Yijun Tian

Yijun Tian, Kaiwen Dong, Chunhui Zhang et al.

Generative self-supervised learning (SSL), especially masked autoencoders, has become one of the most exciting learning paradigms and has shown great potential in handling graph data. However, real-world graphs are always heterogeneous, which poses three critical challenges that existing methods ignore: 1) how to capture complex graph structure? 2) how to incorporate various node attributes? and 3) how to encode different node positions? In light of this, we study the problem of generative SSL on heterogeneous graphs and propose HGMAE, a novel heterogeneous graph masked autoencoder model to address these challenges. HGMAE captures comprehensive graph information via two innovative masking techniques and three unique training strategies. In particular, we first develop metapath masking and adaptive attribute masking with dynamic mask rate to enable effective and stable learning on heterogeneous graphs. We then design several training strategies including metapath-based edge reconstruction to adopt complex structural information, target attribute restoration to incorporate various node attributes, and positional feature prediction to encode node positional information. Extensive experiments demonstrate that HGMAE outperforms both contrastive and generative state-of-the-art baselines on several tasks across multiple datasets. Codes are available at https://github.com/meettyj/HGMAE.

Yijun Tian, Huan Song, Zichen Wang et al.

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

Yihong Ma, Yijun Tian, Nuno Moniz et al.

The rapid advancement in data-driven research has increased the demand for effective graph data analysis. However, real-world data often exhibits class imbalance, leading to poor performance of machine learning models. To overcome this challenge, class-imbalanced learning on graphs (CILG) has emerged as a promising solution that combines the strengths of graph representation learning and class-imbalanced learning. In recent years, significant progress has been made in CILG. Anticipating that such a trend will continue, this survey aims to offer a comprehensive understanding of the current state-of-the-art in CILG and provide insights for future research directions. Concerning the former, we introduce the first taxonomy of existing work and its connection to existing imbalanced learning literature. Concerning the latter, we critically analyze recent work in CILG and discuss urgent lines of inquiry within the topic. Moreover, we provide a continuously maintained reading list of papers and code at https://github.com/yihongma/CILG-Papers.

Yijun Tian, Chuxu Zhang, Zhichun Guo et al.

Recipe recommendation systems play an essential role in helping people decide what to eat. Existing recipe recommendation systems typically focused on content-based or collaborative filtering approaches, ignoring the higher-order collaborative signal such as relational structure information among users, recipes and food items. In this paper, we formalize the problem of recipe recommendation with graphs to incorporate the collaborative signal into recipe recommendation through graph modeling. In particular, we first present URI-Graph, a new and large-scale user-recipe-ingredient graph. We then propose RecipeRec, a novel heterogeneous graph learning model for recipe recommendation. The proposed model can capture recipe content and collaborative signal through a heterogeneous graph neural network with hierarchical attention and an ingredient set transformer. We also introduce a graph contrastive augmentation strategy to extract informative graph knowledge in a self-supervised manner. Finally, we design a joint objective function of recommendation and contrastive learning to optimize the model. Extensive experiments demonstrate that RecipeRec outperforms state-of-the-art methods for recipe recommendation. Dataset and codes are available at https://github.com/meettyj/RecipeRec.

Yijun Tian, Chuxu Zhang, Zhichun Guo et al.

Learning effective recipe representations is essential in food studies. Unlike what has been developed for image-based recipe retrieval or learning structural text embeddings, the combined effect of multi-modal information (i.e., recipe images, text, and relation data) receives less attention. In this paper, we formalize the problem of multi-modal recipe representation learning to integrate the visual, textual, and relational information into recipe embeddings. In particular, we first present Large-RG, a new recipe graph data with over half a million nodes, making it the largest recipe graph to date. We then propose Recipe2Vec, a novel graph neural network based recipe embedding model to capture multi-modal information. Additionally, we introduce an adversarial attack strategy to ensure stable learning and improve performance. Finally, we design a joint objective function of node classification and adversarial learning to optimize the model. Extensive experiments demonstrate that Recipe2Vec outperforms state-of-the-art baselines on two classic food study tasks, i.e., cuisine category classification and region prediction. Dataset and codes are available at https://github.com/meettyj/Recipe2Vec.

Yijun Tian, Chuxu Zhang, Zhichun Guo et al.

While Graph Neural Networks (GNNs) have demonstrated their efficacy in dealing with non-Euclidean structural data, they are difficult to be deployed in real applications due to the scalability constraint imposed by multi-hop data dependency. Existing methods attempt to address this scalability issue by training multi-layer perceptrons (MLPs) exclusively on node content features using labels derived from trained GNNs. Even though the performance of MLPs can be significantly improved, two issues prevent MLPs from outperforming GNNs and being used in practice: the ignorance of graph structural information and the sensitivity to node feature noises. In this paper, we propose to learn NOise-robust Structure-aware MLPs On Graphs (NOSMOG) to overcome the challenges. Specifically, we first complement node content with position features to help MLPs capture graph structural information. We then design a novel representational similarity distillation strategy to inject structural node similarities into MLPs. Finally, we introduce the adversarial feature augmentation to ensure stable learning against feature noises and further improve performance. Extensive experiments demonstrate that NOSMOG outperforms GNNs and the state-of-the-art method in both transductive and inductive settings across seven datasets, while maintaining a competitive inference efficiency. Codes are available at https://github.com/meettyj/NOSMOG.

