Jiliang Tang

Hongzhi Wen, Jiayuan Ding, Wei Jin et al.

Recent advances in multimodal single-cell technologies have enabled simultaneous acquisitions of multiple omics data from the same cell, providing deeper insights into cellular states and dynamics. However, it is challenging to learn the joint representations from the multimodal data, model the relationship between modalities, and, more importantly, incorporate the vast amount of single-modality datasets into the downstream analyses. To address these challenges and correspondingly facilitate multimodal single-cell data analyses, three key tasks have been introduced: $\textit{modality prediction}$, $\textit{modality matching}$ and $\textit{joint embedding}$. In this work, we present a general Graph Neural Network framework $\textit{scMoGNN}$ to tackle these three tasks and show that $\textit{scMoGNN}$ demonstrates superior results in all three tasks compared with the state-of-the-art and conventional approaches. Our method is an official winner in the overall ranking of $\textit{Modality prediction}$ from NeurIPS 2021 Competition, and all implementations of our methods have been integrated into DANCE package~\url{https://github.com/OmicsML/dance}.

Jiatong Li, Yunqing Liu, Wenqi Fan et al.

Molecule discovery plays a crucial role in various scientific fields, advancing the design of tailored materials and drugs. However, most of the existing methods heavily rely on domain experts, require excessive computational cost, or suffer from sub-optimal performance. On the other hand, Large Language Models (LLMs), like ChatGPT, have shown remarkable performance in various cross-modal tasks due to their powerful capabilities in natural language understanding, generalization, and in-context learning (ICL), which provides unprecedented opportunities to advance molecule discovery. Despite several previous works trying to apply LLMs in this task, the lack of domain-specific corpus and difficulties in training specialized LLMs still remain challenges. In this work, we propose a novel LLM-based framework (MolReGPT) for molecule-caption translation, where an In-Context Few-Shot Molecule Learning paradigm is introduced to empower molecule discovery with LLMs like ChatGPT to perform their in-context learning capability without domain-specific pre-training and fine-tuning. MolReGPT leverages the principle of molecular similarity to retrieve similar molecules and their text descriptions from a local database to enable LLMs to learn the task knowledge from context examples. We evaluate the effectiveness of MolReGPT on molecule-caption translation, including molecule understanding and text-based molecule generation. Experimental results show that compared to fine-tuned models, MolReGPT outperforms MolT5-base and is comparable to MolT5-large without additional training. To the best of our knowledge, MolReGPT is the first work to leverage LLMs via in-context learning in molecule-caption translation for advancing molecule discovery. Our work expands the scope of LLM applications, as well as providing a new paradigm for molecule discovery and design.

Pengfei He, Zhenwei Dai, Xianfeng Tang et al.

Large Language Model-based Multi-Agent Systems (LLM-MAS) have demonstrated strong capabilities in solving complex tasks but remain vulnerable when agents receive unreliable messages. This vulnerability stems from a fundamental gap: LLM agents treat all incoming messages equally without evaluating their trustworthiness. While some existing studies approach trustworthiness, they focus on a single type of harmfulness rather than analyze it in a holistic approach from multiple trustworthiness perspectives. We address this gap by proposing a comprehensive definition of trustworthiness inspired by human communication theory (Grice, 1975). Our definition identifies six orthogonal trust dimensions that provide interpretable measures of trustworthiness. Building on this definition, we introduce the Attention Trust Score (A -Trust), a lightweight, attention-based method for evaluating the trustworthiness of messages. We then develop a principled trust management system (TMS) for LLM -MAS that supports both message-level and agent-level trust assessments. Experiments across diverse multi-agent settings and tasks demonstrate that our TMS significantly improves robustness against malicious inputs.

Yingqian Cui, Jie Ren, Yuping Lin et al.

Text-to-image generative models, especially those based on latent diffusion models (LDMs), have demonstrated outstanding ability in generating high-quality and high-resolution images from textual prompts. With this advancement, various fine-tuning methods have been developed to personalize text-to-image models for specific applications such as artistic style adaptation and human face transfer. However, such advancements have raised copyright concerns, especially when the data are used for personalization without authorization. For example, a malicious user can employ fine-tuning techniques to replicate the style of an artist without consent. In light of this concern, we propose FT-Shield, a watermarking solution tailored for the fine-tuning of text-to-image diffusion models. FT-Shield addresses copyright protection challenges by designing new watermark generation and detection strategies. In particular, it introduces an innovative algorithm for watermark generation. It ensures the seamless transfer of watermarks from training images to generated outputs, facilitating the identification of copyrighted material use. To tackle the variability in fine-tuning methods and their impact on watermark detection, FT-Shield integrates a Mixture of Experts (MoE) approach for watermark detection. Comprehensive experiments validate the effectiveness of our proposed FT-Shield.

