arXiv subjects

Jia Wu

Publications and source records attributed to Jia Wu.

At least 37 records · Page 2Linked to original sources

arXiv2025

LLM-based Agents Suffer from Hallucinations: A Survey of Taxonomy, Methods, and Directions

Driven by the rapid advancements of Large Language Models (LLMs), LLM-based agents have emerged as powerful intelligent systems capable of human-like cognition, reasoning, and interaction. These agents are increasingly being deployed across diverse real-world applications, including student education, scientific research, and financial analysis. However, despite their remarkable potential, LLM-based agents remain vulnerable to hallucination issues, which can result in erroneous task execution and undermine the reliability of the overall system design. Addressing this critical challenge requires a deep understanding and a systematic consolidation of recent advances on LLM-based agents. To this end, we present the first comprehensive survey of hallucinations in LLM-based agents. By carefully analyzing the complete workflow of agents, we propose a new taxonomy that identifies different types of agent hallucinations occurring at different stages. Furthermore, we conduct an in-depth examination of eighteen triggering causes underlying the emergence of agent hallucinations. Through a detailed review of a large number of existing studies, we summarize approaches for hallucination mitigation and detection, and highlight promising directions for future research. We hope this survey will inspire further efforts toward addressing hallucinations in LLM-based agents, ultimately contributing to the development of more robust and reliable agent systems.

cs.AI↗

arXiv2025

FP-AbDiff: Improving Score-based Antibody Design by Capturing Nonequilibrium Dynamics through the Underlying Fokker-Planck Equation

Computational antibody design holds immense promise for therapeutic discovery, yet existing generative models are fundamentally limited by two core challenges: (i) a lack of dynamical consistency, which yields physically implausible structures, and (ii) poor generalization due to data scarcity and structural bias. We introduce FP-AbDiff, the first antibody generator to enforce Fokker-Planck Equation (FPE) physics along the entire generative trajectory. Our method minimizes a novel FPE residual loss over the mixed manifold of CDR geometries (R^3 x SO(3)), compelling locally-learned denoising scores to assemble into a globally coherent probability flow. This physics-informed regularizer is synergistically integrated with deep biological priors within a state-of-the-art SE(3)-equivariant diffusion framework. Rigorous evaluation on the RAbD benchmark confirms that FP-AbDiff establishes a new state-of-the-art. In de novo CDR-H3 design, it achieves a mean Root Mean Square Deviation of 0.99 Å when superposing on the variable region, a 25% improvement over the previous state-of-the-art model, AbX, and the highest reported Contact Amino Acid Recovery of 39.91%. This superiority is underscored in the more challenging six-CDR co-design task, where our model delivers consistently superior geometric precision, cutting the average full-chain Root Mean Square Deviation by ~15%, and crucially, achieves the highest full-chain Amino Acid Recovery on the functionally dominant CDR-H3 loop (45.67%). By aligning generative dynamics with physical laws, FP-AbDiff enhances robustness and generalizability, establishing a principled approach for physically faithful and functionally viable antibody design.

cs.LG↗

arXiv2025

From ID-based to ID-free: Rethinking ID Effectiveness in Multimodal Collaborative Filtering Recommendation

Most existing multimodal collaborative filtering recommendation (MCFRec) methods rely heavily on ID features and multimodal content to enhance recommendation performance. However, this paper reveals that ID features are effective but have limited benefits in multimodal collaborative filtering recommendation. Therefore, this paper systematically deconstruct the pros and cons of ID features: (i) they provide initial embedding but lack semantic richness, (ii) they provide a unique identifier for each user and item but hinder generalization to untrained data, and (iii) they assist in aligning and fusing multimodal features but may lead to representation shift. Based on these insights, this paper proposes IDFREE, an ID-free multimodal collaborative Filtering REcommEndation baseline. IDFREE replaces ID features with multimodal features and positional encodings to generate semantically meaningful ID-free embeddings. For ID-free multimodal collaborative filtering, it further proposes an adaptive similarity graph module to construct dynamic user-user and item-item graphs based on multimodal features. Then, an augmented user-item graph encoder is proposed to construct more effective user and item encoding. Finally, IDFREE achieves inter-multimodal alignment based on the contrastive learning and uses Softmax loss as recommendation loss. Basic experiments on three public datasets demonstrate that IDFREE outperforms existing ID-based MCFRec methods, achieving an average performance gain of 72.24% across standard metrics (Recall@5, 10, 20, 50 and NDCG@5, 10, 20, 50). Exploratory and extended experiments further validate our findings on the limitations of ID features in MCFRec. The code is released at https://github.com/G-H-Li/IDFREE.

