Daily Papers

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.

Attention mechanisms have been widely used to capture long-range dependencies among nodes in Graph Transformers. Bottlenecked by the quadratic computational cost, attention mechanisms fail to scale in large graphs. Recent improvements in computational efficiency are mainly achieved by attention sparsification with random or heuristic-based graph subsampling, which falls short in data-dependent context reasoning. State space models (SSMs), such as Mamba, have gained prominence for their effectiveness and efficiency in modeling long-range dependencies in sequential data. However, adapting SSMs to non-sequential graph data presents a notable challenge. In this work, we introduce Graph-Mamba, the first attempt to enhance long-range context modeling in graph networks by integrating a Mamba block with the input-dependent node selection mechanism. Specifically, we formulate graph-centric node prioritization and permutation strategies to enhance context-aware reasoning, leading to a substantial improvement in predictive performance. Extensive experiments on ten benchmark datasets demonstrate that Graph-Mamba outperforms state-of-the-art methods in long-range graph prediction tasks, with a fraction of the computational cost in both FLOPs and GPU memory consumption. The code and models are publicly available at https://github.com/bowang-lab/Graph-Mamba.

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.

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.

In today's digital age, conspiracies and information campaigns can emerge rapidly and erode social and democratic cohesion. While recent deep learning approaches have made progress in modeling engagement through language and propagation models, they struggle with irregularly sampled data and early trajectory assessment. We present IC-Mamba, a novel state space model that forecasts social media engagement by modeling interval-censored data with integrated temporal embeddings. Our model excels at predicting engagement patterns within the crucial first 15-30 minutes of posting (RMSE 0.118-0.143), enabling rapid assessment of content reach. By incorporating interval-censored modeling into the state space framework, IC-Mamba captures fine-grained temporal dynamics of engagement growth, achieving a 4.72% improvement over state-of-the-art across multiple engagement metrics (likes, shares, comments, and emojis). Our experiments demonstrate IC-Mamba's effectiveness in forecasting both post-level dynamics and broader narrative patterns (F1 0.508-0.751 for narrative-level predictions). The model maintains strong predictive performance across extended time horizons, successfully forecasting opinion-level engagement up to 28 days ahead using observation windows of 3-10 days. These capabilities enable earlier identification of potentially problematic content, providing crucial lead time for designing and implementing countermeasures. Code is available at: https://github.com/ltian678/ic-mamba. An interactive dashboard demonstrating our results is available at: https://ic-mamba.behavioral-ds.science.

The Transformer architecture has shown a remarkable ability in modeling global relationships. However, it poses a significant computational challenge when processing high-dimensional medical images. This hinders its development and widespread adoption in this task. Mamba, as a State Space Model (SSM), recently emerged as a notable manner for long-range dependencies in sequential modeling, excelling in natural language processing filed with its remarkable memory efficiency and computational speed. Inspired by its success, we introduce SegMamba, a novel 3D medical image Segmentation Mamba model, designed to effectively capture long-range dependencies within whole volume features at every scale. Our SegMamba, in contrast to Transformer-based methods, excels in whole volume feature modeling from a state space model standpoint, maintaining superior processing speed, even with volume features at a resolution of {64times 64times 64}. Comprehensive experiments on the BraTS2023 dataset demonstrate the effectiveness and efficiency of our SegMamba. The code for SegMamba is available at: https://github.com/ge-xing/SegMamba

Recently, State Space Models (SSMs), with Mamba as a prime example, have shown great promise for long-range dependency modeling with linear complexity. Then, Vision Mamba and the subsequent architectures are presented successively, and they perform well on visual tasks. The crucial step of applying Mamba to visual tasks is to construct 2D visual features in sequential manners. To effectively organize and construct visual features within the 2D image space through 1D selective scan, we propose a novel Multi-Head Scan (MHS) module. The embeddings extracted from the preceding layer are projected into multiple lower-dimensional subspaces. Subsequently, within each subspace, the selective scan is performed along distinct scan routes. The resulting sub-embeddings, obtained from the multi-head scan process, are then integrated and ultimately projected back into the high-dimensional space. Moreover, we incorporate a Scan Route Attention (SRA) mechanism to enhance the module's capability to discern complex structures. To validate the efficacy of our module, we exclusively substitute the 2D-Selective-Scan (SS2D) block in VM-UNet with our proposed module, and we train our models from scratch without using any pre-trained weights. The results indicate a significant improvement in performance while reducing the parameters of the original VM-UNet. The code for this study is publicly available at https://github.com/PixDeep/MHS-VM.

In the realm of time series forecasting (TSF), it is imperative for models to adeptly discern and distill hidden patterns within historical time series data to forecast future states. Transformer-based models exhibit formidable efficacy in TSF, primarily attributed to their advantage in apprehending these patterns. However, the quadratic complexity of the Transformer leads to low computational efficiency and high costs, which somewhat hinders the deployment of the TSF model in real-world scenarios. Recently, Mamba, a selective state space model, has gained traction due to its ability to process dependencies in sequences while maintaining near-linear complexity. For TSF tasks, these characteristics enable Mamba to comprehend hidden patterns as the Transformer and reduce computational overhead compared to the Transformer. Therefore, we propose a Mamba-based model named Simple-Mamba (S-Mamba) for TSF. Specifically, we tokenize the time points of each variate autonomously via a linear layer. A bidirectional Mamba layer is utilized to extract inter-variate correlations and a Feed-Forward Network is set to learn temporal dependencies. Finally, the generation of forecast outcomes through a linear mapping layer. Experiments on thirteen public datasets prove that S-Mamba maintains low computational overhead and achieves leading performance. Furthermore, we conduct extensive experiments to explore Mamba's potential in TSF tasks. Our code is available at https://github.com/wzhwzhwzh0921/S-D-Mamba.

The diffusion model has long been plagued by scalability and quadratic complexity issues, especially within transformer-based structures. In this study, we aim to leverage the long sequence modeling capability of a State-Space Model called Mamba to extend its applicability to visual data generation. Firstly, we identify a critical oversight in most current Mamba-based vision methods, namely the lack of consideration for spatial continuity in the scan scheme of Mamba. Secondly, building upon this insight, we introduce a simple, plug-and-play, zero-parameter method named Zigzag Mamba, which outperforms Mamba-based baselines and demonstrates improved speed and memory utilization compared to transformer-based baselines. Lastly, we integrate Zigzag Mamba with the Stochastic Interpolant framework to investigate the scalability of the model on large-resolution visual datasets, such as FacesHQ 1024times 1024 and UCF101, MultiModal-CelebA-HQ, and MS COCO 256times 256. Code will be released at https://taohu.me/zigma/

State space models and Mamba-based models have been increasingly applied across various domains, achieving state-of-the-art performance. This technical report introduces the first attempt to train a transferable Mamba model utilizing contrastive language-image pretraining (CLIP). We have trained Mamba models of varying sizes and undertaken comprehensive evaluations of these models on 26 zero-shot classification datasets and 16 out-of-distribution (OOD) datasets. Our findings reveal that a Mamba model with 67 million parameters is on par with a 307 million-parameter Vision Transformer (ViT) model in zero-shot classification tasks, highlighting the parameter efficiency of Mamba models. In tests of OOD generalization, Mamba-based models exhibit exceptional performance in conditions of OOD image contrast or when subjected to high-pass filtering. However, a Hessian analysis indicates that Mamba models feature a sharper and more non-convex landscape compared to ViT-based models, making them more challenging to train. The source code is available at https://github.com/raytrun/mamba-clip.

Precise lesion resection depends on accurately identifying fine-grained anatomical structures. While many coarse-grained segmentation (CGS) methods have been successful in large-scale segmentation (e.g., organs), they fall short in clinical scenarios requiring fine-grained segmentation (FGS), which remains challenging due to frequent individual variations in small-scale anatomical structures. Although recent Mamba-based models have advanced medical image segmentation, they often rely on fixed manually-defined scanning orders, which limit their adaptability to individual variations in FGS. To address this, we propose ASM-UNet, a novel Mamba-based architecture for FGS. It introduces adaptive scan scores to dynamically guide the scanning order, generated by combining group-level commonalities and individual-level variations. Experiments on two public datasets (ACDC and Synapse) and a newly proposed challenging biliary tract FGS dataset, namely BTMS, demonstrate that ASM-UNet achieves superior performance in both CGS and FGS tasks. Our code and dataset are available at https://github.com/YqunYang/ASM-UNet.

We propose a novel hybrid Mamba-Transformer backbone, denoted as MambaVision, which is specifically tailored for vision applications. Our core contribution includes redesigning the Mamba formulation to enhance its capability for efficient modeling of visual features. In addition, we conduct a comprehensive ablation study on the feasibility of integrating Vision Transformers (ViT) with Mamba. Our results demonstrate that equipping the Mamba architecture with several self-attention blocks at the final layers greatly improves the modeling capacity to capture long-range spatial dependencies. Based on our findings, we introduce a family of MambaVision models with a hierarchical architecture to meet various design criteria. For Image classification on ImageNet-1K dataset, MambaVision model variants achieve a new State-of-the-Art (SOTA) performance in terms of Top-1 accuracy and image throughput. In downstream tasks such as object detection, instance segmentation and semantic segmentation on MS COCO and ADE20K datasets, MambaVision outperforms comparably-sized backbones and demonstrates more favorable performance. Code: https://github.com/NVlabs/MambaVision.

We introduce AiM, an autoregressive (AR) image generative model based on Mamba architecture. AiM employs Mamba, a novel state-space model characterized by its exceptional performance for long-sequence modeling with linear time complexity, to supplant the commonly utilized Transformers in AR image generation models, aiming to achieve both superior generation quality and enhanced inference speed. Unlike existing methods that adapt Mamba to handle two-dimensional signals via multi-directional scan, AiM directly utilizes the next-token prediction paradigm for autoregressive image generation. This approach circumvents the need for extensive modifications to enable Mamba to learn 2D spatial representations. By implementing straightforward yet strategically targeted modifications for visual generative tasks, we preserve Mamba's core structure, fully exploiting its efficient long-sequence modeling capabilities and scalability. We provide AiM models in various scales, with parameter counts ranging from 148M to 1.3B. On the ImageNet1K 256*256 benchmark, our best AiM model achieves a FID of 2.21, surpassing all existing AR models of comparable parameter counts and demonstrating significant competitiveness against diffusion models, with 2 to 10 times faster inference speed. Code is available at https://github.com/hp-l33/AiM

Despite their frequent use for change detection, both ConvNets and Vision transformers (ViT) exhibit well-known limitations, namely the former struggle to model long-range dependencies while the latter are computationally inefficient, rendering them challenging to train on large-scale datasets. Vision Mamba, an architecture based on State Space Models has emerged as an alternative addressing the aforementioned deficiencies and has been already applied to remote sensing change detection, though mostly as a feature extracting backbone. In this article the Change State Space Model is introduced, that has been specifically designed for change detection by focusing on the relevant changes between bi-temporal images, effectively filtering out irrelevant information. By concentrating solely on the changed features, the number of network parameters is reduced, enhancing significantly computational efficiency while maintaining high detection performance and robustness against input degradation. The proposed model has been evaluated via three benchmark datasets, where it outperformed ConvNets, ViTs, and Mamba-based counterparts at a fraction of their computational complexity. The implementation will be made available at https://github.com/Elman295/CSSM upon acceptance.

Associating unstructured data with structured information is crucial for real-world tasks that require relevance search. However, existing graph learning benchmarks often overlook the rich semantic information associate with each node. To bridge such gap, we introduce the Multimodal Graph Benchmark (MM-GRAPH), the first comprehensive multi-modal graph benchmark that incorporates both textual and visual information. MM-GRAPH surpasses previous efforts, which have primarily focused on text-attributed graphs with various connectivity patterns. MM-GRAPH consists of five graph learning datasets of various scales that are appropriate for different learning tasks. Their multimodal node features, enabling a more comprehensive evaluation of graph learning algorithms in real-world scenarios. To facilitate research on multimodal graph learning, we further provide an extensive study on the performance of various graph neural networks in the presence of features from various modalities. MM-GRAPH aims to foster research on multimodal graph learning and drive the development of more advanced and robust graph learning algorithms. By providing a diverse set of datasets and benchmarks, MM-GRAPH enables researchers to evaluate and compare their models in realistic settings, ultimately leading to improved performance on real-world applications that rely on multimodal graph data.

The analysis of tabular data has traditionally been dominated by gradient-boosted decision trees (GBDTs), known for their proficiency with mixed categorical and numerical features. However, recent deep learning innovations are challenging this dominance. We introduce Mambular, an adaptation of the Mamba architecture optimized for tabular data. We extensively benchmark Mambular against state-of-the-art models, including neural networks and tree-based methods, and demonstrate its competitive performance across diverse datasets. Additionally, we explore various adaptations of Mambular to understand its effectiveness for tabular data. We investigate different pooling strategies, feature interaction mechanisms, and bi-directional processing. Our analysis shows that interpreting features as a sequence and passing them through Mamba layers results in surprisingly performant models. The results highlight Mambulars potential as a versatile and powerful architecture for tabular data analysis, expanding the scope of deep learning applications in this domain. The source code is available at https://github.com/basf/mamba-tabular.

Recently, the state space model Mamba has demonstrated efficient long-sequence modeling capabilities, particularly for addressing long-sequence visual tasks in 3D medical imaging. However, existing generative self-supervised learning methods have not yet fully unleashed Mamba's potential for handling long-range dependencies because they overlook the inherent causal properties of state space sequences in masked modeling. To address this challenge, we propose a general-purpose pre-training framework called MambaMIM, a masked image modeling method based on a novel TOKen-Interpolation strategy (TOKI) for the selective structure state space sequence, which learns causal relationships of state space within the masked sequence. Further, MambaMIM introduces a bottom-up 3D hybrid masking strategy to maintain a masking consistency across different architectures and can be used on any single or hybrid Mamba architecture to enhance its multi-scale and long-range representation capability. We pre-train MambaMIM on a large-scale dataset of 6.8K CT scans and evaluate its performance across eight public medical segmentation benchmarks. Extensive downstream experiments reveal the feasibility and advancement of using Mamba for medical image pre-training. In particular, when we apply the MambaMIM to a customized architecture that hybridizes MedNeXt and Vision Mamba, we consistently obtain the state-of-the-art segmentation performance. The code is available at: https://github.com/FengheTan9/MambaMIM.

Global dependency modeling and spatial position modeling are two core issues of the foundational architecture design in current deep learning frameworks. Recently, Vision Transformers (ViTs) have achieved remarkable success in computer vision, leveraging the powerful global dependency modeling capability of the self-attention mechanism. Furthermore, Mamba2 has demonstrated its significant potential in natural language processing tasks by explicitly modeling the spatial adjacency prior through the structured mask. In this paper, we propose Polyline Path Masked Attention (PPMA) that integrates the self-attention mechanism of ViTs with an enhanced structured mask of Mamba2, harnessing the complementary strengths of both architectures. Specifically, we first ameliorate the traditional structured mask of Mamba2 by introducing a 2D polyline path scanning strategy and derive its corresponding structured mask, polyline path mask, which better preserves the adjacency relationships among image tokens. Notably, we conduct a thorough theoretical analysis on the structural characteristics of the proposed polyline path mask and design an efficient algorithm for the computation of the polyline path mask. Next, we embed the polyline path mask into the self-attention mechanism of ViTs, enabling explicit modeling of spatial adjacency prior. Extensive experiments on standard benchmarks, including image classification, object detection, and segmentation, demonstrate that our model outperforms previous state-of-the-art approaches based on both state-space models and Transformers. For example, our proposed PPMA-T/S/B models achieve 48.7%/51.1%/52.3% mIoU on the ADE20K semantic segmentation task, surpassing RMT-T/S/B by 0.7%/1.3%/0.3%, respectively. Code is available at https://github.com/zhongchenzhao/PPMA.

