show that our framework learns meaningful user embeddings and can help better understand political polarization. Notable differences in user descriptions, topics, images, and levels of retweet/quote activities are observed. Our framework for decoding user-content interaction shows wide applicability in understanding political polarization. Furthermore, it can be extended to user-item bipartite information networks for other applications such as content and product recommendation.

Recently, many mesh-based graph neural network (GNN) models have been proposed for modeling complex high-dimensional physical systems. Remarkable achievements have been made in significantly reducing the solving time compared to traditional numerical solvers. These methods are typically designed to i) reduce the computational cost in solving physical dynamics and/or ii) propose techniques to enhance the solution accuracy in fluid and rigid body dynamics. However, it remains under-explored whether they are effective in addressing the challenges of flexible body dynamics, where instantaneous collisions occur within a very short timeframe. In this paper, we present Hierarchical Contact Mesh Transformer (HCMT), which uses hierarchical mesh structures and can learn long-range dependencies (occurred by collisions) among spatially distant positions of a body -- two close positions in a higher-level mesh correspond to two distant positions in a lower-level mesh. HCMT enables long-range interactions, and the hierarchical mesh structure quickly propagates collision effects to faraway positions. To this end, it consists of a contact mesh Transformer and a hierarchical mesh Transformer (CMT and HMT, respectively). Lastly, we propose a flexible body dynamics dataset, consisting of trajectories that reflect experimental settings frequently used in the display industry for product designs. We also compare the performance of several baselines using well-known benchmark datasets. Our results show that HCMT provides significant performance improvements over existing methods. Our code is available at https://github.com/yuyudeep/hcmt.

We present RelBench, a public benchmark for solving predictive tasks over relational databases with graph neural networks. RelBench provides databases and tasks spanning diverse domains and scales, and is intended to be a foundational infrastructure for future research. We use RelBench to conduct the first comprehensive study of Relational Deep Learning (RDL) (Fey et al., 2024), which combines graph neural network predictive models with (deep) tabular models that extract initial entity-level representations from raw tables. End-to-end learned RDL models fully exploit the predictive signal encoded in primary-foreign key links, marking a significant shift away from the dominant paradigm of manual feature engineering combined with tabular models. To thoroughly evaluate RDL against this prior gold-standard, we conduct an in-depth user study where an experienced data scientist manually engineers features for each task. In this study, RDL learns better models whilst reducing human work needed by more than an order of magnitude. This demonstrates the power of deep learning for solving predictive tasks over relational databases, opening up many new research opportunities enabled by RelBench.

Online social media works as a source of various valuable and actionable information during disasters. These information might be available in multiple languages due to the nature of user generated content. An effective system to automatically identify and categorize these actionable information should be capable to handle multiple languages and under limited supervision. However, existing works mostly focus on English language only with the assumption that sufficient labeled data is available. To overcome these challenges, we propose a multilingual disaster related text classification system which is capable to work under \{mono, cross and multi\} lingual scenarios and under limited supervision. Our end-to-end trainable framework combines the versatility of graph neural networks, by applying over the corpus, with the power of transformer based large language models, over examples, with the help of cross-attention between the two. We evaluate our framework over total nine English, Non-English and monolingual datasets in \{mono, cross and multi\} lingual classification scenarios. Our framework outperforms state-of-the-art models in disaster domain and multilingual BERT baseline in terms of Weighted F_1 score. We also show the generalizability of the proposed model under limited supervision.

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.

Foundation models, or large atomistic models (LAMs), aim to universally represent the ground-state potential energy surface (PES) of atomistic systems as defined by density functional theory (DFT). The scaling law is pivotal in the development of large models, suggesting that their generalizability in downstream tasks consistently improves with increased model size, expanded training datasets, and larger computational budgets. In this study, we present DPA3, a multi-layer graph neural network founded on line graph series (LiGS), designed explicitly for the era of LAMs. We demonstrate that the generalization error of the DPA3 model adheres to the scaling law. The scalability in the number of model parameters is attained by stacking additional layers within DPA3. Additionally, the model employs a dataset encoding mechanism that decouples the scaling of training data size from the model size within its multi-task training framework. When trained as problem-oriented potential energy models, the DPA3 model exhibits superior accuracy in the majority of benchmark cases, encompassing systems with diverse features, including molecules, bulk materials, surface and cluster catalysts, two-dimensional materials, and battery materials. When trained as a LAM on the OpenLAM-v1 dataset, the DPA-3.1-3M model exhibits state-of-the-art performance in the LAMBench benchmark suite for LAMs, demonstrating lowest overall zero-shot generalization error across 17 downstream tasks from a broad spectrum of research domains. This performance suggests superior accuracy as an out-of-the-box potential model, requiring minimal fine-tuning data for downstream scientific applications.

Machine learning (ML) and deep learning (DL) techniques have gained significant attention as reduced order models (ROMs) to computationally expensive structural analysis methods, such as finite element analysis (FEA). Graph neural network (GNN) is a particular type of neural network which processes data that can be represented as graphs. This allows for efficient representation of complex geometries that can change during conceptual design of a structure or a product. In this study, we propose a novel graph embedding technique for efficient representation of 3D stiffened panels by considering separate plate domains as vertices. This approach is considered using Graph Sampling and Aggregation (GraphSAGE) to predict stress distributions in stiffened panels with varying geometries. A comparison between a finite-element-vertex graph representation is conducted to demonstrate the effectiveness of the proposed approach. A comprehensive parametric study is performed to examine the effect of structural geometry on the prediction performance. Our results demonstrate the immense potential of graph neural networks with the proposed graph embedding method as robust reduced-order models for 3D structures.

Deep neural networks (DNN) can approximate value functions or policies for reinforcement learning, which makes the reinforcement learning algorithms more powerful. However, some DNNs, such as convolutional neural networks (CNN), cannot extract enough information or take too long to obtain enough features from the inputs under specific circumstances of reinforcement learning. For example, the input data of Google Research Football, a reinforcement learning environment which trains agents to play football, is the small map of players' locations. The information is contained not only in the coordinates of players, but also in the relationships between different players. CNNs can neither extract enough information nor take too long to train. To address this issue, this paper proposes a deep q-learning network (DQN) with a graph neural network (GNN) as its model. The GNN transforms the input data into a graph which better represents the football players' locations so that it extracts more information of the interactions between different players. With two GNNs to approximate its local and target value functions, this DQN allows players to learn from their experience by using value functions to see the prospective value of each intended action. The proposed model demonstrated the power of GNN in the football game by outperforming other DRL models with significantly fewer steps.

Large Language Models (LLMs) have shown remarkable generalization capability with exceptional performance in various language modeling tasks. However, they still exhibit inherent limitations in precisely capturing and returning grounded knowledge. While existing work has explored utilizing knowledge graphs to enhance language modeling via joint training and customized model architectures, applying this to LLMs is problematic owing to their large number of parameters and high computational cost. In addition, how to leverage the pre-trained LLMs and avoid training a customized model from scratch remains an open question. In this work, we propose Graph Neural Prompting (GNP), a novel plug-and-play method to assist pre-trained LLMs in learning beneficial knowledge from KGs. GNP encompasses various designs, including a standard graph neural network encoder, a cross-modality pooling module, a domain projector, and a self-supervised link prediction objective. Extensive experiments on multiple datasets demonstrate the superiority of GNP on both commonsense and biomedical reasoning tasks across different LLM sizes and settings.

We present an end-to-end deep learning segmentation method by combining a 3D UNet architecture with a graph neural network (GNN) model. In this approach, the convolutional layers at the deepest level of the UNet are replaced by a GNN-based module with a series of graph convolutions. The dense feature maps at this level are transformed into a graph input to the GNN module. The incorporation of graph convolutions in the UNet provides nodes in the graph with information that is based on node connectivity, in addition to the local features learnt through the downsampled paths. This information can help improve segmentation decisions. By stacking several graph convolution layers, the nodes can access higher order neighbourhood information without substantial increase in computational expense. We propose two types of node connectivity in the graph adjacency: i) one predefined and based on a regular node neighbourhood, and ii) one dynamically computed during training and using the nearest neighbour nodes in the feature space. We have applied this method to the task of segmenting the airway tree from chest CT scans. Experiments have been performed on 32 CTs from the Danish Lung Cancer Screening Trial dataset. We evaluate the performance of the UNet-GNN models with two types of graph adjacency and compare it with the baseline UNet.

Despite recent community revelations about the advancements and potential applications of Large Language Models (LLMs) in understanding Text-Attributed Graph (TAG), the deployment of LLMs for production is hindered by its high computational and storage requirements, as well as long latencies during model inference. Simultaneously, although traditional Graph Neural Networks (GNNs) are light weight and adept at learning structural features of graphs, their ability to grasp the complex semantics in TAG is somewhat constrained for real applications. To address these limitations, we concentrate on the downstream task of node classification in TAG and propose a novel graph knowledge distillation framework, termed Linguistic Graph Knowledge Distillation (LinguGKD), using LLMs as teacher models and GNNs as student models for knowledge distillation. It involves TAG-oriented instruction tuning of LLM on designed tailored prompts, followed by propagating knowledge and aligning the hierarchically learned node features from the teacher LLM to the student GNN in latent space, employing a layer-adaptive contrastive learning strategy. Through extensive experiments on a variety of LLM and GNN models and multiple benchmark datasets, the proposed LinguGKD significantly boosts the student GNN's predictive accuracy and convergence rate, without the need of extra data or model parameters. Compared to teacher LLM, distilled GNN achieves superior inference speed equipped with much fewer computing and storage demands, when surpassing the teacher LLM's classification accuracy on some of benchmark datasets.

Recent research on integrating Large Language Models (LLMs) with Graph Neural Networks (GNNs) typically follows two approaches: LLM-centered models, which convert graph data into tokens for LLM processing, and GNN-centered models, which use LLMs to encode text features into node and edge representations for GNN input. LLM-centered models often struggle to capture graph structures effectively, while GNN-centered models compress variable-length textual data into fixed-size vectors, limiting their ability to understand complex semantics. Additionally, GNN-centered approaches require converting tasks into a uniform, manually-designed format, restricting them to classification tasks and preventing language output. To address these limitations, we introduce a new architecture that deeply integrates GNN with LLM, featuring three key innovations: (1) Structure-Aware Transformers, which incorporate GNN's message-passing capabilities directly into LLM's transformer layers, allowing simultaneous processing of textual and structural information and generating outputs from both GNN and LLM; (2) Graph-Text Cross-Attention, which processes full, uncompressed text from graph nodes and edges, ensuring complete semantic integration; and (3) GNN-LLM Twin Predictor, enabling LLM's flexible autoregressive generation alongside GNN's scalable one-pass prediction. GL-Fusion achieves outstand performance on various tasks. Notably, it achieves state-of-the-art performance on OGBN-Arxiv and OGBG-Code2.

Recent prevailing works on graph machine learning typically follow a similar methodology that involves designing advanced variants of graph neural networks (GNNs) to maintain the superior performance of GNNs on different graphs. In this paper, we aim to streamline the GNN design process and leverage the advantages of Large Language Models (LLMs) to improve the performance of GNNs on downstream tasks. We formulate a new paradigm, coined "LLMs-as-Consultants," which integrates LLMs with GNNs in an interactive manner. A framework named LOGIN (LLM Consulted GNN training) is instantiated, empowering the interactive utilization of LLMs within the GNN training process. First, we attentively craft concise prompts for spotted nodes, carrying comprehensive semantic and topological information, and serving as input to LLMs. Second, we refine GNNs by devising a complementary coping mechanism that utilizes the responses from LLMs, depending on their correctness. We empirically evaluate the effectiveness of LOGIN on node classification tasks across both homophilic and heterophilic graphs. The results illustrate that even basic GNN architectures, when employed within the proposed LLMs-as-Consultants paradigm, can achieve comparable performance to advanced GNNs with intricate designs. Our codes are available at https://github.com/QiaoYRan/LOGIN.

Over the past few years, neural networks have re-emerged as powerful machine-learning models, yielding state-of-the-art results in fields such as image recognition and speech processing. More recently, neural network models started to be applied also to textual natural language signals, again with very promising results. This tutorial surveys neural network models from the perspective of natural language processing research, in an attempt to bring natural-language researchers up to speed with the neural techniques. The tutorial covers input encoding for natural language tasks, feed-forward networks, convolutional networks, recurrent networks and recursive networks, as well as the computation graph abstraction for automatic gradient computation.

Graph representation learning has emerged as a powerful technique for addressing real-world problems. Various downstream graph learning tasks have benefited from its recent developments, such as node classification, similarity search, and graph classification. However, prior arts on graph representation learning focus on domain specific problems and train a dedicated model for each graph dataset, which is usually non-transferable to out-of-domain data. Inspired by the recent advances in pre-training from natural language processing and computer vision, we design Graph Contrastive Coding (GCC) -- a self-supervised graph neural network pre-training framework -- to capture the universal network topological properties across multiple networks. We design GCC's pre-training task as subgraph instance discrimination in and across networks and leverage contrastive learning to empower graph neural networks to learn the intrinsic and transferable structural representations. We conduct extensive experiments on three graph learning tasks and ten graph datasets. The results show that GCC pre-trained on a collection of diverse datasets can achieve competitive or better performance to its task-specific and trained-from-scratch counterparts. This suggests that the pre-training and fine-tuning paradigm presents great potential for graph representation learning.

Post-Training Quantization (PTQ) is pivotal for deploying large language models (LLMs) within resource-limited settings by significantly reducing resource demands. However, existing PTQ strategies underperform at low bit levels < 3 bits due to the significant difference between the quantized and original weights. To enhance the quantization performance at low bit widths, we introduce a Mixed-precision Graph Neural PTQ (MG-PTQ) approach, employing a graph neural network (GNN) module to capture dependencies among weights and adaptively assign quantization bit-widths. Through the information propagation of the GNN module, our method more effectively captures dependencies among target weights, leading to a more accurate assessment of weight importance and optimized allocation of quantization strategies. Extensive experiments on the WikiText2 and C4 datasets demonstrate that our MG-PTQ method outperforms previous state-of-the-art PTQ method GPTQ, setting new benchmarks for quantization performance under low-bit conditions.

While deep learning models have achieved state-of-the-art accuracies for many prediction tasks, understanding these models remains a challenge. Despite the recent interest in developing visual tools to help users interpret deep learning models, the complexity and wide variety of models deployed in industry, and the large-scale datasets that they used, pose unique design challenges that are inadequately addressed by existing work. Through participatory design sessions with over 15 researchers and engineers at Facebook, we have developed, deployed, and iteratively improved ActiVis, an interactive visualization system for interpreting large-scale deep learning models and results. By tightly integrating multiple coordinated views, such as a computation graph overview of the model architecture, and a neuron activation view for pattern discovery and comparison, users can explore complex deep neural network models at both the instance- and subset-level. ActiVis has been deployed on Facebook's machine learning platform. We present case studies with Facebook researchers and engineers, and usage scenarios of how ActiVis may work with different models.

In Multi-Label Text Classification (MLTC), one sample can belong to more than one class. It is observed that most MLTC tasks, there are dependencies or correlations among labels. Existing methods tend to ignore the relationship among labels. In this paper, a graph attention network-based model is proposed to capture the attentive dependency structure among the labels. The graph attention network uses a feature matrix and a correlation matrix to capture and explore the crucial dependencies between the labels and generate classifiers for the task. The generated classifiers are applied to sentence feature vectors obtained from the text feature extraction network (BiLSTM) to enable end-to-end training. Attention allows the system to assign different weights to neighbor nodes per label, thus allowing it to learn the dependencies among labels implicitly. The results of the proposed model are validated on five real-world MLTC datasets. The proposed model achieves similar or better performance compared to the previous state-of-the-art models.

Jupyter notebook allows data scientists to write machine learning code together with its documentation in cells. In this paper, we propose a new task of code documentation generation (CDG) for computational notebooks. In contrast to the previous CDG tasks which focus on generating documentation for single code snippets, in a computational notebook, one documentation in a markdown cell often corresponds to multiple code cells, and these code cells have an inherent structure. We proposed a new model (HAConvGNN) that uses a hierarchical attention mechanism to consider the relevant code cells and the relevant code tokens information when generating the documentation. Tested on a new corpus constructed from well-documented Kaggle notebooks, we show that our model outperforms other baseline models.

We present a data-driven approach for forecasting global weather using graph neural networks. The system learns to step forward the current 3D atmospheric state by six hours, and multiple steps are chained together to produce skillful forecasts going out several days into the future. The underlying model is trained on reanalysis data from ERA5 or forecast data from GFS. Test performance on metrics such as Z500 (geopotential height) and T850 (temperature) improves upon previous data-driven approaches and is comparable to operational, full-resolution, physical models from GFS and ECMWF, at least when evaluated on 1-degree scales and when using reanalysis initial conditions. We also show results from connecting this data-driven model to live, operational forecasts from GFS.

Graph-based collaborative filtering methods have prevailing performance for recommender systems since they can capture high-order information between users and items, in which the graphs are constructed from the observed user-item interactions that might miss links or contain spurious positive interactions in industrial scenarios. The Bayesian Graph Neural Network framework approaches this issue with generative models for the interaction graphs. The critical problem is to devise a proper family of graph generative models tailored to recommender systems. We propose an efficient generative model that jointly considers the preferences of users, the concurrence of items and some important graph structure information. Experiments on four popular benchmark datasets demonstrate the effectiveness of our proposed graph generative methods for recommender systems.

This paper presents SYBILGAT, a novel approach to Sybil detection in social networks using Graph Attention Networks (GATs). Traditional methods for Sybil detection primarily leverage structural properties of networks; however, they tend to struggle with a large number of attack edges and are often unable to simultaneously utilize both known Sybil and honest nodes. Our proposed method addresses these limitations by dynamically assigning attention weights to different nodes during aggregations, enhancing detection performance. We conducted extensive experiments in various scenarios, including pretraining in sampled subgraphs, synthetic networks, and networks under targeted attacks. The results show that SYBILGAT significantly outperforms the state-of-the-art algorithms, particularly in scenarios with high attack complexity and when the number of attack edges increases. Our approach shows robust performance across different network models and sizes, even as the detection task becomes more challenging. We successfully applied the model to a real-world Twitter graph with more than 269k nodes and 6.8M edges. The flexibility and generalizability of SYBILGAT make it a promising tool to defend against Sybil attacks in online social networks with only structural information.

Recent works have demonstrated the benefits of capturing long-distance dependency in graphs by deeper graph neural networks (GNNs). But deeper GNNs suffer from the long-lasting scalability challenge due to the neighborhood explosion problem in large-scale graphs. In this work, we propose to capture long-distance dependency in graphs by shallower models instead of deeper models, which leads to a much more efficient model, LazyGNN, for graph representation learning. Moreover, we demonstrate that LazyGNN is compatible with existing scalable approaches (such as sampling methods) for further accelerations through the development of mini-batch LazyGNN. Comprehensive experiments demonstrate its superior prediction performance and scalability on large-scale benchmarks. The implementation of LazyGNN is available at https://github.com/RXPHD/Lazy_GNN.

Graph neural networks (GNN) has been successfully applied to operate on the graph-structured data. Given a specific scenario, rich human expertise and tremendous laborious trials are usually required to identify a suitable GNN architecture. It is because the performance of a GNN architecture is significantly affected by the choice of graph convolution components, such as aggregate function and hidden dimension. Neural architecture search (NAS) has shown its potential in discovering effective deep architectures for learning tasks in image and language modeling. However, existing NAS algorithms cannot be directly applied to the GNN search problem. First, the search space of GNN is different from the ones in existing NAS work. Second, the representation learning capacity of GNN architecture changes obviously with slight architecture modifications. It affects the search efficiency of traditional search methods. Third, widely used techniques in NAS such as parameter sharing might become unstable in GNN. To bridge the gap, we propose the automated graph neural networks (AGNN) framework, which aims to find an optimal GNN architecture within a predefined search space. A reinforcement learning based controller is designed to greedily validate architectures via small steps. AGNN has a novel parameter sharing strategy that enables homogeneous architectures to share parameters, based on a carefully-designed homogeneity definition. Experiments on real-world benchmark datasets demonstrate that the GNN architecture identified by AGNN achieves the best performance, comparing with existing handcrafted models and tradistional search methods.

We introduce the FRactional-Order graph Neural Dynamical network (FROND), a new continuous graph neural network (GNN) framework. Unlike traditional continuous GNNs that rely on integer-order differential equations, FROND employs the Caputo fractional derivative to leverage the non-local properties of fractional calculus. This approach enables the capture of long-term dependencies in feature updates, moving beyond the Markovian update mechanisms in conventional integer-order models and offering enhanced capabilities in graph representation learning. We offer an interpretation of the node feature updating process in FROND from a non-Markovian random walk perspective when the feature updating is particularly governed by a diffusion process. We demonstrate analytically that oversmoothing can be mitigated in this setting. Experimentally, we validate the FROND framework by comparing the fractional adaptations of various established integer-order continuous GNNs, demonstrating their consistently improved performance and underscoring the framework's potential as an effective extension to enhance traditional continuous GNNs. The code is available at https://github.com/zknus/ICLR2024-FROND.

Tactile feedback is critical for understanding the dynamics of both rigid and deformable objects in many manipulation tasks, such as non-prehensile manipulation and dense packing. We introduce an approach that combines visual and tactile sensing for robotic manipulation by learning a neural, tactile-informed dynamics model. Our proposed framework, RoboPack, employs a recurrent graph neural network to estimate object states, including particles and object-level latent physics information, from historical visuo-tactile observations and to perform future state predictions. Our tactile-informed dynamics model, learned from real-world data, can solve downstream robotics tasks with model-predictive control. We demonstrate our approach on a real robot equipped with a compliant Soft-Bubble tactile sensor on non-prehensile manipulation and dense packing tasks, where the robot must infer the physics properties of objects from direct and indirect interactions. Trained on only an average of 30 minutes of real-world interaction data per task, our model can perform online adaptation and make touch-informed predictions. Through extensive evaluations in both long-horizon dynamics prediction and real-world manipulation, our method demonstrates superior effectiveness compared to previous learning-based and physics-based simulation systems.

As a branch of advanced artificial intelligence, dialogue systems are prospering. Multi-turn response selection is a general research problem in dialogue systems. With the assistance of background information and pre-trained language models, the performance of state-of-the-art methods on this problem gains impressive improvement. However, existing studies neglect the importance of external commonsense knowledge. Hence, we design a Siamese network where a pre-trained Language model merges with a Graph neural network (SinLG). SinLG takes advantage of Pre-trained Language Models (PLMs) to catch the word correlations in the context and response candidates and utilizes a Graph Neural Network (GNN) to reason helpful common sense from an external knowledge graph. The GNN aims to assist the PLM in fine-tuning, and arousing its related memories to attain better performance. Specifically, we first extract related concepts as nodes from an external knowledge graph to construct a subgraph with the context response pair as a super node for each sample. Next, we learn two representations for the context response pair via both the PLM and GNN. A similarity loss between the two representations is utilized to transfer the commonsense knowledge from the GNN to the PLM. Then only the PLM is used to infer online so that efficiency can be guaranteed. Finally, we conduct extensive experiments on two variants of the PERSONA-CHAT dataset, which proves that our solution can not only improve the performance of the PLM but also achieve an efficient inference.

Cross-domain alignment between two sets of entities (e.g., objects in an image, words in a sentence) is fundamental to both computer vision and natural language processing. Existing methods mainly focus on designing advanced attention mechanisms to simulate soft alignment, with no training signals to explicitly encourage alignment. The learned attention matrices are also dense and lacks interpretability. We propose Graph Optimal Transport (GOT), a principled framework that germinates from recent advances in Optimal Transport (OT). In GOT, cross-domain alignment is formulated as a graph matching problem, by representing entities into a dynamically-constructed graph. Two types of OT distances are considered: (i) Wasserstein distance (WD) for node (entity) matching; and (ii) Gromov-Wasserstein distance (GWD) for edge (structure) matching. Both WD and GWD can be incorporated into existing neural network models, effectively acting as a drop-in regularizer. The inferred transport plan also yields sparse and self-normalized alignment, enhancing the interpretability of the learned model. Experiments show consistent outperformance of GOT over baselines across a wide range of tasks, including image-text retrieval, visual question answering, image captioning, machine translation, and text summarization.

Online recruitment platforms typically employ Person-Job Fit models in the core service that automatically match suitable job seekers with appropriate job positions. While existing works leverage historical or contextual information, they often disregard a crucial aspect: job seekers' social relationships in professional networks. This paper emphasizes the importance of incorporating professional networks into the Person-Job Fit model. Our innovative approach consists of two stages: (1) defining a Workplace Heterogeneous Information Network (WHIN) to capture heterogeneous knowledge, including professional connections and pre-training representations of various entities using a heterogeneous graph neural network; (2) designing a Contextual Social Attention Graph Neural Network (CSAGNN) that supplements users' missing information with professional connections' contextual information. We introduce a job-specific attention mechanism in CSAGNN to handle noisy professional networks, leveraging pre-trained entity representations from WHIN. We demonstrate the effectiveness of our approach through experimental evaluations conducted across three real-world recruitment datasets from LinkedIn, showing superior performance compared to baseline models.

Many machine learning tasks involve learning functions that are known to be invariant or equivariant to certain symmetries of the input data. However, it is often challenging to design neural network architectures that respect these symmetries while being expressive and computationally efficient. For example, Euclidean motion invariant/equivariant graph or point cloud neural networks. We introduce Frame Averaging (FA), a general purpose and systematic framework for adapting known (backbone) architectures to become invariant or equivariant to new symmetry types. Our framework builds on the well known group averaging operator that guarantees invariance or equivariance but is intractable. In contrast, we observe that for many important classes of symmetries, this operator can be replaced with an averaging operator over a small subset of the group elements, called a frame. We show that averaging over a frame guarantees exact invariance or equivariance while often being much simpler to compute than averaging over the entire group. Furthermore, we prove that FA-based models have maximal expressive power in a broad setting and in general preserve the expressive power of their backbone architectures. Using frame averaging, we propose a new class of universal Graph Neural Networks (GNNs), universal Euclidean motion invariant point cloud networks, and Euclidean motion invariant Message Passing (MP) GNNs. We demonstrate the practical effectiveness of FA on several applications including point cloud normal estimation, beyond 2-WL graph separation, and n-body dynamics prediction, achieving state-of-the-art results in all of these benchmarks.

Implicit-depth neural networks have grown as powerful alternatives to traditional networks in various applications in recent years. However, these models often lack guarantees of existence and uniqueness, raising stability, performance, and reproducibility issues. In this paper, we present a new analysis of the existence and uniqueness of fixed points for implicit-depth neural networks based on the concept of subhomogeneous operators and the nonlinear Perron-Frobenius theory. Compared to previous similar analyses, our theory allows for weaker assumptions on the parameter matrices, thus yielding a more flexible framework for well-defined implicit networks. We illustrate the performance of the resulting subhomogeneous networks on feedforward, convolutional, and graph neural network examples.