cs.IR↗

arXiv2025

Adversarial Attacks Against Automated Fact-Checking: A Survey

In an era where misinformation spreads freely, fact-checking (FC) plays a crucial role in verifying claims and promoting reliable information. While automated fact-checking (AFC) has advanced significantly, existing systems remain vulnerable to adversarial attacks that manipulate or generate claims, evidence, or claim-evidence pairs. These attacks can distort the truth, mislead decision-makers, and ultimately undermine the reliability of FC models. Despite growing research interest in adversarial attacks against AFC systems, a comprehensive, holistic overview of key challenges remains lacking. These challenges include understanding attack strategies, assessing the resilience of current models, and identifying ways to enhance robustness. This survey provides the first in-depth review of adversarial attacks targeting FC, categorizing existing attack methodologies and evaluating their impact on AFC systems. Additionally, we examine recent advancements in adversary-aware defenses and highlight open research questions that require further exploration. Our findings underscore the urgent need for resilient FC frameworks capable of withstanding adversarial manipulations in pursuit of preserving high verification accuracy.

cs.CL↗

arXiv2025

Explicit and Implicit Data Augmentation for Social Event Detection

Social event detection involves identifying and categorizing important events from social media, which relies on labeled data, but annotation is costly and labor-intensive. To address this problem, we propose Augmentation framework for Social Event Detection (SED-Aug), a plug-and-play dual augmentation framework, which combines explicit text-based and implicit feature-space augmentation to enhance data diversity and model robustness. The explicit augmentation utilizes large language models to enhance textual information through five diverse generation strategies. For implicit augmentation, we design five novel perturbation techniques that operate in the feature space on structural fused embeddings. These perturbations are crafted to keep the semantic and relational properties of the embeddings and make them more diverse. Specifically, SED-Aug outperforms the best baseline model by approximately 17.67% on the Twitter2012 dataset and by about 15.57% on the Twitter2018 dataset in terms of the average F1 score. The code is available at GitHub: https://github.com/congboma/SED-Aug.

cs.CL↗

arXiv2025

MorphGen: Morphology-Guided Representation Learning for Robust Single-Domain Generalization in Histopathological Cancer Classification

Domain generalization in computational histopathology is hindered by heterogeneity in whole slide images (WSIs), caused by variations in tissue preparation, staining, and imaging conditions across institutions. Unlike machine learning systems, pathologists rely on domain-invariant morphological cues such as nuclear atypia (enlargement, irregular contours, hyperchromasia, chromatin texture, spatial disorganization), structural atypia (abnormal architecture and gland formation), and overall morphological atypia that remain diagnostic across diverse settings. Motivated by this, we hypothesize that explicitly modeling biologically robust nuclear morphology and spatial organization will enable the learning of cancer representations that are resilient to domain shifts. We propose MorphGen (Morphology-Guided Generalization), a method that integrates histopathology images, augmentations, and nuclear segmentation masks within a supervised contrastive learning framework. By aligning latent representations of images and nuclear masks, MorphGen prioritizes diagnostic features such as nuclear and morphological atypia and spatial organization over staining artifacts and domain-specific features. To further enhance out-of-distribution robustness, we incorporate stochastic weight averaging (SWA), steering optimization toward flatter minima. Attention map analyses revealed that MorphGen primarily relies on nuclear morphology, cellular composition, and spatial cell organization within tumors or normal regions for final classification. Finally, we demonstrate resilience of the learned representations to image corruptions (such as staining artifacts) and adversarial attacks, showcasing not only OOD generalization but also addressing critical vulnerabilities in current deep learning systems for digital pathology. Code, datasets, and trained models are available at: https://github.com/hikmatkhan/MorphGen