The vision community has started to build with the recently developed state space model, Mamba, as the new backbone for a range of tasks. This paper shows that Mamba's visual capability can be significantly enhanced through autoregressive pretraining, a direction not previously explored. Efficiency-wise, the autoregressive nature can well capitalize on the Mamba's unidirectional recurrent structure, enabling faster overall training speed compared to other training strategies like mask modeling. Performance-wise, autoregressive pretraining equips the Mamba architecture with markedly higher accuracy over its supervised-trained counterparts and, more importantly, successfully unlocks its scaling potential to large and even huge model sizes. For example, with autoregressive pretraining, a base-size Mamba attains 83.2\% ImageNet accuracy, outperforming its supervised counterpart by 2.0\%; our huge-size Mamba, the largest Vision Mamba to date, attains 85.0\% ImageNet accuracy (85.5\% when finetuned with 384times384 inputs), notably surpassing all other Mamba variants in vision. The code is available at https://github.com/OliverRensu/ARM.

Multimodal Large Language Models (MLLMs) have attracted much attention due to their multifunctionality. However, traditional Transformer architectures incur significant overhead due to their secondary computational complexity. To address this issue, we introduce ML-Mamba, a multimodal language model that utilizes the latest and efficient Mamba-2 model for inference. Mamba-2 is known for its linear extension and fast processing of long sequences. We replace the Transformer based backbone with a pre-trained Mamba-2 model and explore methods for integrating 2D visual selective scanning mechanisms into multimodal learning. We also try various visual encoders and Mamba-2 model variants. Our extensive experiments conducted in various multimodal benchmark tests have demonstrated the competitive performance of ML-Mamba and highlighted the potential of state space models in multimodal tasks. The experimental results show that: (1) ML-Mamba achieves performance comparable to state-of-the-art methods such as TinyLaVA and MobileVLM v2 through its linear sequential modeling, while also having faster inference speed; (2) ML-Mamba performs well in visual hallucinations and spatial relationship judgment in closed set benchmark tests; (3) ML-Mamba achieves performance comparable to LLaVA while reducing the number of parameters by 40\%.(4) Compared to the multimodal model using the original Mamba model, the Mamba-2 based large-scale multimodal language model has stronger inference performance and effectiveness.

We present PlainMamba: a simple non-hierarchical state space model (SSM) designed for general visual recognition. The recent Mamba model has shown how SSMs can be highly competitive with other architectures on sequential data and initial attempts have been made to apply it to images. In this paper, we further adapt the selective scanning process of Mamba to the visual domain, enhancing its ability to learn features from two-dimensional images by (i) a continuous 2D scanning process that improves spatial continuity by ensuring adjacency of tokens in the scanning sequence, and (ii) direction-aware updating which enables the model to discern the spatial relations of tokens by encoding directional information. Our architecture is designed to be easy to use and easy to scale, formed by stacking identical PlainMamba blocks, resulting in a model with constant width throughout all layers. The architecture is further simplified by removing the need for special tokens. We evaluate PlainMamba on a variety of visual recognition tasks including image classification, semantic segmentation, object detection, and instance segmentation. Our method achieves performance gains over previous non-hierarchical models and is competitive with hierarchical alternatives. For tasks requiring high-resolution inputs, in particular, PlainMamba requires much less computing while maintaining high performance. Code and models are available at https://github.com/ChenhongyiYang/PlainMamba

Recent Learned image compression (LIC) leverages Mamba-style state-space models (SSMs) for global receptive fields with linear complexity. However, vanilla Mamba is content-agnostic, relying on fixed and predefined selective scans, which restricts its ability to dynamically and fully exploit content dependencies. We introduce Content-Adaptive Mamba (CAM), a dynamic SSM that addresses two critical limitations. First, it employs content-aware token reorganization, clustering and reordering tokens based on content similarity to prioritize proximity in feature space over Euclidean space. Second, it integrates global priors into SSM via a prompt dictionary, effectively mitigating the strict causality and long-range decay in the token interactions of Mamba. These innovations enable CAM to better capture global dependencies while preserving computational efficiency. Leveraging CAM, our Content-Adaptive Mamba-based LIC model (CMIC) achieves state-of-the-art rate-distortion performance, surpassing VTM-21.0 by -15.91\%, -21.34\%, and -17.58\% BD-rate on Kodak, Tecnick, and CLIC benchmarks, respectively.

The Mamba-based image restoration backbones have recently demonstrated significant potential in balancing global reception and computational efficiency. However, the inherent causal modeling limitation of Mamba, where each token depends solely on its predecessors in the scanned sequence, restricts the full utilization of pixels across the image and thus presents new challenges in image restoration. In this work, we propose MambaIRv2, which equips Mamba with the non-causal modeling ability similar to ViTs to reach the attentive state space restoration model. Specifically, the proposed attentive state-space equation allows to attend beyond the scanned sequence and facilitate image unfolding with just one single scan. Moreover, we further introduce a semantic-guided neighboring mechanism to encourage interaction between distant but similar pixels. Extensive experiments show our MambaIRv2 outperforms SRFormer by even 0.35dB PSNR for lightweight SR even with 9.3\% less parameters and suppresses HAT on classic SR by up to 0.29dB. Code is available at https://github.com/csguoh/MambaIR.

The Mamba layer offers an efficient selective state space model (SSM) that is highly effective in modeling multiple domains including NLP, long-range sequences processing, and computer vision. Selective SSMs are viewed as dual models, in which one trains in parallel on the entire sequence via IO-aware parallel scan, and deploys in an autoregressive manner. We add a third view and show that such models can be viewed as attention-driven models. This new perspective enables us to compare the underlying mechanisms to that of the self-attention layers in transformers and allows us to peer inside the inner workings of the Mamba model with explainability methods. Our code is publicly available.

Remote sensing image classification forms the foundation of various understanding tasks, serving a crucial function in remote sensing image interpretation. The recent advancements of Convolutional Neural Networks (CNNs) and Transformers have markedly enhanced classification accuracy. Nonetheless, remote sensing scene classification remains a significant challenge, especially given the complexity and diversity of remote sensing scenarios and the variability of spatiotemporal resolutions. The capacity for whole-image understanding can provide more precise semantic cues for scene discrimination. In this paper, we introduce RSMamba, a novel architecture for remote sensing image classification. RSMamba is based on the State Space Model (SSM) and incorporates an efficient, hardware-aware design known as the Mamba. It integrates the advantages of both a global receptive field and linear modeling complexity. To overcome the limitation of the vanilla Mamba, which can only model causal sequences and is not adaptable to two-dimensional image data, we propose a dynamic multi-path activation mechanism to augment Mamba's capacity to model non-causal data. Notably, RSMamba maintains the inherent modeling mechanism of the vanilla Mamba, yet exhibits superior performance across multiple remote sensing image classification datasets. This indicates that RSMamba holds significant potential to function as the backbone of future visual foundation models. The code will be available at https://github.com/KyanChen/RSMamba.

Semantic Change Detection (SCD) from remote sensing imagery requires models balancing extensive spatial context, computational efficiency, and sensitivity to class-imbalanced land-cover transitions. While Convolutional Neural Networks excel at local feature extraction but lack global context, Transformers provide global modeling at high computational costs. Recent Mamba architectures based on state-space models offer compelling solutions through linear complexity and efficient long-range modeling. In this study, we introduce Mamba-FCS, a SCD framework built upon Visual State Space Model backbone incorporating, a Joint Spatio-Frequency Fusion block incorporating log-amplitude frequency domain features to enhance edge clarity and suppress illumination artifacts, a Change-Guided Attention (CGA) module that explicitly links the naturally intertwined BCD and SCD tasks, and a Separated Kappa (SeK) loss tailored for class-imbalanced performance optimization. Extensive evaluation on SECOND and Landsat-SCD datasets shows that Mamba-FCS achieves state-of-the-art metrics, 88.62% Overall Accuracy, 65.78% F_scd, and 25.50% SeK on SECOND, 96.25% Overall Accuracy, 89.27% F_scd, and 60.26% SeK on Landsat-SCD. Ablation analyses confirm distinct contributions of each novel component, with qualitative assessments highlighting significant improvements in SCD. Our results underline the substantial potential of Mamba architectures, enhanced by proposed techniques, setting a new benchmark for effective and scalable semantic change detection in remote sensing applications. The complete source code, configuration files, and pre-trained models will be publicly available upon publication.

State-Space Models (SSMs) have recently emerged as a powerful and efficient alternative to the long-standing transformer architecture. However, existing SSM conceptualizations retain deeply rooted biases from their roots in natural language processing. This constrains their ability to appropriately model the spatially-dependent characteristics of visual inputs. In this paper, we address these limitations by re-deriving modern selective state-space techniques, starting from a natively multidimensional formulation. Currently, prior works attempt to apply natively 1D SSMs to 2D data (i.e. images) by relying on arbitrary combinations of 1D scan directions to capture spatial dependencies. In contrast, Mamba2D improves upon this with a single 2D scan direction that factors in both dimensions of the input natively, effectively modelling spatial dependencies when constructing hidden states. Mamba2D shows comparable performance to prior adaptations of SSMs for vision tasks, on standard image classification evaluations with the ImageNet-1K dataset. Source code is available at https://github.com/cocoalex00/Mamba2D.

UNet and its variants have been widely used in medical image segmentation. However, these models, especially those based on Transformer architectures, pose challenges due to their large number of parameters and computational loads, making them unsuitable for mobile health applications. Recently, State Space Models (SSMs), exemplified by Mamba, have emerged as competitive alternatives to CNN and Transformer architectures. Building upon this, we employ Mamba as a lightweight substitute for CNN and Transformer within UNet, aiming at tackling challenges stemming from computational resource limitations in real medical settings. To this end, we introduce the Lightweight Mamba UNet (LightM-UNet) that integrates Mamba and UNet in a lightweight framework. Specifically, LightM-UNet leverages the Residual Vision Mamba Layer in a pure Mamba fashion to extract deep semantic features and model long-range spatial dependencies, with linear computational complexity. Extensive experiments conducted on two real-world 2D/3D datasets demonstrate that LightM-UNet surpasses existing state-of-the-art literature. Notably, when compared to the renowned nnU-Net, LightM-UNet achieves superior segmentation performance while drastically reducing parameter and computation costs by 116x and 21x, respectively. This highlights the potential of Mamba in facilitating model lightweighting. Our code implementation is publicly available at https://github.com/MrBlankness/LightM-UNet.

A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in studying numerous subgraph problems, on top of the ordinary graph problems. Many algorithms are proposed in studying subgraph problems, where one common approach is by extracting the patterns and structures of a given graph. Due to the complex structures of certain types of graphs and to improve overall performances of the existing frameworks, machine learning techniques have recently been employed in dealing with various subgraph problems. In this article, we present a comprehensive review on five well known subgraph problems that have been tackled by using machine learning methods. They are subgraph isomorphism (both counting and matching), maximum common subgraph, community detection and community search problems. We provide an outline of each proposed method, and examine its designs and performances. We also explore non-learning-based algorithms for each problem and a brief discussion is given. We then suggest some promising research directions in this area, hoping that relevant subgraph problems can be tackled by using a similar strategy. Since there is a huge growth in employing machine learning techniques in recent years, we believe that this survey will serve as a good reference point to relevant research communities.

Recently, a novel visual state space (VSS) model, referred to as Mamba, has demonstrated significant progress in modeling long sequences with linear complexity, comparable to Transformer models, thereby enhancing its adaptability for processing visual data. Although most methods aim to enhance the global receptive field by directly modifying Mamba's scanning mechanism, they tend to overlook the critical importance of local information in dense prediction tasks. Additionally, whether Mamba can effectively extract local features as convolutional neural networks (CNNs) do remains an open question that merits further investigation. In this paper, We propose a novel model, AtrousMamba, which effectively balances the extraction of fine-grained local details with the integration of global contextual information. Specifically, our method incorporates an atrous-window selective scan mechanism, enabling a gradual expansion of the scanning range with adjustable rates. This design shortens the distance between adjacent tokens, enabling the model to effectively capture fine-grained local features and global context. By leveraging the atrous window scan visual state space (AWVSS) module, we design dedicated end-to-end Mamba-based frameworks for binary change detection (BCD) and semantic change detection (SCD), referred to as AWMambaBCD and AWMambaSCD, respectively. Experimental results on six benchmark datasets show that the proposed framework outperforms existing CNN-based, Transformer-based, and Mamba-based methods. These findings clearly demonstrate that Mamba not only captures long-range dependencies in visual data but also effectively preserves fine-grained local details.

Tracking by detection has been the prevailing paradigm in the field of Multi-object Tracking (MOT). These methods typically rely on the Kalman Filter to estimate the future locations of objects, assuming linear object motion. However, they fall short when tracking objects exhibiting nonlinear and diverse motion in scenarios like dancing and sports. In addition, there has been limited focus on utilizing learning-based motion predictors in MOT. To address these challenges, we resort to exploring data-driven motion prediction methods. Inspired by the great expectation of state space models (SSMs), such as Mamba, in long-term sequence modeling with near-linear complexity, we introduce a Mamba-based motion model named Mamba moTion Predictor (MTP). MTP is designed to model the complex motion patterns of objects like dancers and athletes. Specifically, MTP takes the spatial-temporal location dynamics of objects as input, captures the motion pattern using a bi-Mamba encoding layer, and predicts the next motion. In real-world scenarios, objects may be missed due to occlusion or motion blur, leading to premature termination of their trajectories. To tackle this challenge, we further expand the application of MTP. We employ it in an autoregressive way to compensate for missing observations by utilizing its own predictions as inputs, thereby contributing to more consistent trajectories. Our proposed tracker, MambaTrack, demonstrates advanced performance on benchmarks such as Dancetrack and SportsMOT, which are characterized by complex motion and severe occlusion.

Despite the significant achievements of Vision Transformers (ViTs) in various vision tasks, they are constrained by the quadratic complexity. Recently, State Space Models (SSMs) have garnered widespread attention due to their global receptive field and linear complexity with respect to the input length, demonstrating substantial potential across fields including natural language processing and computer vision. To improve the performance of SSMs in vision tasks, a multi-scan strategy is widely adopted, which leads to significant redundancy of SSMs. For a better trade-off between efficiency and performance, we analyze the underlying reasons behind the success of the multi-scan strategy, where long-range dependency plays an important role. Based on the analysis, we introduce Multi-Scale Vision Mamba (MSVMamba) to preserve the superiority of SSMs in vision tasks with limited parameters. It employs a multi-scale 2D scanning technique on both original and downsampled feature maps, which not only benefits long-range dependency learning but also reduces computational costs. Additionally, we integrate a Convolutional Feed-Forward Network (ConvFFN) to address the lack of channel mixing. Our experiments demonstrate that MSVMamba is highly competitive, with the MSVMamba-Tiny model achieving 82.8% top-1 accuracy on ImageNet, 46.9% box mAP, and 42.2% instance mAP with the Mask R-CNN framework, 1x training schedule on COCO, and 47.6% mIoU with single-scale testing on ADE20K.Code is available at https://github.com/YuHengsss/MSVMamba.