Zheyuan Liu, Guangyao Dou, Zhaoxuan Tan et al.

Generative AI technologies have been deployed in many places, such as (multimodal) large language models and vision generative models. Their remarkable performance should be attributed to massive training data and emergent reasoning abilities. However, the models would memorize and generate sensitive, biased, or dangerous information originated from the training data especially those from web crawl. New machine unlearning (MU) techniques are being developed to reduce or eliminate undesirable knowledge and its effects from the models, because those that were designed for traditional classification tasks could not be applied for Generative AI. We offer a comprehensive survey on many things about MU in Generative AI, such as a new problem formulation, evaluation methods, and a structured discussion on the advantages and limitations of different kinds of MU techniques. It also presents several critical challenges and promising directions in MU research. A curated list of readings can be found: https://github.com/franciscoliu/GenAI-MU-Reading.

Zheyuan Liu, Guangyao Dou, Yijun Tian et al.

Machine Unlearning (MU) algorithms have become increasingly critical due to the imperative adherence to data privacy regulations. The primary objective of MU is to erase the influence of specific data samples on a given model without the need to retrain it from scratch. Accordingly, existing methods focus on maximizing user privacy protection. However, there are different degrees of privacy regulations for each real-world web-based application. Exploring the full spectrum of trade-offs between privacy, model utility, and runtime efficiency is critical for practical unlearning scenarios. Furthermore, designing the MU algorithm with simple control of the aforementioned trade-off is desirable but challenging due to the inherent complex interaction. To address the challenges, we present Controllable Machine Unlearning (ConMU), a novel framework designed to facilitate the calibration of MU. The ConMU framework contains three integral modules: an important data selection module that reconciles the runtime efficiency and model generalization, a progressive Gaussian mechanism module that balances privacy and model generalization, and an unlearning proxy that controls the trade-offs between privacy and runtime efficiency. Comprehensive experiments on various benchmark datasets have demonstrated the robust adaptability of our control mechanism and its superiority over established unlearning methods. ConMU explores the full spectrum of the Privacy-Utility-Efficiency trade-off and allows practitioners to account for different real-world regulations. Source code available at: https://github.com/guangyaodou/ConMU.

Zhichun Guo, Kehan Guo, Bozhao Nan et al.

Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top of which the downstream tasks (e.g., property prediction) can be performed. Recently, MRL has achieved considerable progress, especially in methods based on deep molecular graph learning. In this survey, we systematically review these graph-based molecular representation techniques, especially the methods incorporating chemical domain knowledge. Specifically, we first introduce the features of 2D and 3D molecular graphs. Then we summarize and categorize MRL methods into three groups based on their input. Furthermore, we discuss some typical chemical applications supported by MRL. To facilitate studies in this fast-developing area, we also list the benchmarks and commonly used datasets in the paper. Finally, we share our thoughts on future research directions.

Yijun Tian, Shichao Pei, Xiangliang Zhang et al.

Graph Neural Networks (GNNs) have attracted tremendous attention by demonstrating their capability to handle graph data. However, they are difficult to be deployed in resource-limited devices due to model sizes and scalability constraints imposed by the multi-hop data dependency. In addition, real-world graphs usually possess complex structural information and features. Therefore, to improve the applicability of GNNs and fully encode the complicated topological information, knowledge distillation on graphs (KDG) has been introduced to build a smaller yet effective model and exploit more knowledge from data, leading to model compression and performance improvement. Recently, KDG has achieved considerable progress with many studies proposed. In this survey, we systematically review these works. Specifically, we first introduce KDG challenges and bases, then categorize and summarize existing works of KDG by answering the following three questions: 1) what to distillate, 2) who to whom, and 3) how to distillate. Finally, we share our thoughts on future research directions.

Zhichun Guo, Chunhui Zhang, Yujie Fan et al.

Graph neural networks (GNNs) have shown remarkable performance on diverse graph mining tasks. Although different GNNs can be unified as the same message passing framework, they learn complementary knowledge from the same graph. Knowledge distillation (KD) is developed to combine the diverse knowledge from multiple models. It transfers knowledge from high-capacity teachers to a lightweight student. However, to avoid oversmoothing, GNNs are often shallow, which deviates from the setting of KD. In this context, we revisit KD by separating its benefits from model compression and emphasizing its power of transferring knowledge. To this end, we need to tackle two challenges: how to transfer knowledge from compact teachers to a student with the same capacity; and, how to exploit student GNN's own strength to learn knowledge. In this paper, we propose a novel adaptive KD framework, called BGNN, which sequentially transfers knowledge from multiple GNNs into a student GNN. We also introduce an adaptive temperature module and a weight boosting module. These modules guide the student to the appropriate knowledge for effective learning. Extensive experiments have demonstrated the effectiveness of BGNN. In particular, we achieve up to 3.05% improvement for node classification and 6.35% improvement for graph classification over vanilla GNNs.

Peiyu Li, Xiaobao Huang, Yijun Tian et al.