Guangliang Liu, Haitao Mao, Jiliang Tang et al.

Large Language Models (LLMs) are capable of producing content that perpetuates stereotypes, discrimination, and toxicity. The recently proposed moral self-correction is a computationally efficient method for reducing harmful content in the responses of LLMs. However, the process of how injecting self-correction instructions can modify the behavior of LLMs remains under-explored. In this paper, we explore the effectiveness of moral self-correction by answering three research questions: (1) In what scenarios does moral self-correction work? (2) What are the internal mechanisms of LLMs, e.g., hidden states, that are influenced by moral self-correction instructions? (3) Is intrinsic moral self-correction actually superficial in terms of reduced immorality in hidden states? We argue that self-correction can help LLMs find a shortcut to more morally correct output, rather than truly reducing the immorality stored in hidden states. Through empirical investigation with tasks of language generation and multi-choice question answering, we conclude:(i) LLMs exhibit good performance across both tasks, and self-correction instructions are particularly beneficial when the correct answer is already top-ranked; (ii) The morality levels in intermediate hidden states are strong indicators as to whether one instruction would be more effective than another; (iii) Based on our analysis of intermediate hidden states and task case studies of self-correction behaviors, we are first to propose the hypothesis that intrinsic moral self-correction is in fact superficial.

Ziwen Zhao, Yuhua Li, Yixiong Zou et al.

Masked graph autoencoders have emerged as a powerful graph self-supervised learning method that has yet to be fully explored. In this paper, we unveil that the existing discrete edge masking and binary link reconstruction strategies are insufficient to learn topologically informative representations, from the perspective of message propagation on graph neural networks. These limitations include blocking message flows, vulnerability to over-smoothness, and suboptimal neighborhood discriminability. Inspired by these understandings, we explore non-discrete edge masks, which are sampled from a continuous and dispersive probability distribution instead of the discrete Bernoulli distribution. These masks restrict the amount of output messages for each edge, referred to as "bandwidths". We propose a novel, informative, and effective topological masked graph autoencoder using bandwidth masking and a layer-wise bandwidth prediction objective. We demonstrate its powerful graph topological learning ability both theoretically and empirically. Our proposed framework outperforms representative baselines in both self-supervised link prediction (improving the discrete edge reconstructors by at most 20%) and node classification on numerous datasets, solely with a structure-learning pretext. Our implementation is available at https://github.com/Newiz430/Bandana.

Guiyao Tie, Zeli Zhao, Dingjie Song et al.

The emergence of Large Language Models (LLMs) has fundamentally transformed natural language processing, making them indispensable across domains ranging from conversational systems to scientific exploration. However, their pre-trained architectures often reveal limitations in specialized contexts, including restricted reasoning capacities, ethical uncertainties, and suboptimal domain-specific performance. These challenges necessitate advanced post-training language models (PoLMs) to address these shortcomings, such as OpenAI-o1/o3 and DeepSeek-R1 (collectively known as Large Reasoning Models, or LRMs). This paper presents the first comprehensive survey of PoLMs, systematically tracing their evolution across five core paradigms: Fine-tuning, which enhances task-specific accuracy; Alignment, which ensures ethical coherence and alignment with human preferences; Reasoning, which advances multi-step inference despite challenges in reward design; Efficiency, which optimizes resource utilization amidst increasing complexity; Integration and Adaptation, which extend capabilities across diverse modalities while addressing coherence issues. Charting progress from ChatGPT's alignment strategies to DeepSeek-R1's innovative reasoning advancements, we illustrate how PoLMs leverage datasets to mitigate biases, deepen reasoning capabilities, and enhance domain adaptability. Our contributions include a pioneering synthesis of PoLM evolution, a structured taxonomy categorizing techniques and datasets, and a strategic agenda emphasizing the role of LRMs in improving reasoning proficiency and domain flexibility. As the first survey of its scope, this work consolidates recent PoLM advancements and establishes a rigorous intellectual framework for future research, fostering the development of LLMs that excel in precision, ethical robustness, and versatility across scientific and societal applications.

