arXiv subjects

Xikun Zhang

Publications and source records attributed to Xikun Zhang.

At least 37 records · Page 2Linked to original sources

arXiv2026

Stable Multimodal Graph Unlearning via Feature-Dimension Aware Quantile Selection

Graph unlearning remains a critical technique for supporting privacy-preserving and sustainable multimodal graph learning. However, we observe that existing unlearning strategies tend to apply uniform parameter selection and editing across all graph neural network (GNN) layers, which is especially harmful for multimodal graphs where high-dimensional input projections encode dominant cross-modal knowledge. As a result, over-editing these sensitive layers often leads to catastrophic utility degradation after forgetting, undermining both stable learning and effective privacy protection. To address this gap, we propose FDQ, a Feature-Dimension Aware Quantile framework for multimodal graph unlearning. FDQ adaptively identifies high-dimensional input projection layers and applies more conservative, FDQ-guided quantile thresholds when constructing suppression sets, while keeping the underlying importance estimation mechanism unchanged. FDQ is seamlessly integrated with diagonal sensitivity-based parameter importance analysis to enable efficient node and edge unlearning under general forget requests. Through extensive experiments on Ele-Fashion and Goodreads-NC, we demonstrate that FDQ consistently achieves strong utility preservation while maintaining effective forgetting against membership inference attacks. Overall, FDQ offers a principled and robust solution for privacy-aware unlearning in high-dimensional multimodal graph systems.

cs.LG↗

arXiv2026

FORGE: Fine-grained Multimodal Evaluation for Manufacturing Scenarios

The manufacturing sector is increasingly adopting Multimodal Large Language Models (MLLMs) to transition from simple perception to autonomous execution, yet current evaluations fail to reflect the rigorous demands of real-world manufacturing environments. Progress is hindered by data scarcity and a lack of fine-grained domain semantics in existing datasets. To bridge this gap, we introduce FORGE. Wefirst construct a high-quality multimodal dataset that combines real-world 2D images and 3D point clouds, annotated with fine-grained domain semantics (e.g., exact model numbers). We then evaluate 18 state-of-the-art MLLMs across three manufacturing tasks, namely workpiece verification, structural surface inspection, and assembly verification, revealing significant performance gaps. Counter to conventional understanding, the bottleneck analysis shows that visual grounding is not the primary limiting factor. Instead, insufficient domain-specific knowledge is the key bottleneck, setting a clear direction for future research. Beyond evaluation, we show that our structured annotations can serve as an actionable training resource: supervised fine-tuning of a compact 3B-parameter model on our data yields up to 90.8% relative improvement in accuracy on held-out manufacturing scenarios, providing preliminary evidence for a practical pathway toward domain-adapted manufacturing MLLMs. The code and datasets are available at https://ai4manufacturing.github.io/forge-web.

cs.CV↗

arXiv2026

Prototype-Enhanced Multi-View Learning for Thyroid Nodule Ultrasound Classification

Thyroid nodule classification using ultrasound imaging is essential for early diagnosis and clinical decision-making; however, despite promising performance on in-distribution data, existing deep learning methods often exhibit limited robustness and generalisation when deployed across different ultrasound devices or clinical environments. This limitation is mainly attributed to the pronounced heterogeneity of thyroid ultrasound images, which can lead models to capture spurious correlations rather than reliable diagnostic cues. To address this challenge, we propose PEMV-thyroid, a Prototype-Enhanced Multi-View learning framework that accounts for data heterogeneity by learning complementary representations from multiple feature perspectives and refining decision boundaries through a prototype-based correction mechanism with mixed prototype information. By integrating multi-view representations with prototype-level guidance, the proposed approach enables more stable representation learning under heterogeneous imaging conditions. Extensive experiments on multiple thyroid ultrasound datasets demonstrate that PEMV-thyroid consistently outperforms state-of-the-art methods, particularly in cross-device and cross-domain evaluation scenarios, leading to improved diagnostic accuracy and generalisation performance in real-world clinical settings. The source code is available at https://github.com/chenyangmeii/Prototype-Enhanced-Multi-View-Learning.