In recent years, the application of multimodal large language models (MLLM) in various fields has achieved remarkable success. However, as the foundation model for many downstream tasks, current MLLMs are composed of the well-known Transformer network, which has a less efficient quadratic computation complexity. To improve the efficiency of such basic models, we propose Cobra, a linear computational complexity MLLM. Specifically, Cobra integrates the efficient Mamba language model into the visual modality. Moreover, we explore and study various modal fusion schemes to create an effective multi-modal Mamba. Extensive experiments demonstrate that (1) Cobra achieves extremely competitive performance with current computationally efficient state-of-the-art methods, e.g., LLaVA-Phi, TinyLLaVA, and MobileVLM v2, and has faster speed due to Cobra's linear sequential modeling. (2) Interestingly, the results of closed-set challenging prediction benchmarks show that Cobra performs well in overcoming visual illusions and spatial relationship judgments. (3) Notably, Cobra even achieves comparable performance to LLaVA with about 43% of the number of parameters. We will make all codes of Cobra open-source and hope that the proposed method can facilitate future research on complexity problems in MLLM. Our project page is available at: https://sites.google.com/view/cobravlm.

Graphs have often been used to answer questions about the interaction between real-world entities by taking advantage of their capacity to represent complex topologies. Complex networks are known to be graphs that capture such non-trivial topologies; they are able to represent human phenomena such as epidemic processes, the dynamics of populations, and the urbanization of cities. The investigation of complex networks has been extrapolated to many fields of science, with particular emphasis on computing techniques, including artificial intelligence. In such a case, the analysis of the interaction between entities of interest is transposed to the internal learning of algorithms, a paradigm whose investigation is able to expand the state of the art in Computer Science. By exploring this paradigm, this thesis puts together complex networks and machine learning techniques to improve the understanding of the human phenomena observed in pandemics, pendular migration, and street networks. Accordingly, we contribute with: (i) a new neural network architecture capable of modeling dynamic processes observed in spatial and temporal data with applications in epidemics propagation, weather forecasting, and patient monitoring in intensive care units; (ii) a machine-learning methodology for analyzing and predicting links in the scope of human mobility between all the cities of Brazil; and, (iii) techniques for identifying inconsistencies in the urban planning of cities while tracking the most influential vertices, with applications over Brazilian and worldwide cities. We obtained results sustained by sound evidence of advances to the state of the art in artificial intelligence, rigorous formalisms, and ample experimentation. Our findings rely upon real-world applications in a range of domains, demonstrating the applicability of our methodologies.

Local graph clustering methods aim to detect small clusters in very large graphs without the need to process the whole graph. They are fundamental and scalable tools for a wide range of tasks such as local community detection, node ranking and node embedding. While prior work on local graph clustering mainly focuses on graphs without node attributes, modern real-world graph datasets typically come with node attributes that provide valuable additional information. We present a simple local graph clustering algorithm for graphs with node attributes, based on the idea of diffusing mass locally in the graph while accounting for both structural and attribute proximities. Using high-dimensional concentration results, we provide statistical guarantees on the performance of the algorithm for the recovery of a target cluster with a single seed node. We give conditions under which a target cluster generated from a fairly general contextual random graph model, which includes both the stochastic block model and the planted cluster model as special cases, can be fully recovered with bounded false positives. Empirically, we validate all theoretical claims using synthetic data, and we show that incorporating node attributes leads to superior local clustering performances using real-world graph datasets.

Long-term forecasting of chaotic systems from short-term observations remains a fundamental and underexplored challenge due to the intrinsic sensitivity to initial conditions and the complex geometry of strange attractors. Existing approaches often rely on long-term training data or focus on short-term sequence correlations, struggling to maintain predictive stability and dynamical coherence over extended horizons. We propose PhyxMamba, a novel framework that integrates a Mamba-based state-space model with physics-informed principles to capture the underlying dynamics of chaotic systems. By reconstructing the attractor manifold from brief observations using time-delay embeddings, PhyxMamba extracts global dynamical features essential for accurate forecasting. Our generative training scheme enables Mamba to replicate the physical process, augmented by multi-token prediction and attractor geometry regularization for physical constraints, enhancing prediction accuracy and preserving key statistical invariants. Extensive evaluations on diverse simulated and real-world chaotic systems demonstrate that PhyxMamba delivers superior long-term forecasting and faithfully captures essential dynamical invariants from short-term data. This framework opens new avenues for reliably predicting chaotic systems under observation-scarce conditions, with broad implications across climate science, neuroscience, epidemiology, and beyond. Our code is open-source at https://github.com/tsinghua-fib-lab/PhyxMamba.

In recent developments, the Mamba architecture, known for its selective state space approach, has shown potential in the efficient modeling of long sequences. However, its application in image generation remains underexplored. Traditional diffusion transformers (DiT), which utilize self-attention blocks, are effective but their computational complexity scales quadratically with the input length, limiting their use for high-resolution images. To address this challenge, we introduce a novel diffusion architecture, Diffusion Mamba (DiM), which foregoes traditional attention mechanisms in favor of a scalable alternative. By harnessing the inherent efficiency of the Mamba architecture, DiM achieves rapid inference times and reduced computational load, maintaining linear complexity with respect to sequence length. Our architecture not only scales effectively but also outperforms existing diffusion transformers in both image and video generation tasks. The results affirm the scalability and efficiency of DiM, establishing a new benchmark for image and video generation techniques. This work advances the field of generative models and paves the way for further applications of scalable architectures.

Event camera-based visual tracking has drawn more and more attention in recent years due to the unique imaging principle and advantages of low energy consumption, high dynamic range, and dense temporal resolution. Current event-based tracking algorithms are gradually hitting their performance bottlenecks, due to the utilization of vision Transformer and the static template for target object localization. In this paper, we propose a novel Mamba-based visual tracking framework that adopts the state space model with linear complexity as a backbone network. The search regions and target template are fed into the vision Mamba network for simultaneous feature extraction and interaction. The output tokens of search regions will be fed into the tracking head for target localization. More importantly, we consider introducing a dynamic template update strategy into the tracking framework using the Memory Mamba network. By considering the diversity of samples in the target template library and making appropriate adjustments to the template memory module, a more effective dynamic template can be integrated. The effective combination of dynamic and static templates allows our Mamba-based tracking algorithm to achieve a good balance between accuracy and computational cost on multiple large-scale datasets, including EventVOT, VisEvent, and FE240hz. The source code will be released on https://github.com/Event-AHU/MambaEVT

With the emergence of data marketplaces, the demand for methods to assess the value of data has increased significantly. While numerous techniques have been proposed for this purpose, none have specifically addressed graphs as the main data modality. Graphs are widely used across various fields, ranging from chemical molecules to social networks. In this study, we break down graphs into two main components: structural and featural, and we focus on evaluating data without relying on specific task-related metrics, making it applicable in practical scenarios where validation requirements may be lacking. We introduce a novel framework called blind message passing, which aligns the seller's and buyer's graphs using a shared node permutation based on graph matching. This allows us to utilize the graph Wasserstein distance to quantify the differences in the structural distribution of graph datasets, called the structural disparities. We then consider featural aspects of buyers' and sellers' graphs for data valuation and capture their statistical similarities and differences, referred to as relevance and diversity, respectively. Our approach ensures that buyers and sellers remain unaware of each other's datasets. Our experiments on real datasets demonstrate the effectiveness of our approach in capturing the relevance, diversity, and structural disparities of seller data for buyers, particularly in graph-based data valuation scenarios.

Spatial-Spectral Mamba (SSM) improves computational efficiency and captures long-range dependencies, addressing Transformer limitations. However, traditional Mamba models overlook rich spectral information in HSIs and struggle with high dimensionality and sequential data. To address these issues, we propose the SSM with multi-head self-attention and token enhancement (MHSSMamba). This model integrates spectral and spatial information by enhancing spectral tokens and using multi-head attention to capture complex relationships between spectral bands and spatial locations. It also manages long-range dependencies and the sequential nature of HSI data, preserving contextual information across spectral bands. MHSSMamba achieved remarkable classification accuracies of 97.62\% on Pavia University, 96.92\% on the University of Houston, 96.85\% on Salinas, and 99.49\% on Wuhan-longKou datasets. The source code is available at https://github.com/MHassaanButt/MHA\_SS\_Mamba{GitHub}.

Sequence modeling plays a vital role across various domains, with recurrent neural networks being historically the predominant method of performing these tasks. However, the emergence of transformers has altered this paradigm due to their superior performance. Built upon these advances, transformers have conjoined CNNs as two leading foundational models for learning visual representations. However, transformers are hindered by the O(N^2) complexity of their attention mechanisms, while CNNs lack global receptive fields and dynamic weight allocation. State Space Models (SSMs), specifically the \textbf{Mamba} model with selection mechanisms and hardware-aware architecture, have garnered immense interest lately in sequential modeling and visual representation learning, challenging the dominance of transformers by providing infinite context lengths and offering substantial efficiency maintaining linear complexity in the input sequence. Capitalizing on the advances in computer vision, medical imaging has heralded a new epoch with Mamba models. Intending to help researchers navigate the surge, this survey seeks to offer an encyclopedic review of Mamba models in medical imaging. Specifically, we start with a comprehensive theoretical review forming the basis of SSMs, including Mamba architecture and its alternatives for sequence modeling paradigms in this context. Next, we offer a structured classification of Mamba models in the medical field and introduce a diverse categorization scheme based on their application, imaging modalities, and targeted organs. Finally, we summarize key challenges, discuss different future research directions of the SSMs in the medical domain, and propose several directions to fulfill the demands of this field. In addition, we have compiled the studies discussed in this paper along with their open-source implementations on our GitHub repository.

Recent advancements in anomaly detection have seen the efficacy of CNN- and transformer-based approaches. However, CNNs struggle with long-range dependencies, while transformers are burdened by quadratic computational complexity. Mamba-based models, with their superior long-range modeling and linear efficiency, have garnered substantial attention. This study pioneers the application of Mamba to multi-class unsupervised anomaly detection, presenting MambaAD, which consists of a pre-trained encoder and a Mamba decoder featuring (Locality-Enhanced State Space) LSS modules at multi-scales. The proposed LSS module, integrating parallel cascaded (Hybrid State Space) HSS blocks and multi-kernel convolutions operations, effectively captures both long-range and local information. The HSS block, utilizing (Hybrid Scanning) HS encoders, encodes feature maps into five scanning methods and eight directions, thereby strengthening global connections through the (State Space Model) SSM. The use of Hilbert scanning and eight directions significantly improves feature sequence modeling. Comprehensive experiments on six diverse anomaly detection datasets and seven metrics demonstrate state-of-the-art performance, substantiating the method's effectiveness. The code and models are available at https://lewandofskee.github.io/projects/MambaAD.

A graph homomorphism is a map between two graphs that preserves adjacency relations. We consider the problem of sampling a random graph homomorphism from a graph into a large network. We propose two complementary MCMC algorithms for sampling random graph homomorphisms and establish bounds on their mixing times and the concentration of their time averages. Based on our sampling algorithms, we propose a novel framework for network data analysis that circumvents some of the drawbacks in methods based on independent and neighborhood sampling. Various time averages of the MCMC trajectory give us various computable observables, including well-known ones such as homomorphism density and average clustering coefficient and their generalizations. Furthermore, we show that these network observables are stable with respect to a suitably renormalized cut distance between networks. We provide various examples and simulations demonstrating our framework through synthetic networks. We also demonstrate the performance of our framework on the tasks of network clustering and subgraph classification on the Facebook100 dataset and on Word Adjacency Networks of a set of classic novels.

Recently, State Space Models (SSMs) with efficient hardware-aware designs, i.e., Mamba, have demonstrated significant potential in computer vision tasks due to their linear computational complexity with respect to token length and their global receptive field. However, Mamba's performance on dense prediction tasks, including human pose estimation and semantic segmentation, has been constrained by three key challenges: insufficient inductive bias, long-range forgetting, and low-resolution output representation. To address these challenges, we introduce the Dynamic Visual State Space (DVSS) block, which utilizes multi-scale convolutional kernels to extract local features across different scales and enhance inductive bias, and employs deformable convolution to mitigate the long-range forgetting problem while enabling adaptive spatial aggregation based on input and task-specific information. By leveraging the multi-resolution parallel design proposed in HRNet, we introduce High-Resolution Visual State Space Model (HRVMamba) based on the DVSS block, which preserves high-resolution representations throughout the entire process while promoting effective multi-scale feature learning. Extensive experiments highlight HRVMamba's impressive performance on dense prediction tasks, achieving competitive results against existing benchmark models without bells and whistles. Code is available at https://github.com/zhanghao5201/HRVMamba.

We consider the problem of graph matching, or learning vertex correspondence, between two correlated stochastic block models (SBMs). The graph matching problem arises in various fields, including computer vision, natural language processing and bioinformatics, and in particular, matching graphs with inherent community structure has significance related to de-anonymization of correlated social networks. Compared to the correlated Erdos-Renyi (ER) model, where various efficient algorithms have been developed, among which a few algorithms have been proven to achieve the exact matching with constant edge correlation, no low-order polynomial algorithm has been known to achieve exact matching for the correlated SBMs with constant correlation. In this work, we propose an efficient algorithm for matching graphs with community structure, based on the comparison between partition trees rooted from each vertex, by extending the idea of Mao et al. (2021) to graphs with communities. The partition tree divides the large neighborhoods of each vertex into disjoint subsets using their edge statistics to different communities. Our algorithm is the first low-order polynomial-time algorithm achieving exact matching between two correlated SBMs with high probability in dense graphs.

We consider the problem of estimating (diagonally dominant) M-matrices as precision matrices in Gaussian graphical models. These models exhibit intriguing properties, such as the existence of the maximum likelihood estimator with merely two observations for M-matrices lauritzen2019maximum,slawski2015estimation and even one observation for diagonally dominant M-matrices truell2021maximum. We propose an adaptive multiple-stage estimation method that refines the estimate by solving a weighted ell_1-regularized problem at each stage. Furthermore, we develop a unified framework based on the gradient projection method to solve the regularized problem, incorporating distinct projections to handle the constraints of M-matrices and diagonally dominant M-matrices. A theoretical analysis of the estimation error is provided. Our method outperforms state-of-the-art methods in precision matrix estimation and graph edge identification, as evidenced by synthetic and financial time-series data sets.