Representation learning on text-attributed graphs (TAGs) has become a critical research problem in recent years. A typical example of a TAG is a paper citation graph, where the text of each paper serves as node attributes. Initial graph neural network (GNN) pipelines handled these text attributes by transforming them into shallow or hand-crafted features, such as skip-gram or bag-of-words features. Recent efforts have focused on enhancing these pipelines with language models (LMs), which typically demand intricate designs and substantial computational resources. With the advent of powerful large language models (LLMs) such as GPT or Llama2, which demonstrate an ability to reason and to utilize general knowledge, there is a growing need for techniques which combine the textual modelling abilities of LLMs with the structural learning capabilities of GNNs. Hence, in this work, we focus on leveraging LLMs to capture textual information as features, which can be used to boost GNN performance on downstream tasks. A key innovation is our use of explanations as features: we prompt an LLM to perform zero-shot classification, request textual explanations for its decision-making process, and design an LLM-to-LM interpreter to translate these explanations into informative features for downstream GNNs. Our experiments demonstrate that our method achieves state-of-the-art results on well-established TAG datasets, including Cora, PubMed, ogbn-arxiv, as well as our newly introduced dataset, tape-arxiv23. Furthermore, our method significantly speeds up training, achieving a 2.88 times improvement over the closest baseline on ogbn-arxiv. Lastly, we believe the versatility of the proposed method extends beyond TAGs and holds the potential to enhance other tasks involving graph-text data. Our codes and datasets are available at: https://github.com/XiaoxinHe/TAPE.

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: 3.6% increase in drug response prediction correlation, 9.6% improvement in single-cell drug classification AUC, and 1.1% average gain in gene perturbation prediction accuracy.

Agent Based Models (ABMs) have emerged as a powerful tool for investigating complex social interactions, particularly in the context of public health and infectious disease investigation. In an effort to enhance the conventional ABM, enabling automated model calibration and reducing the computational resources needed for scaling up the model, we have developed a tensorized and differentiable agent-based model by coupling Graph Neural Network (GNN) and Long Short-Term Memory (LSTM) network. The model was employed to investigate the 2019 measles outbreak occurred in New Zealand, demonstrating a promising ability to accurately simulate the outbreak dynamics, particularly during the peak period of repeated cases. This paper shows that by leveraging the latest Artificial Intelligence (AI) technology and the capabilities of traditional ABMs, we gain deeper insights into the dynamics of infectious disease outbreaks. This, in turn, helps us make more informed decision when developing effective strategies that strike a balance between managing outbreaks and minimizing disruptions to everyday life.

Molecular representation is a foundational element in our understanding of the physical world. Its importance ranges from the fundamentals of chemical reactions to the design of new therapies and materials. Previous molecular machine learning models have employed strings, fingerprints, global features, and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a novel approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects. We show that the explicit addition of stereoelectronic interactions significantly improves the performance of molecular machine learning models. Furthermore, stereoelectronics-infused representations can be learned and deployed with a tailored double graph neural network workflow, enabling its application to any downstream molecular machine learning task. Finally, we show that the learned representations allow for facile stereoelectronic evaluation of previously intractable systems, such as entire proteins, opening new avenues of molecular design.

Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work, we generate a big dataset of structure-property relationships for strut-based lattices. The dataset is made available to the community which can fuel the development of methods anchored in physical principles for the fitting of fourth-order tensors. In addition, we present a higher-order GNN model trained on this dataset. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate its benefits in terms of predictive performance and reduced training requirements. Finally, we demonstrate an example application of the model to an architected material design task. The methods which we developed are applicable to fourth-order tensors beyond elasticity such as piezo-optical tensor etc.

Although Answer Set Programming (ASP) allows constraining neural-symbolic (NeSy) systems, its employment is hindered by the prohibitive costs of computing stable models and the CPU-bound nature of state-of-the-art solvers. To this end, we propose Answer Set Networks (ASN), a NeSy solver. Based on Graph Neural Networks (GNN), ASNs are a scalable approach to ASP-based Deep Probabilistic Logic Programming (DPPL). Specifically, we show how to translate ASPs into ASNs and demonstrate how ASNs can efficiently solve the encoded problem by leveraging GPU's batching and parallelization capabilities. Our experimental evaluations demonstrate that ASNs outperform state-of-the-art CPU-bound NeSy systems on multiple tasks. Simultaneously, we make the following two contributions based on the strengths of ASNs. Namely, we are the first to show the finetuning of Large Language Models (LLM) with DPPLs, employing ASNs to guide the training with logic. Further, we show the "constitutional navigation" of drones, i.e., encoding public aviation laws in an ASN for routing Unmanned Aerial Vehicles in uncertain environments.

We introduce PICA, a novel representation for high-fidelity animatable clothed human avatars with physics-accurate dynamics, even for loose clothing. Previous neural rendering-based representations of animatable clothed humans typically employ a single model to represent both the clothing and the underlying body. While efficient, these approaches often fail to accurately represent complex garment dynamics, leading to incorrect deformations and noticeable rendering artifacts, especially for sliding or loose garments. Furthermore, previous works represent garment dynamics as pose-dependent deformations and facilitate novel pose animations in a data-driven manner. This often results in outcomes that do not faithfully represent the mechanics of motion and are prone to generating artifacts in out-of-distribution poses. To address these issues, we adopt two individual 3D Gaussian Splatting (3DGS) models with different deformation characteristics, modeling the human body and clothing separately. This distinction allows for better handling of their respective motion characteristics. With this representation, we integrate a graph neural network (GNN)-based clothed body physics simulation module to ensure an accurate representation of clothing dynamics. Our method, through its carefully designed features, achieves high-fidelity rendering of clothed human bodies in complex and novel driving poses, significantly outperforming previous methods under the same settings.

Clinical predictive models often rely on patients' electronic health records (EHR), but integrating medical knowledge to enhance predictions and decision-making is challenging. This is because personalized predictions require personalized knowledge graphs (KGs), which are difficult to generate from patient EHR data. To address this, we propose GraphCare, an open-world framework that uses external KGs to improve EHR-based predictions. Our method extracts knowledge from large language models (LLMs) and external biomedical KGs to build patient-specific KGs, which are then used to train our proposed Bi-attention AugmenTed (BAT) graph neural network (GNN) for healthcare predictions. On two public datasets, MIMIC-III and MIMIC-IV, GraphCare surpasses baselines in four vital healthcare prediction tasks: mortality, readmission, length of stay (LOS), and drug recommendation. On MIMIC-III, it boosts AUROC by 17.6\% and 6.6\% for mortality and readmission, and F1-score by 7.9\% and 10.8\% for LOS and drug recommendation, respectively. Notably, GraphCare demonstrates a substantial edge in scenarios with limited data availability. Our findings highlight the potential of using external KGs in healthcare prediction tasks and demonstrate the promise of GraphCare in generating personalized KGs for promoting personalized medicine.

Enabling Large Language Models (LLMs) to understand the 3D physical world is an emerging yet challenging research direction. Current strategies for processing point clouds typically downsample the scene or divide it into smaller parts for separate analysis. However, both approaches risk losing key local details or global contextual information. In this paper, we introduce PerLA, a 3D language assistant designed to be more perceptive to both details and context, making visual representations more informative for the LLM. PerLA captures high-resolution (local) details in parallel from different point cloud areas and integrates them with (global) context obtained from a lower-resolution whole point cloud. We present a novel algorithm that preserves point cloud locality through the Hilbert curve and effectively aggregates local-to-global information via cross-attention and a graph neural network. Lastly, we introduce a novel loss for local representation consensus to promote training stability. PerLA outperforms state-of-the-art 3D language assistants, with gains of up to +1.34 CiDEr on ScanQA for question answering, and +4.22 on ScanRefer and +3.88 on Nr3D for dense captioning.https://gfmei.github.io/PerLA/

The recent success of natural language understanding (NLU) systems has been troubled by results highlighting the failure of these models to generalize in a systematic and robust way. In this work, we introduce a diagnostic benchmark suite, named CLUTRR, to clarify some key issues related to the robustness and systematicity of NLU systems. Motivated by classic work on inductive logic programming, CLUTRR requires that an NLU system infer kinship relations between characters in short stories. Successful performance on this task requires both extracting relationships between entities, as well as inferring the logical rules governing these relationships. CLUTRR allows us to precisely measure a model's ability for systematic generalization by evaluating on held-out combinations of logical rules, and it allows us to evaluate a model's robustness by adding curated noise facts. Our empirical results highlight a substantial performance gap between state-of-the-art NLU models (e.g., BERT and MAC) and a graph neural network model that works directly with symbolic inputs---with the graph-based model exhibiting both stronger generalization and greater robustness.

The advancement of polymer informatics has been significantly propelled by the integration of machine learning (ML) techniques, enabling the rapid prediction of polymer properties and expediting the discovery of high-performance polymeric materials. However, the field lacks a standardized workflow that encompasses prediction accuracy, uncertainty quantification, ML interpretability, and polymer synthesizability. In this study, we introduce POINT^{2} (POlymer INformatics Training and Testing), a comprehensive benchmark database and protocol designed to address these critical challenges. Leveraging the existing labeled datasets and the unlabeled PI1M dataset, a collection of approximately one million virtual polymers generated via a recurrent neural network trained on the realistic polymers, we develop an ensemble of ML models, including Quantile Random Forests, Multilayer Perceptrons with dropout, Graph Neural Networks, and pretrained large language models. These models are coupled with diverse polymer representations such as Morgan, MACCS, RDKit, Topological, Atom Pair fingerprints, and graph-based descriptors to achieve property predictions, uncertainty estimations, model interpretability, and template-based polymerization synthesizability across a spectrum of properties, including gas permeability, thermal conductivity, glass transition temperature, melting temperature, fractional free volume, and density. The POINT^{2} database can serve as a valuable resource for the polymer informatics community for polymer discovery and optimization.

Graph Convolutional Neural Networks (GCNs) possess strong capabilities for processing graph data in non-grid domains. They can capture the topological logical structure and node features in graphs and integrate them into nodes' final representations. GCNs have been extensively studied in various fields, such as recommendation systems, social networks, and protein molecular structures. With the increasing application of graph neural networks, research has focused on improving their performance while compressing their size. In this work, a plug-in module named Graph Knowledge Enhancement and Distillation Module (GKEDM) is proposed. GKEDM can enhance node representations and improve the performance of GCNs by extracting and aggregating graph information via multi-head attention mechanism. Furthermore, GKEDM can serve as an auxiliary transferor for knowledge distillation. With a specially designed attention distillation method, GKEDM can distill the knowledge of large teacher models into high-performance and compact student models. Experiments on multiple datasets demonstrate that GKEDM can significantly improve the performance of various GCNs with minimal overhead. Furthermore, it can efficiently transfer distilled knowledge from large teacher networks to small student networks via attention distillation.

GraphRAG addresses significant challenges in Retrieval-Augmented Generation (RAG) by leveraging graphs with embedded knowledge to enhance the reasoning capabilities of Large Language Models (LLMs). Despite its promising potential, the GraphRAG community currently lacks a unified framework for fine-grained decomposition of the graph-based knowledge retrieval process. Furthermore, there is no systematic categorization or evaluation of existing solutions within the retrieval process. In this paper, we present LEGO-GraphRAG, a modular framework that decomposes the retrieval process of GraphRAG into three interconnected modules: subgraph-extraction, path-filtering, and path-refinement. We systematically summarize and classify the algorithms and neural network (NN) models relevant to each module, providing a clearer understanding of the design space for GraphRAG instances. Additionally, we identify key design factors, such as Graph Coupling and Computational Cost, that influence the effectiveness of GraphRAG implementations. Through extensive empirical studies, we construct high-quality GraphRAG instances using a representative selection of solutions and analyze their impact on retrieval and reasoning performance. Our findings offer critical insights into optimizing GraphRAG instance design, ultimately contributing to the advancement of more accurate and contextually relevant LLM applications.

DL compiler's primary function is to translate DNN programs written in high-level DL frameworks such as PyTorch and TensorFlow into portable executables. These executables can then be flexibly executed by the deployed host programs. However, existing DL compilers rely on a tracing mechanism, which involves feeding a runtime input to a neural network program and tracing the program execution paths to generate the computational graph necessary for compilation. Unfortunately, this mechanism falls short when dealing with modern dynamic neural networks (DyNNs) that possess varying computational graphs depending on the inputs. Consequently, conventional DL compilers struggle to accurately compile DyNNs into executable code. To address this limitation, we propose \tool, a general approach that enables any existing DL compiler to successfully compile DyNNs. \tool tackles the dynamic nature of DyNNs by introducing a compilation mechanism that redistributes the control and data flow of the original DNN programs during the compilation process. Specifically, \tool develops program analysis and program transformation techniques to convert a dynamic neural network into multiple sub-neural networks. Each sub-neural network is devoid of conditional statements and is compiled independently. Furthermore, \tool synthesizes a host module that models the control flow of the DyNNs and facilitates the invocation of the sub-neural networks. Our evaluation demonstrates the effectiveness of \tool, achieving a 100\% success rate in compiling all dynamic neural networks. Moreover, the compiled executables generated by \tool exhibit significantly improved performance, running between 1.12times and 20.21times faster than the original DyNNs executed on general-purpose DL frameworks.

Volatility forecasting is essential for risk management and decision-making in financial markets. Traditional models like Generalized Autoregressive Conditional Heteroskedasticity (GARCH) effectively capture volatility clustering but often fail to model complex, non-linear interdependencies between multiple indices. This paper proposes a novel approach using Graph Neural Networks (GNNs) to represent global financial markets as dynamic graphs. The Temporal Graph Attention Network (Temporal GAT) combines Graph Convolutional Networks (GCNs) and Graph Attention Networks (GATs) to capture the temporal and structural dynamics of volatility spillovers. By utilizing correlation-based and volatility spillover indices, the Temporal GAT constructs directed graphs that enhance the accuracy of volatility predictions. Empirical results from a 15-year study of eight major global indices show that the Temporal GAT outperforms traditional GARCH models and other machine learning methods, particularly in short- to mid-term forecasts. The sensitivity and scenario-based analysis over a range of parameters and hyperparameters further demonstrate the significance of the proposed technique. Hence, this work highlights the potential of GNNs in modeling complex market behaviors, providing valuable insights for financial analysts and investors.

Locating the source of an epidemic, or patient zero (P0), can provide critical insights into the infection's transmission course and allow efficient resource allocation. Existing methods use graph-theoretic centrality measures and expensive message-passing algorithms, requiring knowledge of the underlying dynamics and its parameters. In this paper, we revisit this problem using graph neural networks (GNNs) to learn P0. We establish a theoretical limit for the identification of P0 in a class of epidemic models. We evaluate our method against different epidemic models on both synthetic and a real-world contact network considering a disease with history and characteristics of COVID-19. % We observe that GNNs can identify P0 close to the theoretical bound on accuracy, without explicit input of dynamics or its parameters. In addition, GNN is over 100 times faster than classic methods for inference on arbitrary graph topologies. Our theoretical bound also shows that the epidemic is like a ticking clock, emphasizing the importance of early contact-tracing. We find a maximum time after which accurate recovery of the source becomes impossible, regardless of the algorithm used.

Recent advancements in large language model (LLM)-based agents have demonstrated that collective intelligence can significantly surpass the capabilities of individual agents, primarily due to well-crafted inter-agent communication topologies. Despite the diverse and high-performing designs available, practitioners often face confusion when selecting the most effective pipeline for their specific task: Which topology is the best choice for my task, avoiding unnecessary communication token overhead while ensuring high-quality solution? In response to this dilemma, we introduce G-Designer, an adaptive, efficient, and robust solution for multi-agent deployment, which dynamically designs task-aware, customized communication topologies. Specifically, G-Designer models the multi-agent system as a multi-agent network, leveraging a variational graph auto-encoder to encode both the nodes (agents) and a task-specific virtual node, and decodes a task-adaptive and high-performing communication topology. Extensive experiments on six benchmarks showcase that G-Designer is: (1) high-performing, achieving superior results on MMLU with accuracy at 84.50% and on HumanEval with pass@1 at 89.90%; (2) task-adaptive, architecting communication protocols tailored to task difficulty, reducing token consumption by up to 95.33% on HumanEval; and (3) adversarially robust, defending against agent adversarial attacks with merely 0.3% accuracy drop.

Molecular interactions often involve high-order relationships that cannot be fully captured by traditional graph-based models limited to pairwise connections. Hypergraphs naturally extend graphs by enabling multi-way interactions, making them well-suited for modeling complex molecular systems. In this work, we introduce EquiHGNN, an Equivariant HyperGraph Neural Network framework that integrates symmetry-aware representations to improve molecular modeling. By enforcing the equivariance under relevant transformation groups, our approach preserves geometric and topological properties, leading to more robust and physically meaningful representations. We examine a range of equivariant architectures and demonstrate that integrating symmetry constraints leads to notable performance gains on large-scale molecular datasets. Experiments on both small and large molecules show that high-order interactions offer limited benefits for small molecules but consistently outperform 2D graphs on larger ones. Adding geometric features to these high-order structures further improves the performance, emphasizing the value of spatial information in molecular learning. Our source code is available at https://github.com/HySonLab/EquiHGNN/

Scene graph generation (SGG) models have suffered from inherent problems regarding the benchmark datasets such as the long-tailed predicate distribution and missing annotation problems. In this work, we aim to alleviate the long-tailed problem of SGG by utilizing unannotated triplets. To this end, we introduce a Self-Training framework for SGG (ST-SGG) that assigns pseudo-labels for unannotated triplets based on which the SGG models are trained. While there has been significant progress in self-training for image recognition, designing a self-training framework for the SGG task is more challenging due to its inherent nature such as the semantic ambiguity and the long-tailed distribution of predicate classes. Hence, we propose a novel pseudo-labeling technique for SGG, called Class-specific Adaptive Thresholding with Momentum (CATM), which is a model-agnostic framework that can be applied to any existing SGG models. Furthermore, we devise a graph structure learner (GSL) that is beneficial when adopting our proposed self-training framework to the state-of-the-art message-passing neural network (MPNN)-based SGG models. Our extensive experiments verify the effectiveness of ST-SGG on various SGG models, particularly in enhancing the performance on fine-grained predicate classes.

Community Question Answering (CQA) in different domains is growing at a large scale because of the availability of several platforms and huge shareable information among users. With the rapid growth of such online platforms, a massive amount of archived data makes it difficult for moderators to retrieve possible duplicates for a new question and identify and confirm existing question pairs as duplicates at the right time. This problem is even more critical in CQAs corresponding to large software systems like askubuntu where moderators need to be experts to comprehend something as a duplicate. Note that the prime challenge in such CQA platforms is that the moderators are themselves experts and are therefore usually extremely busy with their time being extraordinarily expensive. To facilitate the task of the moderators, in this work, we have tackled two significant issues for the askubuntu CQA platform: (1) retrieval of duplicate questions given a new question and (2) duplicate question confirmation time prediction. In the first task, we focus on retrieving duplicate questions from a question pool for a particular newly posted question. In the second task, we solve a regression problem to rank a pair of questions that could potentially take a long time to get confirmed as duplicates. For duplicate question retrieval, we propose a Siamese neural network based approach by exploiting both text and network-based features, which outperforms several state-of-the-art baseline techniques. Our method outperforms DupPredictor and DUPE by 5% and 7% respectively. For duplicate confirmation time prediction, we have used both the standard machine learning models and neural network along with the text and graph-based features. We obtain Spearman's rank correlation of 0.20 and 0.213 (statistically significant) for text and graph based features respectively.

This paper presents a motion data augmentation scheme incorporating motion synthesis encouraging diversity and motion correction imposing physical plausibility. This motion synthesis consists of our modified Variational AutoEncoder (VAE) and Inverse Kinematics (IK). In this VAE, our proposed sampling-near-samples method generates various valid motions even with insufficient training motion data. Our IK-based motion synthesis method allows us to generate a variety of motions semi-automatically. Since these two schemes generate unrealistic artifacts in the synthesized motions, our motion correction rectifies them. This motion correction scheme consists of imitation learning with physics simulation and subsequent motion debiasing. For this imitation learning, we propose the PD-residual force that significantly accelerates the training process. Furthermore, our motion debiasing successfully offsets the motion bias induced by imitation learning to maximize the effect of augmentation. As a result, our method outperforms previous noise-based motion augmentation methods by a large margin on both Recurrent Neural Network-based and Graph Convolutional Network-based human motion prediction models. The code is available at https://github.com/meaten/MotionAug.

Syntax-incorporated machine translation models have been proven successful in improving the model's reasoning and meaning preservation ability. In this paper, we propose a simple yet effective graph-structured encoder, the Recurrent Graph Syntax Encoder, dubbed RGSE, which enhances the ability to capture useful syntactic information. The RGSE is done over a standard encoder (recurrent or self-attention encoder), regarding recurrent network units as graph nodes and injects syntactic dependencies as edges, such that RGSE models syntactic dependencies and sequential information (i.e., word order) simultaneously. Our approach achieves considerable improvements over several syntax-aware NMT models in EnglishRightarrowGerman and EnglishRightarrowCzech translation tasks. And RGSE-equipped big model obtains competitive result compared with the state-of-the-art model in WMT14 En-De task. Extensive analysis further verifies that RGSE could benefit long sentence modeling, and produces better translations.

In this paper, we propose XG-BoT, an explainable deep graph neural network model for botnet node detection. The proposed model comprises a botnet detector and an explainer for automatic forensics. The XG-BoT detector can effectively detect malicious botnet nodes in large-scale networks. Specifically, it utilizes a grouped reversible residual connection with a graph isomorphism network to learn expressive node representations from botnet communication graphs. The explainer, based on the GNNExplainer and saliency map in XG-BoT, can perform automatic network forensics by highlighting suspicious network flows and related botnet nodes. We evaluated XG-BoT using real-world, large-scale botnet network graph datasets. Overall, XG-BoT outperforms state-of-the-art approaches in terms of key evaluation metrics. Additionally, we demonstrate that the XG-BoT explainers can generate useful explanations for automatic network forensics.

Islamophobic language is a prevalent challenge on online social interaction platforms. Identifying and eliminating such hatred is a crucial step towards a future of harmony and peace. This study presents a novel paradigm for identifying and explaining hate speech towards Islam using graph neural networks. Utilizing the intrinsic ability of graph neural networks to find, extract, and use relationships across disparate data points, our model consistently achieves outstanding performance while offering explanations for the underlying correlations and causation.

Recent years have seen the advent of molecular simulation datasets that are orders of magnitude larger and more diverse. These new datasets differ substantially in four aspects of complexity: 1. Chemical diversity (number of different elements), 2. system size (number of atoms per sample), 3. dataset size (number of data samples), and 4. domain shift (similarity of the training and test set). Despite these large differences, benchmarks on small and narrow datasets remain the predominant method of demonstrating progress in graph neural networks (GNNs) for molecular simulation, likely due to cheaper training compute requirements. This raises the question -- does GNN progress on small and narrow datasets translate to these more complex datasets? This work investigates this question by first developing the GemNet-OC model based on the large Open Catalyst 2020 (OC20) dataset. GemNet-OC outperforms the previous state-of-the-art on OC20 by 16% while reducing training time by a factor of 10. We then compare the impact of 18 model components and hyperparameter choices on performance in multiple datasets. We find that the resulting model would be drastically different depending on the dataset used for making model choices. To isolate the source of this discrepancy we study six subsets of the OC20 dataset that individually test each of the above-mentioned four dataset aspects. We find that results on the OC-2M subset correlate well with the full OC20 dataset while being substantially cheaper to train on. Our findings challenge the common practice of developing GNNs solely on small datasets, but highlight ways of achieving fast development cycles and generalizable results via moderately-sized, representative datasets such as OC-2M and efficient models such as GemNet-OC. Our code and pretrained model weights are open-sourced.

Vulnerability identification is crucial to protect the software systems from attacks for cyber security. It is especially important to localize the vulnerable functions among the source code to facilitate the fix. However, it is a challenging and tedious process, and also requires specialized security expertise. Inspired by the work on manually-defined patterns of vulnerabilities from various code representation graphs and the recent advance on graph neural networks, we propose Devign, a general graph neural network based model for graph-level classification through learning on a rich set of code semantic representations. It includes a novel Conv module to efficiently extract useful features in the learned rich node representations for graph-level classification. The model is trained over manually labeled datasets built on 4 diversified large-scale open-source C projects that incorporate high complexity and variety of real source code instead of synthesis code used in previous works. The results of the extensive evaluation on the datasets demonstrate that Devign outperforms the state of the arts significantly with an average of 10.51% higher accuracy and 8.68\% F1 score, increases averagely 4.66% accuracy and 6.37% F1 by the Conv module.

Document layout analysis has a wide range of requirements across various domains, languages, and business scenarios. However, most current state-of-the-art algorithms are language-dependent, with architectures that rely on transformer encoders or language-specific text encoders, such as BERT, for feature extraction. These approaches are limited in their ability to handle very long documents due to input sequence length constraints and are closely tied to language-specific tokenizers. Additionally, training a cross-language text encoder can be challenging due to the lack of labeled multilingual document datasets that consider privacy. Furthermore, some layout tasks require a clean separation between different layout components without overlap, which can be difficult for image segmentation-based algorithms to achieve. In this paper, we present Paragraph2Graph, a language-independent graph neural network (GNN)-based model that achieves competitive results on common document layout datasets while being adaptable to business scenarios with strict separation. With only 19.95 million parameters, our model is suitable for industrial applications, particularly in multi-language scenarios.

Floor labels of crowdsourced RF signals are crucial for many smart-city applications, such as multi-floor indoor localization, geofencing, and robot surveillance. To build a prediction model to identify the floor number of a new RF signal upon its measurement, conventional approaches using the crowdsourced RF signals assume that at least few labeled signal samples are available on each floor. In this work, we push the envelope further and demonstrate that it is technically feasible to enable such floor identification with only one floor-labeled signal sample on the bottom floor while having the rest of signal samples unlabeled. We propose FIS-ONE, a novel floor identification system with only one labeled sample. FIS-ONE consists of two steps, namely signal clustering and cluster indexing. We first build a bipartite graph to model the RF signal samples and obtain a latent representation of each node (each signal sample) using our attention-based graph neural network model so that the RF signal samples can be clustered more accurately. Then, we tackle the problem of indexing the clusters with proper floor labels, by leveraging the observation that signals from an access point can be detected on different floors, i.e., signal spillover. Specifically, we formulate a cluster indexing problem as a combinatorial optimization problem and show that it is equivalent to solving a traveling salesman problem, whose (near-)optimal solution can be found efficiently. We have implemented FIS-ONE and validated its effectiveness on the Microsoft dataset and in three large shopping malls. Our results show that FIS-ONE outperforms other baseline algorithms significantly, with up to 23% improvement in adjusted rand index and 25% improvement in normalized mutual information using only one floor-labeled signal sample.

Traffic prediction is essential for the progression of Intelligent Transportation Systems (ITS) and the vision of smart cities. While Spatial-Temporal Graph Neural Networks (STGNNs) have shown promise in this domain by leveraging Graph Neural Networks (GNNs) integrated with either RNNs or Transformers, they present challenges such as computational complexity, gradient issues, and resource-intensiveness. This paper addresses these challenges, advocating for three main solutions: a node-embedding approach, time series decomposition, and periodicity learning. We introduce STLinear, a minimalist model architecture designed for optimized efficiency and performance. Unlike traditional STGNNs, STlinear operates fully locally, avoiding inter-node data exchanges, and relies exclusively on linear layers, drastically cutting computational demands. Our empirical studies on real-world datasets confirm STLinear's prowess, matching or exceeding the accuracy of leading STGNNs, but with significantly reduced complexity and computation overhead (more than 95% reduction in MACs per epoch compared to state-of-the-art STGNN baseline published in 2023). In summary, STLinear emerges as a potent, efficient alternative to conventional STGNNs, with profound implications for the future of ITS and smart city initiatives.