cs.CV↗

arXiv2026

FairGC: Fairness-aware Graph Condensation

Graph condensation (GC) has become a vital strategy for scaling Graph Neural Networks by compressing massive datasets into small, synthetic node sets. While current GC methods effectively maintain predictive accuracy, they are primarily designed for utility and often ignore fairness constraints. Because these techniques are bias-blind, they frequently capture and even amplify demographic disparities found in the original data. This leads to synthetic proxies that are unsuitable for sensitive applications like credit scoring or social recommendations. To solve this problem, we introduce FairGC, a unified framework that embeds fairness directly into the graph distillation process. Our approach consists of three key components. First, a Distribution-Preserving Condensation module synchronizes the joint distributions of labels and sensitive attributes to stop bias from spreading. Second, a Spectral Encoding module uses Laplacian eigen-decomposition to preserve essential global structural patterns. Finally, a Fairness-Enhanced Neural Architecture employs multi-domain fusion and a label-smoothing curriculum to produce equitable predictions. Rigorous evaluations on four real-world datasets, show that FairGC provides a superior balance between accuracy and fairness. Our results confirm that FairGC significantly reduces disparity in Statistical Parity and Equal Opportunity compared to existing state-of-the-art condensation models. The codes are available at https://github.com/LuoRenqiang/FairGC.

cs.LG↗

arXiv2026

When to Trust: A Causality-Aware Calibration Framework for Accurate Knowledge Graph Retrieval-Augmented Generation

Knowledge Graph Retrieval-Augmented Generation (KG-RAG) extends the RAG paradigm by incorporating structured knowledge from knowledge graphs, enabling Large Language Models (LLMs) to perform more precise and explainable reasoning. While KG-RAG improves factual accuracy in complex tasks, existing KG-RAG models are often severely overconfident, producing high-confidence predictions even when retrieved sub-graphs are incomplete or unreliable, which raises concerns for deployment in high-stakes domains. To address this issue, we propose Ca2KG, a Causality-aware Calibration framework for KG-RAG. Ca2KG integrates counterfactual prompting, which exposes retrieval-dependent uncertainties in knowledge quality and reasoning reliability, with a panel-based re-scoring mechanism that stabilises predictions across interventions. Extensive experiments on two complex QA datasets demonstrate that Ca2KG consistently improves calibration while maintaining or even enhancing predictive accuracy.

cs.CL↗

arXiv2026

FTSCommDetector: Discovering Behavioral Communities through Temporal Synchronization

Why do trillion-dollar tech giants AAPL and MSFT diverge into different response patterns during market disruptions despite identical sector classifications? This paradox reveals a fundamental limitation: traditional community detection methods fail to capture synchronization-desynchronization patterns where entities move independently yet align during critical moments. To this end, we introduce FTSCommDetector, implementing our Temporal Coherence Architecture (TCA) to discover similar and dissimilar communities in continuous multivariate time series. Unlike existing methods that process each timestamp independently, causing unstable community assignments and missing evolving relationships, our approach maintains coherence through dual-scale encoding and static topology with dynamic attention. Furthermore, we establish information-theoretic foundations demonstrating how scale separation maximizes complementary information and introduce Normalized Temporal Profiles (NTP) for scale-invariant evaluation. As a result, FTSCommDetector achieves consistent improvements across four diverse financial markets (SP100, SP500, SP1000, Nikkei 225), with gains ranging from 3.5% to 11.1% over the strongest baselines. The method demonstrates remarkable robustness with only 2% performance variation across window sizes from 60 to 120 days, making dataset-specific tuning unnecessary, providing practical insights for portfolio construction and risk management.

cs.SI↗

arXiv2026

Debiasing Large Language Models via Adaptive Causal Prompting with Sketch-of-Thought

Despite notable advancements in prompting methods for Large Language Models (LLMs), such as Chain-of-Thought (CoT), existing strategies still suffer from excessive token usage and limited generalisability across diverse reasoning tasks. To address these limitations, we propose an Adaptive Causal Prompting with Sketch-of-Thought (ACPS) framework, which leverages structural causal models to infer the causal effect of a query on its answer and adaptively select an appropriate intervention (i.e., standard front-door and conditional front-door adjustments). This design enables generalisable causal reasoning across heterogeneous tasks without task-specific retraining. By replacing verbose CoT with concise Sketch-of-Thought, ACPS enables efficient reasoning that significantly reduces token usage and inference cost. Extensive experiments on multiple reasoning benchmarks and LLMs demonstrate that ACPS consistently outperforms existing prompting baselines in terms of accuracy, robustness, and computational efficiency.

cs.CL↗

arXiv2025

Effective Policy Learning for Multi-Agent Online Coordination Beyond Submodular Objectives