Significant work has been conducted in the domain of food computing, yet these studies typically focus on single tasks such as t2t (instruction generation from food titles and ingredients), i2t (recipe generation from food images), or t2i (food image generation from recipes). None of these approaches integrate all modalities simultaneously. To address this gap, we introduce a novel food computing foundation model that achieves true multimodality, encompassing tasks such as t2t, t2i, i2t, it2t, and t2ti. By leveraging large language models (LLMs) and pre-trained image encoder and decoder models, our model can perform a diverse array of food computing-related tasks, including food understanding, food recognition, recipe generation, and food image generation. Compared to previous models, our foundation model demonstrates a significantly broader range of capabilities and exhibits superior performance, particularly in food image generation and recipe generation tasks. We open-sourced ChefFusion at GitHub.

Kaiwen Dong, Yijun Tian, Zhichun Guo et al.

Link prediction is a crucial problem in graph-structured data. Due to the recent success of graph neural networks (GNNs), a variety of GNN-based models were proposed to tackle the link prediction task. Specifically, GNNs leverage the message passing paradigm to obtain node representation, which relies on link connectivity. However, in a link prediction task, links in the training set are always present while ones in the testing set are not yet formed, resulting in a discrepancy of the connectivity pattern and bias of the learned representation. It leads to a problem of dataset shift which degrades the model performance. In this paper, we first identify the dataset shift problem in the link prediction task and provide theoretical analyses on how existing link prediction methods are vulnerable to it. We then propose FakeEdge, a model-agnostic technique, to address the problem by mitigating the graph topological gap between training and testing sets. Extensive experiments demonstrate the applicability and superiority of FakeEdge on multiple datasets across various domains.

Chunhui Zhang, Chao Huang, Yijun Tian et al.

Even pruned by the state-of-the-art network compression methods, Graph Neural Networks (GNNs) training upon non-Euclidean graph data often encounters relatively higher time costs, due to its irregular and nasty density properties, compared with data in the regular Euclidean space. Another natural property concomitantly with graph is class-imbalance which cannot be alleviated by the massive graph data while hindering GNNs' generalization. To fully tackle these unpleasant properties, (i) theoretically, we introduce a hypothesis about what extent a subset of the training data can approximate the full dataset's learning effectiveness. The effectiveness is further guaranteed and proved by the gradients' distance between the subset and the full set; (ii) empirically, we discover that during the learning process of a GNN, some samples in the training dataset are informative for providing gradients to update model parameters. Moreover, the informative subset is not fixed during training process. Samples that are informative in the current training epoch may not be so in the next one. We also notice that sparse subnets pruned from a well-trained GNN sometimes forget the information provided by the informative subset, reflected in their poor performances upon the subset. Based on these findings, we develop a unified data-model dynamic sparsity framework named Graph Decantation (GraphDec) to address challenges brought by training upon a massive class-imbalanced graph data. The key idea of GraphDec is to identify the informative subset dynamically during the training process by adopting sparse graph contrastive learning. Extensive experiments on benchmark datasets demonstrate that GraphDec outperforms baselines for graph and node tasks, with respect to classification accuracy and data usage efficiency.

Xiaoxin He, Yijun Tian, Yifei Sun et al.

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

Ziming Li, Xiaoming Wu, Zehong Wang et al.

Graphs provide a natural representation of relational structure that arises across diverse domains. Despite this ubiquity, graph structure is typically learned in a modality- and task-isolated manner, where graph representations are constructed within individual task contexts and discarded thereafter. As a result, structural regularities across modalities and tasks are repeatedly reconstructed rather than accumulated at the level of intermediate graph representations. This motivates a representation-learning question: how should graph structure be organized so that it can persist and accumulate across heterogeneous modalities and tasks? We adopt a representation-centric perspective in which graph structure is treated as a structural substrate that persists across learning contexts. To instantiate this perspective, we propose G-Substrate, a graph substrate framework that organizes learning around shared graph structures. G-Substrate comprises two complementary mechanisms: a unified structural schema that ensures compatibility among graph representations across heterogeneous modalities and tasks, and an interleaved role-based training strategy that exposes the same graph structure to multiple functional roles during learning. Experiments across multiple domains, modalities, and tasks show that G-Substrate outperforms task-isolated and naive multi-task learning methods.

Wenqian Ye, Bo Yuan, Zhichao Xu et al.

We study a class of emergent misalignment in multi-agent systems (MAS), with a focus on automated workflows, which we refer to agentic misalignment. Although these systems can solve complex tasks, they often fail because agents act according to implicit proxy utilities that do not align with the intended human goals. We formally define these behaviors and analyze them within a Bayesian framework, showing that generic utilities naturally lead to posterior collapse of agents in automated workflows. To address this issue, we propose Agentic Evidence Attribution (AEA), a novel alignment paradigm that improves agent posteriors using context-specific evidence. AEA reasons over agent actions and provides structured evidence to correct misaligned behavior during collaboration. To better understand the role of evidence, we study two instantiations of AEA: self-reflection (internal evidence from the model) and weak-to-strong generalization (external evidence on the agentic trajectory). We show that a small evidence model effectively aligns the MAS by providing orthogonal failure attribution. Our results clarify the sources of agentic misalignment in automated workflows and show that evidence-based alignment can effectively improve agent collaboration and leads to reliable multi-agent systems built on automated workflows.