Compared to single view medical image classification, using multiple views can significantly enhance predictive accuracy as it can account for the complementarity of each view while leveraging correlations between views. Existing multi-view approaches typically employ separate convolutional or transformer branches combined with simplistic feature fusion strategies. However, these approaches inadvertently disregard essential cross-view correlations, leading to suboptimal classification performance, and suffer from challenges with limited receptive field (CNNs) or quadratic computational complexity (transformers). Inspired by state space sequence models, we propose XFMamba, a pure Mamba-based cross-fusion architecture to address the challenge of multi-view medical image classification. XFMamba introduces a novel two-stage fusion strategy, facilitating the learning of single-view features and their cross-view disparity. This mechanism captures spatially long-range dependencies in each view while enhancing seamless information transfer between views. Results on three public datasets, MURA, CheXpert and DDSM, illustrate the effectiveness of our approach across diverse multi-view medical image classification tasks, showing that it outperforms existing convolution-based and transformer-based multi-view methods. Code is available at https://github.com/XZheng0427/XFMamba.

Recent advancements in Mamba have shown promising results in image restoration. These methods typically flatten 2D images into multiple distinct 1D sequences along rows and columns, process each sequence independently using selective scan operation, and recombine them to form the outputs. However, such a paradigm overlooks two vital aspects: i) the local relationships and spatial continuity inherent in natural images, and ii) the discrepancies among sequences unfolded through totally different ways. To overcome the drawbacks, we explore two problems in Mamba-based restoration methods: i) how to design a scanning strategy preserving both locality and continuity while facilitating restoration, and ii) how to aggregate the distinct sequences unfolded in totally different ways. To address these problems, we propose a novel Mamba-based Image Restoration model (MaIR), which consists of Nested S-shaped Scanning strategy (NSS) and Sequence Shuffle Attention block (SSA). Specifically, NSS preserves locality and continuity of the input images through the stripe-based scanning region and the S-shaped scanning path, respectively. SSA aggregates sequences through calculating attention weights within the corresponding channels of different sequences. Thanks to NSS and SSA, MaIR surpasses 40 baselines across 14 challenging datasets, achieving state-of-the-art performance on the tasks of image super-resolution, denoising, deblurring and dehazing. The code is available at https://github.com/XLearning-SCU/2025-CVPR-MaIR.

Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very interesting applications, ranging from drug discovery to recommender systems. To achieve such tasks, tremendous work has been accomplished to learn embedding of nodes and edges into finite-dimension vector spaces. This task is called Graph Representation Learning. However, Graph Representation Learning techniques often display prohibitive time and memory complexities, preventing their use in real-time with business size graphs. In this paper, we address this issue by leveraging a degeneracy property of Graphs - the K-Core Decomposition. We present two techniques taking advantage of this decomposition to reduce the time and memory consumption of walk-based Graph Representation Learning algorithms. We evaluate the performances, expressed in terms of quality of embedding and computational resources, of the proposed techniques on several academic datasets. Our code is available at https://github.com/SBrandeis/kcore-embedding

Multi-modal semantic segmentation significantly enhances AI agents' perception and scene understanding, especially under adverse conditions like low-light or overexposed environments. Leveraging additional modalities (X-modality) like thermal and depth alongside traditional RGB provides complementary information, enabling more robust and reliable segmentation. In this work, we introduce Sigma, a Siamese Mamba network for multi-modal semantic segmentation, utilizing the Selective Structured State Space Model, Mamba. Unlike conventional methods that rely on CNNs, with their limited local receptive fields, or Vision Transformers (ViTs), which offer global receptive fields at the cost of quadratic complexity, our model achieves global receptive fields coverage with linear complexity. By employing a Siamese encoder and innovating a Mamba fusion mechanism, we effectively select essential information from different modalities. A decoder is then developed to enhance the channel-wise modeling ability of the model. Our method, Sigma, is rigorously evaluated on both RGB-Thermal and RGB-Depth segmentation tasks, demonstrating its superiority and marking the first successful application of State Space Models (SSMs) in multi-modal perception tasks. Code is available at https://github.com/zifuwan/Sigma.

Food classification is the foundation for developing food vision tasks and plays a key role in the burgeoning field of computational nutrition. Due to the complexity of food requiring fine-grained classification, recent academic research mainly modifies Convolutional Neural Networks (CNNs) and/or Vision Transformers (ViTs) to perform food category classification. However, to learn fine-grained features, the CNN backbone needs additional structural design, whereas ViT, containing the self-attention module, has increased computational complexity. In recent months, a new Sequence State Space (S4) model, through a Selection mechanism and computation with a Scan (S6), colloquially termed Mamba, has demonstrated superior performance and computation efficiency compared to the Transformer architecture. The VMamba model, which incorporates the Mamba mechanism into image tasks (such as classification), currently establishes the state-of-the-art (SOTA) on the ImageNet dataset. In this research, we introduce an academically underestimated food dataset CNFOOD-241, and pioneer the integration of a residual learning framework within the VMamba model to concurrently harness both global and local state features inherent in the original VMamba architectural design. The research results show that VMamba surpasses current SOTA models in fine-grained and food classification. The proposed Res-VMamba further improves the classification accuracy to 79.54\% without pretrained weight. Our findings elucidate that our proposed methodology establishes a new benchmark for SOTA performance in food recognition on the CNFOOD-241 dataset. The code can be obtained on GitHub: https://github.com/ChiShengChen/ResVMamba.

Mining cohesive subgraphs in attributed graphs is an essential problem in the domain of graph data analysis. The integration of fairness considerations significantly fuels interest in models and algorithms for mining fairness-aware cohesive subgraphs. Notably, the relative fair clique emerges as a robust model, ensuring not only comprehensive attribute coverage but also greater flexibility in distributing attribute vertices. Motivated by the strength of this model, we for the first time pioneer an investigation into the identification of the maximum relative fair clique in large-scale graphs. We introduce a novel concept of colorful support, which serves as the foundation for two innovative graph reduction techniques. These techniques effectively narrow the graph's size by iteratively removing edges that do not belong to relative fair cliques. Furthermore, a series of upper bounds of the maximum relative fair clique size is proposed by incorporating consideration of vertex attributes and colors. The pruning techniques derived from these upper bounds can significantly trim unnecessary search space during the branch-and-bound procedure. Adding to this, we present a heuristic algorithm with a linear time complexity, employing both a degree-based greedy strategy and a colored degree-based greedy strategy to identify a larger relative fair clique. This heuristic algorithm can serve a dual purpose by aiding in branch pruning, thereby enhancing overall search efficiency. Extensive experiments conducted on six real-life datasets demonstrate the efficiency, scalability, and effectiveness of our algorithms.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Deep neural networks (DNNs) have remarkably succeeded in various image processing tasks. However, their large size and computational complexity present significant challenges for deploying them in resource-constrained environments. This paper presents an innovative approach for integrating Mamba Architecture within a Progressive Knowledge Distillation (PKD) process to address the challenge of reducing model complexity while maintaining accuracy in image classification tasks. The proposed framework distills a large teacher model into progressively smaller student models, designed using Mamba blocks. Each student model is trained using Selective-State-Space Models (S-SSM) within the Mamba blocks, focusing on important input aspects while reducing computational complexity. The work's preliminary experiments use MNIST and CIFAR-10 as datasets to demonstrate the effectiveness of this approach. For MNIST, the teacher model achieves 98% accuracy. A set of seven student models as a group retained 63% of the teacher's FLOPs, approximating the teacher's performance with 98% accuracy. The weak student used only 1% of the teacher's FLOPs and maintained 72% accuracy. Similarly, for CIFAR-10, the students achieved 1% less accuracy compared to the teacher, with the small student retaining 5% of the teacher's FLOPs to achieve 50% accuracy. These results confirm the flexibility and scalability of Mamba Architecture, which can be integrated into PKD, succeeding in the process of finding students as weak learners. The framework provides a solution for deploying complex neural networks in real-time applications with a reduction in computational cost.

Diffusion models, as a novel generative paradigm, have achieved remarkable success in various image generation tasks such as image inpainting, image-to-text translation, and video generation. Graph generation is a crucial computational task on graphs with numerous real-world applications. It aims to learn the distribution of given graphs and then generate new graphs. Given the great success of diffusion models in image generation, increasing efforts have been made to leverage these techniques to advance graph generation in recent years. In this paper, we first provide a comprehensive overview of generative diffusion models on graphs, In particular, we review representative algorithms for three variants of graph diffusion models, i.e., Score Matching with Langevin Dynamics (SMLD), Denoising Diffusion Probabilistic Model (DDPM), and Score-based Generative Model (SGM). Then, we summarize the major applications of generative diffusion models on graphs with a specific focus on molecule and protein modeling. Finally, we discuss promising directions in generative diffusion models on graph-structured data. For this survey, we also created a GitHub project website by collecting the supporting resources for generative diffusion models on graphs, at the link: https://github.com/ChengyiLIU-cs/Generative-Diffusion-Models-on-Graphs

We study a new connection between a technical measure called mu-conductance that arises in the study of Markov chains for sampling convex bodies and the network community profile that characterizes size-resolved properties of clusters and communities in social and information networks. The idea of mu-conductance is similar to the traditional graph conductance, but disregards sets with small volume. We derive a sequence of optimization problems including a low-rank semi-definite program from which we can derive a lower bound on the optimal mu-conductance value. These ideas give the first theoretically sound bound on the behavior of the network community profile for a wide range of cluster sizes. The algorithm scales up to graphs with hundreds of thousands of nodes and we demonstrate how our framework validates the predicted structures of real-world graphs.

Mamba, an architecture with RNN-like token mixer of state space model (SSM), was recently introduced to address the quadratic complexity of the attention mechanism and subsequently applied to vision tasks. Nevertheless, the performance of Mamba for vision is often underwhelming when compared with convolutional and attention-based models. In this paper, we delve into the essence of Mamba, and conceptually conclude that Mamba is ideally suited for tasks with long-sequence and autoregressive characteristics. For vision tasks, as image classification does not align with either characteristic, we hypothesize that Mamba is not necessary for this task; Detection and segmentation tasks are also not autoregressive, yet they adhere to the long-sequence characteristic, so we believe it is still worthwhile to explore Mamba's potential for these tasks. To empirically verify our hypotheses, we construct a series of models named MambaOut through stacking Mamba blocks while removing their core token mixer, SSM. Experimental results strongly support our hypotheses. Specifically, our MambaOut model surpasses all visual Mamba models on ImageNet image classification, indicating that Mamba is indeed unnecessary for this task. As for detection and segmentation, MambaOut cannot match the performance of state-of-the-art visual Mamba models, demonstrating the potential of Mamba for long-sequence visual tasks. The code is available at https://github.com/yuweihao/MambaOut

We consider a number of graph kernels and proximity measures including commute time kernel, regularized Laplacian kernel, heat kernel, exponential diffusion kernel (also called "communicability"), etc., and the corresponding distances as applied to clustering nodes in random graphs and several well-known datasets. The model of generating random graphs involves edge probabilities for the pairs of nodes that belong to the same class or different predefined classes of nodes. It turns out that in most cases, logarithmic measures (i.e., measures resulting after taking logarithm of the proximities) perform better while distinguishing underlying classes than the "plain" measures. A comparison in terms of reject curves of inter-class and intra-class distances confirms this conclusion. A similar conclusion can be made for several well-known datasets. A possible origin of this effect is that most kernels have a multiplicative nature, while the nature of distances used in cluster algorithms is an additive one (cf. the triangle inequality). The logarithmic transformation is a tool to transform the first nature to the second one. Moreover, some distances corresponding to the logarithmic measures possess a meaningful cutpoint additivity property. In our experiments, the leader is usually the logarithmic Communicability measure. However, we indicate some more complicated cases in which other measures, typically, Communicability and plain Walk, can be the winners.

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

Human motion generation is a cut-edge area of research in generative computer vision, with promising applications in video creation, game development, and robotic manipulation. The recent Mamba architecture shows promising results in efficiently modeling long and complex sequences, yet two significant challenges remain: Firstly, directly applying Mamba to extended motion generation is ineffective, as the limited capacity of the implicit memory leads to memory decay. Secondly, Mamba struggles with multimodal fusion compared to Transformers, and lack alignment with textual queries, often confusing directions (left or right) or omitting parts of longer text queries. To address these challenges, our paper presents three key contributions: Firstly, we introduce KMM, a novel architecture featuring Key frame Masking Modeling, designed to enhance Mamba's focus on key actions in motion segments. This approach addresses the memory decay problem and represents a pioneering method in customizing strategic frame-level masking in SSMs. Additionally, we designed a contrastive learning paradigm for addressing the multimodal fusion problem in Mamba and improving the motion-text alignment. Finally, we conducted extensive experiments on the go-to dataset, BABEL, achieving state-of-the-art performance with a reduction of more than 57% in FID and 70% parameters compared to previous state-of-the-art methods. See project website: https://steve-zeyu-zhang.github.io/KMM

Graphs can be used to represent and reason about systems and a variety of metrics have been devised to quantify their global characteristics. However, little is currently known about how to construct a graph or improve an existing one given a target objective. In this work, we formulate the construction of a graph as a decision-making process in which a central agent creates topologies by trial and error and receives rewards proportional to the value of the target objective. By means of this conceptual framework, we propose an algorithm based on reinforcement learning and graph neural networks to learn graph construction and improvement strategies. Our core case study focuses on robustness to failures and attacks, a property relevant for the infrastructure and communication networks that power modern society. Experiments on synthetic and real-world graphs show that this approach can outperform existing methods while being cheaper to evaluate. It also allows generalization to out-of-sample graphs, as well as to larger out-of-distribution graphs in some cases. The approach is applicable to the optimization of other global structural properties of graphs.

Graph measures that express closeness or distance between nodes can be employed for graph nodes clustering using metric clustering algorithms. There are numerous measures applicable to this task, and which one performs better is an open question. We study the performance of 25 graph measures on generated graphs with different parameters. While usually measure comparisons are limited to general measure ranking on a particular dataset, we aim to explore the performance of various measures depending on graph features. Using an LFR graph generator, we create a dataset of 11780 graphs covering the whole LFR parameter space. For each graph, we assess the quality of clustering with k-means algorithm for each considered measure. Based on this, we determine the best measure for each area of the parameter space. We find that the parameter space consists of distinct zones where one particular measure is the best. We analyze the geometry of the resulting zones and describe it with simple criteria. Given particular graph parameters, this allows us to recommend a particular measure to use for clustering.

Multi-task dense scene understanding, which learns a model for multiple dense prediction tasks, has a wide range of application scenarios. Modeling long-range dependency and enhancing cross-task interactions are crucial to multi-task dense prediction. In this paper, we propose MTMamba, a novel Mamba-based architecture for multi-task scene understanding. It contains two types of core blocks: self-task Mamba (STM) block and cross-task Mamba (CTM) block. STM handles long-range dependency by leveraging Mamba, while CTM explicitly models task interactions to facilitate information exchange across tasks. Experiments on NYUDv2 and PASCAL-Context datasets demonstrate the superior performance of MTMamba over Transformer-based and CNN-based methods. Notably, on the PASCAL-Context dataset, MTMamba achieves improvements of +2.08, +5.01, and +4.90 over the previous best methods in the tasks of semantic segmentation, human parsing, and object boundary detection, respectively. The code is available at https://github.com/EnVision-Research/MTMamba.

