A large language model for predicting T cell receptor-antigen binding specificity

The human immune response depends on the binding of T-cell receptors (TCRs) to antigens (pTCR), which elicits the T cells to eliminate viruses, tumor cells, and other pathogens. The ability of human immunity system responding to unknown viruses and bacteria stems from the TCR diversity. However, this vast diversity poses challenges on the TCR-antigen binding prediction methods. In this study, we propose a Masked Language Model (MLM), referred to as tcrLM, to overcome limitations in model generalization. Specifically, we randomly masked sequence segments and train tcrLM to infer the masked segment, thereby extract expressive feature from TCR sequences. Meanwhile, we introduced virtual adversarial training techniques to enhance the model's robustness. We built the largest TCR CDR3 sequence dataset to date (comprising 2,277,773,840 residuals), and pre-trained tcrLM on this dataset. Our extensive experimental results demonstrate that tcrLM achieved AUC values of 0.937 and 0.933 on independent test sets and external validation sets, respectively, which remarkably outperformed four previously published prediction methods. On a large-scale COVID-19 pTCR binding test set, our method outperforms the current state-of-the-art method by at least 8%, highlighting the generalizability of our method. Furthermore, we validated that our approach effectively predicts immunotherapy response and clinical outcomes on a clinical cohorts. These findings clearly indicate that tcrLM exhibits significant potential in predicting antigenic immunogenicity.

Six-CD: Benchmarking Concept Removals for Benign Text-to-image Diffusion Models

Text-to-image (T2I) diffusion models have shown exceptional capabilities in generating images that closely correspond to textual prompts. However, the advancement of T2I diffusion models presents significant risks, as the models could be exploited for malicious purposes, such as generating images with violence or nudity, or creating unauthorized portraits of public figures in inappropriate contexts. To mitigate these risks, concept removal methods have been proposed. These methods aim to modify diffusion models to prevent the generation of malicious and unwanted concepts. Despite these efforts, existing research faces several challenges: (1) a lack of consistent comparisons on a comprehensive dataset, (2) ineffective prompts in harmful and nudity concepts, (3) overlooked evaluation of the ability to generate the benign part within prompts containing malicious concepts. To address these gaps, we propose to benchmark the concept removal methods by introducing a new dataset, Six-CD, along with a novel evaluation metric. In this benchmark, we conduct a thorough evaluation of concept removals, with the experimental observations and discussions offering valuable insights in the field.

A Pure Transformer Pretraining Framework on Text-attributed Graphs

Pretraining plays a pivotal role in acquiring generalized knowledge from large-scale data, achieving remarkable successes as evidenced by large models in CV and NLP. However, progress in the graph domain remains limited due to fundamental challenges such as feature heterogeneity and structural heterogeneity. Recently, increasing efforts have been made to enhance node feature quality with Large Language Models (LLMs) on text-attributed graphs (TAGs), demonstrating superiority to traditional bag-of-words or word2vec techniques. These high-quality node features reduce the previously critical role of graph structure, resulting in a modest performance gap between Graph Neural Networks (GNNs) and structure-agnostic Multi-Layer Perceptrons (MLPs). Motivated by this, we introduce a feature-centric pretraining perspective by treating graph structure as a prior and leveraging the rich, unified feature space to learn refined interaction patterns that generalizes across graphs. Our framework, Graph Sequence Pretraining with Transformer (GSPT), samples node contexts through random walks and employs masked feature reconstruction to capture pairwise proximity in the LLM-unified feature space using a standard Transformer. By utilizing unified text representations rather than varying structures, our framework achieves significantly better transferability among graphs within the same domain. GSPT can be easily adapted to both node classification and link prediction, demonstrating promising empirical success on various datasets.

Towards Understanding Jailbreak Attacks in LLMs: A Representation Space Analysis

Large language models (LLMs) are susceptible to a type of attack known as jailbreaking, which misleads LLMs to output harmful contents. Although there are diverse jailbreak attack strategies, there is no unified understanding on why some methods succeed and others fail. This paper explores the behavior of harmful and harmless prompts in the LLM's representation space to investigate the intrinsic properties of successful jailbreak attacks. We hypothesize that successful attacks share some similar properties: They are effective in moving the representation of the harmful prompt towards the direction to the harmless prompts. We leverage hidden representations into the objective of existing jailbreak attacks to move the attacks along the acceptance direction, and conduct experiments to validate the above hypothesis using the proposed objective. We hope this study provides new insights into understanding how LLMs understand harmfulness information.

Text-space Graph Foundation Models: Comprehensive Benchmarks and New Insights

Given the ubiquity of graph data and its applications in diverse domains, building a Graph Foundation Model (GFM) that can work well across different graphs and tasks with a unified backbone has recently garnered significant interests. A major obstacle to achieving this goal stems from the fact that graphs from different domains often exhibit diverse node features. Inspired by multi-modal models that align different modalities with natural language, the text has recently been adopted to provide a unified feature space for diverse graphs. Despite the great potential of these text-space GFMs, current research in this field is hampered by two problems. First, the absence of a comprehensive benchmark with unified problem settings hinders a clear understanding of the comparative effectiveness and practical value of different text-space GFMs. Second, there is a lack of sufficient datasets to thoroughly explore the methods' full potential and verify their effectiveness across diverse settings. To address these issues, we conduct a comprehensive benchmark providing novel text-space datasets and comprehensive evaluation under unified problem settings. Empirical results provide new insights and inspire future research directions. Our code and data are publicly available from \url{https://github.com/CurryTang/TSGFM}.