Jiongxiao Wang, Qiaojing Yan, Yawei Wang et al.

Large Language Model (LLM)-based agents have demonstrated remarkable capabilities in complex reasoning and multi-turn interactions but struggle to continuously improve and adapt when deployed in new environments. One promising approach is implementing skill libraries that allow agents to learn, validate, and apply new skills. However, current skill library approaches rely primarily on LLM prompting, making consistent skill library implementation challenging. To overcome these challenges, we propose a Reinforcement Learning (RL)-based approach to enhance agents' self-improvement capabilities with a skill library. Specifically, we introduce Skill Augmented GRPO for self-Evolution (SAGE), a novel RL framework that systematically incorporates skills into learning. The framework's key component, Sequential Rollout, iteratively deploys agents across a chain of similar tasks for each rollout. As agents navigate through the task chain, skills generated from previous tasks accumulate in the library and become available for subsequent tasks. Additionally, the framework enhances skill generation and utilization through a Skill-integrated Reward that complements the original outcome-based rewards. Experimental results on AppWorld demonstrate that SAGE, when applied to supervised-finetuned model with expert experience, achieves 8.9% higher Scenario Goal Completion while requiring 26% fewer interaction steps and generating 59% fewer tokens, substantially outperforming existing approaches in both accuracy and efficiency.

Yijun Tian, Yikun Han, Xiusi Chen et al.

Transferring the reasoning capability from stronger large language models (LLMs) to smaller ones has been quite appealing, as smaller LLMs are more flexible to deploy with less expense. Among the existing solutions, knowledge distillation stands out due to its outstanding efficiency and generalization. However, existing methods suffer from several drawbacks, including limited knowledge diversity and the lack of rich contextual information. To solve the problems and facilitate the learning of compact language models, we propose TinyLLM, a new knowledge distillation paradigm to learn a small student LLM from multiple large teacher LLMs. In particular, we encourage the student LLM to not only generate the correct answers but also understand the rationales behind these answers. Given that different LLMs possess diverse reasoning skills, we guide the student model to assimilate knowledge from various teacher LLMs. We further introduce an in-context example generator and a teacher-forcing Chain-of-Thought strategy to ensure that the rationales are accurate and grounded in contextually appropriate scenarios. Extensive experiments on six datasets across two reasoning tasks demonstrate the superiority of our method. Results show that TinyLLM can outperform large teacher LLMs significantly, despite a considerably smaller model size. The source code is available at: https://github.com/YikunHan42/TinyLLM.

Lincan Li, Wei Shao, Wei Dong et al.

The aspiration of the next generation's autonomous driving (AD) technology relies on the dedicated integration and interaction among intelligent perception, prediction, planning, and low-level control. There has been a huge bottleneck regarding the upper bound of autonomous driving algorithm performance, a consensus from academia and industry believes that the key to surmount the bottleneck lies in data-centric autonomous driving technology. Recent advancement in AD simulation, closed-loop model training, and AD big data engine have gained some valuable experience. However, there is a lack of systematic knowledge and deep understanding regarding how to build efficient data-centric AD technology for AD algorithm self-evolution and better AD big data accumulation. To fill in the identified research gaps, this article will closely focus on reviewing the state-of-the-art data-driven autonomous driving technologies, with an emphasis on the comprehensive taxonomy of autonomous driving datasets characterized by milestone generations, key features, data acquisition settings, etc. Furthermore, we provide a systematic review of the existing benchmark closed-loop AD big data pipelines from the industrial frontier, including the procedure of closed-loop frameworks, key technologies, and empirical studies. Finally, the future directions, potential applications, limitations and concerns are discussed to arouse efforts from both academia and industry for promoting the further development of autonomous driving. The project repository is available at: https://github.com/LincanLi98/Awesome-Data-Centric-Autonomous-Driving.

Zheyuan Liu, Guangyao Dou, Zhaoxuan Tan et al.

The rapid advancement of Large Language Models (LLMs) has demonstrated their vast potential across various domains, attributed to their extensive pretraining knowledge and exceptional generalizability. However, LLMs often encounter challenges in generating harmful content when faced with problematic prompts. To address this problem, existing work attempted to implement a gradient ascent based approach to prevent LLMs from producing harmful output. While these methods can be effective, they frequently impact the model utility in responding to normal prompts. To address this gap, we introduce Selective Knowledge negation Unlearning (SKU), a novel unlearning framework for LLMs, designed to eliminate harmful knowledge while preserving utility on normal prompts. Specifically, SKU is consisted of two stages: harmful knowledge acquisition stage and knowledge negation stage. The first stage aims to identify and acquire harmful knowledge within the model, whereas the second is dedicated to remove this knowledge. SKU selectively isolates and removes harmful knowledge in model parameters, ensuring the model's performance remains robust on normal prompts. Our experiments conducted across various LLM architectures demonstrate that SKU identifies a good balance point between removing harmful information and preserving utility.

Tianyu Yang, Terry Ruas, Yijun Tian et al.