State space models (SSMs) like Mamba have recently attracted much attention. Compared to Transformer-based large language models (LLMs), Mamba achieves linear computation complexity with the sequence length and demonstrates superior performance. However, Mamba is hard to accelerate due to the scattered activation outliers and the complex computation dependency, rendering existing LLM accelerators inefficient. In this paper, we propose LightMamba that co-designs the quantization algorithm and FPGA accelerator architecture for efficient Mamba inference. We first propose an FPGA-friendly post-training quantization algorithm that features rotation-assisted quantization and power-of-two SSM quantization to reduce the majority of computation to 4-bit. We further design an FPGA accelerator that partially unrolls the Mamba computation to balance the efficiency and hardware costs. Through computation reordering as well as fine-grained tiling and fusion, the hardware utilization and memory efficiency of the accelerator get drastically improved. We implement LightMamba on Xilinx Versal VCK190 FPGA and achieve 4.65x to 6.06x higher energy efficiency over the GPU baseline. When evaluated on Alveo U280 FPGA, LightMamba reaches 93 tokens/s, which is 1.43x that of the GPU baseline.

Convolutional neural networks (CNN) and Transformers have made impressive progress in the field of remote sensing change detection (CD). However, both architectures have inherent shortcomings: CNN are constrained by a limited receptive field that may hinder their ability to capture broader spatial contexts, while Transformers are computationally intensive, making them costly to train and deploy on large datasets. Recently, the Mamba architecture, based on state space models, has shown remarkable performance in a series of natural language processing tasks, which can effectively compensate for the shortcomings of the above two architectures. In this paper, we explore for the first time the potential of the Mamba architecture for remote sensing CD tasks. We tailor the corresponding frameworks, called MambaBCD, MambaSCD, and MambaBDA, for binary change detection (BCD), semantic change detection (SCD), and building damage assessment (BDA), respectively. All three frameworks adopt the cutting-edge Visual Mamba architecture as the encoder, which allows full learning of global spatial contextual information from the input images. For the change decoder, which is available in all three architectures, we propose three spatio-temporal relationship modeling mechanisms, which can be naturally combined with the Mamba architecture and fully utilize its attribute to achieve spatio-temporal interaction of multi-temporal features, thereby obtaining accurate change information. On five benchmark datasets, our proposed frameworks outperform current CNN- and Transformer-based approaches without using any complex training strategies or tricks, fully demonstrating the potential of the Mamba architecture in CD tasks. Further experiments show that our architecture is quite robust to degraded data. The source code will be available in https://github.com/ChenHongruixuan/MambaCD

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.

The growing interest in machine learning problems over graphs with additional node information such as texts, images, or labels has popularized methods that require the costly operation of processing the entire graph. Yet, little effort has been made to the development of fast local methods (i.e. without accessing the entire graph) that extract useful information from such data. To that end, we propose a study of local graph clustering using noisy node labels as a proxy for additional node information. In this setting, nodes receive initial binary labels based on cluster affiliation: 1 if they belong to the target cluster and 0 otherwise. Subsequently, a fraction of these labels is flipped. We investigate the benefits of incorporating noisy labels for local graph clustering. By constructing a weighted graph with such labels, we study the performance of graph diffusion-based local clustering method on both the original and the weighted graphs. From a theoretical perspective, we consider recovering an unknown target cluster with a single seed node in a random graph with independent noisy node labels. We provide sufficient conditions on the label noise under which, with high probability, using diffusion in the weighted graph yields a more accurate recovery of the target cluster. This approach proves more effective than using the given labels alone or using diffusion in the label-free original graph. Empirically, we show that reliable node labels can be obtained with just a few samples from an attributed graph. Moreover, utilizing these labels via diffusion in the weighted graph leads to significantly better local clustering performance across several real-world datasets, improving F1 scores by up to 13%.

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

Assume n, m are positive integers and G is a graph. Let P_{n,m} be the graph obtained from the path with vertices {-m, -(m-1), ldots, 0, ldots, n} by adding a loop at vertex 0. The double cone Delta_{n,m}(G) over a graph G is obtained from the direct product G times P_{n,m} by identifying V(G) times {n} into a single vertex (star, n), identifying V(G) times {-m} into a single vertex (star, -m), and adding an edge connecting (star, -m) and (star, n). This paper determines the fractional chromatic number of Delta_{n,m}(G). In particular, if n < m or n=m is even, then chi_f(Delta_{n,m}(G)) = chi_f(Delta_n(G)), where Delta_n(G) is the nth cone over G. If n=m is odd, then chi_f(Delta_{n,m}(G)) > chi_f(Delta_n(G)). The chromatic number of Delta_{n,m}(G) is also discussed.

How might one test the hypothesis that networks were sampled from the same distribution? Here, we compare two statistical tests that use subgraph counts to address this question. The first uses the empirical subgraph densities themselves as estimates of those of the underlying distribution. The second test uses a new approach that converts these subgraph densities into estimates of the graph cumulants of the distribution (without any increase in computational complexity). We demonstrate -- via theory, simulation, and application to real data -- the superior statistical power of using graph cumulants. In summary, when analyzing data using subgraph/motif densities, we suggest using the corresponding graph cumulants instead.

Gesture synthesis is a vital realm of human-computer interaction, with wide-ranging applications across various fields like film, robotics, and virtual reality. Recent advancements have utilized the diffusion model and attention mechanisms to improve gesture synthesis. However, due to the high computational complexity of these techniques, generating long and diverse sequences with low latency remains a challenge. We explore the potential of state space models (SSMs) to address the challenge, implementing a two-stage modeling strategy with discrete motion priors to enhance the quality of gestures. Leveraging the foundational Mamba block, we introduce MambaTalk, enhancing gesture diversity and rhythm through multimodal integration. Extensive experiments demonstrate that our method matches or exceeds the performance of state-of-the-art models.

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.\

Hypergraphs offer a powerful framework for modeling higher-order interactions that traditional pairwise graphs cannot fully capture. However, practical constraints often lead to their simplification into projected graphs, resulting in substantial information loss and ambiguity in representing higher-order relationships. In this work, we propose MARIOH, a supervised approach for reconstructing the original hypergraph from its projected graph by leveraging edge multiplicity. To overcome the difficulties posed by the large search space, MARIOH integrates several key ideas: (a) identifying provable size-2 hyperedges, which reduces the candidate search space, (b) predicting the likelihood of candidates being hyperedges by utilizing both structural and multiplicity-related features, and (c) not only targeting promising hyperedge candidates but also examining less confident ones to explore alternative possibilities. Together, these ideas enable MARIOH to efficiently and effectively explore the search space. In our experiments using 10 real-world datasets, MARIOH achieves up to 74.51% higher reconstruction accuracy compared to state-of-the-art methods.

Human motion generation stands as a significant pursuit in generative computer vision, while achieving long-sequence and efficient motion generation remains challenging. Recent advancements in state space models (SSMs), notably Mamba, have showcased considerable promise in long sequence modeling with an efficient hardware-aware design, which appears to be a promising direction to build motion generation model upon it. Nevertheless, adapting SSMs to motion generation faces hurdles since the lack of a specialized design architecture to model motion sequence. To address these challenges, we propose Motion Mamba, a simple and efficient approach that presents the pioneering motion generation model utilized SSMs. Specifically, we design a Hierarchical Temporal Mamba (HTM) block to process temporal data by ensemble varying numbers of isolated SSM modules across a symmetric U-Net architecture aimed at preserving motion consistency between frames. We also design a Bidirectional Spatial Mamba (BSM) block to bidirectionally process latent poses, to enhance accurate motion generation within a temporal frame. Our proposed method achieves up to 50% FID improvement and up to 4 times faster on the HumanML3D and KIT-ML datasets compared to the previous best diffusion-based method, which demonstrates strong capabilities of high-quality long sequence motion modeling and real-time human motion generation. See project website https://steve-zeyu-zhang.github.io/MotionMamba/

To characterize the location (mean, median) of a set of graphs, one needs a notion of centrality that is adapted to metric spaces, since graph sets are not Euclidean spaces. A standard approach is to consider the Frechet mean. In this work, we equip a set of graphs with the pseudometric defined by the norm between the eigenvalues of their respective adjacency matrix. Unlike the edit distance, this pseudometric reveals structural changes at multiple scales, and is well adapted to studying various statistical problems for graph-valued data. We describe an algorithm to compute an approximation to the sample Frechet mean of a set of undirected unweighted graphs with a fixed size using this pseudometric.

Previous research on lightweight models has primarily focused on CNNs and Transformer-based designs. CNNs, with their local receptive fields, struggle to capture long-range dependencies, while Transformers, despite their global modeling capabilities, are limited by quadratic computational complexity in high-resolution scenarios. Recently, state-space models have gained popularity in the visual domain due to their linear computational complexity. Despite their low FLOPs, current lightweight Mamba-based models exhibit suboptimal throughput. In this work, we propose the MobileMamba framework, which balances efficiency and performance. We design a three-stage network to enhance inference speed significantly. At a fine-grained level, we introduce the Multi-Receptive Field Feature Interaction(MRFFI) module, comprising the Long-Range Wavelet Transform-Enhanced Mamba(WTE-Mamba), Efficient Multi-Kernel Depthwise Convolution(MK-DeConv), and Eliminate Redundant Identity components. This module integrates multi-receptive field information and enhances high-frequency detail extraction. Additionally, we employ training and testing strategies to further improve performance and efficiency. MobileMamba achieves up to 83.6% on Top-1, surpassing existing state-of-the-art methods which is maximum x21 faster than LocalVim on GPU. Extensive experiments on high-resolution downstream tasks demonstrate that MobileMamba surpasses current efficient models, achieving an optimal balance between speed and accuracy.

In this paper, the causal bandit problem is investigated, in which the objective is to select an optimal sequence of interventions on nodes in a causal graph. It is assumed that the graph is governed by linear structural equations; it is further assumed that both the causal topology and the distribution of interventions are unknown. By exploiting the causal relationships between the nodes whose signals contribute to the reward, interventions are optimized. First, based on the difference between the two types of graph identification errors (false positives and negatives), a causal graph learning method is proposed, which strongly reduces sample complexity relative to the prior art by learning sub-graphs. Under the assumption of Gaussian exogenous inputs and minimum-mean squared error weight estimation, a new uncertainty bound tailored to the causal bandit problem is derived. This uncertainty bound drives an upper confidence bound based intervention selection to optimize the reward. To cope with non-stationary bandits, a sub-graph change detection mechanism is proposed, with high sample efficiency. Numerical results compare the new methodology to existing schemes and show a substantial performance improvement in both stationary and non-stationary settings. Compared to existing approaches, the proposed scheme takes 67% fewer samples to learn the causal structure and achieves an average reward gain of 85%.

Relational databases (RDBs) are composed of interconnected tables, where relationships between them are defined through foreign keys. Recent research on applying machine learning to RDBs has explored graph-based representations of RDBs, where rows of tables are modeled as nodes, and foreign key relationships are modeled as edges. RDB-to-graph modeling helps capture cross-table dependencies, ultimately leading to enhanced performance across diverse tasks. However, there are numerous ways to model RDBs as graphs, and performance varies significantly depending on the chosen graph model. In our analysis, applying a common heuristic rule for graph modeling leads to up to a 10% drop in performance compared to the best-performing graph model, which remains non-trivial to identify. To foster research on intelligent RDB-to-graph modeling, we introduce RDB2G-Bench, the first benchmark framework for evaluating such methods. We construct extensive datasets covering 5 real-world RDBs and 12 predictive tasks, resulting in around 50k graph-performance pairs for efficient and reproducible evaluations. Thanks to our precomputed datasets, we were able to benchmark 9 automatic RDB-to-graph modeling methods on the 12 tasks over 600x faster than on-the-fly evaluation, which requires repeated model training. Our analysis of the datasets and benchmark results reveals key structural patterns affecting graph model effectiveness, along with practical implications for effective graph modeling.

Existing Transformer-based models for point cloud analysis suffer from quadratic complexity, leading to compromised point cloud resolution and information loss. In contrast, the newly proposed Mamba model, based on state space models (SSM), outperforms Transformer in multiple areas with only linear complexity. However, the straightforward adoption of Mamba does not achieve satisfactory performance on point cloud tasks. In this work, we present Mamba3D, a state space model tailored for point cloud learning to enhance local feature extraction, achieving superior performance, high efficiency, and scalability potential. Specifically, we propose a simple yet effective Local Norm Pooling (LNP) block to extract local geometric features. Additionally, to obtain better global features, we introduce a bidirectional SSM (bi-SSM) with both a token forward SSM and a novel backward SSM that operates on the feature channel. Extensive experimental results show that Mamba3D surpasses Transformer-based counterparts and concurrent works in multiple tasks, with or without pre-training. Notably, Mamba3D achieves multiple SoTA, including an overall accuracy of 92.6% (train from scratch) on the ScanObjectNN and 95.1% (with single-modal pre-training) on the ModelNet40 classification task, with only linear complexity.

In this paper, we introduce a novel graph-based method to classify the regions with similar climate in a local area. We refer our proposed method as Graph Partition Based Method (GPBM). Our proposed method attempts to overcome the shortcomings of the current state-of-the-art methods in the literature. It has no limit on the number of variables that can be used and also preserves the nature of climate data. To illustrate the capability of our proposed algorithm, we benchmark its performance with other state-of-the-art climate classification techniques. The climate data is collected from 24 synoptic stations in Fars province in southern Iran. The data includes seven climate variables stored as time series from 1951 to 2017. Our results exhibit that our proposed method performs a more realistic climate classification with less computational time. It can save more information during the climate classification process and is therefore efficient in further data analysis. Furthermore, using our method, we can introduce seasonal graphs to better investigate seasonal climate changes. To the best of our knowledge, our proposed method is the first graph-based climate classification system.

Large multimodal models (LMMs) have exhibited proficiencies across many visual tasks. Although numerous well-known benchmarks exist to evaluate model performance, they increasingly have insufficient headroom. As such, there is a pressing need for a new generation of benchmarks challenging enough for the next generation of LMMs. One area that LMMs show potential is graph analysis, specifically, the tasks an analyst might typically perform when interpreting figures such as estimating the mean, intercepts or correlations of functions and data series. In this work, we introduce GRAB, a graph analysis benchmark, fit for current and future frontier LMMs. Our benchmark is entirely synthetic, ensuring high-quality, noise-free questions. GRAB is comprised of 2170 questions, covering four tasks and 23 graph properties. We evaluate 20 LMMs on GRAB, finding it to be a challenging benchmark, with the highest performing model attaining a score of just 21.7%. Finally, we conduct various ablations to investigate where the models succeed and struggle. We release GRAB to encourage progress in this important, growing domain.