cs.CV↗

arXiv2025

The Next Layer: Augmenting Foundation Models with Structure-Preserving and Attention-Guided Learning for Local Patches to Global Context Awareness in Computational Pathology

Foundation models have recently emerged as powerful feature extractors in computational pathology, yet they typically omit mechanisms for leveraging the global spatial structure of tissues and the local contextual relationships among diagnostically relevant regions - key elements for understanding the tumor microenvironment. Multiple instance learning (MIL) remains an essential next step following foundation model, designing a framework to aggregate patch-level features into slide-level predictions. We present EAGLE-Net, a structure-preserving, attention-guided MIL architecture designed to augment prediction and interpretability. EAGLE-Net integrates multi-scale absolute spatial encoding to capture global tissue architecture, a top-K neighborhood-aware loss to focus attention on local microenvironments, and background suppression loss to minimize false positives. We benchmarked EAGLE-Net on large pan-cancer datasets, including three cancer types for classification (10,260 slides) and seven cancer types for survival prediction (4,172 slides), using three distinct histology foundation backbones (REMEDIES, Uni-V1, Uni2-h). Across tasks, EAGLE-Net achieved up to 3% higher classification accuracy and the top concordance indices in 6 of 7 cancer types, producing smooth, biologically coherent attention maps that aligned with expert annotations and highlighted invasive fronts, necrosis, and immune infiltration. These results position EAGLE-Net as a generalizable, interpretable framework that complements foundation models, enabling improved biomarker discovery, prognostic modeling, and clinical decision support

q-bio.QM↗

arXiv2025

Towards Faithful Class-level Self-explainability in Graph Neural Networks by Subgraph Dependencies

Enhancing the interpretability of graph neural networks (GNNs) is crucial to ensure their safe and fair deployment. Recent work has introduced self-explainable GNNs that generate explanations as part of training, improving both faithfulness and efficiency. Some of these models, such as ProtGNN and PGIB, learn class-specific prototypes, offering a potential pathway toward class-level explanations. However, their evaluations focus solely on instance-level explanations, leaving open the question of whether these prototypes meaningfully generalize across instances of the same class. In this paper, we introduce GraphOracle, a novel self-explainable GNN framework designed to generate and evaluate class-level explanations for GNNs. Our model jointly learns a GNN classifier and a set of structured, sparse subgraphs that are discriminative for each class. We propose a novel integrated training that captures graph$\unicode{x2013}$subgraph$\unicode{x2013}$prediction dependencies efficiently and faithfully, validated through a masking-based evaluation strategy. This strategy enables us to retroactively assess whether prior methods like ProtGNN and PGIB deliver effective class-level explanations. Our results show that they do not. In contrast, GraphOracle achieves superior fidelity, explainability, and scalability across a range of graph classification tasks. We further demonstrate that GraphOracle avoids the computational bottlenecks of previous methods$\unicode{x2014}$like Monte Carlo Tree Search$\unicode{x2014}$by using entropy-regularized subgraph selection and lightweight random walk extraction, enabling faster and more scalable training. These findings position GraphOracle as a practical and principled solution for faithful class-level self-explainability in GNNs.