Vision-language models (VLMs) excel at interpreting text-rich images but struggle with long, visually complex documents that demand analysis and integration of information spread across multiple pages. Existing approaches typically rely on fixed reasoning templates or rigid pipelines, which force VLMs into a passive role and hinder both efficiency and generalization. We present Active Long-DocumEnt Navigation (ALDEN), a multi-turn reinforcement learning framework that fine-tunes VLMs as interactive agents capable of actively navigating long, visually rich documents. ALDEN introduces a novel fetch action that directly accesses the page by index, complementing the classic search action and better exploiting document structure. For dense process supervision and efficient training, we propose a rule-based cross-level reward that provides both turn- and token-level signals. To address the empirically observed training instability caused by numerous visual tokens from long documents, we further propose a visual-semantic anchoring mechanism that applies a dual-path KL-divergence constraint to stabilize visual and textual representations separately during training. Trained on a corpus constructed from three open-source datasets, ALDEN achieves state-of-the-art performance on five long-document benchmarks. Overall, ALDEN marks a step beyond passive document reading toward agents that autonomously navigate and reason across long, visually rich documents, offering a robust path to more accurate and efficient long-document understanding.

Zhichao Xu, Minheng Wang, Yawei Wang et al.

Retrieval-augmented generation (RAG) systems trained using reinforcement learning (RL) with reasoning are hampered by inefficient context management, where long, noisy retrieved documents increase costs and degrade performance. We introduce RECON (REasoning with CONdensation), a framework that integrates an explicit summarization module to compress evidence within the reasoning loop. Our summarizer is trained via a two-stage process: relevance pretraining on QA datasets, followed by multi-aspect distillation from proprietary LLMs to ensure factuality and clarity. Integrated into the Search-R1 pipeline, RECON reduces total context length by 35\%, leading to improved training speed and inference latency, while simultaneously improving RAG performance on downstream QA benchmarks. Notably, it boosts the average EM score of the 3B model by 14.5\% and the 7B model by 3.0\%, showing particular strength in multi-hop QA. RECON demonstrates that learned context compression is essential for building practical, scalable, and performant RAG systems. Our code implementation is made available at https://github.com/allfornancy/RECON.

Zhaoxuan Tan, Qingkai Zeng, Yijun Tian et al.

Personalization in large language models (LLMs) is increasingly important, aiming to align the LLMs' interactions, content, and recommendations with individual user preferences. Recent advances have highlighted effective prompt design by enriching user queries with non-parametric knowledge through behavior history retrieval and textual profiles. However, these methods faced limitations due to a lack of model ownership, resulting in constrained customization and privacy issues, and often failed to capture complex, dynamic user behavior patterns. To address these shortcomings, we introduce One PEFT Per User (OPPU), employing personalized parameter-efficient fine-tuning (PEFT) modules to store user-specific behavior patterns and preferences. By plugging in personal PEFT parameters, users can own and use their LLMs individually. OPPU integrates parametric user knowledge in the personal PEFT parameters with non-parametric knowledge from retrieval and profiles, adapting LLMs to user behavior shifts. Experimental results demonstrate that OPPU significantly outperforms existing prompt-based methods across seven diverse tasks in the LaMP benchmark. Further studies reveal OPPU's enhanced capabilities in handling user behavior shifts, modeling users at different activity levels, maintaining robustness across various user history formats, and displaying versatility with different PEFT methods.

Wenqian Ye, Luyang Jiang, Eric Xie et al.

Back in the early 20th century, a horse named Hans appeared to perform arithmetic and other intellectual tasks during exhibitions in Germany, while it actually relied solely on involuntary cues in the body language from the human trainer. Modern machine learning models are no different. These models are known to be sensitive to spurious correlations between non-essential features of the inputs (e.g., background, texture, and secondary objects) and the corresponding labels. Such features and their correlations with the labels are known as "spurious" because they tend to change with shifts in real-world data distributions, which can negatively impact the model's generalization and robustness. In this paper, we provide a comprehensive survey of this emerging issue, along with a fine-grained taxonomy of existing state-of-the-art methods for addressing spurious correlations in machine learning models. Additionally, we summarize existing datasets, benchmarks, and metrics to facilitate future research. The paper concludes with a discussion of the broader impacts, the recent advancements, and future challenges in the era of generative AI, aiming to provide valuable insights for researchers in the related domains of the machine learning community.

Zheyuan Liu, Xiaoxin He, Yijun Tian et al.

Graph plays an important role in representing complex relationships in real-world applications such as social networks, biological data and citation networks. In recent years, Large Language Models (LLMs) have achieved tremendous success in various domains, which makes applying LLMs to graphs particularly appealing. However, directly applying LLMs to graph modalities presents unique challenges due to the discrepancy and mismatch between the graph and text modalities. Hence, to further investigate LLMs' potential for comprehending graph information, we introduce GraphPrompter, a novel framework designed to align graph information with LLMs via soft prompts. Specifically, GraphPrompter consists of two main components: a graph neural network to encode complex graph information and an LLM that effectively processes textual information. Comprehensive experiments on various benchmark datasets under node classification and link prediction tasks demonstrate the effectiveness of our proposed method. The GraphPrompter framework unveils the substantial capabilities of LLMs as predictors in graph-related tasks, enabling researchers to utilize LLMs across a spectrum of real-world graph scenarios more effectively.