Recently the state space models (SSMs) with efficient hardware-aware designs, i.e., Mamba, have shown great potential for long sequence modeling. Building efficient and generic vision backbones purely upon SSMs is an appealing direction. However, representing visual data is challenging for SSMs due to the position-sensitivity of visual data and the requirement of global context for visual understanding. In this paper, we show that the reliance of visual representation learning on self-attention is not necessary and propose a new generic vision backbone with bidirectional Mamba blocks (Vim), which marks the image sequences with position embeddings and compresses the visual representation with bidirectional state space models. On ImageNet classification, COCO object detection, and ADE20k semantic segmentation tasks, Vim achieves higher performance compared to well-established vision transformers like DeiT, while also demonstrating significantly improved computation & memory efficiency. For example, Vim is 2.8times faster than DeiT and saves 86.8% GPU memory when performing batch inference to extract features on images with a resolution of 1248times1248. The results demonstrate that Vim is capable of overcoming the computation & memory constraints on performing Transformer-style understanding for high-resolution images and it has great potential to become the next-generation backbone for vision foundation models. Code is available at https://github.com/hustvl/Vim.

Capturing long-range dependencies efficiently is essential for visual recognition tasks, yet existing methods face limitations. Convolutional neural networks (CNNs) struggle with restricted receptive fields, while Vision Transformers (ViTs) achieve global context and long-range modeling at a high computational cost. State-space models (SSMs) offer an alternative, but their application in vision remains underexplored. This work introduces vGamba, a hybrid vision backbone that integrates SSMs with attention mechanisms to enhance efficiency and expressiveness. At its core, the Gamba bottleneck block that includes, Gamba Cell, an adaptation of Mamba for 2D spatial structures, alongside a Multi-Head Self-Attention (MHSA) mechanism and a Gated Fusion Module for effective feature representation. The interplay of these components ensures that vGamba leverages the low computational demands of SSMs while maintaining the accuracy of attention mechanisms for modeling long-range dependencies in vision tasks. Additionally, the Fusion module enables seamless interaction between these components. Extensive experiments on classification, detection, and segmentation tasks demonstrate that vGamba achieves a superior trade-off between accuracy and computational efficiency, outperforming several existing models.

Pixel-level segmentation of structural cracks across various scenarios remains a considerable challenge. Current methods encounter challenges in effectively modeling crack morphology and texture, facing challenges in balancing segmentation quality with low computational resource usage. To overcome these limitations, we propose a lightweight Structure-Aware Vision Mamba Network (SCSegamba), capable of generating high-quality pixel-level segmentation maps by leveraging both the morphological information and texture cues of crack pixels with minimal computational cost. Specifically, we developed a Structure-Aware Visual State Space module (SAVSS), which incorporates a lightweight Gated Bottleneck Convolution (GBC) and a Structure-Aware Scanning Strategy (SASS). The key insight of GBC lies in its effectiveness in modeling the morphological information of cracks, while the SASS enhances the perception of crack topology and texture by strengthening the continuity of semantic information between crack pixels. Experiments on crack benchmark datasets demonstrate that our method outperforms other state-of-the-art (SOTA) methods, achieving the highest performance with only 2.8M parameters. On the multi-scenario dataset, our method reached 0.8390 in F1 score and 0.8479 in mIoU. The code is available at https://github.com/Karl1109/SCSegamba.

Given a graph G and the desired size k in bits, how can we summarize G within k bits, while minimizing the information loss? Large-scale graphs have become omnipresent, posing considerable computational challenges. Analyzing such large graphs can be fast and easy if they are compressed sufficiently to fit in main memory or even cache. Graph summarization, which yields a coarse-grained summary graph with merged nodes, stands out with several advantages among graph compression techniques. Thus, a number of algorithms have been developed for obtaining a concise summary graph with little information loss or equivalently small reconstruction error. However, the existing methods focus solely on reducing the number of nodes, and they often yield dense summary graphs, failing to achieve better compression rates. Moreover, due to their limited scalability, they can be applied only to moderate-size graphs. In this work, we propose SSumM, a scalable and effective graph-summarization algorithm that yields a sparse summary graph. SSumM not only merges nodes together but also sparsifies the summary graph, and the two strategies are carefully balanced based on the minimum description length principle. Compared with state-of-the-art competitors, SSumM is (a) Concise: yields up to 11.2X smaller summary graphs with similar reconstruction error, (b) Accurate: achieves up to 4.2X smaller reconstruction error with similarly concise outputs, and (c) Scalable: summarizes 26X larger graphs while exhibiting linear scalability. We validate these advantages through extensive experiments on 10 real-world graphs.

We propose a novel framework that leverages LLMs for full causal graph discovery. While previous LLM-based methods have used a pairwise query approach, this requires a quadratic number of queries which quickly becomes impractical for larger causal graphs. In contrast, the proposed framework uses a breadth-first search (BFS) approach which allows it to use only a linear number of queries. We also show that the proposed method can easily incorporate observational data when available, to improve performance. In addition to being more time and data-efficient, the proposed framework achieves state-of-the-art results on real-world causal graphs of varying sizes. The results demonstrate the effectiveness and efficiency of the proposed method in discovering causal relationships, showcasing its potential for broad applicability in causal graph discovery tasks across different domains.

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.

In the realm of medical image segmentation, both CNN-based and Transformer-based models have been extensively explored. However, CNNs exhibit limitations in long-range modeling capabilities, whereas Transformers are hampered by their quadratic computational complexity. Recently, State Space Models (SSMs), exemplified by Mamba, have emerged as a promising approach. They not only excel in modeling long-range interactions but also maintain a linear computational complexity. In this paper, leveraging state space models, we propose a U-shape architecture model for medical image segmentation, named Vision Mamba UNet (VM-UNet). Specifically, the Visual State Space (VSS) block is introduced as the foundation block to capture extensive contextual information, and an asymmetrical encoder-decoder structure is constructed with fewer convolution layers to save calculation cost. We conduct comprehensive experiments on the ISIC17, ISIC18, and Synapse datasets, and the results indicate that VM-UNet performs competitively in medical image segmentation tasks. To our best knowledge, this is the first medical image segmentation model constructed based on the pure SSM-based model. We aim to establish a baseline and provide valuable insights for the future development of more efficient and effective SSM-based segmentation systems. Our code is available at https://github.com/JCruan519/VM-UNet.

Video anomaly detection (VAD) methods are mostly CNN-based or Transformer-based, achieving impressive results, but the focus on detection accuracy often comes at the expense of inference speed. The emergence of state space models in computer vision, exemplified by the Mamba model, demonstrates improved computational efficiency through selective scans and showcases the great potential for long-range modeling. Our study pioneers the application of Mamba to VAD, dubbed VADMamba, which is based on multi-task learning for frame prediction and optical flow reconstruction. Specifically, we propose the VQ-Mamba Unet (VQ-MaU) framework, which incorporates a Vector Quantization (VQ) layer and Mamba-based Non-negative Visual State Space (NVSS) block. Furthermore, two individual VQ-MaU networks separately predict frames and reconstruct corresponding optical flows, further boosting accuracy through a clip-level fusion evaluation strategy. Experimental results validate the efficacy of the proposed VADMamba across three benchmark datasets, demonstrating superior performance in inference speed compared to previous work. Code is available at https://github.com/jLooo/VADMamba.

Multi-task dense scene understanding, which trains a model for multiple dense prediction tasks, has a wide range of application scenarios. Capturing long-range dependency and enhancing cross-task interactions are crucial to multi-task dense prediction. In this paper, we propose MTMamba++, a novel architecture for multi-task scene understanding featuring with a Mamba-based decoder. It contains two types of core blocks: self-task Mamba (STM) block and cross-task Mamba (CTM) block. STM handles long-range dependency by leveraging state-space models, while CTM explicitly models task interactions to facilitate information exchange across tasks. We design two types of CTM block, namely F-CTM and S-CTM, to enhance cross-task interaction from feature and semantic perspectives, respectively. Experiments on NYUDv2, PASCAL-Context, and Cityscapes datasets demonstrate the superior performance of MTMamba++ over CNN-based and Transformer-based methods. The code is available at https://github.com/EnVision-Research/MTMamba.

Real-world networks, with their evolving relations, are best captured as temporal graphs. However, existing software libraries are largely designed for static graphs where the dynamic nature of temporal graphs is ignored. Bridging this gap, we introduce TGX, a Python package specially designed for analysis of temporal networks that encompasses an automated pipeline for data loading, data processing, and analysis of evolving graphs. TGX provides access to eleven built-in datasets and eight external Temporal Graph Benchmark (TGB) datasets as well as any novel datasets in the .csv format. Beyond data loading, TGX facilitates data processing functionalities such as discretization of temporal graphs and node subsampling to accelerate working with larger datasets. For comprehensive investigation, TGX offers network analysis by providing a diverse set of measures, including average node degree and the evolving number of nodes and edges per timestamp. Additionally, the package consolidates meaningful visualization plots indicating the evolution of temporal patterns, such as Temporal Edge Appearance (TEA) and Temporal Edge Trafficc (TET) plots. The TGX package is a robust tool for examining the features of temporal graphs and can be used in various areas like studying social networks, citation networks, and tracking user interactions. We plan to continuously support and update TGX based on community feedback. TGX is publicly available on: https://github.com/ComplexData-MILA/TGX.

Graphs are widely used for modeling relational data in real-world scenarios, such as social networks and urban computing. Existing LLM-based graph analysis approaches either integrate graph neural networks (GNNs) for specific machine learning tasks, limiting their transferability, or rely solely on LLMs' internal reasoning ability, resulting in suboptimal performance. To address these limitations, we take advantage of recent advances in LLM-based agents, which have shown capabilities of utilizing external knowledge or tools for problem solving. By simulating human problem-solving strategies such as analogy and collaboration, we propose a multi-agent system based on LLMs named GraphTeam, for graph analysis. GraphTeam consists of five LLM-based agents from three modules, and the agents with different specialities can collaborate with each other to address complex problems. Specifically, (1) input-output normalization module: the question agent extracts and refines four key arguments from the original question, facilitating the problem understanding, and the answer agent organizes the results to meet the output requirement; (2) external knowledge retrieval module: we first build a knowledge base consisting of relevant documentation and experience information, and then the search agent retrieves the most relevant entries for each question. (3) problem-solving module: given the retrieved information from search agent, the coding agent uses established algorithms via programming to generate solutions, and in case the coding agent does not work, the reasoning agent will directly compute the results without programming. Extensive experiments on six graph analysis benchmarks demonstrate that GraphTeam achieves state-of-the-art performance with an average 25.85% improvement over the best baseline in terms of accuracy. The code and data are available at https://github.com/BUPT-GAMMA/GraphTeam.

We introduce fast algorithms for correlation clustering with respect to the Min Max objective that provide constant factor approximations on complete graphs. Our algorithms are the first purely combinatorial approximation algorithms for this problem. We construct a novel semi-metric on the set of vertices, which we call the correlation metric, that indicates to our clustering algorithms whether pairs of nodes should be in the same cluster. The paper demonstrates empirically that, compared to prior work, our algorithms sacrifice little in the objective quality to obtain significantly better run-time. Moreover, our algorithms scale to larger networks that are effectively intractable for known algorithms.

Federated learning is an active research topic since it enables several participants to jointly train a model without sharing local data. Currently, cross-silo federated learning is a popular training setting that utilizes a few hundred reliable data silos with high-speed access links to training a model. While this approach has been widely applied in real-world scenarios, designing a robust topology to reduce the training time remains an open problem. In this paper, we present a new multigraph topology for cross-silo federated learning. We first construct the multigraph using the overlay graph. We then parse this multigraph into different simple graphs with isolated nodes. The existence of isolated nodes allows us to perform model aggregation without waiting for other nodes, hence effectively reducing the training time. Intensive experiments on three public datasets show that our proposed method significantly reduces the training time compared with recent state-of-the-art topologies while maintaining the accuracy of the learned model. Our code can be found at https://github.com/aioz-ai/MultigraphFL

In the last few years, graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. This emerging field has witnessed an extensive growth of promising techniques that have been applied with success to computer science, mathematics, biology, physics and chemistry. But for any successful field to become mainstream and reliable, benchmarks must be developed to quantify progress. This led us in March 2020 to release a benchmark framework that i) comprises of a diverse collection of mathematical and real-world graphs, ii) enables fair model comparison with the same parameter budget to identify key architectures, iii) has an open-source, easy-to-use and reproducible code infrastructure, and iv) is flexible for researchers to experiment with new theoretical ideas. As of December 2022, the GitHub repository has reached 2,000 stars and 380 forks, which demonstrates the utility of the proposed open-source framework through the wide usage by the GNN community. In this paper, we present an updated version of our benchmark with a concise presentation of the aforementioned framework characteristics, an additional medium-sized molecular dataset AQSOL, similar to the popular ZINC, but with a real-world measured chemical target, and discuss how this framework can be leveraged to explore new GNN designs and insights. As a proof of value of our benchmark, we study the case of graph positional encoding (PE) in GNNs, which was introduced with this benchmark and has since spurred interest of exploring more powerful PE for Transformers and GNNs in a robust experimental setting.

In this paper we introduce a novel family of attributed graphs for the purpose of shape discrimination. Our graphs typically arise from variations on the Mapper graph construction, which is an approximation of the Reeb graph for point cloud data. Our attributions enrich these constructions with (persistent) homology in ways that are provably stable, thereby recording extra topological information that is typically lost in these graph constructions. We provide experiments which illustrate the use of these invariants for shape representation and classification. In particular, we obtain competitive shape classification results when using our topologically attributed graphs as inputs to a simple graph neural network classifier.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

Graph structure learning aims to learn connectivity in a graph from data. It is particularly important for many computer vision related tasks since no explicit graph structure is available for images for most cases. A natural way to construct a graph among images is to treat each image as a node and assign pairwise image similarities as weights to corresponding edges. It is well known that pairwise similarities between images are sensitive to the noise in feature representations, leading to unreliable graph structures. We address this problem from the viewpoint of statistical tests. By viewing the feature vector of each node as an independent sample, the decision of whether creating an edge between two nodes based on their similarity in feature representation can be thought as a {it single} statistical test. To improve the robustness in the decision of creating an edge, multiple samples are drawn and integrated by {it multiple} statistical tests to generate a more reliable similarity measure, consequentially more reliable graph structure. The corresponding elegant matrix form named B-Attention is designed for efficiency. The effectiveness of multiple tests for graph structure learning is verified both theoretically and empirically on multiple clustering and ReID benchmark datasets. Source codes are available at https://github.com/Thomas-wyh/B-Attention.

Linear structural equation models are multivariate statistical models encoded by mixed graphs. In particular, the set of covariance matrices for distributions belonging to a linear structural equation model for a fixed mixed graph G=(V, D,B) is parameterized by a rational function with parameters for each vertex and edge in G. This rational parametrization naturally allows for the study of these models from an algebraic and combinatorial point of view. Indeed, this point of view has led to a collection of results in the literature, mainly focusing on questions related to identifiability and determining relationships between covariances (i.e., finding polynomials in the Gaussian vanishing ideal). So far, a large proportion of these results has focused on the case when D, the directed part of the mixed graph G, is acyclic. This is due to the fact that in the acyclic case, the parametrization becomes polynomial and there is a description of the entries of the covariance matrices in terms of a finite sum. We move beyond the acyclic case and give a closed form expression for the entries of the covariance matrices in terms of the one-connections in a graph obtained from D through some small operations. This closed form expression then allows us to show that if G is simple, then the parametrization map is generically finite-to-one. Finally, having a closed form expression for the covariance matrices allows for the development of an algorithm for systematically exploring possible polynomials in the Gaussian vanishing ideal.