Estimating the 6-DoF pose of a rigid object from a single RGB image is a crucial yet challenging task. Recent studies have shown the great potential of dense correspondence-based solutions, yet improvements are still needed to reach practical deployment. In this paper, we propose a novel pose estimation algorithm named CheckerPose, which improves on three main aspects. Firstly, CheckerPose densely samples 3D keypoints from the surface of the 3D object and finds their 2D correspondences progressively in the 2D image. Compared to previous solutions that conduct dense sampling in the image space, our strategy enables the correspondence searching in a 2D grid (i.e., pixel coordinate). Secondly, for our 3D-to-2D correspondence, we design a compact binary code representation for 2D image locations. This representation not only allows for progressive correspondence refinement but also converts the correspondence regression to a more efficient classification problem. Thirdly, we adopt a graph neural network to explicitly model the interactions among the sampled 3D keypoints, further boosting the reliability and accuracy of the correspondences. Together, these novel components make CheckerPose a strong pose estimation algorithm. When evaluated on the popular Linemod, Linemod-O, and YCB-V object pose estimation benchmarks, CheckerPose clearly boosts the accuracy of correspondence-based methods and achieves state-of-the-art performances. Code is available at https://github.com/RuyiLian/CheckerPose.

This study introduces DrivAerNet, a large-scale high-fidelity CFD dataset of 3D industry-standard car shapes, and RegDGCNN, a dynamic graph convolutional neural network model, both aimed at aerodynamic car design through machine learning. DrivAerNet, with its 4000 detailed 3D car meshes using 0.5 million surface mesh faces and comprehensive aerodynamic performance data comprising of full 3D pressure, velocity fields, and wall-shear stresses, addresses the critical need for extensive datasets to train deep learning models in engineering applications. It is 60\% larger than the previously available largest public dataset of cars, and is the only open-source dataset that also models wheels and underbody. RegDGCNN leverages this large-scale dataset to provide high-precision drag estimates directly from 3D meshes, bypassing traditional limitations such as the need for 2D image rendering or Signed Distance Fields (SDF). By enabling fast drag estimation in seconds, RegDGCNN facilitates rapid aerodynamic assessments, offering a substantial leap towards integrating data-driven methods in automotive design. Together, DrivAerNet and RegDGCNN promise to accelerate the car design process and contribute to the development of more efficient vehicles. To lay the groundwork for future innovations in the field, the dataset and code used in our study are publicly accessible at https://github.com/Mohamedelrefaie/DrivAerNet

The presence of point defects such as vacancies plays an important role in material design. Here, we demonstrate that a graph neural network (GNN) model trained only on perfect materials can also be used to predict vacancy formation energies (E_{vac}) of defect structures without the need for additional training data. Such GNN-based predictions are considerably faster than density functional theory (DFT) calculations with reasonable accuracy and show the potential that GNNs are able to capture a functional form for energy predictions. To test this strategy, we developed a DFT dataset of 508 E_{vac} consisting of 3D elemental solids, alloys, oxides, nitrides, and 2D monolayer materials. We analyzed and discussed the applicability of such direct and fast predictions. We applied the model to predict 192494 E_{vac} for 55723 materials in the JARVIS-DFT database.

Understanding the road genome is essential to realize autonomous driving. This highly intelligent problem contains two aspects - the connection relationship of lanes, and the assignment relationship between lanes and traffic elements, where a comprehensive topology reasoning method is vacant. On one hand, previous map learning techniques struggle in deriving lane connectivity with segmentation or laneline paradigms; or prior lane topology-oriented approaches focus on centerline detection and neglect the interaction modeling. On the other hand, the traffic element to lane assignment problem is limited in the image domain, leaving how to construct the correspondence from two views an unexplored challenge. To address these issues, we present TopoNet, the first end-to-end framework capable of abstracting traffic knowledge beyond conventional perception tasks. To capture the driving scene topology, we introduce three key designs: (1) an embedding module to incorporate semantic knowledge from 2D elements into a unified feature space; (2) a curated scene graph neural network to model relationships and enable feature interaction inside the network; (3) instead of transmitting messages arbitrarily, a scene knowledge graph is devised to differentiate prior knowledge from various types of the road genome. We evaluate TopoNet on the challenging scene understanding benchmark, OpenLane-V2, where our approach outperforms all previous works by a great margin on all perceptual and topological metrics. The code is released at https://github.com/OpenDriveLab/TopoNet

Although deep learning models have demonstrated remarkable potential in weather prediction, most of them overlook either the physics of the underlying weather evolution or the topology of the Earth's surface. In light of these disadvantages, we develop PASSAT, a novel Physics-ASSisted And Topology-informed deep learning model for weather prediction. PASSAT attributes the weather evolution to two key factors: (i) the advection process that can be characterized by the advection equation and the Navier-Stokes equation; (ii) the Earth-atmosphere interaction that is difficult to both model and calculate. PASSAT also takes the topology of the Earth's surface into consideration, other than simply treating it as a plane. With these considerations, PASSAT numerically solves the advection equation and the Navier-Stokes equation on the spherical manifold, utilizes a spherical graph neural network to capture the Earth-atmosphere interaction, and generates the initial velocity fields that are critical to solving the advection equation from the same spherical graph neural network. In the 5.625^circ-resolution ERA5 data set, PASSAT outperforms both the state-of-the-art deep learning-based weather prediction models and the operational numerical weather prediction model IFS T42. Code and checkpoint are available at https://github.com/Yumenomae/PASSAT_5p625.

Recommender systems increasingly aim to combine signals from both user reviews and purchase (or other interaction) behaviors. While user-written comments provide explicit insights about preferences, merging these textual representations from large language models (LLMs) with graph-based embeddings of user actions remains a challenging task. In this work, we propose a framework that employs both a Graph Neural Network (GNN)-based model and an LLM to produce review-aware representations, preserving review semantics while mitigating textual noise. Our approach utilizes a hybrid objective that balances user-item interactions against text-derived features, ensuring that user's both behavioral and linguistic signals are effectively captured. We evaluate this method on multiple datasets from diverse application domains, demonstrating consistent improvements over a baseline GNN-based recommender model. Notably, our model achieves significant gains in recommendation accuracy when review data is sparse or unevenly distributed. These findings highlight the importance of integrating LLM-driven textual feedback with GNN-derived user behavioral patterns to develop robust, context-aware recommender systems.

Tabular data is a crucial form of information expression, which can organize data in a standard structure for easy information retrieval and comparison. However, in financial industry and many other fields tables are often disclosed in unstructured digital files, e.g. Portable Document Format (PDF) and images, which are difficult to be extracted directly. In this paper, to facilitate deep learning based table extraction from unstructured digital files, we publish a standard Chinese dataset named FinTab, which contains more than 1,600 financial tables of diverse kinds and their corresponding structure representation in JSON. In addition, we propose a novel graph-based convolutional neural network model named GFTE as a baseline for future comparison. GFTE integrates image feature, position feature and textual feature together for precise edge prediction and reaches overall good results.

Graph Neural Networks (GNNs), especially message-passing neural networks (MPNNs), have emerged as powerful architectures for learning on graphs in diverse applications. However, MPNNs face challenges when modeling non-local interactions in graphs such as large conjugated molecules, and social networks due to oversmoothing and oversquashing. Although Spectral GNNs and traditional neural networks such as recurrent neural networks and transformers mitigate these challenges, they often lack generalizability, or fail to capture detailed structural relationships or symmetries in the data. To address these concerns, we introduce Matrix Function Neural Networks (MFNs), a novel architecture that parameterizes non-local interactions through analytic matrix equivariant functions. Employing resolvent expansions offers a straightforward implementation and the potential for linear scaling with system size. The MFN architecture achieves stateof-the-art performance in standard graph benchmarks, such as the ZINC and TU datasets, and is able to capture intricate non-local interactions in quantum systems, paving the way to new state-of-the-art force fields.

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance, but the vast chemical space and the limited availability of property labels make supervised learning challenging. Recently, unsupervised transformer-based language models pretrained on a large unlabelled corpus have produced state-of-the-art results in many downstream natural language processing tasks. Inspired by this development, we present molecular embeddings obtained by training an efficient transformer encoder model, MoLFormer, which uses rotary positional embeddings. This model employs a linear attention mechanism, coupled with highly distributed training, on SMILES sequences of 1.1 billion unlabelled molecules from the PubChem and ZINC datasets. We show that the learned molecular representation outperforms existing baselines, including supervised and self-supervised graph neural networks and language models, on several downstream tasks from ten benchmark datasets. They perform competitively on two others. Further analyses, specifically through the lens of attention, demonstrate that MoLFormer trained on chemical SMILES indeed learns the spatial relationships between atoms within a molecule. These results provide encouraging evidence that large-scale molecular language models can capture sufficient chemical and structural information to predict various distinct molecular properties, including quantum-chemical properties.

Graph mining is an important area in data mining and machine learning that involves extracting valuable information from graph-structured data. In recent years, significant progress has been made in this field through the development of graph neural networks (GNNs). However, GNNs are still deficient in generalizing to diverse graph data. Aiming to this issue, Large Language Models (LLMs) could provide new solutions for graph mining tasks with their superior semantic understanding. In this review, we systematically review the combination and application techniques of LLMs and GNNs and present a novel taxonomy for research in this interdisciplinary field, which involves three main categories: GNN-driving-LLM, LLM-driving-GNN, and GNN-LLM-co-driving. Within this framework, we reveal the capabilities of LLMs in enhancing graph feature extraction as well as improving the effectiveness of downstream tasks such as node classification, link prediction, and community detection. Although LLMs have demonstrated their great potential in handling graph-structured data, their high computational requirements and complexity remain challenges. Future research needs to continue to explore how to efficiently fuse LLMs and GNNs to achieve more powerful graph learning and reasoning capabilities and provide new impetus for the development of graph mining techniques.

Polynomial filters, a kind of Graph Neural Networks, typically use a predetermined polynomial basis and learn the coefficients from the training data. It has been observed that the effectiveness of the model is highly dependent on the property of the polynomial basis. Consequently, two natural and fundamental questions arise: Can we learn a suitable polynomial basis from the training data? Can we determine the optimal polynomial basis for a given graph and node features? In this paper, we propose two spectral GNN models that provide positive answers to the questions posed above. First, inspired by Favard's Theorem, we propose the FavardGNN model, which learns a polynomial basis from the space of all possible orthonormal bases. Second, we examine the supposedly unsolvable definition of optimal polynomial basis from Wang & Zhang (2022) and propose a simple model, OptBasisGNN, which computes the optimal basis for a given graph structure and graph signal. Extensive experiments are conducted to demonstrate the effectiveness of our proposed models.

Graph Neural Networks (GNNs) are neural models that leverage the dependency structure in graphical data via message passing among the graph nodes. GNNs have emerged as pivotal architectures in analyzing graph-structured data, and their expansive application in sensitive domains requires a comprehensive understanding of their decision-making processes -- necessitating a framework for GNN explainability. An explanation function for GNNs takes a pre-trained GNN along with a graph as input, to produce a `sufficient statistic' subgraph with respect to the graph label. A main challenge in studying GNN explainability is to provide fidelity measures that evaluate the performance of these explanation functions. This paper studies this foundational challenge, spotlighting the inherent limitations of prevailing fidelity metrics, including Fid_+, Fid_-, and Fid_Delta. Specifically, a formal, information-theoretic definition of explainability is introduced and it is shown that existing metrics often fail to align with this definition across various statistical scenarios. The reason is due to potential distribution shifts when subgraphs are removed in computing these fidelity measures. Subsequently, a robust class of fidelity measures are introduced, and it is shown analytically that they are resilient to distribution shift issues and are applicable in a wide range of scenarios. Extensive empirical analysis on both synthetic and real datasets are provided to illustrate that the proposed metrics are more coherent with gold standard metrics. The source code is available at https://trustai4s-lab.github.io/fidelity.

Graph Neural Networks (GNNs) are popular models for graph learning problems. GNNs show strong empirical performance in many practical tasks. However, the theoretical properties have not been completely elucidated. In this paper, we investigate whether GNNs can exploit the graph structure from the perspective of the expressive power of GNNs. In our analysis, we consider graph generation processes that are controlled by hidden (or latent) node features, which contain all information about the graph structure. A typical example of this framework is kNN graphs constructed from the hidden features. In our main results, we show that GNNs can recover the hidden node features from the input graph alone, even when all node features, including the hidden features themselves and any indirect hints, are unavailable. GNNs can further use the recovered node features for downstream tasks. These results show that GNNs can fully exploit the graph structure by themselves, and in effect, GNNs can use both the hidden and explicit node features for downstream tasks. In the experiments, we confirm the validity of our results by showing that GNNs can accurately recover the hidden features using a GNN architecture built based on our theoretical analysis.

Graph neural networks (GNNs) are effective models for representation learning on relational data. However, standard GNNs are limited in their expressive power, as they cannot distinguish graphs beyond the capability of the Weisfeiler-Leman graph isomorphism heuristic. In order to break this expressiveness barrier, GNNs have been enhanced with random node initialization (RNI), where the idea is to train and run the models with randomized initial node features. In this work, we analyze the expressive power of GNNs with RNI, and prove that these models are universal, a first such result for GNNs not relying on computationally demanding higher-order properties. This universality result holds even with partially randomized initial node features, and preserves the invariance properties of GNNs in expectation. We then empirically analyze the effect of RNI on GNNs, based on carefully constructed datasets. Our empirical findings support the superior performance of GNNs with RNI over standard GNNs.

Graph neural networks (GNNs) have recently become the standard approach for learning with graph-structured data. Prior work has shed light into their potential, but also their limitations. Unfortunately, it was shown that standard GNNs are limited in their expressive power. These models are no more powerful than the 1-dimensional Weisfeiler-Leman (1-WL) algorithm in terms of distinguishing non-isomorphic graphs. In this paper, we propose Path Neural Networks (PathNNs), a model that updates node representations by aggregating paths emanating from nodes. We derive three different variants of the PathNN model that aggregate single shortest paths, all shortest paths and all simple paths of length up to K. We prove that two of these variants are strictly more powerful than the 1-WL algorithm, and we experimentally validate our theoretical results. We find that PathNNs can distinguish pairs of non-isomorphic graphs that are indistinguishable by 1-WL, while our most expressive PathNN variant can even distinguish between 3-WL indistinguishable graphs. The different PathNN variants are also evaluated on graph classification and graph regression datasets, where in most cases, they outperform the baseline methods.

Many real-world data come in the form of graphs. Graph neural networks (GNNs), a new family of machine learning (ML) models, have been proposed to fully leverage graph data to build powerful applications. In particular, the inductive GNNs, which can generalize to unseen data, become mainstream in this direction. Machine learning models have shown great potential in various tasks and have been deployed in many real-world scenarios. To train a good model, a large amount of data as well as computational resources are needed, leading to valuable intellectual property. Previous research has shown that ML models are prone to model stealing attacks, which aim to steal the functionality of the target models. However, most of them focus on the models trained with images and texts. On the other hand, little attention has been paid to models trained with graph data, i.e., GNNs. In this paper, we fill the gap by proposing the first model stealing attacks against inductive GNNs. We systematically define the threat model and propose six attacks based on the adversary's background knowledge and the responses of the target models. Our evaluation on six benchmark datasets shows that the proposed model stealing attacks against GNNs achieve promising performance.

Graph neural network (GNN), as a powerful representation learning model on graph data, attracts much attention across various disciplines. However, recent studies show that GNN is vulnerable to adversarial attacks. How to make GNN more robust? What are the key vulnerabilities in GNN? How to address the vulnerabilities and defense GNN against the adversarial attacks? In this paper, we propose DefNet, an effective adversarial defense framework for GNNs. In particular, we first investigate the latent vulnerabilities in every layer of GNNs and propose corresponding strategies including dual-stage aggregation and bottleneck perceptron. Then, to cope with the scarcity of training data, we propose an adversarial contrastive learning method to train the GNN in a conditional GAN manner by leveraging the high-level graph representation. Extensive experiments on three public datasets demonstrate the effectiveness of DefNet in improving the robustness of popular GNN variants, such as Graph Convolutional Network and GraphSAGE, under various types of adversarial attacks.

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

Graph Neural Networks (GNNs) have become increasingly important due to their representational power and state-of-the-art predictive performance on many fundamental learning tasks. Despite this success, GNNs suffer from fairness issues that arise as a result of the underlying graph data and the fundamental aggregation mechanism that lies at the heart of the large class of GNN models. In this article, we examine and categorize fairness techniques for improving the fairness of GNNs. Previous work on fair GNN models and techniques are discussed in terms of whether they focus on improving fairness during a preprocessing step, during training, or in a post-processing phase. Furthermore, we discuss how such techniques can be used together whenever appropriate, and highlight the advantages and intuition as well. We also introduce an intuitive taxonomy for fairness evaluation metrics including graph-level fairness, neighborhood-level fairness, embedding-level fairness, and prediction-level fairness metrics. In addition, graph datasets that are useful for benchmarking the fairness of GNN models are summarized succinctly. Finally, we highlight key open problems and challenges that remain to be addressed.

Graph Neural Networks have gained huge interest in the past few years. These powerful algorithms expanded deep learning models to non-Euclidean space and were able to achieve state of art performance in various applications including recommender systems and social networks. However, this performance is based on static graph structures assumption which limits the Graph Neural Networks performance when the data varies with time. Spatiotemporal Graph Neural Networks are extension of Graph Neural Networks that takes the time factor into account. Recently, various Spatiotemporal Graph Neural Network algorithms were proposed and achieved superior performance compared to other deep learning algorithms in several time dependent applications. This survey discusses interesting topics related to Spatiotemporal Graph Neural Networks, including algorithms, applications, and open challenges.

Graph Neural Networks (GNNs) are a powerful technique for machine learning on graph-structured data, yet they pose challenges in interpretability. Existing GNN explanation methods usually yield technical outputs, such as subgraphs and feature importance scores, that are difficult for non-data scientists to understand and thereby violate the purpose of explanations. Motivated by recent Explainable AI (XAI) research, we propose GraphXAIN, a method that generates natural language narratives explaining GNN predictions. GraphXAIN is a model- and explainer-agnostic method that uses Large Language Models (LLMs) to translate explanatory subgraphs and feature importance scores into coherent, story-like explanations of GNN decision-making processes. Evaluations on real-world datasets demonstrate GraphXAIN's ability to improve graph explanations. A survey of machine learning researchers and practitioners reveals that GraphXAIN enhances four explainability dimensions: understandability, satisfaction, convincingness, and suitability for communicating model predictions. When combined with another graph explainer method, GraphXAIN further improves trustworthiness, insightfulness, confidence, and usability. Notably, 95% of participants found GraphXAIN to be a valuable addition to the GNN explanation method. By incorporating natural language narratives, our approach serves both graph practitioners and non-expert users by providing clearer and more effective explanations.

As the field of Graph Neural Networks (GNN) continues to grow, it experiences a corresponding increase in the need for large, real-world datasets to train and test new GNN models on challenging, realistic problems. Unfortunately, such graph datasets are often generated from online, highly privacy-restricted ecosystems, which makes research and development on these datasets hard, if not impossible. This greatly reduces the amount of benchmark graphs available to researchers, causing the field to rely only on a handful of publicly-available datasets. To address this problem, we introduce a novel graph generative model, Computation Graph Transformer (CGT) that learns and reproduces the distribution of real-world graphs in a privacy-controlled way. More specifically, CGT (1) generates effective benchmark graphs on which GNNs show similar task performance as on the source graphs, (2) scales to process large-scale graphs, (3) incorporates off-the-shelf privacy modules to guarantee end-user privacy of the generated graph. Extensive experiments across a vast body of graph generative models show that only our model can successfully generate privacy-controlled, synthetic substitutes of large-scale real-world graphs that can be effectively used to benchmark GNN models.

Conventional recommender systems are required to train the recommendation model using a centralized database. However, due to data privacy concerns, this is often impractical when multi-parties are involved in recommender system training. Federated learning appears as an excellent solution to the data isolation and privacy problem. Recently, Graph neural network (GNN) is becoming a promising approach for federated recommender systems. However, a key challenge is to conduct embedding propagation while preserving the privacy of the graph structure. Few studies have been conducted on the federated GNN-based recommender system. Our study proposes the first vertical federated GNN-based recommender system, called VerFedGNN. We design a framework to transmit: (i) the summation of neighbor embeddings using random projection, and (ii) gradients of public parameter perturbed by ternary quantization mechanism. Empirical studies show that VerFedGNN has competitive prediction accuracy with existing privacy preserving GNN frameworks while enhanced privacy protection for users' interaction information.

Transformer-based models dominate NLP tasks like sentiment analysis, machine translation, and claim verification. However, their massive computational demands and lack of interpretability pose challenges for real-world applications requiring efficiency and transparency. In this work, we explore Graph Neural Networks (GNNs) and Hyperbolic Graph Neural Networks (HGNNs) as lightweight yet effective alternatives for Environmental Claim Detection, reframing it as a graph classification problem. We construct dependency parsing graphs to explicitly model syntactic structures, using simple word embeddings (word2vec) for node features with dependency relations encoded as edge features. Our results demonstrate that these graph-based models achieve comparable or superior performance to state-of-the-art transformers while using 30x fewer parameters. This efficiency highlights the potential of structured, interpretable, and computationally efficient graph-based approaches.

Understanding the decision-making process of Graph Neural Networks (GNNs) is crucial to their interpretability. Most existing methods for explaining GNNs typically rely on training auxiliary models, resulting in the explanations remain black-boxed. This paper introduces Graph Output Attribution (GOAt), a novel method to attribute graph outputs to input graph features, creating GNN explanations that are faithful, discriminative, as well as stable across similar samples. By expanding the GNN as a sum of scalar products involving node features, edge features and activation patterns, we propose an efficient analytical method to compute contribution of each node or edge feature to each scalar product and aggregate the contributions from all scalar products in the expansion form to derive the importance of each node and edge. Through extensive experiments on synthetic and real-world data, we show that our method not only outperforms various state-ofthe-art GNN explainers in terms of the commonly used fidelity metric, but also exhibits stronger discriminability, and stability by a remarkable margin.

Safe deployment of graph neural networks (GNNs) under distribution shift requires models to provide accurate confidence indicators (CI). However, while it is well-known in computer vision that CI quality diminishes under distribution shift, this behavior remains understudied for GNNs. Hence, we begin with a case study on CI calibration under controlled structural and feature distribution shifts and demonstrate that increased expressivity or model size do not always lead to improved CI performance. Consequently, we instead advocate for the use of epistemic uncertainty quantification (UQ) methods to modulate CIs. To this end, we propose G-DeltaUQ, a new single model UQ method that extends the recently proposed stochastic centering framework to support structured data and partial stochasticity. Evaluated across covariate, concept, and graph size shifts, G-DeltaUQ not only outperforms several popular UQ methods in obtaining calibrated CIs, but also outperforms alternatives when CIs are used for generalization gap prediction or OOD detection. Overall, our work not only introduces a new, flexible GNN UQ method, but also provides novel insights into GNN CIs on safety-critical tasks.

In recent years, graph pre-training has gained significant attention, focusing on acquiring transferable knowledge from unlabeled graph data to improve downstream performance. Despite these recent endeavors, the problem of negative transfer remains a major concern when utilizing graph pre-trained models to downstream tasks. Previous studies made great efforts on the issue of what to pre-train and how to pre-train by designing a variety of graph pre-training and fine-tuning strategies. However, there are cases where even the most advanced "pre-train and fine-tune" paradigms fail to yield distinct benefits. This paper introduces a generic framework W2PGNN to answer the crucial question of when to pre-train (i.e., in what situations could we take advantage of graph pre-training) before performing effortful pre-training or fine-tuning. We start from a new perspective to explore the complex generative mechanisms from the pre-training data to downstream data. In particular, W2PGNN first fits the pre-training data into graphon bases, each element of graphon basis (i.e., a graphon) identifies a fundamental transferable pattern shared by a collection of pre-training graphs. All convex combinations of graphon bases give rise to a generator space, from which graphs generated form the solution space for those downstream data that can benefit from pre-training. In this manner, the feasibility of pre-training can be quantified as the generation probability of the downstream data from any generator in the generator space. W2PGNN offers three broad applications: providing the application scope of graph pre-trained models, quantifying the feasibility of pre-training, and assistance in selecting pre-training data to enhance downstream performance. We provide a theoretically sound solution for the first application and extensive empirical justifications for the latter two applications.

Graph neural networks have shown significant success in the field of graph representation learning. Graph convolutions perform neighborhood aggregation and represent one of the most important graph operations. Nevertheless, one layer of these neighborhood aggregation methods only consider immediate neighbors, and the performance decreases when going deeper to enable larger receptive fields. Several recent studies attribute this performance deterioration to the over-smoothing issue, which states that repeated propagation makes node representations of different classes indistinguishable. In this work, we study this observation systematically and develop new insights towards deeper graph neural networks. First, we provide a systematical analysis on this issue and argue that the key factor compromising the performance significantly is the entanglement of representation transformation and propagation in current graph convolution operations. After decoupling these two operations, deeper graph neural networks can be used to learn graph node representations from larger receptive fields. We further provide a theoretical analysis of the above observation when building very deep models, which can serve as a rigorous and gentle description of the over-smoothing issue. Based on our theoretical and empirical analysis, we propose Deep Adaptive Graph Neural Network (DAGNN) to adaptively incorporate information from large receptive fields. A set of experiments on citation, co-authorship, and co-purchase datasets have confirmed our analysis and insights and demonstrated the superiority of our proposed methods.

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs.GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models, and explaining predictions made by GNNs remains unsolved. Here we propose GNNExplainer, the first general, model-agnostic approach for providing interpretable explanations for predictions of any GNN-based model on any graph-based machine learning task. Given an instance, GNNExplainer identifies a compact subgraph structure and a small subset of node features that have a crucial role in GNN's prediction. Further, GNNExplainer can generate consistent and concise explanations for an entire class of instances. We formulate GNNExplainer as an optimization task that maximizes the mutual information between a GNN's prediction and distribution of possible subgraph structures. Experiments on synthetic and real-world graphs show that our approach can identify important graph structures as well as node features, and outperforms baselines by 17.1% on average. GNNExplainer provides a variety of benefits, from the ability to visualize semantically relevant structures to interpretability, to giving insights into errors of faulty GNNs.