Lirong Wu, Yijun Tian, Yufei Huang et al.

Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction. While existing methods rely heavily on protein sequence for PPI prediction, it is the protein structure that is the key to determine the interactions. To take both protein modalities into account, we define the microenvironment of an amino acid residue by its sequence and structural contexts, which describe the surrounding chemical properties and geometric features. In addition, microenvironments defined in previous work are largely based on experimentally assayed physicochemical properties, for which the "vocabulary" is usually extremely small. This makes it difficult to cover the diversity and complexity of microenvironments. In this paper, we propose Microenvironment-Aware Protein Embedding for PPI prediction (MPAE-PPI), which encodes microenvironments into chemically meaningful discrete codes via a sufficiently large microenvironment "vocabulary" (i.e., codebook). Moreover, we propose a novel pre-training strategy, namely Masked Codebook Modeling (MCM), to capture the dependencies between different microenvironments by randomly masking the codebook and reconstructing the input. With the learned microenvironment codebook, we can reuse it as an off-the-shelf tool to efficiently and effectively encode proteins of different sizes and functions for large-scale PPI prediction. Extensive experiments show that MAPE-PPI can scale to PPI prediction with millions of PPIs with superior trade-offs between effectiveness and computational efficiency than the state-of-the-art competitors.

Tianfan Peng, Yuntao Du, Pengzhou Ji et al.

Large multimodal models (LMMs) often suffer from severe inference inefficiency due to the large number of visual tokens introduced by image encoders. While recent token compression methods, such as pruning and merging, have shown promise in reducing redundancy, their evaluation remains fragmented and inconsistent. In this work, we present UniPruneBench, a unified and extensible benchmark for visual token pruning in multimodal LLMs. UniPruneBench provides standardized protocols across six ability dimensions and ten datasets, covering ten representative compression algorithms and three families of LMMs (LLaVA-v1.5, Intern-VL3, and Qwen2.5-VL). Beyond task accuracy, it incorporates system-level metrics such as runtime and prefilling latency to provide a holistic view. Our experiments uncover several key findings: (1) random pruning is a surprisingly strong baseline, (2) no single method consistently outperforms others across scenarios, (3) pruning sensitivity varies significantly across tasks, with OCR being most vulnerable, and (4) pruning ratio is the dominant factor governing performance degradation. We believe UniPruneBench will serve as a reliable foundation for future research on efficient multimodal modeling.

Lirong Wu, Yijun Tian, Haitao Lin et al.

Protein-protein bindings play a key role in a variety of fundamental biological processes, and thus predicting the effects of amino acid mutations on protein-protein binding is crucial. To tackle the scarcity of annotated mutation data, pre-training with massive unlabeled data has emerged as a promising solution. However, this process faces a series of challenges: (1) complex higher-order dependencies among multiple (more than paired) structural scales have not yet been fully captured; (2) it is rarely explored how mutations alter the local conformation of the surrounding microenvironment; (3) pre-training is costly, both in data size and computational burden. In this paper, we first construct a hierarchical prompt codebook to record common microenvironmental patterns at different structural scales independently. Then, we develop a novel codebook pre-training task, namely masked microenvironment modeling, to model the joint distribution of each mutation with their residue types, angular statistics, and local conformational changes in the microenvironment. With the constructed prompt codebook, we encode the microenvironment around each mutation into multiple hierarchical prompts and combine them to flexibly provide information to wild-type and mutated protein complexes about their microenvironmental differences. Such a hierarchical prompt learning framework has demonstrated superior performance and training efficiency over state-of-the-art pre-training-based methods in mutation effect prediction and a case study of optimizing human antibodies against SARS-CoV-2.

Zhichao Xu, Aosong Feng, Yijun Tian et al.

In recent years, dense retrieval has been the focus of information retrieval (IR) research. While effective, dense retrieval produces uninterpretable dense vectors, and suffers from the drawback of large index size. Learned sparse retrieval (LSR) has emerged as promising alternative, achieving competitive retrieval performance while also being able to leverage the classical inverted index data structure for efficient retrieval. However, limited works have explored scaling LSR beyond BERT scale. In this work, we identify two challenges in training large language models (LLM) for LSR: (1) training instability during the early stage of contrastive training; (2) suboptimal performance due to pre-trained LLM's unidirectional attention. To address these challenges, we propose two corresponding techniques: (1) a lightweight adaptation training phase to eliminate training instability; (2) two model variants to enable bidirectional information. With these techniques, we are able to train LSR models with 8B scale LLM, and achieve competitive retrieval performance with reduced index size. Furthermore, we are among the first to analyze the performance-efficiency tradeoff of LLM-based LSR model through the lens of model quantization. Our findings provide insights into adapting LLMs for efficient retrieval modeling.

Yijun Tian, Chuxu Zhang, Ziyi Kou et al.