For a broad range of research, governmental and commercial applications it is important to understand the allegiances, communities and structure of key players in society. One promising direction towards extracting this information is to exploit the rich relational data in digital social networks (the social graph). As social media data sets are very large, most approaches make use of distributed computing systems for this purpose. Distributing graph processing requires solving many difficult engineering problems, which has lead some researchers to look at single-machine solutions that are faster and easier to maintain. In this article, we present a single-machine real-time system for large-scale graph processing that allows analysts to interactively explore graph structures. The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates user similarities while being robust to noise and queryable in real-time. We achieve single machine real-time performance by compressing the neighbourhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing. These techniques reduce query times from hours using industrial desktop machines operating on the full graph to milliseconds on standard laptops. Our method allows exploration of strongly associated regions (i.e. communities) of large graphs in real-time on a laptop. It has been deployed in software that is actively used by social network analysts and offers another channel for media owners to monetise their data, helping them to continue to provide free services that are valued by billions of people globally.

This paper proposes a simple but effective graph-based agglomerative algorithm, for clustering high-dimensional data. We explore the different roles of two fundamental concepts in graph theory, indegree and outdegree, in the context of clustering. The average indegree reflects the density near a sample, and the average outdegree characterizes the local geometry around a sample. Based on such insights, we define the affinity measure of clusters via the product of average indegree and average outdegree. The product-based affinity makes our algorithm robust to noise. The algorithm has three main advantages: good performance, easy implementation, and high computational efficiency. We test the algorithm on two fundamental computer vision problems: image clustering and object matching. Extensive experiments demonstrate that it outperforms the state-of-the-arts in both applications.

Random walks are widely used for mining networks due to the computational efficiency of computing them. For instance, graph representation learning learns a d-dimensional embedding space, so that the nodes that tend to co-occur on random walks (a proxy of being in the same network neighborhood) are close in the embedding space. Specific local network topology (i.e., structure) influences the co-occurrence of nodes on random walks, so random walks of limited length capture only partial topological information, hence diminishing the performance of downstream methods. We explicitly capture all topological neighborhood information and improve performance by introducing orbit adjacencies that quantify the adjacencies of two nodes as co-occurring on a given pair of graphlet orbits, which are symmetric positions on graphlets (small, connected, non-isomorphic, induced subgraphs of a large network). Importantly, we mathematically prove that random walks on up to k nodes capture only a subset of all the possible orbit adjacencies for up to k-node graphlets. Furthermore, we enable orbit adjacency-based analysis of networks by developing an efficient GRaphlet-orbit ADjacency COunter (GRADCO), which exhaustively computes all 28 orbit adjacency matrices for up to four-node graphlets. Note that four-node graphlets suffice, because real networks are usually small-world. In large networks on around 20,000 nodes, GRADCOcomputesthe28matricesinminutes. Onsixrealnetworksfromvarious domains, we compare the performance of node-label predictors obtained by using the network embeddings based on our orbit adjacencies to those based on random walks. We find that orbit adjacencies, which include those unseen by random walks, outperform random walk-based adjacencies, demonstrating the importance of the inclusion of the topological neighborhood information that is unseen by random walks.

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.

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

The exponential growth of scientific literature requires effective management and extraction of valuable insights. While existing scientific search engines excel at delivering search results based on relational databases, they often neglect the analysis of collaborations between scientific entities and the evolution of ideas, as well as the in-depth analysis of content within scientific publications. The representation of heterogeneous graphs and the effective measurement, analysis, and mining of such graphs pose significant challenges. To address these challenges, we present AceMap, an academic system designed for knowledge discovery through academic graph. We present advanced database construction techniques to build the comprehensive AceMap database with large-scale academic entities that contain rich visual, textual, and numerical information. AceMap also employs innovative visualization, quantification, and analysis methods to explore associations and logical relationships among academic entities. AceMap introduces large-scale academic network visualization techniques centered on nebular graphs, providing a comprehensive view of academic networks from multiple perspectives. In addition, AceMap proposes a unified metric based on structural entropy to quantitatively measure the knowledge content of different academic entities. Moreover, AceMap provides advanced analysis capabilities, including tracing the evolution of academic ideas through citation relationships and concept co-occurrence, and generating concise summaries informed by this evolutionary process. In addition, AceMap uses machine reading methods to generate potential new ideas at the intersection of different fields. Exploring the integration of large language models and knowledge graphs is a promising direction for future research in idea evolution. Please visit https://www.acemap.info for further exploration.

Selective state space models (SSMs), such as Mamba, highly excel at capturing long-range dependencies in 1D sequential data, while their applications to 2D vision tasks still face challenges. Current visual SSMs often convert images into 1D sequences and employ various scanning patterns to incorporate local spatial dependencies. However, these methods are limited in effectively capturing the complex image spatial structures and the increased computational cost caused by the lengthened scanning paths. To address these limitations, we propose Spatial-Mamba, a novel approach that establishes neighborhood connectivity directly in the state space. Instead of relying solely on sequential state transitions, we introduce a structure-aware state fusion equation, which leverages dilated convolutions to capture image spatial structural dependencies, significantly enhancing the flow of visual contextual information. Spatial-Mamba proceeds in three stages: initial state computation in a unidirectional scan, spatial context acquisition through structure-aware state fusion, and final state computation using the observation equation. Our theoretical analysis shows that Spatial-Mamba unifies the original Mamba and linear attention under the same matrix multiplication framework, providing a deeper understanding of our method. Experimental results demonstrate that Spatial-Mamba, even with a single scan, attains or surpasses the state-of-the-art SSM-based models in image classification, detection and segmentation. Source codes and trained models can be found at https://github.com/EdwardChasel/Spatial-Mamba.

Referring Image Segmentation~(RIS) leveraging transformers has achieved great success on the interpretation of complex visual-language tasks. However, the quadratic computation cost makes it resource-consuming in capturing long-range visual-language dependencies. Fortunately, Mamba addresses this with efficient linear complexity in processing. However, directly applying Mamba to multi-modal interactions presents challenges, primarily due to inadequate channel interactions for the effective fusion of multi-modal data. In this paper, we propose ReMamber, a novel RIS architecture that integrates the power of Mamba with a multi-modal Mamba Twister block. The Mamba Twister explicitly models image-text interaction, and fuses textual and visual features through its unique channel and spatial twisting mechanism. We achieve competitive results on three challenging benchmarks with a simple and efficient architecture. Moreover, we conduct thorough analyses of ReMamber and discuss other fusion designs using Mamba. These provide valuable perspectives for future research. The code has been released at: https://github.com/yyh-rain-song/ReMamber.

Learning the behavior of large agent populations is an important task for numerous research areas. Although the field of multi-agent reinforcement learning (MARL) has made significant progress towards solving these systems, solutions for many agents often remain computationally infeasible and lack theoretical guarantees. Mean Field Games (MFGs) address both of these issues and can be extended to Graphon MFGs (GMFGs) to include network structures between agents. Despite their merits, the real world applicability of GMFGs is limited by the fact that graphons only capture dense graphs. Since most empirically observed networks show some degree of sparsity, such as power law graphs, the GMFG framework is insufficient for capturing these network topologies. Thus, we introduce the novel concept of Graphex MFGs (GXMFGs) which builds on the graph theoretical concept of graphexes. Graphexes are the limiting objects to sparse graph sequences that also have other desirable features such as the small world property. Learning equilibria in these games is challenging due to the rich and sparse structure of the underlying graphs. To tackle these challenges, we design a new learning algorithm tailored to the GXMFG setup. This hybrid graphex learning approach leverages that the system mainly consists of a highly connected core and a sparse periphery. After defining the system and providing a theoretical analysis, we state our learning approach and demonstrate its learning capabilities on both synthetic graphs and real-world networks. This comparison shows that our GXMFG learning algorithm successfully extends MFGs to a highly relevant class of hard, realistic learning problems that are not accurately addressed by current MARL and MFG methods.

Action detection in real-world scenarios is particularly challenging due to densely distributed actions in hour-long untrimmed videos. It requires modeling both short- and long-term temporal relationships while handling significant intra-class temporal variations. Previous state-of-the-art (SOTA) Transformer-based architectures, though effective, are impractical for real-world deployment due to their high parameter count, GPU memory usage, and limited throughput, making them unsuitable for very long videos. In this work, we innovatively adapt the Mamba architecture for action detection and propose Multi-scale Temporal Mamba (MS-Temba), comprising two key components: Temporal Mamba (Temba) Blocks and the Temporal Mamba Fuser. Temba Blocks include the Temporal Local Module (TLM) for short-range temporal modeling and the Dilated Temporal SSM (DTS) for long-range dependencies. By introducing dilations, a novel concept for Mamba, TLM and DTS capture local and global features at multiple scales. The Temba Fuser aggregates these scale-specific features using Mamba to learn comprehensive multi-scale representations of untrimmed videos. MS-Temba is validated on three public datasets, outperforming SOTA methods on long videos and matching prior methods on short videos while using only one-eighth of the parameters.

While machine learning on graphs has demonstrated promise in drug design and molecular property prediction, significant benchmarking challenges hinder its further progress and relevance. Current benchmarking practices often lack focus on transformative, real-world applications, favoring narrow domains like two-dimensional molecular graphs over broader, impactful areas such as combinatorial optimization, relational databases, or chip design. Additionally, many benchmark datasets poorly represent the underlying data, leading to inadequate abstractions and misaligned use cases. Fragmented evaluations and an excessive focus on accuracy further exacerbate these issues, incentivizing overfitting rather than fostering generalizable insights. These limitations have prevented the development of truly useful graph foundation models. This position paper calls for a paradigm shift toward more meaningful benchmarks, rigorous evaluation protocols, and stronger collaboration with domain experts to drive impactful and reliable advances in graph learning research, unlocking the potential of graph learning.

White blood cell (WBC) classification assists in assessing immune health and diagnosing various diseases, yet manual classification is labor-intensive and prone to inconsistencies. Recent advancements in deep learning have shown promise over traditional methods; however, challenges such as data imbalance and the computational demands of modern technologies, such as Transformer-based models which do not scale well with input size, limit their practical application. This paper introduces a novel framework that leverages Mamba models integrated with ensemble learning to improve WBC classification. Mamba models, known for their linear complexity, provide a scalable alternative to Transformer-based approaches, making them suitable for deployment in resource-constrained environments. Additionally, we introduce a new WBC dataset, Chula-WBC-8, for benchmarking. Our approach not only validates the effectiveness of Mamba models in this domain but also demonstrates their potential to significantly enhance classification efficiency without compromising accuracy. The source code can be found at https://github.com/LewisClifton/Mamba-WBC-Classification.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

Real-world tasks consist of multiple inter-dependent subtasks (e.g., a dirty pan needs to be washed before it can be used for cooking). In this work, we aim to model the causal dependencies between such subtasks from instructional videos describing the task. This is a challenging problem since complete information about the world is often inaccessible from videos, which demands robust learning mechanisms to understand the causal structure of events. We present Multimodal Subtask Graph Generation (MSG2), an approach that constructs a Subtask Graph defining the dependency between a task's subtasks relevant to a task from noisy web videos. Graphs generated by our multimodal approach are closer to human-annotated graphs compared to prior approaches. MSG2 further performs the downstream task of next subtask prediction 85% and 30% more accurately than recent video transformer models in the ProceL and CrossTask datasets, respectively.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

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.

Graph generation is integral to various engineering and scientific disciplines. Nevertheless, existing methodologies tend to overlook the generation of edge attributes. However, we identify critical applications where edge attributes are essential, making prior methods potentially unsuitable in such contexts. Moreover, while trivial adaptations are available, empirical investigations reveal their limited efficacy as they do not properly model the interplay among graph components. To address this, we propose a joint score-based model of nodes and edges for graph generation that considers all graph components. Our approach offers two key novelties: (i) node and edge attributes are combined in an attention module that generates samples based on the two ingredients; and (ii) node, edge and adjacency information are mutually dependent during the graph diffusion process. We evaluate our method on challenging benchmarks involving real-world and synthetic datasets in which edge features are crucial. Additionally, we introduce a new synthetic dataset that incorporates edge values. Furthermore, we propose a novel application that greatly benefits from the method due to its nature: the generation of traffic scenes represented as graphs. Our method outperforms other graph generation methods, demonstrating a significant advantage in edge-related measures.

We present the Temporal Graph Benchmark (TGB), a collection of challenging and diverse benchmark datasets for realistic, reproducible, and robust evaluation of machine learning models on temporal graphs. TGB datasets are of large scale, spanning years in duration, incorporate both node and edge-level prediction tasks and cover a diverse set of domains including social, trade, transaction, and transportation networks. For both tasks, we design evaluation protocols based on realistic use-cases. We extensively benchmark each dataset and find that the performance of common models can vary drastically across datasets. In addition, on dynamic node property prediction tasks, we show that simple methods often achieve superior performance compared to existing temporal graph models. We believe that these findings open up opportunities for future research on temporal graphs. Finally, TGB provides an automated machine learning pipeline for reproducible and accessible temporal graph research, including data loading, experiment setup and performance evaluation. TGB will be maintained and updated on a regular basis and welcomes community feedback. TGB datasets, data loaders, example codes, evaluation setup, and leaderboards are publicly available at https://tgb.complexdatalab.com/.

Attributed bipartite graphs (ABGs) are an expressive data model for describing the interactions between two sets of heterogeneous nodes that are associated with rich attributes, such as customer-product purchase networks and author-paper authorship graphs. Partitioning the target node set in such graphs into k disjoint clusters (referred to as k-ABGC) finds widespread use in various domains, including social network analysis, recommendation systems, information retrieval, and bioinformatics. However, the majority of existing solutions towards k-ABGC either overlook attribute information or fail to capture bipartite graph structures accurately, engendering severely compromised result quality. The severity of these issues is accentuated in real ABGs, which often encompass millions of nodes and a sheer volume of attribute data, rendering effective k-ABGC over such graphs highly challenging. In this paper, we propose TPO, an effective and efficient approach to k-ABGC that achieves superb clustering performance on multiple real datasets. TPO obtains high clustering quality through two major contributions: (i) a novel formulation and transformation of the k-ABGC problem based on multi-scale attribute affinity specialized for capturing attribute affinities between nodes with the consideration of their multi-hop connections in ABGs, and (ii) a highly efficient solver that includes a suite of carefully-crafted optimizations for sidestepping explicit affinity matrix construction and facilitating faster convergence. Extensive experiments, comparing TPO against 19 baselines over 5 real ABGs, showcase the superior clustering quality of TPO measured against ground-truth labels. Moreover, compared to the state of the arts, TPO is often more than 40x faster over both small and large ABGs.

Recently similarity graphs became the leading paradigm for efficient nearest neighbor search, outperforming traditional tree-based and LSH-based methods. Similarity graphs perform the search via greedy routing: a query traverses the graph and in each vertex moves to the adjacent vertex that is the closest to this query. In practice, similarity graphs are often susceptible to local minima, when queries do not reach its nearest neighbors, getting stuck in suboptimal vertices. In this paper we propose to learn the routing function that overcomes local minima via incorporating information about the graph global structure. In particular, we augment the vertices of a given graph with additional representations that are learned to provide the optimal routing from the start vertex to the query nearest neighbor. By thorough experiments, we demonstrate that the proposed learnable routing successfully diminishes the local minima problem and significantly improves the overall search performance.