Unraveling the Mechanics of Learning-Based Demonstration Selection for In-Context Learning

Large Language Models (LLMs) have demonstrated impressive in-context learning (ICL) capabilities from few-shot demonstration exemplars. While recent learning-based demonstration selection methods have proven beneficial to ICL by choosing more useful exemplars, their underlying mechanisms are opaque, hindering efforts to address limitations such as high training costs and poor generalization across tasks. These methods generally assume the selection process captures similarities between the exemplar and the target instance, however, it remains unknown what kinds of similarities are captured and vital to performing ICL. To dive into this question, we analyze the working mechanisms of the learning-based demonstration selection methods and empirically identify two important factors related to similarity measurement: 1) The ability to integrate different levels of task-agnostic text similarities between the input of exemplars and test cases enhances generalization power across different tasks. 2) Incorporating task-specific labels when measuring the similarities significantly improves the performance on each specific task. We validate these two findings through extensive quantitative and qualitative analyses across ten datasets and various LLMs. Based on our findings, we introduce two effective yet simplified exemplar selection methods catering to task-agnostic and task-specific demands, eliminating the costly LLM inference overhead.

Node-wise Filtering in Graph Neural Networks: A Mixture of Experts Approach

Graph Neural Networks (GNNs) have proven to be highly effective for node classification tasks across diverse graph structural patterns. Traditionally, GNNs employ a uniform global filter, typically a low-pass filter for homophilic graphs and a high-pass filter for heterophilic graphs. However, real-world graphs often exhibit a complex mix of homophilic and heterophilic patterns, rendering a single global filter approach suboptimal. In this work, we theoretically demonstrate that a global filter optimized for one pattern can adversely affect performance on nodes with differing patterns. To address this, we introduce a novel GNN framework Node-MoE that utilizes a mixture of experts to adaptively select the appropriate filters for different nodes. Extensive experiments demonstrate the effectiveness of Node-MoE on both homophilic and heterophilic graphs.

UniOQA: A Unified Framework for Knowledge Graph Question Answering with Large Language Models

OwnThink stands as the most extensive Chinese open-domain knowledge graph introduced in recent times. Despite prior attempts in question answering over OwnThink (OQA), existing studies have faced limitations in model representation capabilities, posing challenges in further enhancing overall accuracy in question answering. In this paper, we introduce UniOQA, a unified framework that integrates two complementary parallel workflows. Unlike conventional approaches, UniOQA harnesses large language models (LLMs) for precise question answering and incorporates a direct-answer-prediction process as a cost-effective complement. Initially, to bolster representation capacity, we fine-tune an LLM to translate questions into the Cypher query language (CQL), tackling issues associated with restricted semantic understanding and hallucinations. Subsequently, we introduce the Entity and Relation Replacement algorithm to ensure the executability of the generated CQL. Concurrently, to augment overall accuracy in question answering, we further adapt the Retrieval-Augmented Generation (RAG) process to the knowledge graph. Ultimately, we optimize answer accuracy through a dynamic decision algorithm. Experimental findings illustrate that UniOQA notably advances SpCQL Logical Accuracy to 21.2% and Execution Accuracy to 54.9%, achieving the new state-of-the-art results on this benchmark. Through ablation experiments, we delve into the superior representation capacity of UniOQA and quantify its performance breakthrough.

NVS-Solver: Video Diffusion Model as Zero-Shot Novel View Synthesizer

By harnessing the potent generative capabilities of pre-trained large video diffusion models, we propose NVS-Solver, a new novel view synthesis (NVS) paradigm that operates \textit{without} the need for training. NVS-Solver adaptively modulates the diffusion sampling process with the given views to enable the creation of remarkable visual experiences from single or multiple views of static scenes or monocular videos of dynamic scenes. Specifically, built upon our theoretical modeling, we iteratively modulate the score function with the given scene priors represented with warped input views to control the video diffusion process. Moreover, by theoretically exploring the boundary of the estimation error, we achieve the modulation in an adaptive fashion according to the view pose and the number of diffusion steps. Extensive evaluations on both static and dynamic scenes substantiate the significant superiority of our NVS-Solver over state-of-the-art methods both quantitatively and qualitatively. \textit{ Source code in } \href{https://github.com/ZHU-Zhiyu/NVS_Solver}{https://github.com/ZHU-Zhiyu/NVS$\_$Solver}.

Modeling Selective Feature Attention for Representation-based Siamese Text Matching

Representation-based Siamese networks have risen to popularity in lightweight text matching due to their low deployment and inference costs. While word-level attention mechanisms have been implemented within Siamese networks to improve performance, we propose Feature Attention (FA), a novel downstream block designed to enrich the modeling of dependencies among embedding features. Employing "squeeze-and-excitation" techniques, the FA block dynamically adjusts the emphasis on individual features, enabling the network to concentrate more on features that significantly contribute to the final classification. Building upon FA, we introduce a dynamic "selection" mechanism called Selective Feature Attention (SFA), which leverages a stacked BiGRU Inception structure. The SFA block facilitates multi-scale semantic extraction by traversing different stacked BiGRU layers, encouraging the network to selectively concentrate on semantic information and embedding features across varying levels of abstraction. Both the FA and SFA blocks offer a seamless integration capability with various Siamese networks, showcasing a plug-and-play characteristic. Experimental evaluations conducted across diverse text matching baselines and benchmarks underscore the indispensability of modeling feature attention and the superiority of the "selection" mechanism.