Generative self-supervised learning on graphs, particularly graph masked autoencoders, has emerged as a popular learning paradigm and demonstrated its efficacy in handling non-Euclidean data. However, several remaining issues limit the capability of existing methods: 1) the disregard of uneven node significance in masking, 2) the underutilization of holistic graph information, 3) the ignorance of semantic knowledge in the representation space due to the exclusive use of reconstruction loss in the output space, and 4) the unstable reconstructions caused by the large volume of masked contents. In light of this, we propose UGMAE, a unified framework for graph masked autoencoders to address these issues from the perspectives of adaptivity, integrity, complementarity, and consistency. Specifically, we first develop an adaptive feature mask generator to account for the unique significance of nodes and sample informative masks (adaptivity). We then design a ranking-based structure reconstruction objective joint with feature reconstruction to capture holistic graph information and emphasize the topological proximity between neighbors (integrity). After that, we present a bootstrapping-based similarity module to encode the high-level semantic knowledge in the representation space, complementary to the low-level reconstruction in the output space (complementarity). Finally, we build a consistency assurance module to provide reconstruction objectives with extra stabilized consistency targets (consistency). Extensive experiments demonstrate that UGMAE outperforms both contrastive and generative state-of-the-art baselines on several tasks across multiple datasets.

Rui Lu, Jinhe Bi, Yunpu Ma et al.

Social media has evolved into a complex multimodal environment where text, images, and other signals interact to shape nuanced meanings, often concealing harmful intent. Identifying such intent, whether sarcasm, hate speech, or misinformation, remains challenging due to cross-modal contradictions, rapid cultural shifts, and subtle pragmatic cues. To address these challenges, we propose MV-Debate, a multi-view agent debate framework with dynamic reflection gating for unified multimodal harmful content detection. MV-Debate assembles four complementary debate agents, a surface analyst, a deep reasoner, a modality contrast, and a social contextualist, to analyze content from diverse interpretive perspectives. Through iterative debate and reflection, the agents refine responses under a reflection-gain criterion, ensuring both accuracy and efficiency. Experiments on three benchmark datasets demonstrate that MV-Debate significantly outperforms strong single-model and existing multi-agent debate baselines. This work highlights the promise of multi-agent debate in advancing reliable social intent detection in safety-critical online contexts.

Guande Wu, Huan Song, Yawei Wang et al.

Reasoning is increasingly crucial for various tasks. While chain-of-thought prompting enables large language models to leverage reasoning effectively, harnessing the reasoning capabilities of Vision-Language Models (VLMs) remains challenging. To solve this problem, we propose a novel self-distillation framework that enhances the reasoning capabilities of the model. The proposed framework introduces several key innovations. We start by employing a prompt library tailored to visual reasoning tasks to generate diverse in-context questions and utilize a two-step reasoning procedure to derive reasoning-guided responses. These responses are then used for self-distillation, enabling the model to internalize the reasoning process. Additionally, we improve the model architecture with several innovative components, including an intervention adapter for efficient parameter updates, a cross-modal skip connection to facilitate information exchange between modalities, and an ensemble learning algorithm to integrate diverse reasoning from multiple in-context questions. Extensive experiments show that our method significantly improves the baseline performance across five VQA datasets.

Zhichao Xu, Shengyao Zhuang, Crystina Zhang et al.

While dense retrieval models have become the standard for state-of-the-art information retrieval, their deployment is often constrained by high memory requirements and reliance on GPU accelerators for vector similarity search. Learned sparse retrieval offers a compelling alternative by enabling efficient search via inverted indices, yet it has historically received less attention than dense approaches. In this report, we introduce LACONIC, a family of learned sparse retrievers based on the Llama-3 architecture (1B, 3B, and 8B). We propose a streamlined two-phase training curriculum consisting of (1) weakly supervised pre-finetuning to adapt causal LLMs for bidirectional contextualization and (2) high-signal finetuning using curated hard negatives. Our results demonstrate that LACONIC effectively bridges the performance gap with dense models: the 8B variant achieves a state-of-the-art 60.2 nDCG on the MTEB Retrieval benchmark, ranking 15th on the leaderboard as of January 1, 2026, while utilizing 71\% less index memory than an equivalent dense model. By delivering high retrieval effectiveness on commodity CPU hardware with a fraction of the compute budget required by competing models, LACONIC provides a scalable and efficient solution for real-world search applications.

Jiazheng Li, Yawei Wang, David Yan et al.

Large Language Models (LLMs) have demonstrated remarkable capabilities, enabling language agents to excel at single-turn tasks. However, their application to complex, multi-step, and long-horizon tasks remains challenging. While reinforcement learning (RL) offers a promising avenue for addressing these challenges, mainstream approaches typically rely solely on sparse, outcome-based rewards, a limitation that becomes especially problematic for group-based RL algorithms lacking critic models, such as Group Relative Policy Optimization (GRPO). In such methods, uniformly rewarding or penalizing all actions within a trajectory can lead to training instability and suboptimal policies, because beneficial and detrimental actions are often entangled across multi-step interactions. To address this challenge, we propose SALT, a novel and lightweight framework that provides a finer-grained advantage assignment, derived solely from outcome rewards. We achieve this by constructing a graph from trajectories of the same prompt, which allows us to quantify the quality of each step and assign advantages accordingly. Crucially, SALT is designed as a plug-and-play module that seamlessly integrates with existing group-based RL algorithms, requiring no modifications to the rollout procedure and introducing negligible computational overhead. Extensive experiments on the WebShop, ALFWorld, and AppWorld benchmarks with various model sizes demonstrate that SALT consistently improves performance. We also conduct a thorough analysis to validate the design choices behind SALT and offer actionable insights.