Robotic odour source localization (OSL) is a critical capability for autonomous systems operating in complex environments. However, current OSL methods often suffer from ambiguities, particularly when robots misattribute odours to incorrect objects due to limitations in olfactory datasets and sensor resolutions. To address this challenge, we introduce a novel machine learning method using diffusion-based molecular generation to enhance odour localization accuracy that can be used by itself or with automated olfactory dataset construction pipelines with vision-language models (VLMs) This generative process of our diffusion model expands the chemical space beyond the limitations of both current olfactory datasets and the training data of VLMs, enabling the identification of potential odourant molecules not previously documented. The generated molecules can then be more accurately validated using advanced olfactory sensors which emulate human olfactory recognition through electronic sensor arrays. By integrating visual analysis, language processing, and molecular generation, our framework enhances the ability of olfaction-vision models on robots to accurately associate odours with their correct sources, thereby improving navigation and decision-making through better sensor selection for a target compound. Our methodology represents a foundational advancement in the field of artificial olfaction, offering a scalable solution to the challenges posed by limited olfactory data and sensor ambiguities.

Roman Numeral analysis is the important task of identifying chords and their functional context in pieces of tonal music. This paper presents a new approach to automatic Roman Numeral analysis in symbolic music. While existing techniques rely on an intermediate lossy representation of the score, we propose a new method based on Graph Neural Networks (GNNs) that enable the direct description and processing of each individual note in the score. The proposed architecture can leverage notewise features and interdependencies between notes but yield onset-wise representation by virtue of our novel edge contraction algorithm. Our results demonstrate that ChordGNN outperforms existing state-of-the-art models, achieving higher accuracy in Roman Numeral analysis on the reference datasets. In addition, we investigate variants of our model using proposed techniques such as NADE, and post-processing of the chord predictions. The full source code for this work is available at https://github.com/manoskary/chordgnn

Developing models that can learn to reason is a notoriously challenging problem. We focus on reasoning in relational domains, where the use of Graph Neural Networks (GNNs) seems like a natural choice. However, previous work has shown that regular GNNs lack the ability to systematically generalize from training examples on test graphs requiring longer inference chains, which fundamentally limits their reasoning abilities. A common solution relies on neuro-symbolic methods that systematically reason by learning rules, but their scalability is often limited and they tend to make unrealistically strong assumptions, e.g.\ that the answer can always be inferred from a single relational path. We propose the Epistemic GNN (EpiGNN), a novel parameter-efficient and scalable GNN architecture with an epistemic inductive bias for systematic reasoning. Node embeddings in EpiGNNs are treated as epistemic states, and message passing is implemented accordingly. We show that EpiGNNs achieve state-of-the-art results on link prediction tasks that require systematic reasoning. Furthermore, for inductive knowledge graph completion, EpiGNNs rival the performance of state-of-the-art specialized approaches. Finally, we introduce two new benchmarks that go beyond standard relational reasoning by requiring the aggregation of information from multiple paths. Here, existing neuro-symbolic approaches fail, yet EpiGNNs learn to reason accurately. Code and datasets are available at https://github.com/erg0dic/gnn-sg.

AutoML systems build machine learning models automatically by performing a search over valid data transformations and learners, along with hyper-parameter optimization for each learner. Many AutoML systems use meta-learning to guide search for optimal pipelines. In this work, we present a novel meta-learning system called KGpip which, (1) builds a database of datasets and corresponding pipelines by mining thousands of scripts with program analysis, (2) uses dataset embeddings to find similar datasets in the database based on its content instead of metadata-based features, (3) models AutoML pipeline creation as a graph generation problem, to succinctly characterize the diverse pipelines seen for a single dataset. KGpip's meta-learning is a sub-component for AutoML systems. We demonstrate this by integrating KGpip with two AutoML systems. Our comprehensive evaluation using 126 datasets, including those used by the state-of-the-art systems, shows that KGpip significantly outperforms these systems.

Accurately predicting the criticalness of ICU patients (such as in-ICU mortality risk) is vital for early intervention in critical care. However, conventional models often treat each patient in isolation and struggle to exploit the relational structure in Electronic Health Records (EHR). We propose a Similarity-Based Self-Construct Graph Model (SBSCGM) that dynamically builds a patient similarity graph from multi-modal EHR data, and a HybridGraphMedGNN architecture that operates on this graph to predict patient mortality and a continuous criticalness score. SBSCGM uses a hybrid similarity measure (combining feature-based and structural similarities) to connect patients with analogous clinical profiles in real-time. The HybridGraphMedGNN integrates Graph Convolutional Network (GCN), GraphSAGE, and Graph Attention Network (GAT) layers to learn robust patient representations, leveraging both local and global graph patterns. In experiments on 6,000 ICU stays from the MIMIC-III dataset, our model achieves state-of-the-art performance (AUC-ROC 0.94) outperforming baseline classifiers and single-type GNN models. We also demonstrate improved precision/recall and show that the attention mechanism provides interpretable insights into model predictions. Our framework offers a scalable and interpretable solution for critical care risk prediction, with potential to support clinicians in real-world ICU deployment.

We propose SAM-Road, an adaptation of the Segment Anything Model (SAM) for extracting large-scale, vectorized road network graphs from satellite imagery. To predict graph geometry, we formulate it as a dense semantic segmentation task, leveraging the inherent strengths of SAM. The image encoder of SAM is fine-tuned to produce probability masks for roads and intersections, from which the graph vertices are extracted via simple non-maximum suppression. To predict graph topology, we designed a lightweight transformer-based graph neural network, which leverages the SAM image embeddings to estimate the edge existence probabilities between vertices. Our approach directly predicts the graph vertices and edges for large regions without expensive and complex post-processing heuristics, and is capable of building complete road network graphs spanning multiple square kilometers in a matter of seconds. With its simple, straightforward, and minimalist design, SAM-Road achieves comparable accuracy with the state-of-the-art method RNGDet++, while being 40 times faster on the City-scale dataset. We thus demonstrate the power of a foundational vision model when applied to a graph learning task. The code is available at https://github.com/htcr/sam_road.

The simulation of large-scale systems with complex electron interactions remains one of the greatest challenges for the atomistic modeling of materials. Although classical force fields often fail to describe the coupling between electronic states and ionic rearrangements, the more accurate ab-initio molecular dynamics suffers from computational complexity that prevents long-time and large-scale simulations, which are essential to study many technologically relevant phenomena, such as reactions, ion migrations, phase transformations, and degradation. In this work, we present the Crystal Hamiltonian Graph neural Network (CHGNet) as a novel machine-learning interatomic potential (MLIP), using a graph-neural-network-based force field to model a universal potential energy surface. CHGNet is pretrained on the energies, forces, stresses, and magnetic moments from the Materials Project Trajectory Dataset, which consists of over 10 years of density functional theory static and relaxation trajectories of sim 1.5 million inorganic structures. The explicit inclusion of magnetic moments enables CHGNet to learn and accurately represent the orbital occupancy of electrons, enhancing its capability to describe both atomic and electronic degrees of freedom. We demonstrate several applications of CHGNet in solid-state materials, including charge-informed molecular dynamics in Li_xMnO_2, the finite temperature phase diagram for Li_xFePO_4 and Li diffusion in garnet conductors. We critically analyze the significance of including charge information for capturing appropriate chemistry, and we provide new insights into ionic systems with additional electronic degrees of freedom that can not be observed by previous MLIPs.

Graph Neural Networks (GNNs) have demonstrated superior performance on various graph learning tasks, including recommendation, where they leverage user-item collaborative filtering signals in graphs. However, theoretical formulations of their capability are scarce, despite their empirical effectiveness in state-of-the-art recommender models. Recently, research has explored the expressiveness of GNNs in general, demonstrating that message passing GNNs are at most as powerful as the Weisfeiler-Lehman test, and that GNNs combined with random node initialization are universal. Nevertheless, the concept of "expressiveness" for GNNs remains vaguely defined. Most existing works adopt the graph isomorphism test as the metric of expressiveness, but this graph-level task may not effectively assess a model's ability in recommendation, where the objective is to distinguish nodes of different closeness. In this paper, we provide a comprehensive theoretical analysis of the expressiveness of GNNs in recommendation, considering three levels of expressiveness metrics: graph isomorphism (graph-level), node automorphism (node-level), and topological closeness (link-level). We propose the topological closeness metric to evaluate GNNs' ability to capture the structural distance between nodes, which aligns closely with the objective of recommendation. To validate the effectiveness of this new metric in evaluating recommendation performance, we introduce a learning-less GNN algorithm that is optimal on the new metric and can be optimal on the node-level metric with suitable modification. We conduct extensive experiments comparing the proposed algorithm against various types of state-of-the-art GNN models to explore the explainability of the new metric in the recommendation task. For reproducibility, implementation codes are available at https://github.com/HKUDS/GTE.

Truck parking on freight corridors faces the major challenge of insufficient parking spaces. This is exacerbated by the Hour-of-Service (HOS) regulations, which often result in unauthorized parking practices, causing safety concerns. It has been shown that providing accurate parking usage prediction can be a cost-effective solution to reduce unsafe parking practices. In light of this, existing studies have developed various methods to predict the usage of a truck parking site and have demonstrated satisfactory accuracy. However, these studies focused on a single parking site, and few approaches have been proposed to predict the usage of multiple truck parking sites considering spatio-temporal dependencies, due to the lack of data. This paper aims to fill this gap and presents the Regional Temporal Graph Convolutional Network (RegT-GCN) to predict parking usage across the entire state to provide more comprehensive truck parking information. The framework leverages the topological structures of truck parking site locations and historical parking data to predict the occupancy rate considering spatio-temporal dependencies across a state. To achieve this, we introduce a Regional Decomposition approach, which effectively captures the geographical characteristics of the truck parking locations and their spatial correlations. Evaluation results demonstrate that the proposed model outperforms other baseline models, showing the effectiveness of our regional decomposition. The code is available at https://github.com/raynbowy23/RegT-GCN.

We present a Morphology-Informed Heterogeneous Graph Neural Network (MI-HGNN) for learning-based contact perception. The architecture and connectivity of the MI-HGNN are constructed from the robot morphology, in which nodes and edges are robot joints and links, respectively. By incorporating the morphology-informed constraints into a neural network, we improve a learning-based approach using model-based knowledge. We apply the proposed MI-HGNN to two contact perception problems, and conduct extensive experiments using both real-world and simulated data collected using two quadruped robots. Our experiments demonstrate the superiority of our method in terms of effectiveness, generalization ability, model efficiency, and sample efficiency. Our MI-HGNN improved the performance of a state-of-the-art model that leverages robot morphological symmetry by 8.4% with only 0.21% of its parameters. Although MI-HGNN is applied to contact perception problems for legged robots in this work, it can be seamlessly applied to other types of multi-body dynamical systems and has the potential to improve other robot learning frameworks. Our code is made publicly available at https://github.com/lunarlab-gatech/Morphology-Informed-HGNN.

Graph Neural Networks (GNNs) with equivariant properties have emerged as powerful tools for modeling complex dynamics of multi-object physical systems. However, their generalization ability is limited by the inadequate consideration of physical inductive biases: (1) Existing studies overlook the continuity of transitions among system states, opting to employ several discrete transformation layers to learn the direct mapping between two adjacent states; (2) Most models only account for first-order velocity information, despite the fact that many physical systems are governed by second-order motion laws. To incorporate these inductive biases, we propose the Second-order Equivariant Graph Neural Ordinary Differential Equation (SEGNO). Specifically, we show how the second-order continuity can be incorporated into GNNs while maintaining the equivariant property. Furthermore, we offer theoretical insights into SEGNO, highlighting that it can learn a unique trajectory between adjacent states, which is crucial for model generalization. Additionally, we prove that the discrepancy between this learned trajectory of SEGNO and the true trajectory is bounded. Extensive experiments on complex dynamical systems including molecular dynamics and motion capture demonstrate that our model yields a significant improvement over the state-of-the-art baselines.

Self-supervised learning (SSL) for graph neural networks (GNNs) has attracted increasing attention from the graph machine learning community in recent years, owing to its capability to learn performant node embeddings without costly label information. One weakness of conventional SSL frameworks for GNNs is that they learn through a single philosophy, such as mutual information maximization or generative reconstruction. When applied to various downstream tasks, these frameworks rarely perform equally well for every task, because one philosophy may not span the extensive knowledge required for all tasks. To enhance the task generalization across tasks, as an important first step forward in exploring fundamental graph models, we introduce PARETOGNN, a multi-task SSL framework for node representation learning over graphs. Specifically, PARETOGNN is self-supervised by manifold pretext tasks observing multiple philosophies. To reconcile different philosophies, we explore a multiple-gradient descent algorithm, such that PARETOGNN actively learns from every pretext task while minimizing potential conflicts. We conduct comprehensive experiments over four downstream tasks (i.e., node classification, node clustering, link prediction, and partition prediction), and our proposal achieves the best overall performance across tasks on 11 widely adopted benchmark datasets. Besides, we observe that learning from multiple philosophies enhances not only the task generalization but also the single task performances, demonstrating that PARETOGNN achieves better task generalization via the disjoint yet complementary knowledge learned from different philosophies. Our code is publicly available at https://github.com/jumxglhf/ParetoGNN.

Deep Graph Neural Networks (GNNs) show promising performance on a range of graph tasks, yet at present are costly to run and lack many of the optimisations applied to DNNs. We show, for the first time, how to systematically quantise GNNs with minimal or no loss in performance using Network Architecture Search (NAS). We define the possible quantisation search space of GNNs. The proposed novel NAS mechanism, named Low Precision Graph NAS (LPGNAS), constrains both architecture and quantisation choices to be differentiable. LPGNAS learns the optimal architecture coupled with the best quantisation strategy for different components in the GNN automatically using back-propagation in a single search round. On eight different datasets, solving the task of classifying unseen nodes in a graph, LPGNAS generates quantised models with significant reductions in both model and buffer sizes but with similar accuracy to manually designed networks and other NAS results. In particular, on the Pubmed dataset, LPGNAS shows a better size-accuracy Pareto frontier compared to seven other manual and searched baselines, offering a 2.3 times reduction in model size but a 0.4% increase in accuracy when compared to the best NAS competitor. Finally, from our collected quantisation statistics on a wide range of datasets, we suggest a W4A8 (4-bit weights, 8-bit activations) quantisation strategy might be the bottleneck for naive GNN quantisations.

Graph neural networks (GNNs) have shown great power in modeling graph structured data. However, similar to other machine learning models, GNNs may make predictions biased on protected sensitive attributes, e.g., skin color and gender. Because machine learning algorithms including GNNs are trained to reflect the distribution of the training data which often contains historical bias towards sensitive attributes. In addition, the discrimination in GNNs can be magnified by graph structures and the message-passing mechanism. As a result, the applications of GNNs in sensitive domains such as crime rate prediction would be largely limited. Though extensive studies of fair classification have been conducted on i.i.d data, methods to address the problem of discrimination on non-i.i.d data are rather limited. Furthermore, the practical scenario of sparse annotations in sensitive attributes is rarely considered in existing works. Therefore, we study the novel and important problem of learning fair GNNs with limited sensitive attribute information. FairGNN is proposed to eliminate the bias of GNNs whilst maintaining high node classification accuracy by leveraging graph structures and limited sensitive information. Our theoretical analysis shows that FairGNN can ensure the fairness of GNNs under mild conditions given limited nodes with known sensitive attributes. Extensive experiments on real-world datasets also demonstrate the effectiveness of FairGNN in debiasing and keeping high accuracy.

Understanding where people go after visiting one business is crucial for urban planning, retail analytics, and location-based services. However, predicting these co-visitation patterns across millions of venues remains challenging due to extreme data sparsity and the complex interplay between spatial proximity and business relationships. Traditional approaches using only geographic distance fail to capture why coffee shops attract different customer flows than fine dining restaurants, even when co-located. We introduce NAICS-aware GraphSAGE, a novel graph neural network that integrates business taxonomy knowledge through learnable embeddings to predict population-scale co-visitation patterns. Our key insight is that business semantics, captured through detailed industry codes, provide crucial signals that pure spatial models cannot explain. The approach scales to massive datasets (4.2 billion potential venue pairs) through efficient state-wise decomposition while combining spatial, temporal, and socioeconomic features in an end-to-end framework. Evaluated on our POI-Graph dataset comprising 94.9 million co-visitation records across 92,486 brands and 48 US states, our method achieves significant improvements over state-of-the-art baselines: the R-squared value increases from 0.243 to 0.625 (a 157 percent improvement), with strong gains in ranking quality (32 percent improvement in NDCG at 10).

Graph neural networks aim to learn representations for graph-structured data and show impressive performance, particularly in node classification. Recently, many methods have studied the representations of GNNs from the perspective of optimization goals and spectral graph theory. However, the feature space that dominates representation learning has not been systematically studied in graph neural networks. In this paper, we propose to fill this gap by analyzing the feature space of both spatial and spectral models. We decompose graph neural networks into determined feature spaces and trainable weights, providing the convenience of studying the feature space explicitly using matrix space analysis. In particular, we theoretically find that the feature space tends to be linearly correlated due to repeated aggregations. Motivated by these findings, we propose 1) feature subspaces flattening and 2) structural principal components to expand the feature space. Extensive experiments verify the effectiveness of our proposed more comprehensive feature space, with comparable inference time to the baseline, and demonstrate its efficient convergence capability.

Graph Neural Networks (GNNs) are a popular technique for modelling graph-structured data and computing node-level representations via aggregation of information from the neighborhood of each node. However, this aggregation implies an increased risk of revealing sensitive information, as a node can participate in the inference for multiple nodes. This implies that standard privacy-preserving machine learning techniques, such as differentially private stochastic gradient descent (DP-SGD) - which are designed for situations where each data point participates in the inference for one point only - either do not apply, or lead to inaccurate models. In this work, we formally define the problem of learning GNN parameters with node-level privacy, and provide an algorithmic solution with a strong differential privacy guarantee. We employ a careful sensitivity analysis and provide a non-trivial extension of the privacy-by-amplification technique to the GNN setting. An empirical evaluation on standard benchmark datasets demonstrates that our method is indeed able to learn accurate privacy-preserving GNNs which outperform both private and non-private methods that completely ignore graph information.

Anatomical segmentation is a fundamental task in medical image computing, generally tackled with fully convolutional neural networks which produce dense segmentation masks. These models are often trained with loss functions such as cross-entropy or Dice, which assume pixels to be independent of each other, thus ignoring topological errors and anatomical inconsistencies. We address this limitation by moving from pixel-level to graph representations, which allow to naturally incorporate anatomical constraints by construction. To this end, we introduce HybridGNet, an encoder-decoder neural architecture that leverages standard convolutions for image feature encoding and graph convolutional neural networks (GCNNs) to decode plausible representations of anatomical structures. We also propose a novel image-to-graph skip connection layer which allows localized features to flow from standard convolutional blocks to GCNN blocks, and show that it improves segmentation accuracy. The proposed architecture is extensively evaluated in a variety of domain shift and image occlusion scenarios, and audited considering different types of demographic domain shift. Our comprehensive experimental setup compares HybridGNet with other landmark and pixel-based models for anatomical segmentation in chest x-ray images, and shows that it produces anatomically plausible results in challenging scenarios where other models tend to fail.

Geometric Deep Learning has recently attracted significant interest in a wide range of machine learning fields, including document analysis. The application of Graph Neural Networks (GNNs) has become crucial in various document-related tasks since they can unravel important structural patterns, fundamental in key information extraction processes. Previous works in the literature propose task-driven models and do not take into account the full power of graphs. We propose Doc2Graph, a task-agnostic document understanding framework based on a GNN model, to solve different tasks given different types of documents. We evaluated our approach on two challenging datasets for key information extraction in form understanding, invoice layout analysis and table detection. Our code is freely accessible on https://github.com/andreagemelli/doc2graph.

Property prediction plays an important role in material discovery. As an initial step to eventually develop a foundation model for material science, we introduce a new autoencoder called the MHG-GNN, which combines graph neural network (GNN) with Molecular Hypergraph Grammar (MHG). Results on a variety of property prediction tasks with diverse materials show that MHG-GNN is promising.

Fairness-aware graph neural networks (GNNs) have gained a surge of attention as they can reduce the bias of predictions on any demographic group (e.g., female) in graph-based applications. Although these methods greatly improve the algorithmic fairness of GNNs, the fairness can be easily corrupted by carefully designed adversarial attacks. In this paper, we investigate the problem of adversarial attacks on fairness of GNNs and propose G-FairAttack, a general framework for attacking various types of fairness-aware GNNs in terms of fairness with an unnoticeable effect on prediction utility. In addition, we propose a fast computation technique to reduce the time complexity of G-FairAttack. The experimental study demonstrates that G-FairAttack successfully corrupts the fairness of different types of GNNs while keeping the attack unnoticeable. Our study on fairness attacks sheds light on potential vulnerabilities in fairness-aware GNNs and guides further research on the robustness of GNNs in terms of fairness.

Graph neural networks (GNNs) have been demonstrated to be powerful in modeling graph-structured data. However, training GNNs usually requires abundant task-specific labeled data, which is often arduously expensive to obtain. One effective way to reduce the labeling effort is to pre-train an expressive GNN model on unlabeled data with self-supervision and then transfer the learned model to downstream tasks with only a few labels. In this paper, we present the GPT-GNN framework to initialize GNNs by generative pre-training. GPT-GNN introduces a self-supervised attributed graph generation task to pre-train a GNN so that it can capture the structural and semantic properties of the graph. We factorize the likelihood of the graph generation into two components: 1) Attribute Generation and 2) Edge Generation. By modeling both components, GPT-GNN captures the inherent dependency between node attributes and graph structure during the generative process. Comprehensive experiments on the billion-scale Open Academic Graph and Amazon recommendation data demonstrate that GPT-GNN significantly outperforms state-of-the-art GNN models without pre-training by up to 9.1% across various downstream tasks.

A new research framework is proposed to incorporate machine learning techniques into the field of experimental chemistry to facilitate chromatographic enantioseparation. A documentary dataset of chiral molecular retention times (CMRT dataset) in high-performance liquid chromatography is established to handle the challenge of data acquisition. Based on the CMRT dataset, a quantile geometry-enhanced graph neural network is proposed to learn the molecular structure-retention time relationship, which shows a satisfactory predictive ability for enantiomers. The domain knowledge of chromatography is incorporated into the machine learning model to achieve multi-column prediction, which paves the way for chromatographic enantioseparation prediction by calculating the separation probability. Experiments confirm that the proposed research framework works well in retention time prediction and chromatographic enantioseparation facilitation, which sheds light on the application of machine learning techniques to the experimental scene and improves the efficiency of experimenters to speed up scientific discovery.

In node classification using graph neural networks (GNNs), a typical model generates logits for different class labels at each node. A softmax layer often outputs a label prediction based on the largest logit. We demonstrate that it is possible to infer hidden graph structural information from the dataset using these logits. We introduce the key notion of label non-uniformity, which is derived from the Wasserstein distance between the softmax distribution of the logits and the uniform distribution. We demonstrate that nodes with small label non-uniformity are harder to classify correctly. We theoretically analyze how the label non-uniformity varies across the graph, which provides insights into boosting the model performance: increasing training samples with high non-uniformity or dropping edges to reduce the maximal cut size of the node set of small non-uniformity. These mechanisms can be easily added to a base GNN model. Experimental results demonstrate that our approach improves the performance of many benchmark base models.

In the field of deep learning, Graph Neural Networks (GNNs) and Graph Transformer models, with their outstanding performance and flexible architectural designs, have become leading technologies for processing structured data, especially graph data. Traditional GNNs often face challenges in capturing information from distant vertices effectively. In contrast, Graph Transformer models are particularly adept at managing long-distance node relationships. Despite these advantages, Graph Transformer models still encounter issues with computational and storage efficiency when scaled to large graph datasets. To address these challenges, we propose an innovative Graph Neural Network (GNN) architecture that integrates a Top-m attention mechanism aggregation component and a neighborhood aggregation component, effectively enhancing the model's ability to aggregate relevant information from both local and extended neighborhoods at each layer. This method not only improves computational efficiency but also enriches the node features, facilitating a deeper analysis of complex graph structures. Additionally, to assess the effectiveness of our proposed model, we have applied it to citation sentiment prediction, a novel task previously unexplored in the GNN field. Accordingly, we constructed a dedicated citation network, ArXivNet. In this dataset, we specifically annotated the sentiment polarity of the citations (positive, neutral, negative) to enable in-depth sentiment analysis. Our approach has shown superior performance across a variety of tasks including vertex classification, link prediction, sentiment prediction, graph regression, and visualization. It outperforms existing methods in terms of effectiveness, as demonstrated by experimental results on multiple datasets.

Learning to represent free text is a core task in many clinical machine learning (ML) applications, as clinical text contains observations and plans not otherwise available for inference. State-of-the-art methods use large language models developed with immense computational resources and training data; however, applying these models is challenging because of the highly varying syntax and vocabulary in clinical free text. Structured information such as International Classification of Disease (ICD) codes often succinctly abstracts the most important facts of a clinical encounter and yields good performance, but is often not as available as clinical text in real-world scenarios. We propose a multi-view learning framework that jointly learns from codes and text to combine the availability and forward-looking nature of text and better performance of ICD codes. The learned text embeddings can be used as inputs to predictive algorithms independent of the ICD codes during inference. Our approach uses a Graph Neural Network (GNN) to process ICD codes, and Bi-LSTM to process text. We apply Deep Canonical Correlation Analysis (DCCA) to enforce the two views to learn a similar representation of each patient. In experiments using planned surgical procedure text, our model outperforms BERT models fine-tuned to clinical data, and in experiments using diverse text in MIMIC-III, our model is competitive to a fine-tuned BERT at a tiny fraction of its computational effort.

In this study, we propose a novel graph neural network called propagate-selector (PS), which propagates information over sentences to understand information that cannot be inferred when considering sentences in isolation. First, we design a graph structure in which each node represents an individual sentence, and some pairs of nodes are selectively connected based on the text structure. Then, we develop an iterative attentive aggregation and a skip-combine method in which a node interacts with its neighborhood nodes to accumulate the necessary information. To evaluate the performance of the proposed approaches, we conduct experiments with the standard HotpotQA dataset. The empirical results demonstrate the superiority of our proposed approach, which obtains the best performances, compared to the widely used answer-selection models that do not consider the intersentential relationship.

Recently, data-driven simulators based on graph neural networks have gained attention in modeling physical systems on unstructured meshes. However, they struggle with long-range dependencies in fluid flows, particularly in refined mesh regions. This challenge, known as the 'over-squashing' problem, hinders information propagation. While existing graph rewiring methods address this issue to some extent, they only consider graph topology, overlooking the underlying physical phenomena. We propose Physics-Informed Ollivier-Ricci Flow (PIORF), a novel rewiring method that combines physical correlations with graph topology. PIORF uses Ollivier-Ricci curvature (ORC) to identify bottleneck regions and connects these areas with nodes in high-velocity gradient nodes, enabling long-range interactions and mitigating over-squashing. Our approach is computationally efficient in rewiring edges and can scale to larger simulations. Experimental results on 3 fluid dynamics benchmark datasets show that PIORF consistently outperforms baseline models and existing rewiring methods, achieving up to 26.2 improvement.