cs.LG↗

arXiv2025

DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery

Large language models (LLMs) integrated with autonomous agents hold significant potential for advancing scientific discovery through automated reasoning and task execution. However, applying LLM agents to drug discovery is still constrained by challenges such as large-scale multimodal data processing, limited task automation, and poor support for domain-specific tools. To overcome these limitations, we introduce DrugPilot, a LLM-based agent system with a parameterized reasoning architecture designed for end-to-end scientific workflows in drug discovery. DrugPilot enables multi-stage research processes by integrating structured tool use with a novel parameterized memory pool. The memory pool converts heterogeneous data from both public sources and user-defined inputs into standardized representations. This design supports efficient multi-turn dialogue, reduces information loss during data exchange, and enhances complex scientific decision-making. To support training and benchmarking, we construct a drug instruction dataset covering eight core drug discovery tasks. Under the Berkeley function-calling benchmark, DrugPilot significantly outperforms state-of-the-art agents such as ReAct and LoT, achieving task completion rates of 98.0%, 93.5%, and 64.0% for simple, multi-tool, and multi-turn scenarios, respectively. These results highlight DrugPilot's potential as a versatile agent framework for computational science domains requiring automated, interactive, and data-integrated reasoning.

cs.AI↗

arXiv2025

Zero-Shot Learning with Subsequence Reordering Pretraining for Compound-Protein Interaction

Given the vastness of chemical space and the ongoing emergence of previously uncharacterized proteins, zero-shot compound-protein interaction (CPI) prediction better reflects the practical challenges and requirements of real-world drug development. Although existing methods perform adequately during certain CPI tasks, they still face the following challenges: (1) Representation learning from local or complete protein sequences often overlooks the complex interdependencies between subsequences, which are essential for predicting spatial structures and binding properties. (2) Dependence on large-scale or scarce multimodal protein datasets demands significant training data and computational resources, limiting scalability and efficiency. To address these challenges, we propose a novel approach that pretrains protein representations for CPI prediction tasks using subsequence reordering, explicitly capturing the dependencies between protein subsequences. Furthermore, we apply length-variable protein augmentation to ensure excellent pretraining performance on small training datasets. To evaluate the model's effectiveness and zero-shot learning ability, we combine it with various baseline methods. The results demonstrate that our approach can improve the baseline model's performance on the CPI task, especially in the challenging zero-shot scenario. Compared to existing pre-training models, our model demonstrates superior performance, particularly in data-scarce scenarios where training samples are limited. Our implementation is available at https://github.com/Hoch-Zhang/PSRP-CPI.

cs.LG↗

arXiv2025

Thinking Beyond Tokens: From Brain-Inspired Intelligence to Cognitive Foundations for Artificial General Intelligence and its Societal Impact

Can machines truly think, reason and act in domains like humans? This enduring question continues to shape the pursuit of Artificial General Intelligence (AGI). Despite the growing capabilities of models such as GPT-4.5, DeepSeek, Claude 3.5 Sonnet, Phi-4, and Grok 3, which exhibit multimodal fluency and partial reasoning, these systems remain fundamentally limited by their reliance on token-level prediction and lack of grounded agency. This paper offers a cross-disciplinary synthesis of AGI development, spanning artificial intelligence, cognitive neuroscience, psychology, generative models, and agent-based systems. We analyze the architectural and cognitive foundations of general intelligence, highlighting the role of modular reasoning, persistent memory, and multi-agent coordination. In particular, we emphasize the rise of Agentic RAG frameworks that combine retrieval, planning, and dynamic tool use to enable more adaptive behavior. We discuss generalization strategies, including information compression, test-time adaptation, and training-free methods, as critical pathways toward flexible, domain-agnostic intelligence. Vision-Language Models (VLMs) are reexamined not just as perception modules but as evolving interfaces for embodied understanding and collaborative task completion. We also argue that true intelligence arises not from scale alone but from the integration of memory and reasoning: an orchestration of modular, interactive, and self-improving components where compression enables adaptive behavior. Drawing on advances in neurosymbolic systems, reinforcement learning, and cognitive scaffolding, we explore how recent architectures begin to bridge the gap between statistical learning and goal-directed cognition. Finally, we identify key scientific, technical, and ethical challenges on the path to AGI.

cs.AI↗

arXiv2025

Antibody Design and Optimization with Multi-scale Equivariant Graph Diffusion Models for Accurate Complex Antigen Binding