With the global refugee crisis at a historic high, there is a growing need to assess the impact of refugee settlements on their hosting countries and surrounding environments. Because fires are an important land management practice in smallholder agriculture in sub-Saharan Africa, burned area (BA) mappings can help provide information about the impacts of land management practices on local environments. However, a lack of BA ground-truth data in much of sub-Saharan Africa limits the use of highly scalable deep learning (DL) techniques for such BA mappings. In this work, we propose a scalable transfer learning approach to study BA dynamics in areas with little to no ground-truth data such as the West Nile region in Northern Uganda. We train a deep learning model on BA ground-truth data in Portugal and propose the application of that model on refugee-hosting districts in West Nile between 2015 and 2020. By comparing the district-level BA dynamic with the wider West Nile region, we aim to add understanding of the land management impacts of refugee settlements on their surrounding environments.

Let T be a rooted and weighted tree, where the weight of any node is equal to the sum of the weights of its children. The popular Treemap algorithm visualizes such a tree as a hierarchical partition of a square into rectangles, where the area of the rectangle corresponding to any node in T is equal to the weight of that node. The aspect ratio of the rectangles in such a rectangular partition necessarily depends on the weights and can become arbitrarily high. We introduce a new hierarchical partition scheme, called a polygonal partition, which uses convex polygons rather than just rectangles. We present two methods for constructing polygonal partitions, both having guarantees on the worst-case aspect ratio of the constructed polygons; in particular, both methods guarantee a bound on the aspect ratio that is independent of the weights of the nodes. We also consider rectangular partitions with slack, where the areas of the rectangles may differ slightly from the weights of the corresponding nodes. We show that this makes it possible to obtain partitions with constant aspect ratio. This result generalizes to hyper-rectangular partitions in R^d. We use these partitions with slack for embedding ultrametrics into d-dimensional Euclidean space: we give a rm polylog(Delta)-approximation algorithm for embedding n-point ultrametrics into R^d with minimum distortion, where Delta denotes the spread of the metric, i.e., the ratio between the largest and the smallest distance between two points. The previously best-known approximation ratio for this problem was polynomial in n. This is the first algorithm for embedding a non-trivial family of weighted-graph metrics into a space of constant dimension that achieves polylogarithmic approximation ratio.

This work introduces DiGress, a discrete denoising diffusion model for generating graphs with categorical node and edge attributes. Our model utilizes a discrete diffusion process that progressively edits graphs with noise, through the process of adding or removing edges and changing the categories. A graph transformer network is trained to revert this process, simplifying the problem of distribution learning over graphs into a sequence of node and edge classification tasks. We further improve sample quality by introducing a Markovian noise model that preserves the marginal distribution of node and edge types during diffusion, and by incorporating auxiliary graph-theoretic features. A procedure for conditioning the generation on graph-level features is also proposed. DiGress achieves state-of-the-art performance on molecular and non-molecular datasets, with up to 3x validity improvement on a planar graph dataset. It is also the first model to scale to the large GuacaMol dataset containing 1.3M drug-like molecules without the use of molecule-specific representations.

Generating graph-structured data requires learning the underlying distribution of graphs. Yet, this is a challenging problem, and the previous graph generative methods either fail to capture the permutation-invariance property of graphs or cannot sufficiently model the complex dependency between nodes and edges, which is crucial for generating real-world graphs such as molecules. To overcome such limitations, we propose a novel score-based generative model for graphs with a continuous-time framework. Specifically, we propose a new graph diffusion process that models the joint distribution of the nodes and edges through a system of stochastic differential equations (SDEs). Then, we derive novel score matching objectives tailored for the proposed diffusion process to estimate the gradient of the joint log-density with respect to each component, and introduce a new solver for the system of SDEs to efficiently sample from the reverse diffusion process. We validate our graph generation method on diverse datasets, on which it either achieves significantly superior or competitive performance to the baselines. Further analysis shows that our method is able to generate molecules that lie close to the training distribution yet do not violate the chemical valency rule, demonstrating the effectiveness of the system of SDEs in modeling the node-edge relationships. Our code is available at https://github.com/harryjo97/GDSS.

There is a surge of interest in image scene graph generation (object, attribute and relationship detection) due to the need of building fine-grained image understanding models that go beyond object detection. Due to the lack of a good benchmark, the reported results of different scene graph generation models are not directly comparable, impeding the research progress. We have developed a much-needed scene graph generation benchmark based on the maskrcnn-benchmark and several popular models. This paper presents main features of our benchmark and a comprehensive ablation study of scene graph generation models using the Visual Genome and OpenImages Visual relationship detection datasets. Our codebase is made publicly available at https://github.com/microsoft/scene_graph_benchmark.

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.

Micro-Aerial Vehicles (MAVs) have the advantage of moving freely in 3D space. However, creating compact and sparse map representations that can be efficiently used for planning for such robots is still an open problem. In this paper, we take maps built from noisy sensor data and construct a sparse graph containing topological information that can be used for 3D planning. We use a Euclidean Signed Distance Field, extract a 3D Generalized Voronoi Diagram (GVD), and obtain a thin skeleton diagram representing the topological structure of the environment. We then convert this skeleton diagram into a sparse graph, which we show is resistant to noise and changes in resolution. We demonstrate global planning over this graph, and the orders of magnitude speed-up it offers over other common planning methods. We validate our planning algorithm in real maps built onboard an MAV, using RGB-D sensing.

We present a novel quasi-Monte Carlo mechanism to improve graph-based sampling, coined repelling random walks. By inducing correlations between the trajectories of an interacting ensemble such that their marginal transition probabilities are unmodified, we are able to explore the graph more efficiently, improving the concentration of statistical estimators whilst leaving them unbiased. The mechanism has a trivial drop-in implementation. We showcase the effectiveness of repelling random walks in a range of settings including estimation of graph kernels, the PageRank vector and graphlet concentrations. We provide detailed experimental evaluation and robust theoretical guarantees. To our knowledge, repelling random walks constitute the first rigorously studied quasi-Monte Carlo scheme correlating the directions of walkers on a graph, inviting new research in this exciting nascent domain.

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. The code is available at https://github.com/Karami-m/HiGen_main.

This work studies a central extremal graph theory problem inspired by a 1975 conjecture of Erdos, which aims to find graphs with a given size (number of nodes) that maximize the number of edges without having 3- or 4-cycles. We formulate this problem as a sequential decision-making problem and compare AlphaZero, a neural network-guided tree search, with tabu search, a heuristic local search method. Using either method, by introducing a curriculum -- jump-starting the search for larger graphs using good graphs found at smaller sizes -- we improve the state-of-the-art lower bounds for several sizes. We also propose a flexible graph-generation environment and a permutation-invariant network architecture for learning to search in the space of graphs.

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.

We study experiment design for unique identification of the causal graph of a simple SCM, where the graph may contain cycles. The presence of cycles in the structure introduces major challenges for experiment design as, unlike acyclic graphs, learning the skeleton of causal graphs with cycles may not be possible from merely the observational distribution. Furthermore, intervening on a variable in such graphs does not necessarily lead to orienting all the edges incident to it. In this paper, we propose an experiment design approach that can learn both cyclic and acyclic graphs and hence, unifies the task of experiment design for both types of graphs. We provide a lower bound on the number of experiments required to guarantee the unique identification of the causal graph in the worst case, showing that the proposed approach is order-optimal in terms of the number of experiments up to an additive logarithmic term. Moreover, we extend our result to the setting where the size of each experiment is bounded by a constant. For this case, we show that our approach is optimal in terms of the size of the largest experiment required for uniquely identifying the causal graph in the worst case.

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.

Multiple Instance Learning (MIL) has emerged as a dominant paradigm to extract discriminative feature representations within Whole Slide Images (WSIs) in computational pathology. Despite driving notable progress, existing MIL approaches suffer from limitations in facilitating comprehensive and efficient interactions among instances, as well as challenges related to time-consuming computations and overfitting. In this paper, we incorporate the Selective Scan Space State Sequential Model (Mamba) in Multiple Instance Learning (MIL) for long sequence modeling with linear complexity, termed as MambaMIL. By inheriting the capability of vanilla Mamba, MambaMIL demonstrates the ability to comprehensively understand and perceive long sequences of instances. Furthermore, we propose the Sequence Reordering Mamba (SR-Mamba) aware of the order and distribution of instances, which exploits the inherent valuable information embedded within the long sequences. With the SR-Mamba as the core component, MambaMIL can effectively capture more discriminative features and mitigate the challenges associated with overfitting and high computational overhead. Extensive experiments on two public challenging tasks across nine diverse datasets demonstrate that our proposed framework performs favorably against state-of-the-art MIL methods. The code is released at https://github.com/isyangshu/MambaMIL.

Recovering causal relationships from data is an important problem. Using observational data, one can typically only recover causal graphs up to a Markov equivalence class and additional assumptions or interventional data are needed for complete recovery. In this work, under some standard assumptions, we study causal graph discovery via adaptive interventions with node-dependent interventional costs. For this setting, we show that no algorithm can achieve an approximation guarantee that is asymptotically better than linear in the number of vertices with respect to the verification number; a well-established benchmark for adaptive search algorithms. Motivated by this negative result, we define a new benchmark that captures the worst-case interventional cost for any search algorithm. Furthermore, with respect to this new benchmark, we provide adaptive search algorithms that achieve logarithmic approximations under various settings: atomic, bounded size interventions and generalized cost objectives.

Network embedding has been widely used in social recommendation and network analysis, such as recommendation systems and anomaly detection with graphs. However, most of previous approaches cannot handle large graphs efficiently, due to that (i) computation on graphs is often costly and (ii) the size of graph or the intermediate results of vectors could be prohibitively large, rendering it difficult to be processed on a single machine. In this paper, we propose an efficient and effective distributed algorithm for network embedding on large graphs using Apache Spark, which recursively partitions a graph into several small-sized subgraphs to capture the internal and external structural information of nodes, and then computes the network embedding for each subgraph in parallel. Finally, by aggregating the outputs on all subgraphs, we obtain the embeddings of nodes in a linear cost. After that, we demonstrate in various experiments that our proposed approach is able to handle graphs with billions of edges within a few hours and is at least 4 times faster than the state-of-the-art approaches. Besides, it achieves up to 4.25% and 4.27% improvements on link prediction and node classification tasks respectively. In the end, we deploy the proposed algorithms in two online games of Tencent with the applications of friend recommendation and item recommendation, which improve the competitors by up to 91.11% in running time and up to 12.80% in the corresponding evaluation metrics.

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.

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.

Existing graph matching methods typically assume that there are similar structures between graphs and they are matchable. However, these assumptions do not align with real-world applications. This work addresses a more realistic scenario where graphs exhibit diverse modes, requiring graph grouping before or along with matching, a task termed mixture graph matching and clustering. We introduce Minorize-Maximization Matching and Clustering (M3C), a learning-free algorithm that guarantees theoretical convergence through the Minorize-Maximization framework and offers enhanced flexibility via relaxed clustering. Building on M3C, we develop UM3C, an unsupervised model that incorporates novel edge-wise affinity learning and pseudo label selection. Extensive experimental results on public benchmarks demonstrate that our method outperforms state-of-the-art graph matching and mixture graph matching and clustering approaches in both accuracy and efficiency. Source code will be made publicly available.

The retroperitoneum hosts a variety of tumors, including rare benign and malignant types, which pose diagnostic and treatment challenges due to their infrequency and proximity to vital structures. Estimating tumor volume is difficult due to their irregular shapes, and manual segmentation is time-consuming. Automatic segmentation using U-Net and its variants, incorporating Vision Transformer (ViT) elements, has shown promising results but struggles with high computational demands. To address this, architectures like the Mamba State Space Model (SSM) and Extended Long-Short Term Memory (xLSTM) offer efficient solutions by handling long-range dependencies with lower resource consumption. This study evaluates U-Net enhancements, including CNN, ViT, Mamba, and xLSTM, on a new in-house CT dataset and a public organ segmentation dataset. The proposed ViLU-Net model integrates Vi-blocks for improved segmentation. Results highlight xLSTM's efficiency in the U-Net framework. The code is publicly accessible on GitHub.

We propose a graph clustering formulation based on multicut (a.k.a. weighted correlation clustering) on the complete graph. Our formulation does not need specification of the graph topology as in the original sparse formulation of multicut, making our approach simpler and potentially better performing. In contrast to unweighted correlation clustering we allow for a more expressive weighted cost structure. In dense multicut, the clustering objective is given in a factorized form as inner products of node feature vectors. This allows for an efficient formulation and inference in contrast to multicut/weighted correlation clustering, which has at least quadratic representation and computation complexity when working on the complete graph. We show how to rewrite classical greedy algorithms for multicut in our dense setting and how to modify them for greater efficiency and solution quality. In particular, our algorithms scale to graphs with tens of thousands of nodes. Empirical evidence on instance segmentation on Cityscapes and clustering of ImageNet datasets shows the merits of our approach.

With the increasing prevalence of graph-structured data, multi-view graph clustering has been widely used in various downstream applications. Existing approaches primarily rely on a unified message passing mechanism, which significantly enhances clustering performance. Nevertheless, this mechanism limits its applicability to heterophilous situations, as it is fundamentally predicated on the assumption of homophily, i.e., the connected nodes often belong to the same class. In reality, this assumption does not always hold; a moderately or even mildly homophilous graph is more common than a fully homophilous one due to inevitable heterophilous information in the graph. To address this issue, in this paper, we propose a novel SiMilarity-enhanced Homophily for Multi-view Heterophilous Graph Clustering (SMHGC) approach. By analyzing the relationship between similarity and graph homophily, we propose to enhance the homophily by introducing three similarity terms, i.e., neighbor pattern similarity, node feature similarity, and multi-view global similarity, in a label-free manner. Then, a consensus-based inter- and intra-view fusion paradigm is proposed to fuse the improved homophilous graph from different views and utilize them for clustering. The state-of-the-art experimental results on both multi-view heterophilous and homophilous datasets collectively demonstrate the strong capacity of similarity for unsupervised multi-view heterophilous graph learning. Additionally, the consistent performance across semi-synthetic datasets with varying levels of homophily serves as further evidence of SMHGC's resilience to heterophily.

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.

Micro-expressions are typically regarded as unconscious manifestations of a person's genuine emotions. However, their short duration and subtle signals pose significant challenges for downstream recognition. We propose a multi-task learning framework named the Adaptive Motion Magnification and Sparse Mamba (AMMSM) to address this. This framework aims to enhance the accurate capture of micro-expressions through self-supervised subtle motion magnification, while the sparse spatial selection Mamba architecture combines sparse activation with the advanced Visual Mamba model to model key motion regions and their valuable representations more effectively. Additionally, we employ evolutionary search to optimize the magnification factor and the sparsity ratios of spatial selection, followed by fine-tuning to improve performance further. Extensive experiments on two standard datasets demonstrate that the proposed AMMSM achieves state-of-the-art (SOTA) accuracy and robustness.