AutoML has demonstrated remarkable success in finding an effective neural architecture for a given machine learning task defined by a specific dataset and an evaluation metric. However, most present AutoML techniques consider each task independently from scratch, which requires exploring many architectures, leading to high computational cost. Here we propose AutoTransfer, an AutoML solution that improves search efficiency by transferring the prior architectural design knowledge to the novel task of interest. Our key innovation includes a task-model bank that captures the model performance over a diverse set of GNN architectures and tasks, and a computationally efficient task embedding that can accurately measure the similarity among different tasks. Based on the task-model bank and the task embeddings, we estimate the design priors of desirable models of the novel task, by aggregating a similarity-weighted sum of the top-K design distributions on tasks that are similar to the task of interest. The computed design priors can be used with any AutoML search algorithm. We evaluate AutoTransfer on six datasets in the graph machine learning domain. Experiments demonstrate that (i) our proposed task embedding can be computed efficiently, and that tasks with similar embeddings have similar best-performing architectures; (ii) AutoTransfer significantly improves search efficiency with the transferred design priors, reducing the number of explored architectures by an order of magnitude. Finally, we release GNN-Bank-101, a large-scale dataset of detailed GNN training information of 120,000 task-model combinations to facilitate and inspire future research.

As an alternative to classical numerical solvers for partial differential equations (PDEs) subject to boundary value constraints, there has been a surge of interest in investigating neural networks that can solve such problems efficiently. In this work, we design a general solution operator for two different time-independent PDEs using graph neural networks (GNNs) and spectral graph convolutions. We train the networks on simulated data from a finite elements solver on a variety of shapes and inhomogeneities. In contrast to previous works, we focus on the ability of the trained operator to generalize to previously unseen scenarios. Specifically, we test generalization to meshes with different shapes and superposition of solutions for a different number of inhomogeneities. We find that training on a diverse dataset with lots of variation in the finite element meshes is a key ingredient for achieving good generalization results in all cases. With this, we believe that GNNs can be used to learn solution operators that generalize over a range of properties and produce solutions much faster than a generic solver. Our dataset, which we make publicly available, can be used and extended to verify the robustness of these models under varying conditions.

The interrupting swap-allowed blocking job shop problem (ISBJSSP) is a complex scheduling problem that is able to model many manufacturing planning and logistics applications realistically by addressing both the lack of storage capacity and unforeseen production interruptions. Subjected to random disruptions due to machine malfunction or maintenance, industry production settings often choose to adopt dispatching rules to enable adaptive, real-time re-scheduling, rather than traditional methods that require costly re-computation on the new configuration every time the problem condition changes dynamically. To generate dispatching rules for the ISBJSSP problem, a method that uses graph neural networks and reinforcement learning is proposed. ISBJSSP is formulated as a Markov decision process. Using proximal policy optimization, an optimal scheduling policy is learnt from randomly generated instances. Employing a set of reported benchmark instances, we conduct a detailed experimental study on ISBJSSP instances with a range of machine shutdown probabilities to show that the scheduling policies generated can outperform or are at least as competitive as existing dispatching rules with predetermined priority. This study shows that the ISBJSSP, which requires real-time adaptive solutions, can be scheduled efficiently with the proposed machine learning method when production interruptions occur with random machine shutdowns.

Relational graph neural networks (RGNNs) are graph neural networks (GNNs) with dedicated structures for modeling the different types of nodes and/or edges in heterogeneous graphs. While RGNNs have been increasingly adopted in many real-world applications due to their versatility and accuracy, they pose performance and system design challenges due to their inherent computation patterns, gap between the programming interface and kernel APIs, and heavy programming efforts in optimizing kernels caused by their coupling with data layout and heterogeneity. To systematically address these challenges, we propose Pigeon, a novel two-level intermediate representation (IR) and its code generator framework, that (a) represents the key properties of the RGNN models to bridge the gap between the programming interface and kernel APIs, (b) decouples model semantics, data layout, and operators-specific optimization from each other to reduce programming efforts, (c) expresses and leverages optimization opportunities in inter-operator transforms, data layout, and operator-specific schedules. By building on one general matrix multiply (GEMM) template and a node/edge traversal template, Pigeon achieves up to 7.8x speed-up in inference and 5.6x speed-up in training compared with the state-of-the-art public systems in select models, i.e., RGCN, RGAT, HGT, when running heterogeneous graphs provided by Deep Graph Library (DGL) and Open Graph Benchmark (OGB). Pigeon also triggers fewer out-of-memory (OOM) errors. In addition, we propose linear operator fusion and compact materialization to further accelerate the system by up to 2.2x.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

Graph Neural Networks (GNNs) have advanced graph structure understanding via recursive information exchange and aggregation among graph nodes. To improve model robustness, self-supervised learning (SSL) has emerged as a promising approach for data augmentation. However, existing methods for generating pre-trained graph embeddings often rely on fine-tuning with specific downstream task labels, which limits their usability in scenarios where labeled data is scarce or unavailable. To address this, our research focuses on advancing the generalization capabilities of graph models in challenging zero-shot learning scenarios. Inspired by the success of large language models (LLMs), we aim to develop a graph-oriented LLM that can achieve high generalization across diverse downstream datasets and tasks, even without any information available from the downstream graph data. In this work, we present the GraphGPT framework that aligns LLMs with graph structural knowledge with a graph instruction tuning paradigm. Our framework incorporates a text-graph grounding component to establish a connection between textual information and graph structures. Additionally, we propose a dual-stage instruction tuning paradigm, accompanied by a lightweight graph-text alignment projector. This paradigm explores self-supervised graph structural signals and task-specific graph instructions, to guide LLMs in understanding complex graph structures and improving their adaptability across different downstream tasks. Our framework is evaluated on supervised and zero-shot graph learning tasks, demonstrating superior generalization and outperforming state-of-the-art baselines.

Graph Neural Networks (GNNs) have shown promising potential in graph representation learning. The majority of GNNs define a local message-passing mechanism, propagating information over the graph by stacking multiple layers. These methods, however, are known to suffer from two major limitations: over-squashing and poor capturing of long-range dependencies. Recently, Graph Transformers (GTs) emerged as a powerful alternative to Message-Passing Neural Networks (MPNNs). GTs, however, have quadratic computational cost, lack inductive biases on graph structures, and rely on complex Positional/Structural Encodings (SE/PE). In this paper, we show that while Transformers, complex message-passing, and SE/PE are sufficient for good performance in practice, neither is necessary. Motivated by the recent success of State Space Models (SSMs), such as Mamba, we present Graph Mamba Networks (GMNs), a general framework for a new class of GNNs based on selective SSMs. We discuss and categorize the new challenges when adopting SSMs to graph-structured data, and present four required and one optional steps to design GMNs, where we choose (1) Neighborhood Tokenization, (2) Token Ordering, (3) Architecture of Bidirectional Selective SSM Encoder, (4) Local Encoding, and dispensable (5) PE and SE. We further provide theoretical justification for the power of GMNs. Experiments demonstrate that despite much less computational cost, GMNs attain an outstanding performance in long-range, small-scale, large-scale, and heterophilic benchmark datasets.

Programming languages possess rich semantic information such as data flow that is represented by graphs and not available from the surface form of source code. Recent code language models have scaled to billions of parameters, but model source code solely as text tokens while ignoring any other structural information. Conversely, models that do encode structural information of code make modifications to the Transformer architecture, limiting their scale and compatibility with pretrained LLMs. In this work, we take the best of both worlds with GALLa - Graph Aligned Large Language Model. GALLa utilizes graph neural networks and cross-modal alignment technologies to inject the structural information of code into LLMs as an auxiliary task during finetuning. This framework is both model-agnostic and task-agnostic, as it can be applied to any code LLM for any code downstream task, and requires the structural graph data only at training time from a corpus unrelated to the finetuning data, while incurring no cost at inference time over the baseline LLM. Experiments on five code tasks with four different baseline LLMs ranging in size from 350M to 8B validate the effectiveness of GALLa, demonstrating consistent improvement over the baseline, even for powerful models such as LLaMA3.

Graph-structured data plays a vital role in numerous domains, such as social networks, citation networks, commonsense reasoning graphs and knowledge graphs. While graph neural networks have been employed for graph processing, recent advancements have explored integrating large language models for graph-based tasks. In this paper, we propose a novel approach named Learnable Graph Pooling Token (LGPT), which addresses the limitations of the scalability issues in node-level projection and information loss in graph-level projection. LGPT enables flexible and efficient graph representation by introducing learnable parameters that act as tokens in large language models, balancing fine-grained and global graph information. Additionally, we investigate an Early Query Fusion technique, which fuses query context before constructing the graph representation, leading to more effective graph embeddings. Our method achieves a 4.13\% performance improvement on the GraphQA benchmark without training the large language model, demonstrating significant gains in handling complex textual-attributed graph data.

Accurate Subseasonal-to-Seasonal (S2S) ocean simulation is critically important for marine research, yet remains challenging due to its substantial thermal inertia and extended time delay. Machine learning (ML)-based models have demonstrated significant advancements in simulation accuracy and computational efficiency compared to traditional numerical methods. Nevertheless, a significant limitation of current ML models for S2S ocean simulation is their inadequate incorporation of physical consistency and the slow-changing properties of the ocean system. In this work, we propose a neural ocean model (NeuralOM) for S2S ocean simulation with a multi-scale interactive graph neural network to emulate diverse physical phenomena associated with ocean systems effectively. Specifically, we propose a multi-stage framework tailored to model the ocean's slowly changing nature. Additionally, we introduce a multi-scale interactive messaging module to capture complex dynamical behaviors, such as gradient changes and multiplicative coupling relationships inherent in ocean dynamics. Extensive experimental evaluations confirm that our proposed NeuralOM outperforms state-of-the-art models in S2S and extreme event simulation. The codes are available at https://github.com/YuanGao-YG/NeuralOM.

Retrieval-augmented generation (RAG) has proven effective in integrating knowledge into large language models (LLMs). However, conventional RAGs struggle to capture complex relationships between pieces of knowledge, limiting their performance in intricate reasoning that requires integrating knowledge from multiple sources. Recently, graph-enhanced retrieval augmented generation (GraphRAG) builds graph structure to explicitly model these relationships, enabling more effective and efficient retrievers. Nevertheless, its performance is still hindered by the noise and incompleteness within the graph structure. To address this, we introduce GFM-RAG, a novel graph foundation model (GFM) for retrieval augmented generation. GFM-RAG is powered by an innovative graph neural network that reasons over graph structure to capture complex query-knowledge relationships. The GFM with 8M parameters undergoes a two-stage training process on large-scale datasets, comprising 60 knowledge graphs with over 14M triples and 700k documents. This results in impressive performance and generalizability for GFM-RAG, making it the first graph foundation model applicable to unseen datasets for retrieval without any fine-tuning required. Extensive experiments on three multi-hop QA datasets and seven domain-specific RAG datasets demonstrate that GFM-RAG achieves state-of-the-art performance while maintaining efficiency and alignment with neural scaling laws, highlighting its potential for further improvement.

While Language Models have become workhorses for NLP, their interplay with textual knowledge graphs (KGs) - structured memories of general or domain knowledge - is actively researched. Current embedding methodologies for such graphs typically either (i) linearize graphs for embedding them using sequential Language Models (LMs), which underutilize structural information, or (ii) use Graph Neural Networks (GNNs) to preserve graph structure, while GNNs cannot represent textual features as well as a pre-trained LM could. In this work we introduce a novel language model, the Graph Language Model (GLM), that integrates the strengths of both approaches, while mitigating their weaknesses. The GLM parameters are initialized from a pretrained LM, to facilitate nuanced understanding of individual concepts and triplets. Simultaneously, its architectural design incorporates graph biases, thereby promoting effective knowledge distribution within the graph. Empirical evaluations on relation classification tasks on ConceptNet subgraphs reveal that GLM embeddings surpass both LM- and GNN-based baselines in supervised and zero-shot settings.

Neural networks that process the parameters of other neural networks find applications in domains as diverse as classifying implicit neural representations, generating neural network weights, and predicting generalization errors. However, existing approaches either overlook the inherent permutation symmetry in the neural network or rely on intricate weight-sharing patterns to achieve equivariance, while ignoring the impact of the network architecture itself. In this work, we propose to represent neural networks as computational graphs of parameters, which allows us to harness powerful graph neural networks and transformers that preserve permutation symmetry. Consequently, our approach enables a single model to encode neural computational graphs with diverse architectures. We showcase the effectiveness of our method on a wide range of tasks, including classification and editing of implicit neural representations, predicting generalization performance, and learning to optimize, while consistently outperforming state-of-the-art methods. The source code is open-sourced at https://github.com/mkofinas/neural-graphs.

Time series are the primary data type used to record dynamic system measurements and generated in great volume by both physical sensors and online processes (virtual sensors). Time series analytics is therefore crucial to unlocking the wealth of information implicit in available data. With the recent advancements in graph neural networks (GNNs), there has been a surge in GNN-based approaches for time series analysis. These approaches can explicitly model inter-temporal and inter-variable relationships, which traditional and other deep neural network-based methods struggle to do. In this survey, we provide a comprehensive review of graph neural networks for time series analysis (GNN4TS), encompassing four fundamental dimensions: forecasting, classification, anomaly detection, and imputation. Our aim is to guide designers and practitioners to understand, build applications, and advance research of GNN4TS. At first, we provide a comprehensive task-oriented taxonomy of GNN4TS. Then, we present and discuss representative research works and introduce mainstream applications of GNN4TS. A comprehensive discussion of potential future research directions completes the survey. This survey, for the first time, brings together a vast array of knowledge on GNN-based time series research, highlighting foundations, practical applications, and opportunities of graph neural networks for time series analysis.

Given the recent impressive accomplishments of language models (LMs) for code generation, we explore the use of LMs as adaptive mutation and crossover operators for an evolutionary neural architecture search (NAS) algorithm. While NAS still proves too difficult a task for LMs to succeed at solely through prompting, we find that the combination of evolutionary prompt engineering with soft prompt-tuning, a method we term EvoPrompting, consistently finds diverse and high performing models. We first demonstrate that EvoPrompting is effective on the computationally efficient MNIST-1D dataset, where EvoPrompting produces convolutional architecture variants that outperform both those designed by human experts and naive few-shot prompting in terms of accuracy and model size. We then apply our method to searching for graph neural networks on the CLRS Algorithmic Reasoning Benchmark, where EvoPrompting is able to design novel architectures that outperform current state-of-the-art models on 21 out of 30 algorithmic reasoning tasks while maintaining similar model size. EvoPrompting is successful at designing accurate and efficient neural network architectures across a variety of machine learning tasks, while also being general enough for easy adaptation to other tasks beyond neural network design.

Foundation models have emerged as critical components in a variety of artificial intelligence applications, and showcase significant success in natural language processing and several other domains. Meanwhile, the field of graph machine learning is witnessing a paradigm transition from shallow methods to more sophisticated deep learning approaches. The capabilities of foundation models to generalize and adapt motivate graph machine learning researchers to discuss the potential of developing a new graph learning paradigm. This paradigm envisions models that are pre-trained on extensive graph data and can be adapted for various graph tasks. Despite this burgeoning interest, there is a noticeable lack of clear definitions and systematic analyses pertaining to this new domain. To this end, this article introduces the concept of Graph Foundation Models (GFMs), and offers an exhaustive explanation of their key characteristics and underlying technologies. We proceed to classify the existing work related to GFMs into three distinct categories, based on their dependence on graph neural networks and large language models. In addition to providing a thorough review of the current state of GFMs, this article also outlooks potential avenues for future research in this rapidly evolving domain.

Answering complex questions about textual narratives requires reasoning over both stated context and the world knowledge that underlies it. However, pretrained language models (LM), the foundation of most modern QA systems, do not robustly represent latent relationships between concepts, which is necessary for reasoning. While knowledge graphs (KG) are often used to augment LMs with structured representations of world knowledge, it remains an open question how to effectively fuse and reason over the KG representations and the language context, which provides situational constraints and nuances. In this work, we propose GreaseLM, a new model that fuses encoded representations from pretrained LMs and graph neural networks over multiple layers of modality interaction operations. Information from both modalities propagates to the other, allowing language context representations to be grounded by structured world knowledge, and allowing linguistic nuances (e.g., negation, hedging) in the context to inform the graph representations of knowledge. Our results on three benchmarks in the commonsense reasoning (i.e., CommonsenseQA, OpenbookQA) and medical question answering (i.e., MedQA-USMLE) domains demonstrate that GreaseLM can more reliably answer questions that require reasoning over both situational constraints and structured knowledge, even outperforming models 8x larger.

Language Models (LMs) are increasingly challenging the dominance of domain-specific models, including Graph Neural Networks (GNNs) and Graph Transformers (GTs), in graph learning tasks. Following this trend, we propose a novel approach that empowers off-the-shelf LMs to achieve performance comparable to state-of-the-art GNNs on node classification tasks, without requiring any architectural modification. By preserving the LM's original architecture, our approach retains a key benefit of LM instruction tuning: the ability to jointly train on diverse datasets, fostering greater flexibility and efficiency. To achieve this, we introduce two key augmentation strategies: (1) Enriching LMs' input using topological and semantic retrieval methods, which provide richer contextual information, and (2) guiding the LMs' classification process through a lightweight GNN classifier that effectively prunes class candidates. Our experiments on real-world datasets show that backbone Flan-T5 models equipped with these augmentation strategies outperform state-of-the-art text-output node classifiers and are comparable to top-performing vector-output node classifiers. By bridging the gap between specialized task-specific node classifiers and general LMs, this work paves the way for more versatile and widely applicable graph learning models. We will open-source the code upon publication.

Large language models (LLMs) have demonstrated remarkable in-context reasoning capabilities across a wide range of tasks, particularly with unstructured inputs such as language or images. However, LLMs struggle to handle structured data, such as graphs, due to their lack of understanding of non-Euclidean structures. As a result, without additional fine-tuning, their performance significantly lags behind that of graph neural networks (GNNs) in graph learning tasks. In this paper, we show that learning on graph data can be conceptualized as a retrieval-augmented generation (RAG) process, where specific instances (e.g., nodes or edges) act as queries, and the graph itself serves as the retrieved context. Building on this insight, we propose a series of RAG frameworks to enhance the in-context learning capabilities of LLMs for graph learning tasks. Comprehensive evaluations demonstrate that our proposed RAG frameworks significantly improve LLM performance on graph-based tasks, particularly in scenarios where a pretrained LLM must be used without modification or accessed via an API.

Statutory article retrieval (SAR), the task of retrieving statute law articles relevant to a legal question, is a promising application of legal text processing. In particular, high-quality SAR systems can improve the work efficiency of legal professionals and provide basic legal assistance to citizens in need at no cost. Unlike traditional ad-hoc information retrieval, where each document is considered a complete source of information, SAR deals with texts whose full sense depends on complementary information from the topological organization of statute law. While existing works ignore these domain-specific dependencies, we propose a novel graph-augmented dense statute retriever (G-DSR) model that incorporates the structure of legislation via a graph neural network to improve dense retrieval performance. Experimental results show that our approach outperforms strong retrieval baselines on a real-world expert-annotated SAR dataset.

Graph neural networks (GNNs) have become the preferred models for node classification in graph data due to their robust capabilities in integrating graph structures and attributes. However, these models heavily depend on a substantial amount of high-quality labeled data for training, which is often costly to obtain. With the rise of large language models (LLMs), a promising approach is to utilize their exceptional zero-shot capabilities and extensive knowledge for node labeling. Despite encouraging results, this approach either requires numerous queries to LLMs or suffers from reduced performance due to noisy labels generated by LLMs. To address these challenges, we introduce Locle, an active self-training framework that does Label-free node Classification with LLMs cost-Effectively. Locle iteratively identifies small sets of "critical" samples using GNNs and extracts informative pseudo-labels for them with both LLMs and GNNs, serving as additional supervision signals to enhance model training. Specifically, Locle comprises three key components: (i) an effective active node selection strategy for initial annotations; (ii) a careful sample selection scheme to identify "critical" nodes based on label disharmonicity and entropy; and (iii) a label refinement module that combines LLMs and GNNs with a rewired topology. Extensive experiments on five benchmark text-attributed graph datasets demonstrate that Locle significantly outperforms state-of-the-art methods under the same query budget to LLMs in terms of label-free node classification. Notably, on the DBLP dataset with 14.3k nodes, Locle achieves an 8.08% improvement in accuracy over the state-of-the-art at a cost of less than one cent. Our code is available at https://github.com/HKBU-LAGAS/Locle.

Graph Neural Networks (GNNs) are popular models for machine learning on graphs that typically follow the message-passing paradigm, whereby the feature of a node is updated recursively upon aggregating information over its neighbors. While exchanging messages over the input graph endows GNNs with a strong inductive bias, it can also make GNNs susceptible to over-squashing, thereby preventing them from capturing long-range interactions in the given graph. To rectify this issue, graph rewiring techniques have been proposed as a means of improving information flow by altering the graph connectivity. In this work, we identify three desiderata for graph-rewiring: (i) reduce over-squashing, (ii) respect the locality of the graph, and (iii) preserve the sparsity of the graph. We highlight fundamental trade-offs that occur between spatial and spectral rewiring techniques; while the former often satisfy (i) and (ii) but not (iii), the latter generally satisfy (i) and (iii) at the expense of (ii). We propose a novel rewiring framework that satisfies all of (i)--(iii) through a locality-aware sequence of rewiring operations. We then discuss a specific instance of such rewiring framework and validate its effectiveness on several real-world benchmarks, showing that it either matches or significantly outperforms existing rewiring approaches.

This paper targets the perceptual task of separating the different interacting voices, i.e., monophonic melodic streams, in a polyphonic musical piece. We target symbolic music, where notes are explicitly encoded, and model this task as a Multi-Trajectory Tracking (MTT) problem from discrete observations, i.e., notes in a pitch-time space. Our approach builds a graph from a musical piece, by creating one node for every note, and separates the melodic trajectories by predicting a link between two notes if they are consecutive in the same voice/stream. This kind of local, greedy prediction is made possible by node embeddings created by a heterogeneous graph neural network that can capture inter- and intra-trajectory information. Furthermore, we propose a new regularization loss that encourages the output to respect the MTT premise of at most one incoming and one outgoing link for every node, favouring monophonic (voice) trajectories; this loss function might also be useful in other general MTT scenarios. Our approach does not use domain-specific heuristics, is scalable to longer sequences and a higher number of voices, and can handle complex cases such as voice inversions and overlaps. We reach new state-of-the-art results for the voice separation task in classical music of different styles.

This paper explores the advancements and applications of large-scale models in the medical field, with a particular focus on Medical Large Models (MedLMs). These models, encompassing Large Language Models (LLMs), Vision Models, 3D Large Models, and Multimodal Models, are revolutionizing healthcare by enhancing disease prediction, diagnostic assistance, personalized treatment planning, and drug discovery. The integration of graph neural networks in medical knowledge graphs and drug discovery highlights the potential of Large Graph Models (LGMs) in understanding complex biomedical relationships. The study also emphasizes the transformative role of Vision-Language Models (VLMs) and 3D Large Models in medical image analysis, anatomical modeling, and prosthetic design. Despite the challenges, these technologies are setting new benchmarks in medical innovation, improving diagnostic accuracy, and paving the way for personalized healthcare solutions. This paper aims to provide a comprehensive overview of the current state and future directions of large models in medicine, underscoring their significance in advancing global health.

Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate change. These calculations are traditionally performed using Density Functional Theory, which is computationally very expensive. Machine learning has the potential to dramatically improve the efficiency of these calculations from days or hours to seconds. We propose the Spherical Channel Network (SCN) to model atomic energies and forces. The SCN is a graph neural network where nodes represent atoms and edges their neighboring atoms. The atom embeddings are a set of spherical functions, called spherical channels, represented using spherical harmonics. We demonstrate, that by rotating the embeddings based on the 3D edge orientation, more information may be utilized while maintaining the rotational equivariance of the messages. While equivariance is a desirable property, we find that by relaxing this constraint in both message passing and aggregation, improved accuracy may be achieved. We demonstrate state-of-the-art results on the large-scale Open Catalyst dataset in both energy and force prediction for numerous tasks and metrics.

We develop a general approach to distill symbolic representations of a learned deep model by introducing strong inductive biases. We focus on Graph Neural Networks (GNNs). The technique works as follows: we first encourage sparse latent representations when we train a GNN in a supervised setting, then we apply symbolic regression to components of the learned model to extract explicit physical relations. We find the correct known equations, including force laws and Hamiltonians, can be extracted from the neural network. We then apply our method to a non-trivial cosmology example-a detailed dark matter simulation-and discover a new analytic formula which can predict the concentration of dark matter from the mass distribution of nearby cosmic structures. The symbolic expressions extracted from the GNN using our technique also generalized to out-of-distribution data better than the GNN itself. Our approach offers alternative directions for interpreting neural networks and discovering novel physical principles from the representations they learn.

Task planning in language agents is emerging as an important research topic alongside the development of large language models (LLMs). It aims to break down complex user requests in natural language into solvable sub-tasks, thereby fulfilling the original requests. In this context, the sub-tasks can be naturally viewed as a graph, where the nodes represent the sub-tasks, and the edges denote the dependencies among them. Consequently, task planning is a decision-making problem that involves selecting a connected path or subgraph within the corresponding graph and invoking it. In this paper, we explore graph learning-based methods for task planning, a direction that is orthogonal to the prevalent focus on prompt design. Our interest in graph learning stems from a theoretical discovery: the biases of attention and auto-regressive loss impede LLMs' ability to effectively navigate decision-making on graphs, which is adeptly addressed by graph neural networks (GNNs). This theoretical insight led us to integrate GNNs with LLMs to enhance overall performance. Extensive experiments demonstrate that GNN-based methods surpass existing solutions even without training, and minimal training can further enhance their performance. The performance gain increases with a larger task graph size.

Large language models record impressive performance on many natural language processing tasks. However, their knowledge capacity is limited to the pretraining corpus. Retrieval augmentation offers an effective solution by retrieving context from external knowledge sources to complement the language model. However, existing retrieval augmentation techniques ignore the structural relationships between these documents. Furthermore, retrieval models are not explored much in scientific tasks, especially in regard to the faithfulness of retrieved documents. In this paper, we propose a novel structure-aware retrieval augmented language model that accommodates document structure during retrieval augmentation. We create a heterogeneous document graph capturing multiple types of relationships (e.g., citation, co-authorship, etc.) that connect documents from more than 15 scientific disciplines (e.g., Physics, Medicine, Chemistry, etc.). We train a graph neural network on the curated document graph to act as a structural encoder for the corresponding passages retrieved during the model pretraining. Particularly, along with text embeddings of the retrieved passages, we obtain structural embeddings of the documents (passages) and fuse them together before feeding them to the language model. We evaluate our model extensively on various scientific benchmarks that include science question-answering and scientific document classification tasks. Experimental results demonstrate that structure-aware retrieval improves retrieving more coherent, faithful and contextually relevant passages, while showing a comparable performance in the overall accuracy.

Transformers have revolutionized machine learning with their simple yet effective architecture. Pre-training Transformers on massive text datasets from the Internet has led to unmatched generalization for natural language understanding (NLU) tasks. However, such language models remain fragile when tasked with algorithmic forms of reasoning, where computations must be precise and robust. To address this limitation, we propose a novel approach that combines the Transformer's language understanding with the robustness of graph neural network (GNN)-based neural algorithmic reasoners (NARs). Such NARs proved effective as generic solvers for algorithmic tasks, when specified in graph form. To make their embeddings accessible to a Transformer, we propose a hybrid architecture with a two-phase training procedure, allowing the tokens in the language model to cross-attend to the node embeddings from the NAR. We evaluate our resulting TransNAR model on CLRS-Text, the text-based version of the CLRS-30 benchmark, and demonstrate significant gains over Transformer-only models for algorithmic reasoning, both in and out of distribution.