Zhichao Xu, Shengyao Zhuang, Xueguang Ma et al.

Recent advances in large language models (LLMs) have led to a surge of interest in query augmentation for information retrieval (IR). Two main approaches have emerged. The first prompts LLMs to generate answers or pseudo-documents that serve as new queries, relying purely on the model's parametric knowledge or contextual information. The second applies reinforcement learning (RL) to fine-tune LLMs for query rewriting, directly optimizing retrieval metrics. While having respective advantages and limitations, the two approaches have not been compared under consistent experimental conditions. In this work, we present the first systematic comparison of prompting-based and RL-based query augmentation across diverse benchmarks, including evidence-seeking, ad hoc, and tool retrieval. Our key finding is that simple, training-free query augmentation often performs on par with, or even surpasses, more expensive RL-based counterparts, especially when using powerful LLMs. Motivated by this discovery, we introduce a novel hybrid method, On-policy Pseudo-document Query Expansion (OPQE), which, instead of rewriting a query, the LLM policy learns to generate a pseudo-document that maximizes retrieval performance, thus merging the flexibility and generative structure of prompting with the targeted optimization of RL. We show OPQE outperforms both standalone prompting and RL-based rewriting, demonstrating that a synergistic approach yields the best results. Our implementation is made available to facilitate reproducibility.

Zhichao Xu, Zongyu Wu, Yun Zhou et al.

Inspired by the success of reinforcement learning (RL) in Large Language Model (LLM) training for domains like math and code, recent works have begun exploring how to train LLMs to use search engines more effectively as tools for retrieval-augmented generation. Although these methods achieve performance improvement across QA benchmarks, many prioritize final answer correctness while overlooking the quality of intermediate reasoning steps, which may lead to chain-of-thought unfaithfulness. In this paper, we first introduce a comprehensive evaluation framework for evaluating RL-based search agents, covering three distinct faithfulness metrics: information-think faithfulness, think-answer faithfulness, and think-search faithfulness. Our evaluations reveal that a prototypical RL-based search agent, Search-R1, has significant room for improvement in this regard. To foster faithful reasoning, we introduce VERITAS (Verifying Entailed Reasoning through Intermediate Traceability in Agentic Search), a novel framework that integrates fine-grained faithfulness rewards into the reinforcement learning process. Our experiments show that models trained with VERITAS not only significantly improve reasoning faithfulness, but also achieve comparable task performance across seven QA benchmarks.

Yijun Tian, Shaoyu Chen, Zhichao Xu et al.

The development of state-of-the-art large language models is commonly understood as a two-stage process involving pre-training and post-training. We point out the need for an additional intermediate stage called reinforcement mid-training with potential for strong performance gains. In this paper, we formally define the problem and identify three key challenges: (1) inefficient training due to excessive reasoning steps, (2) disregard of the imbalanced token entropy distribution, and (3) underutilization of token information. To address these challenges, we propose RMT, a framework for efficient, adaptive, and unified reinforcement mid-training with various innovative components. In particular, we first introduce a dynamic token budget mechanism that constrains unnecessary reasoning steps and mitigates model overthinking. Next, we design a curriculum-based adaptive sampling method that fosters a progressive learning trajectory from easy to hard tokens. Finally, we present a dual training strategy that combines reinforcement learning with next-token prediction, ensuring targeted learning on key tokens and full exploitation of all token information. Extensive experiments demonstrate the superiority of RMT over state-of-the-art methods, achieving up to +64.91% performance improvement with only 21% of the reasoning length in language modeling. We also show that checkpoints obtained after reinforcement mid-training can benefit the subsequent post-training, yielding up to +18.76% improvement in the mathematical domain.

Chengyuan Deng, Yiqun Duan, Xin Jin et al.

Large Language Models (LLMs) have achieved unparalleled success across diverse language modeling tasks in recent years. However, this progress has also intensified ethical concerns, impacting the deployment of LLMs in everyday contexts. This paper provides a comprehensive survey of ethical challenges associated with LLMs, from longstanding issues such as copyright infringement, systematic bias, and data privacy, to emerging problems like truthfulness and social norms. We critically analyze existing research aimed at understanding, examining, and mitigating these ethical risks. Our survey underscores integrating ethical standards and societal values into the development of LLMs, thereby guiding the development of responsible and ethically aligned language models.

Yijun Tian

Determining the localization of specific protein in human cells is important for understanding cellular functions and biological processes of underlying diseases. Among imaging techniques, high-throughput fluorescence microscopy imaging is an efficient biotechnology to stain the protein of interest in a cell. In this work, we present a novel classification model Twin U-Net (TUNet) for processing and classifying the belonging of protein in the Atlas images. Several notable Deep Learning models including GoogleNet and Resnet have been employed for comparison. Results have shown that our system obtaining competitive performance.