Yingqian Cui, Jie Ren, Pengfei He et al.

We present a theoretical analysis of the performance of transformer with softmax attention in in-context learning with linear regression tasks. While the existing literature predominantly focuses on the convergence of transformers with single-/multi-head attention, our research centers on comparing their performance. We conduct an exact theoretical analysis to demonstrate that multi-head attention with a substantial embedding dimension performs better than single-head attention. When the number of in-context examples D increases, the prediction loss using single-/multi-head attention is in O(1/D), and the one for multi-head attention has a smaller multiplicative constant. In addition to the simplest data distribution setting, we consider more scenarios, e.g., noisy labels, local examples, correlated features, and prior knowledge. We observe that, in general, multi-head attention is preferred over single-head attention. Our results verify the effectiveness of the design of multi-head attention in the transformer architecture.

Shenglai Zeng, Jiankun Zhang, Bingheng Li et al.

Retrieval-Augmented Generation (RAG) systems have shown promise in enhancing the performance of Large Language Models (LLMs). However, these systems face challenges in effectively integrating external knowledge with the LLM's internal knowledge, often leading to issues with misleading or unhelpful information. This work aims to provide a systematic study on knowledge checking in RAG systems. We conduct a comprehensive analysis of LLM representation behaviors and demonstrate the significance of using representations in knowledge checking. Motivated by the findings, we further develop representation-based classifiers for knowledge filtering. We show substantial improvements in RAG performance, even when dealing with noisy knowledge databases. Our study provides new insights into leveraging LLM representations for enhancing the reliability and effectiveness of RAG systems.

Soo Yong Lee, Sunwoo Kim, Fanchen Bu et al.

How would randomly shuffling feature vectors among nodes from the same class affect graph neural networks (GNNs)? The feature shuffle, intuitively, perturbs the dependence between graph topology and features (A-X dependence) for GNNs to learn from. Surprisingly, we observe a consistent and significant improvement in GNN performance following the feature shuffle. Having overlooked the impact of A-X dependence on GNNs, the prior literature does not provide a satisfactory understanding of the phenomenon. Thus, we raise two research questions. First, how should A-X dependence be measured, while controlling for potential confounds? Second, how does A-X dependence affect GNNs? In response, we (i) propose a principled measure for A-X dependence, (ii) design a random graph model that controls A-X dependence, (iii) establish a theory on how A-X dependence relates to graph convolution, and (iv) present empirical analysis on real-world graphs that align with the theory. We conclude that A-X dependence mediates the effect of graph convolution, such that smaller dependence improves GNN-based node classification.

Jingzhe Liu, Haitao Mao, Zhikai Chen et al.

Graph Neural Networks (GNNs) have emerged as a powerful tool to capture intricate network patterns, achieving success across different domains. However, existing GNNs require careful domain-specific architecture designs and training from scratch on each dataset, leading to an expertise-intensive process with difficulty in generalizing across graphs from different domains. Therefore, it can be hard for practitioners to infer which GNN model can generalize well to graphs from their domains. To address this challenge, we propose a novel cross-domain pretraining framework, "one model for one graph," which overcomes the limitations of previous approaches that failed to use a single GNN to capture diverse graph patterns across domains with significant gaps. Specifically, we pretrain a bank of expert models, with each one corresponding to a specific dataset. When inferring to a new graph, gating functions choose a subset of experts to effectively integrate prior model knowledge while avoiding negative transfer. Extensive experiments consistently demonstrate the superiority of our proposed method on both link prediction and node classification tasks.

Pengfei He, Zitao Li, Yue Xing et al.