In designing and applying graph neural networks, we often fall into some optimization pitfalls, the most deceptive of which is that we can only build a deep model by solving over-smoothing. The fundamental reason is that we do not understand how graph neural networks work. Stress graph drawing can offer a unique viewpoint to message iteration in the graph, such as the root of the over-smoothing problem lies in the inability of graph models to maintain an ideal distance between nodes. We further elucidate the trigger conditions of over-smoothing and propose Stress Graph Neural Networks. By introducing the attractive and repulsive message passing from stress iteration, we show how to build a deep model without preventing over-smoothing, how to use repulsive information, and how to optimize the current message-passing scheme to approximate the full stress message propagation. By performing different tasks on 23 datasets, we verified the effectiveness of our attractive and repulsive models and the derived relationship between stress iteration and graph neural networks. We believe that stress graph drawing will be a popular resource for understanding and designing graph neural networks.

While large language models (LLMs) have integrated images, adapting them to graphs remains challenging, limiting their applications in materials and drug design. This difficulty stems from the need for coherent autoregressive generation across texts and graphs. To address this, we introduce Llamole, the first multimodal LLM capable of interleaved text and graph generation, enabling molecular inverse design with retrosynthetic planning. Llamole integrates a base LLM with the Graph Diffusion Transformer and Graph Neural Networks for multi-conditional molecular generation and reaction inference within texts, while the LLM, with enhanced molecular understanding, flexibly controls activation among the different graph modules. Additionally, Llamole integrates A* search with LLM-based cost functions for efficient retrosynthetic planning. We create benchmarking datasets and conduct extensive experiments to evaluate Llamole against in-context learning and supervised fine-tuning. Llamole significantly outperforms 14 adapted LLMs across 12 metrics for controllable molecular design and retrosynthetic planning.

Communication is a key bottleneck for distributed graph neural network (GNN) training. This paper proposes GNNPipe, a new approach that scales the distributed full-graph deep GNN training. Being the first to use layer-level model parallelism for GNN training, GNNPipe partitions GNN layers among GPUs, each device performs the computation for a disjoint subset of consecutive GNN layers on the whole graph. Compared to graph parallelism with each GPU handling a graph partition, GNNPipe reduces the communication volume by a factor of the number of GNN layers. GNNPipe overcomes the unique challenges for pipelined layer-level model parallelism on the whole graph by partitioning it into dependent chunks, allowing the use of historical vertex embeddings, and applying specific training techniques to ensure convergence. We also propose a hybrid approach by combining GNNPipe with graph parallelism to handle large graphs, achieve better computer resource utilization and ensure model convergence. We build a general GNN training system supporting all three parallelism setting. Extensive experiments show that our method reduces the per-epoch training time by up to 2.45x (on average 1.58x) and reduces the communication volume and overhead by up to 22.89x and 27.21x (on average 8.69x and 11.60x), respectively, while achieving a comparable level of model accuracy and convergence speed compared to graph parallelism.

In recent years, there have been remarkable advancements in node classification achieved by Graph Neural Networks (GNNs). However, they necessitate abundant high-quality labels to ensure promising performance. In contrast, Large Language Models (LLMs) exhibit impressive zero-shot proficiency on text-attributed graphs. Yet, they face challenges in efficiently processing structural data and suffer from high inference costs. In light of these observations, this work introduces a label-free node classification on graphs with LLMs pipeline, LLM-GNN. It amalgamates the strengths of both GNNs and LLMs while mitigating their limitations. Specifically, LLMs are leveraged to annotate a small portion of nodes and then GNNs are trained on LLMs' annotations to make predictions for the remaining large portion of nodes. The implementation of LLM-GNN faces a unique challenge: how can we actively select nodes for LLMs to annotate and consequently enhance the GNN training? How can we leverage LLMs to obtain annotations of high quality, representativeness, and diversity, thereby enhancing GNN performance with less cost? To tackle this challenge, we develop an annotation quality heuristic and leverage the confidence scores derived from LLMs to advanced node selection. Comprehensive experimental results validate the effectiveness of LLM-GNN. In particular, LLM-GNN can achieve an accuracy of 74.9% on a vast-scale dataset \products with a cost less than 1 dollar.

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}

Modeling dynamic graphs, such as those found in social networks, recommendation systems, and e-commerce platforms, is crucial for capturing evolving relationships and delivering relevant insights over time. Traditional approaches primarily rely on graph neural networks with temporal components or sequence generation models, which often focus narrowly on the historical context of target nodes. This limitation restricts the ability to adapt to new and emerging patterns in dynamic graphs. To address this challenge, we propose a novel framework, Retrieval-Augmented Generation for Dynamic Graph modeling (RAG4DyG), which enhances dynamic graph predictions by incorporating contextually and temporally relevant examples from broader graph structures. Our approach includes a time- and context-aware contrastive learning module to identify high-quality demonstrations and a graph fusion strategy to effectively integrate these examples with historical contexts. The proposed framework is designed to be effective in both transductive and inductive scenarios, ensuring adaptability to previously unseen nodes and evolving graph structures. Extensive experiments across multiple real-world datasets demonstrate the effectiveness of RAG4DyG in improving predictive accuracy and adaptability for dynamic graph modeling. The code and datasets are publicly available at https://github.com/YuxiaWu/RAG4DyG.

Learning on text-attributed graphs (TAGs), in which nodes are associated with one or more texts, has been the subject of much recent work. However, most approaches tend to make strong assumptions about the downstream task of interest, are reliant on hand-labeled data, or fail to equally balance the importance of both text and graph representations. In this work, we propose Contrastive Graph-Text pretraining (ConGraT), a general, self-supervised approach for jointly learning separate representations of texts and nodes in a TAG. Our method trains a language model (LM) and a graph neural network (GNN) to align their representations in a common latent space using a batch-wise contrastive learning objective inspired by CLIP. We further propose an extension to the CLIP objective that leverages graph structure to incorporate information about inter-node similarity. Extensive experiments demonstrate that ConGraT outperforms baselines on various downstream tasks, including node and text category classification, link prediction, and language modeling. Finally, we present an application of our method to community detection in social graphs, which enables finding more textually grounded communities, rather than purely graph-based ones. Code and certain datasets are available at https://github.com/wwbrannon/congrat.

This study proposes a hybrid deep-learning-metaheuristic framework with a bi-level architecture for road network design problems (NDPs). We train a graph neural network (GNN) to approximate the solution of the user equilibrium (UE) traffic assignment problem and use inferences made by the trained model to calculate fitness function evaluations of a genetic algorithm (GA) to approximate solutions for NDPs. Using three test networks, two NDP variants and an exact solver as benchmark, we show that on average, our proposed framework can provide solutions within 1.5% gap of the best results in less than 0.5% of the time used by the exact solution procedure. Our framework can be utilized within an expert system for infrastructure planning to determine the best infrastructure planning and management decisions under different scenarios. Given the flexibility of the framework, it can easily be adapted to many other decision problems that can be modeled as bi-level problems on graphs. Moreover, we foreseen interesting future research directions, thus we also put forward a brief research agenda for this topic. The key observation from our research that can shape future research is that the fitness function evaluation time using the inferences made by the GNN model was in the order of milliseconds, which points to an opportunity and a need for novel heuristics that 1) can cope well with noisy fitness function values provided by deep learning models, and 2) can use the significantly enlarged efficiency of the evaluation step to explore the search space effectively (rather than efficiently). This opens a new avenue for a modern class of metaheuristics that are crafted for use with AI-powered predictors.

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

The problem of answering questions using knowledge from pre-trained language models (LMs) and knowledge graphs (KGs) presents two challenges: given a QA context (question and answer choice), methods need to (i) identify relevant knowledge from large KGs, and (ii) perform joint reasoning over the QA context and KG. In this work, we propose a new model, QA-GNN, which addresses the above challenges through two key innovations: (i) relevance scoring, where we use LMs to estimate the importance of KG nodes relative to the given QA context, and (ii) joint reasoning, where we connect the QA context and KG to form a joint graph, and mutually update their representations through graph neural networks. We evaluate our model on QA benchmarks in the commonsense (CommonsenseQA, OpenBookQA) and biomedical (MedQA-USMLE) domains. QA-GNN outperforms existing LM and LM+KG models, and exhibits capabilities to perform interpretable and structured reasoning, e.g., correctly handling negation in questions.

Knowledge about the hidden factors that determine particular system dynamics is crucial for both explaining them and pursuing goal-directed interventions. Inferring these factors from time series data without supervision remains an open challenge. Here, we focus on spatiotemporal processes, including wave propagation and weather dynamics, for which we assume that universal causes (e.g. physics) apply throughout space and time. A recently introduced DIstributed SpatioTemporal graph Artificial Neural network Architecture (DISTANA) is used and enhanced to learn such processes, requiring fewer parameters and achieving significantly more accurate predictions compared to temporal convolutional neural networks and other related approaches. We show that DISTANA, when combined with a retrospective latent state inference principle called active tuning, can reliably derive location-respective hidden causal factors. In a current weather prediction benchmark, DISTANA infers our planet's land-sea mask solely by observing temperature dynamics and, meanwhile, uses the self inferred information to improve its own future temperature predictions.

Multimodal Attributed Graphs (MAGs) are ubiquitous in real-world applications, encompassing extensive knowledge through multimodal attributes attached to nodes (e.g., texts and images) and topological structure representing node interactions. Despite its potential to advance diverse research fields like social networks and e-commerce, MAG representation learning (MAGRL) remains underexplored due to the lack of standardized datasets and evaluation frameworks. In this paper, we first propose MAGB, a comprehensive MAG benchmark dataset, featuring curated graphs from various domains with both textual and visual attributes. Based on MAGB dataset, we further systematically evaluate two mainstream MAGRL paradigms: GNN-as-Predictor, which integrates multimodal attributes via Graph Neural Networks (GNNs), and VLM-as-Predictor, which harnesses Vision Language Models (VLMs) for zero-shot reasoning. Extensive experiments on MAGB reveal following critical insights: (i) Modality significances fluctuate drastically with specific domain characteristics. (ii) Multimodal embeddings can elevate the performance ceiling of GNNs. However, intrinsic biases among modalities may impede effective training, particularly in low-data scenarios. (iii) VLMs are highly effective at generating multimodal embeddings that alleviate the imbalance between textual and visual attributes. These discoveries, which illuminate the synergy between multimodal attributes and graph topologies, contribute to reliable benchmarks, paving the way for future MAG research. The MAGB dataset and evaluation pipeline are publicly available at https://github.com/sktsherlock/MAGB.

Graph representation learning is a fundamental research theme and can be generalized to benefit multiple downstream tasks from the node and link levels to the higher graph level. In practice, it is desirable to develop task-agnostic general graph representation learning methods that are typically trained in an unsupervised manner. Related research reveals that the power of graph representation learning methods depends on whether they can differentiate distinct graph structures as different embeddings and map isomorphic graphs to consistent embeddings (i.e., the isomorphic consistency of graph models). However, for task-agnostic general graph representation learning, existing unsupervised graph models, represented by the variational graph auto-encoders (VGAEs), can only keep the isomorphic consistency within the subgraphs of 1-hop neighborhoods and thus usually manifest inferior performance on the more difficult higher-level tasks. To overcome the limitations of existing unsupervised methods, in this paper, we propose the Isomorphic-Consistent VGAE (IsoC-VGAE) for multi-level task-agnostic graph representation learning. We first devise a decoding scheme to provide a theoretical guarantee of keeping the isomorphic consistency under the settings of unsupervised learning. We then propose the Inverse Graph Neural Network (Inv-GNN) decoder as its intuitive realization, which trains the model via reconstructing the GNN node embeddings with multi-hop neighborhood information, so as to maintain the high-order isomorphic consistency within the VGAE framework. We conduct extensive experiments on the representative graph learning tasks at different levels, including node classification, link prediction and graph classification, and the results verify that our proposed model generally outperforms both the state-of-the-art unsupervised methods and representative supervised methods.

Drug-target interaction (DTI) prediction is crucial for identifying new therapeutics and detecting mechanisms of action. While structure-based methods accurately model physical interactions between a drug and its protein target, cell-based assays such as Cell Painting can better capture complex DTI interactions. This paper introduces MOTIVE, a Morphological cOmpound Target Interaction Graph dataset that comprises Cell Painting features for 11,000 genes and 3,600 compounds along with their relationships extracted from seven publicly available databases. We provide random, cold-source (new drugs), and cold-target (new genes) data splits to enable rigorous evaluation under realistic use cases. Our benchmark results show that graph neural networks that use Cell Painting features consistently outperform those that learn from graph structure alone, feature-based models, and topological heuristics. MOTIVE accelerates both graph ML research and drug discovery by promoting the development of more reliable DTI prediction models. MOTIVE resources are available at https://github.com/carpenter-singh-lab/motive.

Recommender systems have seen significant advancements with the influence of deep learning and graph neural networks, particularly in capturing complex user-item relationships. However, these graph-based recommenders heavily depend on ID-based data, potentially disregarding valuable textual information associated with users and items, resulting in less informative learned representations. Moreover, the utilization of implicit feedback data introduces potential noise and bias, posing challenges for the effectiveness of user preference learning. While the integration of large language models (LLMs) into traditional ID-based recommenders has gained attention, challenges such as scalability issues, limitations in text-only reliance, and prompt input constraints need to be addressed for effective implementation in practical recommender systems. To address these challenges, we propose a model-agnostic framework RLMRec that aims to enhance existing recommenders with LLM-empowered representation learning. It proposes a recommendation paradigm that integrates representation learning with LLMs to capture intricate semantic aspects of user behaviors and preferences. RLMRec incorporates auxiliary textual signals, develops a user/item profiling paradigm empowered by LLMs, and aligns the semantic space of LLMs with the representation space of collaborative relational signals through a cross-view alignment framework. This work further establish a theoretical foundation demonstrating that incorporating textual signals through mutual information maximization enhances the quality of representations. In our evaluation, we integrate RLMRec with state-of-the-art recommender models, while also analyzing its efficiency and robustness to noise data. Our implementation codes are available at https://github.com/HKUDS/RLMRec.

Text-attributed graphs have recently garnered significant attention due to their wide range of applications in web domains. Existing methodologies employ word embedding models for acquiring text representations as node features, which are subsequently fed into Graph Neural Networks (GNNs) for training. Recently, the advent of Large Language Models (LLMs) has introduced their powerful capabilities in information retrieval and text generation, which can greatly enhance the text attributes of graph data. Furthermore, the acquisition and labeling of extensive datasets are both costly and time-consuming endeavors. Consequently, few-shot learning has emerged as a crucial problem in the context of graph learning tasks. In order to tackle this challenge, we propose a lightweight paradigm called LLM4NG, which adopts a plug-and-play approach to empower text-attributed graphs through node generation using LLMs. Specifically, we utilize LLMs to extract semantic information from the labels and generate samples that belong to these categories as exemplars. Subsequently, we employ an edge predictor to capture the structural information inherent in the raw dataset and integrate the newly generated samples into the original graph. This approach harnesses LLMs for enhancing class-level information and seamlessly introduces labeled nodes and edges without modifying the raw dataset, thereby facilitating the node classification task in few-shot scenarios. Extensive experiments demonstrate the outstanding performance of our proposed paradigm, particularly in low-shot scenarios. For instance, in the 1-shot setting of the ogbn-arxiv dataset, LLM4NG achieves a 76% improvement over the baseline model.

Retrieval-augmented generation (RAG) has revitalized Large Language Models (LLMs) by injecting non-parametric factual knowledge. Compared with long-context LLMs, RAG is considered an effective summarization tool in a more concise and lightweight manner, which can interact with LLMs multiple times using diverse queries to get comprehensive responses. However, the LLM-generated historical responses, which contain potentially insightful information, are largely neglected and discarded by existing approaches, leading to suboptimal results. In this paper, we propose graph of records (GoR), which leverages historical responses generated by LLMs to enhance RAG for long-context global summarization. Inspired by the retrieve-then-generate paradigm of RAG, we construct a graph by establishing an edge between the retrieved text chunks and the corresponding LLM-generated response. To further uncover the intricate correlations between them, GoR further features a graph neural network and an elaborately designed BERTScore-based objective for self-supervised model training, enabling seamless supervision signal backpropagation between reference summaries and node embeddings. We comprehensively compare GoR with 12 baselines across four long-context summarization datasets, and the results indicate that our proposed method reaches the best performance e.g., 15\%, 8\%, and 19\% improvement over retrievers w.r.t. Rouge-L, Rouge-1, and Rouge-2 on the WCEP dataset). Extensive experiments further demonstrate the effectiveness of GoR. Code is available at https://github.com/ulab-uiuc/GoR

Natural language explanations (NLEs) are commonly used to provide plausible free-text explanations of a model's reasoning about its predictions. However, recent work has questioned the faithfulness of NLEs, as they may not accurately reflect the model's internal reasoning process regarding its predicted answer. In contrast, highlight explanations -- input fragments identified as critical for the model's predictions -- exhibit measurable faithfulness, which has been incrementally improved through existing research. Building on this foundation, we propose G-Tex, a Graph-Guided Textual Explanation Generation framework designed to enhance the faithfulness of NLEs by leveraging highlight explanations. Specifically, highlight explanations are extracted as highly faithful cues representing the model's reasoning and are subsequently encoded through a graph neural network layer, which explicitly guides the NLE generation process. This alignment ensures that the generated explanations closely reflect the model's underlying reasoning. Experiments on T5 and BART using three reasoning datasets show that G-Tex improves NLE faithfulness by up to 17.59% compared to baseline methods. Additionally, G-Tex generates NLEs with greater semantic and lexical similarity to human-written ones. Human evaluations show that G-Tex can decrease redundant content and enhance the overall quality of NLEs. As our work introduces a novel method for explicitly guiding NLE generation to improve faithfulness, we hope it will serve as a stepping stone for addressing additional criteria for NLE and generated text overall.

The RNA structure-function relationship has recently garnered significant attention within the deep learning community, promising to grow in importance as nucleic acid structure models advance. However, the absence of standardized and accessible benchmarks for deep learning on RNA 3D structures has impeded the development of models for RNA functional characteristics. In this work, we introduce a set of seven benchmarking datasets for RNA structure-function prediction, designed to address this gap. Our library builds on the established Python library rnaglib, and offers easy data distribution and encoding, splitters and evaluation methods, providing a convenient all-in-one framework for comparing models. Datasets are implemented in a fully modular and reproducible manner, facilitating for community contributions and customization. Finally, we provide initial baseline results for all tasks using a graph neural network. Source code: https://github.com/cgoliver/rnaglib Documentation: https://rnaglib.org

Peptides are essential in biological processes and therapeutics. In this study, we introduce Multi-Peptide, an innovative approach that combines transformer-based language models with Graph Neural Networks (GNNs) to predict peptide properties. We combine PeptideBERT, a transformer model tailored for peptide property prediction, with a GNN encoder to capture both sequence-based and structural features. By employing Contrastive Language-Image Pre-training (CLIP), Multi-Peptide aligns embeddings from both modalities into a shared latent space, thereby enhancing the model's predictive accuracy. Evaluations on hemolysis and nonfouling datasets demonstrate Multi-Peptide's robustness, achieving state-of-the-art 86.185% accuracy in hemolysis prediction. This study highlights the potential of multimodal learning in bioinformatics, paving the way for accurate and reliable predictions in peptide-based research and applications.

Vision-Language models (VLMs) pre-trained on large corpora have demonstrated notable success across a range of downstream tasks. In light of the rapidly increasing size of pre-trained VLMs, parameter-efficient transfer learning (PETL) has garnered attention as a viable alternative to full fine-tuning. One such approach is the adapter, which introduces a few trainable parameters into the pre-trained models while preserving the original parameters during adaptation. In this paper, we present a novel modeling framework that recasts adapter tuning after attention as a graph message passing process on attention graphs, where the projected query and value features and attention matrix constitute the node features and the graph adjacency matrix, respectively. Within this framework, tuning adapters in VLMs necessitates handling heterophilic graphs, owing to the disparity between the projected query and value space. To address this challenge, we propose a new adapter architecture, p-adapter, which employs p-Laplacian message passing in Graph Neural Networks (GNNs). Specifically, the attention weights are re-normalized based on the features, and the features are then aggregated using the calibrated attention matrix, enabling the dynamic exploitation of information with varying frequencies in the heterophilic attention graphs. We conduct extensive experiments on different pre-trained VLMs and multi-modal tasks, including visual question answering, visual entailment, and image captioning. The experimental results validate our method's significant superiority over other PETL methods.

Graph neural networks (GNNs) are machine learning models specialized for graph data and widely used in many applications. To train GNNs on large graphs that exceed CPU memory, several systems store data on disk and conduct out-of-core processing. However, these systems suffer from either read amplification when reading node features that are usually smaller than a disk page or degraded model accuracy by treating the graph as disconnected partitions. To close this gap, we build a system called DiskGNN, which achieves high I/O efficiency and thus fast training without hurting model accuracy. The key technique used by DiskGNN is offline sampling, which helps decouple graph sampling from model computation. In particular, by conducting graph sampling beforehand, DiskGNN acquires the node features that will be accessed by model computation, and such information is utilized to pack the target node features contiguously on disk to avoid read amplification. Besides, also adopts designs including four-level feature store to fully utilize the memory hierarchy to cache node features and reduce disk access, batched packing to accelerate the feature packing process, and pipelined training to overlap disk access with other operations. We compare DiskGNN with Ginex and MariusGNN, which are state-of-the-art systems for out-of-core GNN training. The results show that DiskGNN can speed up the baselines by over 8x while matching their best model accuracy.

A ChatGPT-like system for drug compounds could be a game-changer in pharmaceutical research, accelerating drug discovery, enhancing our understanding of structure-activity relationships, guiding lead optimization, aiding drug repurposing, reducing the failure rate, and streamlining clinical trials. In this work, we make an initial attempt towards enabling ChatGPT-like capabilities on drug molecule graphs, by developing a prototype system DrugChat. DrugChat works in a similar way as ChatGPT. Users upload a compound molecule graph and ask various questions about this compound. DrugChat will answer these questions in a multi-turn, interactive manner. The DrugChat system consists of a graph neural network (GNN), a large language model (LLM), and an adaptor. The GNN takes a compound molecule graph as input and learns a representation for this graph. The adaptor transforms the graph representation produced by the GNN into another representation that is acceptable to the LLM. The LLM takes the compound representation transformed by the adaptor and users' questions about this compound as inputs and generates answers. All these components are trained end-to-end. To train DrugChat, we collected instruction tuning datasets which contain 10,834 drug compounds and 143,517 question-answer pairs. The code and data is available at https://github.com/UCSD-AI4H/drugchat

In order to communicate, humans flatten a complex representation of ideas and their attributes into a single word or a sentence. We investigate the impact of representation learning in artificial agents by developing graph referential games. We empirically show that agents parametrized by graph neural networks develop a more compositional language compared to bag-of-words and sequence models, which allows them to systematically generalize to new combinations of familiar features.

Disinformation on social media poses both societal and technical challenges. While previous studies have integrated textual information into propagation networks, they have yet to fully leverage the advancements in Transformer-based language models for high-quality contextual text representations. This work investigates the impact of incorporating textual features into Graph Neural Networks (GNNs) for fake news detection. Our experiments demonstrate that contextual representations improve performance by 9.3% in Macro F1 over static ones and 33.8% over GNNs without textual features. However, noisy data augmentation degrades performance and increases instability. We expect our methodology to open avenues for further research, and all code is made publicly available.

Emotions are an inherent part of human interactions, and consequently, it is imperative to develop AI systems that understand and recognize human emotions. During a conversation involving various people, a person's emotions are influenced by the other speaker's utterances and their own emotional state over the utterances. In this paper, we propose COntextualized Graph Neural Network based Multimodal Emotion recognitioN (COGMEN) system that leverages local information (i.e., inter/intra dependency between speakers) and global information (context). The proposed model uses Graph Neural Network (GNN) based architecture to model the complex dependencies (local and global information) in a conversation. Our model gives state-of-the-art (SOTA) results on IEMOCAP and MOSEI datasets, and detailed ablation experiments show the importance of modeling information at both levels.

Logs play a crucial role in system monitoring and debugging by recording valuable system information, including events and states. Although various methods have been proposed to detect anomalies in log sequences, they often overlook the significance of considering relations among system components, such as services and users, which can be identified from log contents. Understanding these relations is vital for detecting anomalies and their underlying causes. To address this issue, we introduce GLAD, a Graph-based Log Anomaly Detection framework designed to detect relational anomalies in system logs. GLAD incorporates log semantics, relational patterns, and sequential patterns into a unified framework for anomaly detection. Specifically, GLAD first introduces a field extraction module that utilizes prompt-based few-shot learning to identify essential fields from log contents. Then GLAD constructs dynamic log graphs for sliding windows by interconnecting extracted fields and log events parsed from the log parser. These graphs represent events and fields as nodes and their relations as edges. Subsequently, GLAD utilizes a temporal-attentive graph edge anomaly detection model for identifying anomalous relations in these dynamic log graphs. This model employs a Graph Neural Network (GNN)-based encoder enhanced with transformers to capture content, structural and temporal features. We evaluate our proposed method on three datasets, and the results demonstrate the effectiveness of GLAD in detecting anomalies indicated by varying relational patterns.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

Small molecules are essential to drug discovery, and graph-language models hold promise for learning molecular properties and functions from text. However, existing molecule-text datasets are limited in scale and informativeness, restricting the training of generalizable multimodal models. We present MolTextNet, a dataset of 2.5 million high-quality molecule-text pairs designed to overcome these limitations. To construct it, we propose a synthetic text generation pipeline that integrates structural features, computed properties, bioactivity data, and synthetic complexity. Using GPT-4o-mini, we create structured descriptions for 2.5 million molecules from ChEMBL35, with text over 10 times longer than prior datasets. MolTextNet supports diverse downstream tasks, including property prediction and structure retrieval. Pretraining CLIP-style models with Graph Neural Networks and ModernBERT on MolTextNet yields improved performance, highlighting its potential for advancing foundational multimodal modeling in molecular science. Our dataset is available at https://huggingface.co/datasets/liuganghuggingface/moltextnet.

Recent advances in deep learning for physics have focused on discovering shared representations of target systems by incorporating physics priors or inductive biases into neural networks. While effective, these methods are limited to the system domain, where the type of system remains consistent and thus cannot ensure the adaptation to new, or unseen physical systems governed by different laws. For instance, a neural network trained on a mass-spring system cannot guarantee accurate predictions for the behavior of a two-body system or any other system with different physical laws. In this work, we take a significant leap forward by targeting cross domain generalization within the field of Hamiltonian dynamics. We model our system with a graph neural network and employ a meta learning algorithm to enable the model to gain experience over a distribution of tasks and make it adapt to new physics. Our approach aims to learn a unified Hamiltonian representation that is generalizable across multiple system domains, thereby overcoming the limitations of system-specific models. Our results demonstrate that the meta-trained model not only adapts effectively to new systems but also captures a generalized Hamiltonian representation that is consistent across different physical domains. Overall, through the use of meta learning, we offer a framework that achieves cross domain generalization, providing a step towards a unified model for understanding a wide array of dynamical systems via deep learning.