Antibody design remains a critical challenge in therapeutic and diagnostic development, particularly for complex antigens with diverse binding interfaces. Current computational methods face two main limitations: (1) capturing geometric features while preserving symmetries, and (2) generalizing novel antigen interfaces. Despite recent advancements, these methods often fail to accurately capture molecular interactions and maintain structural integrity. To address these challenges, we propose \textbf{AbMEGD}, an end-to-end framework integrating \textbf{M}ulti-scale \textbf{E}quivariant \textbf{G}raph \textbf{D}iffusion for antibody sequence and structure co-design. Leveraging advanced geometric deep learning, AbMEGD combines atomic-level geometric features with residue-level embeddings, capturing local atomic details and global sequence-structure interactions. Its E(3)-equivariant diffusion method ensures geometric precision, computational efficiency, and robust generalizability for complex antigens. Furthermore, experiments using the SAbDab database demonstrate a 10.13\% increase in amino acid recovery, 3.32\% rise in improvement percentage, and a 0.062~Å reduction in root mean square deviation within the critical CDR-H3 region compared to DiffAb, a leading antibody design model. These results highlight AbMEGD's ability to balance structural integrity with improved functionality, establishing a new benchmark for sequence-structure co-design and affinity optimization. The code is available at: https://github.com/Patrick221215/AbMEGD.

cs.LG↗

arXiv2025

STAMImputer: Spatio-Temporal Attention MoE for Traffic Data Imputation

Traffic data imputation is fundamentally important to support various applications in intelligent transportation systems such as traffic flow prediction. However, existing time-to-space sequential methods often fail to effectively extract features in block-wise missing data scenarios. Meanwhile, the static graph structure for spatial feature propagation significantly constrains the models flexibility in handling the distribution shift issue for the nonstationary traffic data. To address these issues, this paper proposes a SpatioTemporal Attention Mixture of experts network named STAMImputer for traffic data imputation. Specifically, we introduce a Mixture of Experts (MoE) framework to capture latent spatio-temporal features and their influence weights, effectively imputing block missing. A novel Low-rank guided Sampling Graph ATtention (LrSGAT) mechanism is designed to dynamically balance the local and global correlations across road networks. The sampled attention vectors are utilized to generate dynamic graphs that capture real-time spatial correlations. Extensive experiments are conducted on four traffic datasets for evaluation. The result shows STAMImputer achieves significantly performance improvement compared with existing SOTA approaches. Our codes are available at https://github.com/RingBDStack/STAMImupter.

cs.LG↗

arXiv2025

Fragment-Masked Diffusion for Molecular Optimization

Molecular optimization is a crucial aspect of drug discovery, aimed at refining molecular structures to enhance drug efficacy and minimize side effects, ultimately accelerating the overall drug development process. Many molecular optimization methods have been proposed, significantly advancing drug discovery. These methods primarily on understanding the specific drug target structures or their hypothesized roles in combating diseases. However, challenges such as a limited number of available targets and a difficulty capturing clear structures hinder innovative drug development. In contrast, phenotypic drug discovery (PDD) does not depend on clear target structures and can identify hits with novel and unbiased polypharmacology signatures. As a result, PDD-based molecular optimization can reduce potential safety risks while optimizing phenotypic activity, thereby increasing the likelihood of clinical success. Therefore, we propose a fragment-masked molecular optimization method based on PDD (FMOP). FMOP employs a regression-free diffusion model to conditionally optimize the molecular masked regions, effectively generating new molecules with similar scaffolds. On the large-scale drug response dataset GDSCv2, we optimize the potential molecules across all 985 cell lines. The overall experiments demonstrate that the in-silico optimization success rate reaches 95.4\%, with an average efficacy increase of 7.5\%. Additionally, we conduct extensive ablation and visualization experiments, confirming that FMOP is an effective and robust molecular optimization method. The code is available at: https://anonymous.4open.science/r/FMOP-98C2.