Zero-shot reasoning methods with Large Language Models (LLMs) offer significant advantages including great generalization to novel tasks and reduced dependency on human-crafted examples. However, the current zero-shot methods still have limitations in complex tasks, e.g., answering questions that require multi-step reasoning. In this paper, we address this limitation by introducing a novel structure-oriented analysis method to help LLMs better understand the question and guide the problem-solving process of LLMs. We first demonstrate how the existing reasoning strategies, Chain-of-Thought and ReAct, can benefit from our structure-oriented analysis. In addition to empirical investigations, we leverage the probabilistic graphical model to theoretically explain why our structure-oriented analysis can improve the LLM reasoning process. To further improve the reliability in complex question-answering tasks, we propose a multi-agent reasoning system, Structure-oriented Autonomous Reasoning Agents (SARA), that can better enforce the reasoning process following our structure-oriented analysis by refinement techniques and is equipped with external knowledge retrieval capability to reduce factual errors. Extensive experiments verify the effectiveness of the proposed reasoning system. Surprisingly, in some cases, the system even surpasses few-shot methods. Finally, the system not only improves reasoning accuracy in complex tasks but also demonstrates robustness against potential attacks that corrupt the reasoning process.

Pengfei He, Zhenwei Dai, Bing He et al.

Large language model (LLM)-based agents increasingly rely on tool use to complete real-world tasks. While existing works evaluate the LLMs' tool use capability, they largely focus on the final answers yet overlook the detailed tool usage trajectory, i.e., whether tools are selected, parameterized, and ordered correctly. We introduce TRAJECT-Bench, a trajectory-aware benchmark to comprehensively evaluate LLMs' tool use capability through diverse tasks with fine-grained evaluation metrics. TRAJECT-Bench pairs high-fidelity, executable tools across practical domains with tasks grounded in production-style APIs, and synthesizes trajectories that vary in breadth (parallel calls) and depth (interdependent chains). Besides final accuracy, TRAJECT-Bench also reports trajectory-level diagnostics, including tool selection and argument correctness, and dependency/order satisfaction. Analyses reveal failure modes such as similar tool confusion and parameter-blind selection, and scaling behavior with tool diversity and trajectory length where the bottleneck of transiting from short to mid-length trajectories is revealed, offering actionable guidance for LLMs' tool use.

Jingzhe Liu, Liam Collins, Jiliang Tang et al.

Recent advancements in generative models have allowed the emergence of a promising paradigm for recommender systems (RS), known as Generative Recommendation (GR), which tries to unify rich item semantics and collaborative filtering signals. One popular modern approach is to use semantic IDs (SIDs), which are discrete codes quantized from the embeddings of modality encoders (e.g., large language or vision models), to represent items in an autoregressive user interaction sequence modeling setup (henceforth, SID-based GR). While generative models in other domains exhibit well-established scaling laws, our work reveals that SID-based GR shows significant bottlenecks while scaling up the model. In particular, the performance of SID-based GR quickly saturates as we enlarge each component: the modality encoder, the quantization tokenizer, and the RS itself. In this work, we identify the limited capacity of SIDs to encode item semantic information as one of the fundamental bottlenecks. Motivated by this observation, as an initial effort to obtain GR models with better scaling behaviors, we revisit another GR paradigm that directly uses large language models (LLMs) as recommenders (henceforth, LLM-as-RS). Our experiments show that the LLM-as-RS paradigm has superior model scaling properties and achieves up to 20 percent improvement over the best achievable performance of SID-based GR through scaling. We also challenge the prevailing belief that LLMs struggle to capture collaborative filtering information, showing that their ability to model user-item interactions improves as LLMs scale up. Our analyses on both SID-based GR and LLMs across model sizes from 44M to 14B parameters underscore the intrinsic scaling limits of SID-based GR and position LLM-as-RS as a promising path toward foundation models for GR.

Quang Truong, Zhikai Chen, Mingxuan Ju et al.

Relational databases underpin critical infrastructure across a wide range of domains, yet the design of generalizable pre-training strategies for learning from relational databases remains an open challenge due to task heterogeneity. Specifically, there exist infinitely many possible downstream tasks, as tasks are defined based on relational schema graphs, temporal dependencies, and SQL-defined label logics. An effective pre-training framework is desired to take these factors into account in order to obtain task-aware representations. By incorporating knowledge of the underlying distribution that drives label generation, downstream tasks can benefit from relevant side-channel information. To bridge this gap, we introduce Task Vector Estimation (TVE), a novel pre-training framework that constructs predictive supervisory signals via set-based aggregation over schema traversal graphs, explicitly modeling next-window relational dynamics. We formalize our approach through an information-theoretic lens, demonstrating that task-informed representations retain more relevant signals than those obtained without task priors. Extensive experiments on the RelBench benchmark show that TVE consistently outperforms traditional pre-training baselines. Our findings advocate for pre-training objectives that encode task heterogeneity and temporal structure as design principles for predictive modeling on relational databases.