Scaling deep learning models has been at the heart of recent revolutions in language modelling and image generation. Practitioners have observed a strong relationship between model size, dataset size, and performance. However, structure-based architectures such as Graph Neural Networks (GNNs) are yet to show the benefits of scale mainly due to the lower efficiency of sparse operations, large data requirements, and lack of clarity about the effectiveness of various architectures. We address this drawback of GNNs by studying their scaling behavior. Specifically, we analyze message-passing networks, graph Transformers, and hybrid architectures on the largest public collection of 2D molecular graphs. For the first time, we observe that GNNs benefit tremendously from the increasing scale of depth, width, number of molecules, number of labels, and the diversity in the pretraining datasets, resulting in a 30.25% improvement when scaling to 1 billion parameters and 28.98% improvement when increasing size of dataset to eightfold. We further demonstrate strong finetuning scaling behavior on 38 tasks, outclassing previous large models. We hope that our work paves the way for an era where foundational GNNs drive pharmaceutical drug discovery.

Humans excel in complex long-horizon soft body manipulation tasks via flexible tool use: bread baking requires a knife to slice the dough and a rolling pin to flatten it. Often regarded as a hallmark of human cognition, tool use in autonomous robots remains limited due to challenges in understanding tool-object interactions. Here we develop an intelligent robotic system, RoboCook, which perceives, models, and manipulates elasto-plastic objects with various tools. RoboCook uses point cloud scene representations, models tool-object interactions with Graph Neural Networks (GNNs), and combines tool classification with self-supervised policy learning to devise manipulation plans. We demonstrate that from just 20 minutes of real-world interaction data per tool, a general-purpose robot arm can learn complex long-horizon soft object manipulation tasks, such as making dumplings and alphabet letter cookies. Extensive evaluations show that RoboCook substantially outperforms state-of-the-art approaches, exhibits robustness against severe external disturbances, and demonstrates adaptability to different materials.

Dynamics models learned from visual observations have shown to be effective in various robotic manipulation tasks. One of the key questions for learning such dynamics models is what scene representation to use. Prior works typically assume representation at a fixed dimension or resolution, which may be inefficient for simple tasks and ineffective for more complicated tasks. In this work, we investigate how to learn dynamic and adaptive representations at different levels of abstraction to achieve the optimal trade-off between efficiency and effectiveness. Specifically, we construct dynamic-resolution particle representations of the environment and learn a unified dynamics model using graph neural networks (GNNs) that allows continuous selection of the abstraction level. During test time, the agent can adaptively determine the optimal resolution at each model-predictive control (MPC) step. We evaluate our method in object pile manipulation, a task we commonly encounter in cooking, agriculture, manufacturing, and pharmaceutical applications. Through comprehensive evaluations both in the simulation and the real world, we show that our method achieves significantly better performance than state-of-the-art fixed-resolution baselines at the gathering, sorting, and redistribution of granular object piles made with various instances like coffee beans, almonds, corn, etc.

Deep neural networks trained on Functional Connectivity (FC) networks extracted from functional Magnetic Resonance Imaging (fMRI) data have gained popularity due to the increasing availability of data and advances in model architectures, including Graph Neural Network (GNN). Recent research on the application of GNN to FC suggests that exploiting the time-varying properties of the FC could significantly improve the accuracy and interpretability of the model prediction. However, the high cost of acquiring high-quality fMRI data and corresponding phenotypic labels poses a hurdle to their application in real-world settings, such that a model na\"ively trained in a supervised fashion can suffer from insufficient performance or a lack of generalization on a small number of data. In addition, most Self-Supervised Learning (SSL) approaches for GNNs to date adopt a contrastive strategy, which tends to lose appropriate semantic information when the graph structure is perturbed or does not leverage both spatial and temporal information simultaneously. In light of these challenges, we propose a generative SSL approach that is tailored to effectively harness spatio-temporal information within dynamic FC. Our empirical results, experimented with large-scale (>50,000) fMRI datasets, demonstrate that our approach learns valuable representations and enables the construction of accurate and robust models when fine-tuned for downstream tasks.

Existing visual place recognition (VPR) datasets predominantly rely on vehicle-mounted imagery, lack multimodal diversity and underrepresent dense, mixed-use street-level spaces, especially in non-Western urban contexts. To address these gaps, we introduce MMS-VPR, a large-scale multimodal dataset for street-level place recognition in complex, pedestrian-only environments. The dataset comprises 78,575 annotated images and 2,512 video clips captured across 207 locations in a ~70,800 m^2 open-air commercial district in Chengdu, China. Each image is labeled with precise GPS coordinates, timestamp, and textual metadata, and covers varied lighting conditions, viewpoints, and timeframes. MMS-VPR follows a systematic and replicable data collection protocol with minimal device requirements, lowering the barrier for scalable dataset creation. Importantly, the dataset forms an inherent spatial graph with 125 edges, 81 nodes, and 1 subgraph, enabling structure-aware place recognition. We further define two application-specific subsets -- Dataset_Edges and Dataset_Points -- to support fine-grained and graph-based evaluation tasks. Extensive benchmarks using conventional VPR models, graph neural networks, and multimodal baselines show substantial improvements when leveraging multimodal and structural cues. MMS-VPR facilitates future research at the intersection of computer vision, geospatial understanding, and multimodal reasoning. The dataset is publicly available at https://huggingface.co/datasets/Yiwei-Ou/MMS-VPR.

An accurate and efficient epileptic seizure onset detection can significantly benefit patients. Traditional diagnostic methods, primarily relying on electroencephalograms (EEGs), often result in cumbersome and non-portable solutions, making continuous patient monitoring challenging. The video-based seizure detection system is expected to free patients from the constraints of scalp or implanted EEG devices and enable remote monitoring in residential settings. Previous video-based methods neither enable all-day monitoring nor provide short detection latency due to insufficient resources and ineffective patient action recognition techniques. Additionally, skeleton-based action recognition approaches remain limitations in identifying subtle seizure-related actions. To address these challenges, we propose a novel Video-based Seizure detection model via a skeleton-based spatiotemporal Vision Graph neural network (VSViG) for its efficient, accurate and timely purpose in real-time scenarios. Our experimental results indicate VSViG outperforms previous state-of-the-art action recognition models on our collected patients' video data with higher accuracy (5.9% error), lower FLOPs (0.4G), and smaller model size (1.4M). Furthermore, by integrating a decision-making rule that combines output probabilities and an accumulative function, we achieve a 5.1 s detection latency after EEG onset, a 13.1 s detection advance before clinical onset, and a zero false detection rate. The project homepage is available at: https://github.com/xuyankun/VSViG/

Out-of-town recommendation is designed for those users who leave their home-town areas and visit the areas they have never been to before. It is challenging to recommend Point-of-Interests (POIs) for out-of-town users since the out-of-town check-in behavior is determined by not only the user's home-town preference but also the user's travel intention. Besides, the user's travel intentions are complex and dynamic, which leads to big difficulties in understanding such intentions precisely. In this paper, we propose a TRAvel-INtention-aware Out-of-town Recommendation framework, named TRAINOR. The proposed TRAINOR framework distinguishes itself from existing out-of-town recommenders in three aspects. First, graph neural networks are explored to represent users' home-town check-in preference and geographical constraints in out-of-town check-in behaviors. Second, a user-specific travel intention is formulated as an aggregation combining home-town preference and generic travel intention together, where the generic travel intention is regarded as a mixture of inherent intentions that can be learned by Neural Topic Model (NTM). Third, a non-linear mapping function, as well as a matrix factorization method, are employed to transfer users' home-town preference and estimate out-of-town POI's representation, respectively. Extensive experiments on real-world data sets validate the effectiveness of the TRAINOR framework. Moreover, the learned travel intention can deliver meaningful explanations for understanding a user's travel purposes.

Program errors can occur in any type of programming, and can manifest in a variety of ways, such as unexpected output, crashes, or performance issues. And program error diagnosis can often be too abstract or technical for developers to understand, especially for beginners. The goal of this paper is to present a novel machine-learning approach for Multi-task Program Error Repair and Explanatory Diagnosis (mPRED). A pre-trained language model is used to encode the source code, and a downstream model is specifically designed to identify and repair errors. Programs and test cases will be augmented and optimized from several perspectives. Additionally, our approach incorporates a "chain of thoughts" method, which enables the models to produce intermediate reasoning explanations before providing the final correction. To aid in visualizing and analyzing the program structure, we use a graph neural network for program structure visualization. Overall, our approach offers a promising approach for repairing program errors across different programming languages and providing helpful explanations to programmers.

Interpretability methods are valuable only if their explanations faithfully describe the explained model. In this work, we consider neural networks whose predictions are invariant under a specific symmetry group. This includes popular architectures, ranging from convolutional to graph neural networks. Any explanation that faithfully explains this type of model needs to be in agreement with this invariance property. We formalize this intuition through the notion of explanation invariance and equivariance by leveraging the formalism from geometric deep learning. Through this rigorous formalism, we derive (1) two metrics to measure the robustness of any interpretability method with respect to the model symmetry group; (2) theoretical robustness guarantees for some popular interpretability methods and (3) a systematic approach to increase the invariance of any interpretability method with respect to a symmetry group. By empirically measuring our metrics for explanations of models associated with various modalities and symmetry groups, we derive a set of 5 guidelines to allow users and developers of interpretability methods to produce robust explanations.

We introduce rLLM (relationLLM), a PyTorch library designed for Relational Table Learning (RTL) with Large Language Models (LLMs). The core idea is to decompose state-of-the-art Graph Neural Networks, LLMs, and Table Neural Networks into standardized modules, to enable the fast construction of novel RTL-type models in a simple "combine, align, and co-train" manner. To illustrate the usage of rLLM, we introduce a simple RTL method named BRIDGE. Additionally, we present three novel relational tabular datasets (TML1M, TLF2K, and TACM12K) by enhancing classic datasets. We hope rLLM can serve as a useful and easy-to-use development framework for RTL-related tasks. Our code is available at: https://github.com/rllm-project/rllm.

Molecules are frequently represented as graphs, but the underlying 3D molecular geometry (the locations of the atoms) ultimately determines most molecular properties. However, most molecules are not static and at room temperature adopt a wide variety of geometries or conformations. The resulting distribution on geometries p(x) is known as the Boltzmann distribution, and many molecular properties are expectations computed under this distribution. Generating accurate samples from the Boltzmann distribution is therefore essential for computing these expectations accurately. Traditional sampling-based methods are computationally expensive, and most recent machine learning-based methods have focused on identifying modes in this distribution rather than generating true samples. Generating such samples requires capturing conformational variability, and it has been widely recognized that the majority of conformational variability in molecules arises from rotatable bonds. In this work, we present VonMisesNet, a new graph neural network that captures conformational variability via a variational approximation of rotatable bond torsion angles as a mixture of von Mises distributions. We demonstrate that VonMisesNet can generate conformations for arbitrary molecules in a way that is both physically accurate with respect to the Boltzmann distribution and orders of magnitude faster than existing sampling methods.

Generative models trained at scale can now produce text, video, and more recently, scientific data such as crystal structures. In applications of generative approaches to materials science, and in particular to crystal structures, the guidance from the domain expert in the form of high-level instructions can be essential for an automated system to output candidate crystals that are viable for downstream research. In this work, we formulate end-to-end language-to-structure generation as a multi-objective optimization problem, and propose Generative Hierarchical Materials Search (GenMS) for controllable generation of crystal structures. GenMS consists of (1) a language model that takes high-level natural language as input and generates intermediate textual information about a crystal (e.g., chemical formulae), and (2) a diffusion model that takes intermediate information as input and generates low-level continuous value crystal structures. GenMS additionally uses a graph neural network to predict properties (e.g., formation energy) from the generated crystal structures. During inference, GenMS leverages all three components to conduct a forward tree search over the space of possible structures. Experiments show that GenMS outperforms other alternatives of directly using language models to generate structures both in satisfying user request and in generating low-energy structures. We confirm that GenMS is able to generate common crystal structures such as double perovskites, or spinels, solely from natural language input, and hence can form the foundation for more complex structure generation in near future.

Recently, large language models (LLMs) have demonstrated superior capabilities in understanding and zero-shot learning on textual data, promising significant advances for many text-related domains. In the graph domain, various real-world scenarios also involve textual data, where tasks and node features can be described by text. These text-attributed graphs (TAGs) have broad applications in social media, recommendation systems, etc. Thus, this paper explores how to utilize LLMs to model TAGs. Previous methods for TAG modeling are based on million-scale LMs. When scaled up to billion-scale LLMs, they face huge challenges in computational costs. Additionally, they also ignore the zero-shot inference capabilities of LLMs. Therefore, we propose GraphAdapter, which uses a graph neural network (GNN) as an efficient adapter in collaboration with LLMs to tackle TAGs. In terms of efficiency, the GNN adapter introduces only a few trainable parameters and can be trained with low computation costs. The entire framework is trained using auto-regression on node text (next token prediction). Once trained, GraphAdapter can be seamlessly fine-tuned with task-specific prompts for various downstream tasks. Through extensive experiments across multiple real-world TAGs, GraphAdapter based on Llama 2 gains an average improvement of approximately 5\% in terms of node classification. Furthermore, GraphAdapter can also adapt to other language models, including RoBERTa, GPT-2. The promising results demonstrate that GNNs can serve as effective adapters for LLMs in TAG modeling.

As deep learning models scale, their training cost has surged significantly. Due to both hardware advancements and limitations in current software stacks, the need for data efficiency has risen. Data efficiency refers to the effective hiding of data access latency and the avoidance of unnecessary data movements. Major challenges arise from the growing disparity between GPU memory bandwidth and computational throughput, imminent GPU memory capacity limitations, and inefficiencies in the PyTorch software stack, including a lack of device-specific PCIe transfer optimizations and high-level domain-specific abstractions. To effectively mitigate these data inefficiencies for deep learning training, this dissertation analyzes data inefficiency in representative deep training tasks, specifically in graph neural networks (GNNs) and large language models (LLMs). It then proposes novel runtime and code generation techniques to mitigate these challenges and implements these optimizations seamlessly within the PyTorch stack while maintaining strong programmability and interoperability. First, PyTorch-Direct is devised to incorporate the GPU-centric PCIe data transfer paradigm in PyTorch for GNN training. Next, Hector intermediate representation (IR) and its code generator are proposed to introduce domain-specific high-level abstraction and systematically address memory-intensive performance challenges for relational GNNs. Finally, in LLM training, the throughput has been increasingly constrained by GPU memory capacity. To mitigate this, the SSDTrain offloading framework is designed and implemented. Together, these contributions show that code generation and runtime techniques can systematically mitigate the data management bottlenecks in deep learning training, which stem from the data-intensive nature of workloads and the oversimplification inherent in the deep learning training software stack.

Signed networks allow us to model conflicting relationships and interactions, such as friend/enemy and support/oppose. These signed interactions happen in real-time. Modeling such dynamics of signed networks is crucial to understanding the evolution of polarization in the network and enabling effective prediction of the signed structure (i.e., link signs and signed weights) in the future. However, existing works have modeled either (static) signed networks or dynamic (unsigned) networks but not dynamic signed networks. Since both sign and dynamics inform the graph structure in different ways, it is non-trivial to model how to combine the two features. In this work, we propose a new Graph Neural Network (GNN)-based approach to model dynamic signed networks, named SEMBA: Signed link's Evolution using Memory modules and Balanced Aggregation. Here, the idea is to incorporate the signs of temporal interactions using separate modules guided by balance theory and to evolve the embeddings from a higher-order neighborhood. Experiments on 4 real-world datasets and 4 different tasks demonstrate that SEMBA consistently and significantly outperforms the baselines by up to 80% on the tasks of predicting signs of future links while matching the state-of-the-art performance on predicting the existence of these links in the future. We find that this improvement is due specifically to the superior performance of SEMBA on the minority negative class.

Future link prediction is a fundamental challenge in various real-world dynamic systems. To address this, numerous temporal graph neural networks (temporal GNNs) and benchmark datasets have been developed. However, these datasets often feature excessive repeated edges and lack complex sequential dynamics, a key characteristic inherent in many real-world applications such as recommender systems and ``Who-To-Follow'' on social networks. This oversight has led existing methods to inadvertently downplay the importance of learning sequential dynamics, focusing primarily on predicting repeated edges. In this study, we demonstrate that existing methods, such as GraphMixer and DyGFormer, are inherently incapable of learning simple sequential dynamics, such as ``a user who has followed OpenAI and Anthropic is more likely to follow AI at Meta next.'' Motivated by this issue, we introduce the Temporal Graph Benchmark with Sequential Dynamics (TGB-Seq), a new benchmark carefully curated to minimize repeated edges, challenging models to learn sequential dynamics and generalize to unseen edges. TGB-Seq comprises large real-world datasets spanning diverse domains, including e-commerce interactions, movie ratings, business reviews, social networks, citation networks and web link networks. Benchmarking experiments reveal that current methods usually suffer significant performance degradation and incur substantial training costs on TGB-Seq, posing new challenges and opportunities for future research. TGB-Seq datasets, leaderboards, and example codes are available at https://tgb-seq.github.io/.

We propose and release a new vulnerable source code dataset. We curate the dataset by crawling security issue websites, extracting vulnerability-fixing commits and source codes from the corresponding projects. Our new dataset contains 18,945 vulnerable functions spanning 150 CWEs and 330,492 non-vulnerable functions extracted from 7,514 commits. Our dataset covers 295 more projects than all previous datasets combined. Combining our new dataset with previous datasets, we present an analysis of the challenges and promising research directions of using deep learning for detecting software vulnerabilities. We study 11 model architectures belonging to 4 families. Our results show that deep learning is still not ready for vulnerability detection, due to high false positive rate, low F1 score, and difficulty of detecting hard CWEs. In particular, we demonstrate an important generalization challenge for the deployment of deep learning-based models. We show that increasing the volume of training data may not further improve the performance of deep learning models for vulnerability detection, but might be useful to improve the generalization ability to unseen projects. We also identify hopeful future research directions. We demonstrate that large language models (LLMs) are a promising research direction for ML-based vulnerability detection, outperforming Graph Neural Networks (GNNs) with code-structure features in our experiments. Moreover, developing source code specific pre-training objectives is a promising research direction to improve the vulnerability detection performance.

Machine-Generated Text (MGT) detection, a task that discriminates MGT from Human-Written Text (HWT), plays a crucial role in preventing misuse of text generative models, which excel in mimicking human writing style recently. Latest proposed detectors usually take coarse text sequence as input and output some good results by fine-tune pretrained models with standard cross-entropy loss. However, these methods fail to consider the linguistic aspect of text (e.g., coherence) and sentence-level structures. Moreover, they lack the ability to handle the low-resource problem which could often happen in practice considering the enormous amount of textual data online. In this paper, we present a coherence-based contrastive learning model named CoCo to detect the possible MGT under low-resource scenario. Inspired by the distinctiveness and permanence properties of linguistic feature, we represent text as a coherence graph to capture its entity consistency, which is further encoded by the pretrained model and graph neural network. To tackle the challenges of data limitations, we employ a contrastive learning framework and propose an improved contrastive loss for making full use of hard negative samples in training stage. The experiment results on two public datasets prove our approach outperforms the state-of-art methods significantly.

Scripting interfaces enable users to automate tasks and customize software workflows, but creating scripts traditionally requires programming expertise and familiarity with specific APIs, posing barriers for many users. While Large Language Models (LLMs) can generate code from natural language queries, runtime code generation is severely limited due to unverified code, security risks, longer response times, and higher computational costs. To bridge the gap, we propose an offline simulation framework to curate a software-specific skillset, a collection of verified scripts, by exploiting LLMs and publicly available scripting guides. Our framework comprises two components: (1) task creation, using top-down functionality guidance and bottom-up API synergy exploration to generate helpful tasks; and (2) skill generation with trials, refining and validating scripts based on execution feedback. To efficiently navigate the extensive API landscape, we introduce a Graph Neural Network (GNN)-based link prediction model to capture API synergy, enabling the generation of skills involving underutilized APIs and expanding the skillset's diversity. Experiments with Adobe Illustrator demonstrate that our framework significantly improves automation success rates, reduces response time, and saves runtime token costs compared to traditional runtime code generation. This is the first attempt to use software scripting interfaces as a testbed for LLM-based systems, highlighting the advantages of leveraging execution feedback in a controlled environment and offering valuable insights into aligning AI capabilities with user needs in specialized software domains.

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depends on the microenvironment of cells specific to each patient. We propose Meta Flow Matching (MFM), a practical approach to integrating along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions unlike previously proposed methods. We demonstrate the ability of MFM to improve prediction of individual treatment responses on a large scale multi-patient single-cell drug screen dataset.

We present PyTorch Frame, a PyTorch-based framework for deep learning over multi-modal tabular data. PyTorch Frame makes tabular deep learning easy by providing a PyTorch-based data structure to handle complex tabular data, introducing a model abstraction to enable modular implementation of tabular models, and allowing external foundation models to be incorporated to handle complex columns (e.g., LLMs for text columns). We demonstrate the usefulness of PyTorch Frame by implementing diverse tabular models in a modular way, successfully applying these models to complex multi-modal tabular data, and integrating our framework with PyTorch Geometric, a PyTorch library for Graph Neural Networks (GNNs), to perform end-to-end learning over relational databases.

Mamba, a special case of the State Space Model, is gaining popularity as an alternative to template-based deep learning approaches in medical image analysis. While transformers are powerful architectures, they have drawbacks, including quadratic computational complexity and an inability to address long-range dependencies efficiently. This limitation affects the analysis of large and complex datasets in medical imaging, where there are many spatial and temporal relationships. In contrast, Mamba offers benefits that make it well-suited for medical image analysis. It has linear time complexity, which is a significant improvement over transformers. Mamba processes longer sequences without attention mechanisms, enabling faster inference and requiring less memory. Mamba also demonstrates strong performance in merging multimodal data, improving diagnosis accuracy and patient outcomes. The organization of this paper allows readers to appreciate the capabilities of Mamba in medical imaging step by step. We begin by defining core concepts of SSMs and models, including S4, S5, and S6, followed by an exploration of Mamba architectures such as pure Mamba, U-Net variants, and hybrid models with convolutional neural networks, transformers, and Graph Neural Networks. We also cover Mamba optimizations, techniques and adaptations, scanning, datasets, applications, experimental results, and conclude with its challenges and future directions in medical imaging. This review aims to demonstrate the transformative potential of Mamba in overcoming existing barriers within medical imaging while paving the way for innovative advancements in the field. A comprehensive list of Mamba architectures applied in the medical field, reviewed in this work, is available at Github.

Text-Attributed Graphs (TAGs) augment graph structures with natural language descriptions, facilitating detailed depictions of data and their interconnections across various real-world settings. However, existing TAG datasets predominantly feature textual information only at the nodes, with edges typically represented by mere binary or categorical attributes. This lack of rich textual edge annotations significantly limits the exploration of contextual relationships between entities, hindering deeper insights into graph-structured data. To address this gap, we introduce Textual-Edge Graphs Datasets and Benchmark (TEG-DB), a comprehensive and diverse collection of benchmark textual-edge datasets featuring rich textual descriptions on nodes and edges. The TEG-DB datasets are large-scale and encompass a wide range of domains, from citation networks to social networks. In addition, we conduct extensive benchmark experiments on TEG-DB to assess the extent to which current techniques, including pre-trained language models, graph neural networks, and their combinations, can utilize textual node and edge information. Our goal is to elicit advancements in textual-edge graph research, specifically in developing methodologies that exploit rich textual node and edge descriptions to enhance graph analysis and provide deeper insights into complex real-world networks. The entire TEG-DB project is publicly accessible as an open-source repository on Github, accessible at https://github.com/Zhuofeng-Li/TEG-Benchmark.

Matbench Discovery simulates the deployment of machine learning (ML) energy models in a high-throughput search for stable inorganic crystals. We address the disconnect between (i) thermodynamic stability and formation energy and (ii) in-domain vs out-of-distribution performance. Alongside this paper, we publish a Python package to aid with future model submissions and a growing online leaderboard with further insights into trade-offs between various performance metrics. To answer the question which ML methodology performs best at materials discovery, our initial release explores a variety of models including random forests, graph neural networks (GNN), one-shot predictors, iterative Bayesian optimizers and universal interatomic potentials (UIP). Ranked best-to-worst by their test set F1 score on thermodynamic stability prediction, we find CHGNet > M3GNet > MACE > ALIGNN > MEGNet > CGCNN > CGCNN+P > Wrenformer > BOWSR > Voronoi tessellation fingerprints with random forest. The top 3 models are UIPs, the winning methodology for ML-guided materials discovery, achieving F1 scores of ~0.6 for crystal stability classification and discovery acceleration factors (DAF) of up to 5x on the first 10k most stable predictions compared to dummy selection from our test set. We also highlight a sharp disconnect between commonly used global regression metrics and more task-relevant classification metrics. Accurate regressors are susceptible to unexpectedly high false-positive rates if those accurate predictions lie close to the decision boundary at 0 eV/atom above the convex hull where most materials are. Our results highlight the need to focus on classification metrics that actually correlate with improved stability hit rate.

Complex cell signaling systems -- governed by varying protein abundances and interactions -- generate diverse cell types across organs. These systems evolve under influences such as age, sex, diet, environmental exposures, and diseases, making them challenging to decode given the involvement of tens of thousands of genes and proteins. Recently, hundreds of millions of single-cell omics data have provided a robust foundation for understanding these signaling networks within various cell subpopulations and conditions. Inspired by the success of large foundation models (for example, large language models and large vision models) pre-trained on massive datasets, we introduce OmniCellTOSG, the first dataset of cell text-omic signaling graphs (TOSGs). Each TOSG represents the signaling network of an individual or meta-cell and is labeled with information such as organ, disease, sex, age, and cell subtype. OmniCellTOSG offers two key contributions. First, it introduces a novel graph model that integrates human-readable annotations -- such as biological functions, cellular locations, signaling pathways, related diseases, and drugs -- with quantitative gene and protein abundance data, enabling graph reasoning to decode cell signaling. This approach calls for new joint models combining large language models and graph neural networks. Second, the dataset is built from single-cell RNA sequencing data of approximately 120 million cells from diverse tissues and conditions (healthy and diseased) and is fully compatible with PyTorch. This facilitates the development of innovative cell signaling models that could transform research in life sciences, healthcare, and precision medicine. The OmniCellTOSG dataset is continuously expanding and will be updated regularly. The dataset and code are available at https://github.com/FuhaiLiAiLab/OmniCellTOSG.

