Daily Papers

Single-nucleus RNA sequencing (snRNA-seq) has significantly advanced our understanding of the disease etiology of neurodegenerative disorders. However, the low quality of specimens derived from postmortem brain tissues, combined with the high variability caused by disease heterogeneity, makes it challenging to integrate snRNA-seq data from multiple sources for precise analyses. To address these challenges, we present scMamba, a pre-trained model designed to improve the quality and utility of snRNA-seq analysis, with a particular focus on neurodegenerative diseases. Inspired by the recent Mamba model, scMamba introduces a novel architecture that incorporates a linear adapter layer, gene embeddings, and bidirectional Mamba blocks, enabling efficient processing of snRNA-seq data while preserving information from the raw input. Notably, scMamba learns generalizable features of cells and genes through pre-training on snRNA-seq data, without relying on dimension reduction or selection of highly variable genes. We demonstrate that scMamba outperforms benchmark methods in various downstream tasks, including cell type annotation, doublet detection, imputation, and the identification of differentially expressed genes.

Existing deep learning approaches leave out the semantic cues that are crucial in semantic segmentation present in complex scenarios including cluttered backgrounds and translucent objects, etc. To handle these challenges, we propose a feature amplification network (FANet) as a backbone network that incorporates semantic information using a novel feature enhancement module at multi-stages. To achieve this, we propose an adaptive feature enhancement (AFE) block that benefits from both a spatial context module (SCM) and a feature refinement module (FRM) in a parallel fashion. SCM aims to exploit larger kernel leverages for the increased receptive field to handle scale variations in the scene. Whereas our novel FRM is responsible for generating semantic cues that can capture both low-frequency and high-frequency regions for better segmentation tasks. We perform experiments over challenging real-world ZeroWaste-f dataset which contains background-cluttered and translucent objects. Our experimental results demonstrate the state-of-the-art performance compared to existing methods.

Pre-trained language models (PLMs) have revolutionized scientific research, yet their application to single-cell analysis remains limited. Text PLMs cannot process single-cell RNA sequencing data, while cell PLMs lack the ability to handle free text, restricting their use in multimodal tasks. Existing efforts to bridge these modalities often suffer from information loss or inadequate single-modal pre-training, leading to suboptimal performances. To address these challenges, we propose Single-Cell MultiModal Generative Pre-trained Transformer (scMMGPT), a unified PLM for joint cell and text modeling. scMMGPT effectively integrates the state-of-the-art cell and text PLMs, facilitating cross-modal knowledge sharing for improved performance. To bridge the text-cell modality gap, scMMGPT leverages dedicated cross-modal projectors, and undergoes extensive pre-training on 27 million cells -- the largest dataset for multimodal cell-text PLMs to date. This large-scale pre-training enables scMMGPT to excel in joint cell-text tasks, achieving an 84\% relative improvement of textual discrepancy for cell description generation, 20.5\% higher accuracy for cell type annotation, and 4\% improvement in k-NN accuracy for text-conditioned pseudo-cell generation, outperforming baselines.

Vision-language pre-trained (VLP) models have been the foundation of numerous vision-language tasks. Given their prevalence, it becomes imperative to assess their adversarial robustness, especially when deploying them in security-crucial real-world applications. Traditionally, adversarial perturbations generated for this assessment target specific VLP models, datasets, and/or downstream tasks. This practice suffers from low transferability and additional computation costs when transitioning to new scenarios. In this work, we thoroughly investigate whether VLP models are commonly sensitive to imperceptible perturbations of a specific pattern for the image modality. To this end, we propose a novel black-box method to generate Universal Adversarial Perturbations (UAPs), which is so called the Effective and T ransferable Universal Adversarial Attack (ETU), aiming to mislead a variety of existing VLP models in a range of downstream tasks. The ETU comprehensively takes into account the characteristics of UAPs and the intrinsic cross-modal interactions to generate effective UAPs. Under this regime, the ETU encourages both global and local utilities of UAPs. This benefits the overall utility while reducing interactions between UAP units, improving the transferability. To further enhance the effectiveness and transferability of UAPs, we also design a novel data augmentation method named ScMix. ScMix consists of self-mix and cross-mix data transformations, which can effectively increase the multi-modal data diversity while preserving the semantics of the original data. Through comprehensive experiments on various downstream tasks, VLP models, and datasets, we demonstrate that the proposed method is able to achieve effective and transferrable universal adversarial attacks.

Large-scale Language Models (LLMs) are constrained by their inability to process lengthy inputs. To address this limitation, we propose the Self-Controlled Memory (SCM) system to unleash infinite-length input capacity for large-scale language models. Our SCM system is composed of three key modules: the language model agent, the memory stream, and the memory controller. The language model agent iteratively processes ultra-long inputs and stores all historical information in the memory stream. The memory controller provides the agent with both long-term memory (archived memory) and short-term memory (flash memory) to generate precise and coherent responses. The controller determines which memories from archived memory should be activated and how to incorporate them into the model input. Our SCM system can be integrated with any LLMs to enable them to process ultra-long texts without any modification or fine-tuning. Experimental results show that our SCM system enables LLMs, which are not optimized for multi-turn dialogue, to achieve multi-turn dialogue capabilities that are comparable to ChatGPT, and to outperform ChatGPT in scenarios involving ultra-long document summarization or long-term conversations. Additionally, we will supply a test set, which covers common long-text input scenarios, for evaluating the abilities of LLMs in processing long documents.~Working in progress.\url{https://github.com/wbbeyourself/SCM4LLMs}

Mixture-of-Experts (MoE) has emerged as a prominent architecture for scaling model size while maintaining computational efficiency. In MoE, each token in the input sequence activates a different subset of experts determined by a routing mechanism. However, the unchosen experts in MoE models do not contribute to the output, potentially leading to underutilization of the model's capacity. In this work, we first conduct exploratory studies to demonstrate that increasing the number of activated experts does not necessarily improve and can even degrade the output quality. Then, we show that output distributions from an MoE model using different routing strategies substantially differ, indicating that different experts do not always act synergistically. Motivated by these findings, we propose Self-Contrast Mixture-of-Experts (SCMoE), a training-free strategy that utilizes unchosen experts in a self-contrast manner during inference. In SCMoE, the next-token probabilities are determined by contrasting the outputs from strong and weak activation using the same MoE model. Our method is conceptually simple and computationally lightweight, as it incurs minimal latency compared to greedy decoding. Experiments on several benchmarks (GSM8K, StrategyQA, MBPP and HumanEval) demonstrate that SCMoE can consistently enhance Mixtral 8x7B's reasoning capability across various domains. For example, it improves the accuracy on GSM8K from 61.79 to 66.94. Moreover, combining SCMoE with self-consistency yields additional gains, increasing major@20 accuracy from 75.59 to 78.31.