Guangliang Liu, Haitao Mao, Bochuan Cao et al.

Large Language Models (LLMs) are able to improve their responses when instructed to do so, a capability known as self-correction. When instructions provide only the task's goal without specific details about potential issues in the response, LLMs must rely on their internal knowledge to improve response quality, a process referred to as intrinsic self-correction. The empirical success of intrinsic self-correction is evident in various applications, but how and why it is effective remains unknown. In this paper, we unveil that intrinsic self-correction can be progressively improved, allowing it to approach a converged state. Our findings are verified in: (1) the scenario of multi-round question answering, by comprehensively demonstrating that intrinsic self-correction can progressively introduce performance gains through iterative interactions, ultimately converging to stable performance; and (2) the context of intrinsic self-correction for enhanced morality, in which we provide empirical evidence that iteratively applying instructions reduces model uncertainty towards convergence, which then leads to convergence of both the calibration error and self-correction performance, ultimately resulting in a stable state of intrinsic self-correction. Furthermore, we introduce a mathematical formulation and a simulation task indicating that the latent concepts activated by self-correction instructions drive the reduction of model uncertainty. Based on our experimental results and analysis of the convergence of intrinsic self-correction, we reveal its underlying mechanism: consistent injected instructions reduce model uncertainty which yields converged, improved performance.

Wenzhuo Tang, Haitao Mao, Danial Dervovic et al.

Models for natural language and images benefit from data scaling behavior: the more data fed into the model, the better they perform. This 'better with more' phenomenon enables the effectiveness of large-scale pre-training on vast amounts of data. However, current graph pre-training methods struggle to scale up data due to heterogeneity across graphs. To achieve effective data scaling, we aim to develop a general model that is able to capture diverse data patterns of graphs and can be utilized to adaptively help the downstream tasks. To this end, we propose UniAug, a universal graph structure augmentor built on a diffusion model. We first pre-train a discrete diffusion model on thousands of graphs across domains to learn the graph structural patterns. In the downstream phase, we provide adaptive enhancement by conducting graph structure augmentation with the help of the pre-trained diffusion model via guided generation. By leveraging the pre-trained diffusion model for structure augmentation, we consistently achieve performance improvements across various downstream tasks in a plug-and-play manner. To the best of our knowledge, this study represents the first demonstration of a data-scaling graph structure augmentor on graphs across domains.

Makoto Yamada, Jiliang Tang, Jose Lugo-Martinez et al.

Machine learning methods are used to discover complex nonlinear relationships in biological and medical data. However, sophisticated learning models are computationally unfeasible for data with millions of features. Here we introduce the first feature selection method for nonlinear learning problems that can scale up to large, ultra-high dimensional biological data. More specifically, we scale up the novel Hilbert-Schmidt Independence Criterion Lasso (HSIC Lasso) to handle millions of features with tens of thousand samples. The proposed method is guaranteed to find an optimal subset of maximally predictive features with minimal redundancy, yielding higher predictive power and improved interpretability. Its effectiveness is demonstrated through applications to classify phenotypes based on module expression in human prostate cancer patients and to detect enzymes among protein structures. We achieve high accuracy with as few as 20 out of one million features --- a dimensionality reduction of 99.998%. Our algorithm can be implemented on commodity cloud computing platforms. The dramatic reduction of features may lead to the ubiquitous deployment of sophisticated prediction models in mobile health care applications.

Yilin Wang, Suhang Wang, Jiliang Tang et al.

Understanding human actions in wild videos is an important task with a broad range of applications. In this paper we propose a novel approach named Hierarchical Attention Network (HAN), which enables to incorporate static spatial information, short-term motion information and long-term video temporal structures for complex human action understanding. Compared to recent convolutional neural network based approaches, HAN has following advantages (1) HAN can efficiently capture video temporal structures in a longer range; (2) HAN is able to reveal temporal transitions between frame chunks with different time steps, i.e. it explicitly models the temporal transitions between frames as well as video segments and (3) with a multiple step spatial temporal attention mechanism, HAN automatically learns important regions in video frames and temporal segments in the video. The proposed model is trained and evaluated on the standard video action benchmarks, i.e., UCF-101 and HMDB-51, and it significantly outperforms the state-of-the arts