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we present a novel generative model, BindGPT which uses a conceptually simple but powerful approach to create 3D molecules within the protein's binding site. Our model produces molecular graphs and conformations jointly, eliminating the need for an extra graph reconstruction step. We pretrain BindGPT on a large-scale dataset and fine-tune it with reinforcement learning using scores from external simulation software. We demonstrate how a single pretrained language model can serve at the same time as a 3D molecular generative model, conformer generator conditioned on the molecular graph, and a pocket-conditioned 3D molecule generator. Notably, the model does not make any representational equivariance assumptions about the domain of generation. We show how such simple conceptual approach combined with pretraining and scaling can perform on par or better than the current best specialized diffusion models, language models, and graph neural networks while being two orders of magnitude cheaper to sample.

In this work we address the problem of landmark-based segmentation for anatomical structures. We propose HybridGNet, an encoder-decoder neural architecture which combines standard convolutions for image feature encoding, with graph convolutional neural networks to decode plausible representations of anatomical structures. We benchmark the proposed architecture considering other standard landmark and pixel-based models for anatomical segmentation in chest x-ray images, and found that HybridGNet is more robust to image occlusions. We also show that it can be used to construct landmark-based segmentations from pixel level annotations. Our experimental results suggest that HybridGNet produces accurate and anatomically plausible landmark-based segmentations, by naturally incorporating shape constraints within the decoding process via spectral convolutions.

The ability to accurately represent sentences is central to language understanding. We describe a convolutional architecture dubbed the Dynamic Convolutional Neural Network (DCNN) that we adopt for the semantic modelling of sentences. The network uses Dynamic k-Max Pooling, a global pooling operation over linear sequences. The network handles input sentences of varying length and induces a feature graph over the sentence that is capable of explicitly capturing short and long-range relations. The network does not rely on a parse tree and is easily applicable to any language. We test the DCNN in four experiments: small scale binary and multi-class sentiment prediction, six-way question classification and Twitter sentiment prediction by distant supervision. The network achieves excellent performance in the first three tasks and a greater than 25% error reduction in the last task with respect to the strongest baseline.

The 2021 NeurIPS Machine Learning for Combinatorial Optimization (ML4CO) competition was designed with the goal of improving state-of-the-art combinatorial optimization solvers by replacing key heuristic components with machine learning models. The competition's main scientific question was the following: is machine learning a viable option for improving traditional combinatorial optimization solvers on specific problem distributions, when historical data is available? This was motivated by the fact that in many practical scenarios, the data changes only slightly between the repetitions of a combinatorial optimization problem, and this is an area where machine learning models are particularly powerful at. This paper summarizes the solution and lessons learned by the Huawei EI-OROAS team in the dual task of the competition. The submission of our team achieved the second place in the final ranking, with a very close distance to the first spot. In addition, our solution was ranked first consistently for several weekly leaderboard updates before the final evaluation. We provide insights gained from a large number of experiments, and argue that a simple Graph Convolutional Neural Network (GCNNs) can achieve state-of-the-art results if trained and tuned properly.

We introduce a new dataset named WikiVitals which contains a large graph of 48k mutually referred Wikipedia articles classified into 32 categories and connected by 2.3M edges. Our aim is to rigorously evaluate the contributions of three distinct sources of information to the label prediction in a semi-supervised node classification setting, namely the content of the articles, their connections with each other and the correlations among their labels. We perform this evaluation using a Graph Markov Neural Network which provides a theoretically principled model for this task and we conduct a detailed evaluation of the contributions of each sources of information using a clear separation of model selection and model assessment. One interesting observation is that including the effect of label dependencies is more relevant for sparse train sets than it is for dense train sets.

Fully automatic cardiac segmentation can be a fast and reproducible method to extract clinical measurements from an echocardiography examination. The U-Net architecture is the current state-of-the-art deep learning architecture for medical segmentation and can segment cardiac structures in real-time with average errors comparable to inter-observer variability. However, this architecture still generates large outliers that are often anatomically incorrect. This work uses the concept of graph convolutional neural networks that predict the contour points of the structures of interest instead of labeling each pixel. We propose a graph architecture that uses two convolutional rings based on cardiac anatomy and show that this eliminates anatomical incorrect multi-structure segmentations on the publicly available CAMUS dataset. Additionally, this work contributes with an ablation study on the graph convolutional architecture and an evaluation of clinical measurements on the clinical HUNT4 dataset. Finally, we propose to use the inter-model agreement of the U-Net and the graph network as a predictor of both the input and segmentation quality. We show this predictor can detect out-of-distribution and unsuitable input images in real-time. Source code is available online: https://github.com/gillesvntnu/GCN_multistructure

Time-series forecasting is one of the most active research topics in artificial intelligence. Applications in real-world time series should consider two factors for achieving reliable predictions: modeling dynamic dependencies among multiple variables and adjusting the model's intrinsic hyperparameters. A still open gap in that literature is that statistical and ensemble learning approaches systematically present lower predictive performance than deep learning methods. They generally disregard the data sequence aspect entangled with multivariate data represented in more than one time series. Conversely, this work presents a novel neural network architecture for time-series forecasting that combines the power of graph evolution with deep recurrent learning on distinct data distributions; we named our method Recurrent Graph Evolution Neural Network (ReGENN). The idea is to infer multiple multivariate relationships between co-occurring time-series by assuming that the temporal data depends not only on inner variables and intra-temporal relationships (i.e., observations from itself) but also on outer variables and inter-temporal relationships (i.e., observations from other-selves). An extensive set of experiments was conducted comparing ReGENN with dozens of ensemble methods and classical statistical ones, showing sound improvement of up to 64.87% over the competing algorithms. Furthermore, we present an analysis of the intermediate weights arising from ReGENN, showing that by looking at inter and intra-temporal relationships simultaneously, time-series forecasting is majorly improved if paying attention to how multiple multivariate data synchronously evolve.

In this paper, we present specially designed automatic speech recognition (ASR) systems for the highly agglutinative and inflective languages of Tamil and Kannada that can recognize unlimited vocabulary of words. We use subwords as the basic lexical units for recognition and construct subword grammar weighted finite state transducer (SG-WFST) graphs for word segmentation that captures most of the complex word formation rules of the languages. We have identified the following category of words (i) verbs, (ii) nouns, (ii) pronouns, and (iv) numbers. The prefix, infix and suffix lists of subwords are created for each of these categories and are used to design the SG-WFST graphs. We also present a heuristic segmentation algorithm that can even segment exceptional words that do not follow the rules encapsulated in the SG-WFST graph. Most of the data-driven subword dictionary creation algorithms are computation driven, and hence do not guarantee morpheme-like units and so we have used the linguistic knowledge of the languages and manually created the subword dictionaries and the graphs. Finally, we train a deep neural network acoustic model and combine it with the pronunciation lexicon of the subword dictionary and the SG-WFST graph to build the subword-ASR systems. Since the subword-ASR produces subword sequences as output for a given test speech, we post-process its output to get the final word sequence, so that the actual number of words that can be recognized is much higher. Upon experimenting the subword-ASR system with the IISc-MILE Tamil and Kannada ASR corpora, we observe an absolute word error rate reduction of 12.39% and 13.56% over the baseline word-based ASR systems for Tamil and Kannada, respectively.

Graph neural networks (GNNs) are one of the most popular research topics for deep learning. GNN methods typically have been designed on top of the graph signal processing theory. In particular, diffusion equations have been widely used for designing the core processing layer of GNNs, and therefore they are inevitably vulnerable to the notorious oversmoothing problem. Recently, a couple of papers paid attention to reaction equations in conjunctions with diffusion equations. However, they all consider limited forms of reaction equations. To this end, we present a reaction-diffusion equation-based GNN method that considers all popular types of reaction equations in addition to one special reaction equation designed by us. To our knowledge, our paper is one of the most comprehensive studies on reaction-diffusion equation-based GNNs. In our experiments with 9 datasets and 28 baselines, our method, called GREAD, outperforms them in a majority of cases. Further synthetic data experiments show that it mitigates the oversmoothing problem and works well for various homophily rates.

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into four categories, namely recurrent graph neural networks, convolutional graph neural networks, graph autoencoders, and spatial-temporal graph neural networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes, benchmark data sets, and model evaluation of graph neural networks. Finally, we propose potential research directions in this rapidly growing field.

In this paper, we propose REASON, a novel framework that enables the automatic discovery of both intra-level (i.e., within-network) and inter-level (i.e., across-network) causal relationships for root cause localization. REASON consists of Topological Causal Discovery and Individual Causal Discovery. The Topological Causal Discovery component aims to model the fault propagation in order to trace back to the root causes. To achieve this, we propose novel hierarchical graph neural networks to construct interdependent causal networks by modeling both intra-level and inter-level non-linear causal relations. Based on the learned interdependent causal networks, we then leverage random walks with restarts to model the network propagation of a system fault. The Individual Causal Discovery component focuses on capturing abrupt change patterns of a single system entity. This component examines the temporal patterns of each entity's metric data (i.e., time series), and estimates its likelihood of being a root cause based on the Extreme Value theory. Combining the topological and individual causal scores, the top K system entities are identified as root causes. Extensive experiments on three real-world datasets with case studies demonstrate the effectiveness and superiority of the proposed framework.

With increasingly more powerful compute capabilities and resources in today's devices, traditionally compute-intensive automatic speech recognition (ASR) has been moving from the cloud to devices to better protect user privacy. However, it is still challenging to implement on-device ASR on resource-constrained devices, such as smartphones, smart wearables, and other smart home automation devices. In this paper, we propose a series of model architecture adaptions, neural network graph transformations, and numerical optimizations to fit an advanced Conformer based end-to-end streaming ASR system on resource-constrained devices without accuracy degradation. We achieve over 5.26 times faster than realtime (0.19 RTF) speech recognition on smart wearables while minimizing energy consumption and achieving state-of-the-art accuracy. The proposed methods are widely applicable to other transformer-based server-free AI applications. In addition, we provide a complete theory on optimal pre-normalizers that numerically stabilize layer normalization in any Lp-norm using any floating point precision.

Document AI aims to automatically analyze documents by leveraging natural language processing and computer vision techniques. One of the major tasks of Document AI is document layout analysis, which structures document pages by interpreting the content and spatial relationships of layout, image, and text. This task can be image-centric, wherein the aim is to identify and label various regions such as authors and paragraphs, or text-centric, where the focus is on classifying individual words in a document. Although there are increasingly sophisticated methods for improving layout analysis, doubts remain about the extent to which their findings can be generalized to a broader context. Specifically, prior work developed systems based on very different architectures, such as transformer-based, graph-based, and CNNs. However, no work has mentioned the effectiveness of these models in a comparative analysis. Moreover, while language-independent Document AI models capable of knowledge transfer have been developed, it remains to be investigated to what degree they can effectively transfer knowledge. In this study, we aim to fill these gaps by conducting a comparative evaluation of state-of-the-art models in document layout analysis and investigating the potential of cross-lingual layout analysis by utilizing machine translation techniques.

Graph neural networks are popular architectures for graph machine learning, based on iterative computation of node representations of an input graph through a series of invariant transformations. A large class of graph neural networks follow a standard message-passing paradigm: at every layer, each node state is updated based on an aggregate of messages from its neighborhood. In this work, we propose a novel framework for training graph neural networks, where every node is viewed as a player that can choose to either 'listen', 'broadcast', 'listen and broadcast', or to 'isolate'. The standard message propagation scheme can then be viewed as a special case of this framework where every node 'listens and broadcasts' to all neighbors. Our approach offers a more flexible and dynamic message-passing paradigm, where each node can determine its own strategy based on their state, effectively exploring the graph topology while learning. We provide a theoretical analysis of the new message-passing scheme which is further supported by an extensive empirical analysis on a synthetic dataset and on real-world datasets.

There is a recent surge in the development of spatio-temporal forecasting models in the transportation domain. Long-range traffic forecasting, however, remains a challenging task due to the intricate and extensive spatio-temporal correlations observed in traffic networks. Current works primarily rely on road networks with graph structures and learn representations using graph neural networks (GNNs), but this approach suffers from over-smoothing problem in deep architectures. To tackle this problem, recent methods introduced the combination of GNNs with residual connections or neural ordinary differential equations (ODE). However, current graph ODE models face two key limitations in feature extraction: (1) they lean towards global temporal patterns, overlooking local patterns that are important for unexpected events; and (2) they lack dynamic semantic edges in their architectural design. In this paper, we propose a novel architecture called Graph-based Multi-ODE Neural Networks (GRAM-ODE) which is designed with multiple connective ODE-GNN modules to learn better representations by capturing different views of complex local and global dynamic spatio-temporal dependencies. We also add some techniques like shared weights and divergence constraints into the intermediate layers of distinct ODE-GNN modules to further improve their communication towards the forecasting task. Our extensive set of experiments conducted on six real-world datasets demonstrate the superior performance of GRAM-ODE compared with state-of-the-art baselines as well as the contribution of different components to the overall performance. The code is available at https://github.com/zbliu98/GRAM-ODE

The last decade has witnessed a boom of deep learning research and applications achieving state-of-the-art results in various domains. However, most advances have been established empirically, and their theoretical analysis remains lacking. One major issue is that our current interpretation of neural networks (NNs) as function approximators is too generic to support in-depth analysis. In this paper, we remedy this by proposing an alternative interpretation that identifies NNs as chain graphs (CGs) and feed-forward as an approximate inference procedure. The CG interpretation specifies the nature of each NN component within the rich theoretical framework of probabilistic graphical models, while at the same time remains general enough to cover real-world NNs with arbitrary depth, multi-branching and varied activations, as well as common structures including convolution / recurrent layers, residual block and dropout. We demonstrate with concrete examples that the CG interpretation can provide novel theoretical support and insights for various NN techniques, as well as derive new deep learning approaches such as the concept of partially collapsed feed-forward inference. It is thus a promising framework that deepens our understanding of neural networks and provides a coherent theoretical formulation for future deep learning research.

An approach to improve neural network interpretability is via clusterability, i.e., splitting a model into disjoint clusters that can be studied independently. We define a measure for clusterability and show that pre-trained models form highly enmeshed clusters via spectral graph clustering. We thus train models to be more modular using a "clusterability loss" function that encourages the formation of non-interacting clusters. Using automated interpretability techniques, we show that our method can help train models that are more modular and learn different, disjoint, and smaller circuits. We investigate CNNs trained on MNIST and CIFAR, small transformers trained on modular addition, and language models. Our approach provides a promising direction for training neural networks that learn simpler functions and are easier to interpret.

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.

Current low-precision quantization algorithms often have the hidden cost of conversion back and forth from floating point to quantized integer values. This hidden cost limits the latency improvement realized by quantizing Neural Networks. To address this, we present HAWQV3, a novel mixed-precision integer-only quantization framework. The contributions of HAWQV3 are the following: (i) An integer-only inference where the entire computational graph is performed only with integer multiplication, addition, and bit shifting, without any floating point operations or even integer division; (ii) A novel hardware-aware mixed-precision quantization method where the bit-precision is calculated by solving an integer linear programming problem that balances the trade-off between model perturbation and other constraints, e.g., memory footprint and latency; (iii) Direct hardware deployment and open source contribution for 4-bit uniform/mixed-precision quantization in TVM, achieving an average speed up of 1.45times for uniform 4-bit, as compared to uniform 8-bit for ResNet50 on T4 GPUs; and (iv) extensive evaluation of the proposed methods on ResNet18/50 and InceptionV3, for various model compression levels with/without mixed precision. For ResNet50, our INT8 quantization achieves an accuracy of 77.58%, which is 2.68% higher than prior integer-only work, and our mixed-precision INT4/8 quantization can reduce INT8 latency by 23% and still achieve 76.73% accuracy. Our framework and the TVM implementation have been open sourced.

Message-passing graph neural networks (MPNNs) emerged as powerful tools for processing graph-structured input. However, they operate on a fixed input graph structure, ignoring potential noise and missing information. Furthermore, their local aggregation mechanism can lead to problems such as over-squashing and limited expressive power in capturing relevant graph structures. Existing solutions to these challenges have primarily relied on heuristic methods, often disregarding the underlying data distribution. Hence, devising principled approaches for learning to infer graph structures relevant to the given prediction task remains an open challenge. In this work, leveraging recent progress in exact and differentiable k-subset sampling, we devise probabilistically rewired MPNNs (PR-MPNNs), which learn to add relevant edges while omitting less beneficial ones. For the first time, our theoretical analysis explores how PR-MPNNs enhance expressive power, and we identify precise conditions under which they outperform purely randomized approaches. Empirically, we demonstrate that our approach effectively mitigates issues like over-squashing and under-reaching. In addition, on established real-world datasets, our method exhibits competitive or superior predictive performance compared to traditional MPNN models and recent graph transformer architectures.

Accumulated clinical studies show that microbes living in humans interact closely with human hosts, and get involved in modulating drug efficacy and drug toxicity. Microbes have become novel targets for the development of antibacterial agents. Therefore, screening of microbe-drug associations can benefit greatly drug research and development. With the increase of microbial genomic and pharmacological datasets, we are greatly motivated to develop an effective computational method to identify new microbe-drug associations. In this paper, we proposed a novel method, Graph2MDA, to predict microbe-drug associations by using variational graph autoencoder (VGAE). We constructed multi-modal attributed graphs based on multiple features of microbes and drugs, such as molecular structures, microbe genetic sequences, and function annotations. Taking as input the multi-modal attribute graphs, VGAE was trained to learn the informative and interpretable latent representations of each node and the whole graph, and then a deep neural network classifier was used to predict microbe-drug associations. The hyperparameter analysis and model ablation studies showed the sensitivity and robustness of our model. We evaluated our method on three independent datasets and the experimental results showed that our proposed method outperformed six existing state-of-the-art methods. We also explored the meaningness of the learned latent representations of drugs and found that the drugs show obvious clustering patterns that are significantly consistent with drug ATC classification. Moreover, we conducted case studies on two microbes and two drugs and found 75\%-95\% predicted associations have been reported in PubMed literature. Our extensive performance evaluations validated the effectiveness of our proposed method.\

Recurrent neural network (RNN) and self-attention mechanism (SAM) are the de facto methods to extract spatial-temporal information for temporal graph learning. Interestingly, we found that although both RNN and SAM could lead to a good performance, in practice neither of them is always necessary. In this paper, we propose GraphMixer, a conceptually and technically simple architecture that consists of three components: (1) a link-encoder that is only based on multi-layer perceptrons (MLP) to summarize the information from temporal links, (2) a node-encoder that is only based on neighbor mean-pooling to summarize node information, and (3) an MLP-based link classifier that performs link prediction based on the outputs of the encoders. Despite its simplicity, GraphMixer attains an outstanding performance on temporal link prediction benchmarks with faster convergence and better generalization performance. These results motivate us to rethink the importance of simpler model architecture.

Stock markets play an important role in the global economy, where accurate stock price predictions can lead to significant financial returns. While existing transformer-based models have outperformed long short-term memory networks and convolutional neural networks in financial time series prediction, their high computational complexity and memory requirements limit their practicality for real-time trading and long-sequence data processing. To address these challenges, we propose SAMBA, an innovative framework for stock return prediction that builds on the Mamba architecture and integrates graph neural networks. SAMBA achieves near-linear computational complexity by utilizing a bidirectional Mamba block to capture long-term dependencies in historical price data and employing adaptive graph convolution to model dependencies between daily stock features. Our experimental results demonstrate that SAMBA significantly outperforms state-of-the-art baseline models in prediction accuracy, maintaining low computational complexity. The code and datasets are available at github.com/Ali-Meh619/SAMBA.

Graph Transformer (GT) recently has emerged as a new paradigm of graph learning algorithms, outperforming the previously popular Message Passing Neural Network (MPNN) on multiple benchmarks. Previous work (Kim et al., 2022) shows that with proper position embedding, GT can approximate MPNN arbitrarily well, implying that GT is at least as powerful as MPNN. In this paper, we study the inverse connection and show that MPNN with virtual node (VN), a commonly used heuristic with little theoretical understanding, is powerful enough to arbitrarily approximate the self-attention layer of GT. In particular, we first show that if we consider one type of linear transformer, the so-called Performer/Linear Transformer (Choromanski et al., 2020; Katharopoulos et al., 2020), then MPNN + VN with only O(1) depth and O(1) width can approximate a self-attention layer in Performer/Linear Transformer. Next, via a connection between MPNN + VN and DeepSets, we prove the MPNN + VN with O(n^d) width and O(1) depth can approximate the self-attention layer arbitrarily well, where d is the input feature dimension. Lastly, under some assumptions, we provide an explicit construction of MPNN + VN with O(1) width and O(n) depth approximating the self-attention layer in GT arbitrarily well. On the empirical side, we demonstrate that 1) MPNN + VN is a surprisingly strong baseline, outperforming GT on the recently proposed Long Range Graph Benchmark (LRGB) dataset, 2) our MPNN + VN improves over early implementation on a wide range of OGB datasets and 3) MPNN + VN outperforms Linear Transformer and MPNN on the climate modeling task.

We present a neural operator architecture to simulate Lagrangian dynamics, such as fluid flow, granular flows, and elastoplasticity. Traditional numerical methods, such as the finite element method (FEM), suffer from long run times and large memory consumption. On the other hand, approaches based on graph neural networks are faster but still suffer from long computation times on dense graphs, which are often required for high-fidelity simulations. Our model, GIOROM or Graph Interaction Operator for Reduced-Order Modeling, learns temporal dynamics within a reduced-order setting, capturing spatial features from a highly sparse graph representation of the input and generalizing to arbitrary spatial locations during inference. The model is geometry-aware and discretization-agnostic and can generalize to different initial conditions, velocities, and geometries after training. We show that point clouds of the order of 100,000 points can be inferred from sparse graphs with sim1000 points, with negligible change in computation time. We empirically evaluate our model on elastic solids, Newtonian fluids, Non-Newtonian fluids, Drucker-Prager granular flows, and von Mises elastoplasticity. On these benchmarks, our approach results in a 25times speedup compared to other neural network-based physics simulators while delivering high-fidelity predictions of complex physical systems and showing better performance on most benchmarks. The code and the demos are provided at https://github.com/HrishikeshVish/GIOROM.

Temporal Graph Neural Networks have garnered substantial attention for their capacity to model evolving structural and temporal patterns while exhibiting impressive performance. However, it is known that these architectures are encumbered by issues that constrain their performance, such as over-squashing and over-smoothing. Meanwhile, Transformers have demonstrated exceptional computational capacity to effectively address challenges related to long-range dependencies. Consequently, we introduce Todyformer-a novel Transformer-based neural network tailored for dynamic graphs. It unifies the local encoding capacity of Message-Passing Neural Networks (MPNNs) with the global encoding of Transformers through i) a novel patchifying paradigm for dynamic graphs to improve over-squashing, ii) a structure-aware parametric tokenization strategy leveraging MPNNs, iii) a Transformer with temporal positional-encoding to capture long-range dependencies, and iv) an encoding architecture that alternates between local and global contextualization, mitigating over-smoothing in MPNNs. Experimental evaluations on public benchmark datasets demonstrate that Todyformer consistently outperforms the state-of-the-art methods for downstream tasks. Furthermore, we illustrate the underlying aspects of the proposed model in effectively capturing extensive temporal dependencies in dynamic graphs.

Mesh-based simulations are central to modeling complex physical systems in many disciplines across science and engineering. Mesh representations support powerful numerical integration methods and their resolution can be adapted to strike favorable trade-offs between accuracy and efficiency. However, high-dimensional scientific simulations are very expensive to run, and solvers and parameters must often be tuned individually to each system studied. Here we introduce MeshGraphNets, a framework for learning mesh-based simulations using graph neural networks. Our model can be trained to pass messages on a mesh graph and to adapt the mesh discretization during forward simulation. Our results show it can accurately predict the dynamics of a wide range of physical systems, including aerodynamics, structural mechanics, and cloth. The model's adaptivity supports learning resolution-independent dynamics and can scale to more complex state spaces at test time. Our method is also highly efficient, running 1-2 orders of magnitude faster than the simulation on which it is trained. Our approach broadens the range of problems on which neural network simulators can operate and promises to improve the efficiency of complex, scientific modeling tasks.

Long-range dependencies are critical for effective graph representation learning, yet most existing datasets focus on small graphs tailored to inductive tasks, offering limited insight into long-range interactions. Current evaluations primarily compare models employing global attention (e.g., graph transformers) with those using local neighborhood aggregation (e.g., message-passing neural networks) without a direct measurement of long-range dependency. In this work, we introduce City-Networks, a novel large-scale transductive learning dataset derived from real-world city roads. This dataset features graphs with over 10^5 nodes and significantly larger diameters than those in existing benchmarks, naturally embodying long-range information. We annotate the graphs using an eccentricity-based approach, ensuring that the classification task inherently requires information from distant nodes. Furthermore, we propose a model-agnostic measurement based on the Jacobians of neighbors from distant hops, offering a principled quantification of long-range dependencies. Finally, we provide theoretical justifications for both our dataset design and the proposed measurement - particularly by focusing on over-smoothing and influence score dilution - which establishes a robust foundation for further exploration of long-range interactions in graph neural networks.

This paper reports the first brain-inspired large language model (BriLLM). This is a non-Transformer, non-GPT, non-traditional machine learning input-output controlled generative language model. The model is based on the Signal Fully-connected flowing (SiFu) definition on the directed graph in terms of the neural network, and has the interpretability of all nodes on the graph of the whole model, instead of the traditional machine learning model that only has limited interpretability at the input and output ends. In the language model scenario, the token is defined as a node in the graph. A randomly shaped or user-defined signal flow flows between nodes on the principle of "least resistance" along paths. The next token or node to be predicted or generated is the target of the signal flow. As a language model, BriLLM theoretically supports infinitely long n-gram models when the model size is independent of the input and predicted length of the model. The model's working signal flow provides the possibility of recall activation and innate multi-modal support similar to the cognitive patterns of the human brain. At present, we released the first BriLLM version in Chinese, with 4000 tokens, 32-dimensional node width, 16-token long sequence prediction ability, and language model prediction performance comparable to GPT-1. More computing power will help us explore the infinite possibilities depicted above.

Large scale deep learning model, such as modern language models and diffusion architectures, have revolutionized applications ranging from natural language processing to computer vision. However, their deployment in distributed or decentralized environments raises significant privacy concerns, as sensitive data may be exposed during inference. Traditional techniques like secure multi-party computation, homomorphic encryption, and differential privacy offer partial remedies but often incur substantial computational overhead, latency penalties, or limited compatibility with non-linear network operations. In this work, we introduce Equivariant Encryption (EE), a novel paradigm designed to enable secure, "blind" inference on encrypted data with near zero performance overhead. Unlike fully homomorphic approaches that encrypt the entire computational graph, EE selectively obfuscates critical internal representations within neural network layers while preserving the exact functionality of both linear and a prescribed set of non-linear operations. This targeted encryption ensures that raw inputs, intermediate activations, and outputs remain confidential, even when processed on untrusted infrastructure. We detail the theoretical foundations of EE, compare its performance and integration complexity against conventional privacy preserving techniques, and demonstrate its applicability across a range of architectures, from convolutional networks to large language models. Furthermore, our work provides a comprehensive threat analysis, outlining potential attack vectors and baseline strategies, and benchmarks EE against standard inference pipelines in decentralized settings. The results confirm that EE maintains high fidelity and throughput, effectively bridging the gap between robust data confidentiality and the stringent efficiency requirements of modern, large scale model inference.