q-bio.BM↗

arXiv2025

Graph-structured Small Molecule Drug Discovery Through Deep Learning: Progress, Challenges, and Opportunities

Due to their excellent drug-like and pharmacokinetic properties, small molecule drugs are widely used to treat various diseases, making them a critical component of drug discovery. In recent years, with the rapid development of deep learning (DL) techniques, DL-based small molecule drug discovery methods have achieved excellent performance in prediction accuracy, speed, and complex molecular relationship modeling compared to traditional machine learning approaches. These advancements enhance drug screening efficiency and optimization and provide more precise and effective solutions for various drug discovery tasks. Contributing to this field's development, this paper aims to systematically summarize and generalize the recent key tasks and representative techniques in graph-structured small molecule drug discovery in recent years. Specifically, we provide an overview of the major tasks in small molecule drug discovery and their interrelationships. Next, we analyze the six core tasks, summarizing the related methods, commonly used datasets, and technological development trends. Finally, we discuss key challenges, such as interpretability and out-of-distribution generalization, and offer our insights into future research directions for small molecule drug discovery.

cs.LG↗

arXiv2025

Exploiting Text Semantics for Few and Zero Shot Node Classification on Text-attributed Graph

Text-attributed graph (TAG) provides a text description for each graph node, and few- and zero-shot node classification on TAGs have many applications in fields such as academia and social networks. Existing work utilizes various graph-based augmentation techniques to train the node and text embeddings, while text-based augmentations are largely unexplored. In this paper, we propose Text Semantics Augmentation (TSA) to improve accuracy by introducing more text semantic supervision signals. Specifically, we design two augmentation techniques, i.e., positive semantics matching and negative semantics contrast, to provide more reference texts for each graph node or text description. Positive semantic matching retrieves texts with similar embeddings to match with a graph node. Negative semantic contrast adds a negative prompt to construct a text description with the opposite semantics, which is contrasted with the original node and text. We evaluate TSA on 5 datasets and compare with 13 state-of-the-art baselines. The results show that TSA consistently outperforms all baselines, and its accuracy improvements over the best-performing baseline are usually over 5%.

cs.CL↗

arXiv2025

Federated Latent Factor Learning for Recovering Wireless Sensor Networks Signal with Privacy-Preserving

Wireless Sensor Networks (WSNs) are a cutting-edge domain in the field of intelligent sensing. Due to sensor failures and energy-saving strategies, the collected data often have massive missing data, hindering subsequent analysis and decision-making. Although Latent Factor Learning (LFL) has been proven effective in recovering missing data, it fails to sufficiently consider data privacy protection. To address this issue, this paper innovatively proposes a federated latent factor learning (FLFL) based spatial signal recovery (SSR) model, named FLFL-SSR. Its main idea is two-fold: 1) it designs a sensor-level federated learning framework, where each sensor uploads only gradient updates instead of raw data to optimize the global model, and 2) it proposes a local spatial sharing strategy, allowing sensors within the same spatial region to share their latent feature vectors, capturing spatial correlations and enhancing recovery accuracy. Experimental results on two real-world WSNs datasets demonstrate that the proposed model outperforms existing federated methods in terms of recovery performance.

cs.LG↗

arXiv2025

A Survey on Location-Driven Influence Maximization

Influence Maximization (IM), which aims to select a set of users from a social network to maximize the expected number of influenced users, is an evergreen hot research topic. Its research outcomes significantly impact real-world applications such as business marketing. The booming location-based network platforms of the last decade appeal to the researchers embedding the location information into traditional IM research. In this survey, we provide a comprehensive review of the existing location-driven IM studies from the perspective of the following key aspects: (1) a review of the application scenarios of these works, (2) the diffusion models to evaluate the influence propagation, and (3) a comprehensive study of the approaches to deal with the location-driven IM problems together with a particular focus on the accelerating techniques. In the end, we draw prospects into the research directions in future IM research.

cs.SI↗