In this paper, we present two effective policy learning algorithms for multi-agent online coordination(MA-OC) problem. The first one, \texttt{MA-SPL}, not only can achieve the optimal $(1-\frac{c}{e})$-approximation guarantee for the MA-OC problem with submodular objectives but also can handle the unexplored $α$-weakly DR-submodular and $(γ,β)$-weakly submodular scenarios, where $c$ is the curvature of the investigated submodular functions, $α$ denotes the diminishing-return(DR) ratio and the tuple $(γ,β)$ represents the submodularity ratios. Subsequently, in order to reduce the reliance on the unknown parameters $α,γ,β$ inherent in the \texttt{MA-SPL} algorithm, we further introduce the second online algorithm named \texttt{MA-MPL}. This \texttt{MA-MPL} algorithm is entirely \emph{parameter-free} and simultaneously can maintain the same approximation ratio as the first \texttt{MA-SPL} algorithm. The core of our \texttt{MA-SPL} and \texttt{MA-MPL} algorithms is a novel continuous-relaxation technique termed as \emph{policy-based continuous extension}. Compared with the well-established \emph{multi-linear extension}, a notable advantage of this new \emph{policy-based continuous extension} is its ability to provide a lossless rounding scheme for any set function, thereby enabling us to tackle the challenging weakly submodular objectives. Finally, extensive simulations are conducted to validate the effectiveness of our proposed algorithms.

cs.MA↗

arXiv2025

R1-VL: Learning to Reason with Multimodal Large Language Models via Step-wise Group Relative Policy Optimization

Recent studies generally enhance MLLMs' reasoning capabilities via supervised fine-tuning on high-quality chain-of-thought reasoning data, which often leads models to merely imitate successful reasoning paths without understanding what the wrong reasoning paths are. In this work, we aim to enhance the MLLMs' reasoning ability beyond passively imitating positive reasoning paths. To this end, we design Step-wise Group Relative Policy Optimization (StepGRPO), a new online reinforcement learning framework that enables MLLMs to self-improve reasoning ability via simple, effective and dense step-wise rewarding. Specifically, StepGRPO introduces two novel rule-based reasoning rewards: Step-wise Reasoning Accuracy Reward (StepRAR) and Step-wise Reasoning Validity Reward (StepRVR). StepRAR rewards the reasoning paths that contain necessary intermediate reasoning steps via a soft key-step matching technique, while StepRAR rewards reasoning paths that follow a well-structured and logically consistent reasoning process through a reasoning completeness and logic evaluation strategy. With the proposed StepGRPO, we introduce R1-VL, a series of MLLMs with outstanding capabilities in step-by-step reasoning. Extensive experiments over 8 benchmarks demonstrate the superiority of our methods.

cs.AI↗

arXiv2025

Benchmarking and Evaluation of AI Models in Biology: Outcomes and Recommendations from the CZI Virtual Cells Workshop

Artificial intelligence holds immense promise for transforming biology, yet a lack of standardized, cross domain, benchmarks undermines our ability to build robust, trustworthy models. Here, we present insights from a recent workshop that convened machine learning and computational biology experts across imaging, transcriptomics, proteomics, and genomics to tackle this gap. We identify major technical and systemic bottlenecks such as data heterogeneity and noise, reproducibility challenges, biases, and the fragmented ecosystem of publicly available resources and propose a set of recommendations for building benchmarking frameworks that can efficiently compare ML models of biological systems across tasks and data modalities. By promoting high quality data curation, standardized tooling, comprehensive evaluation metrics, and open, collaborative platforms, we aim to accelerate the development of robust benchmarks for AI driven Virtual Cells. These benchmarks are crucial for ensuring rigor, reproducibility, and biological relevance, and will ultimately advance the field toward integrated models that drive new discoveries, therapeutic insights, and a deeper understanding of cellular systems.

cs.LG↗

arXiv2025

MMReason: An Open-Ended Multi-Modal Multi-Step Reasoning Benchmark for MLLMs Toward AGI

Reasoning plays a crucial role in advancing Multimodal Large Language Models (MLLMs) toward Artificial General Intelligence. However, existing MLLM benchmarks often fall short in precisely and comprehensively evaluating long-chain reasoning abilities from three key aspects: (1) lack of difficulty and diversity, (2) susceptibility to guessability and memorization, (3) inadequate assessment of intermediate reasoning steps. To fill this gap, we introduce MMReason, a new benchmark designed to precisely and comprehensively evaluate MLLM long-chain reasoning capability with diverse, open-ended, challenging questions. First, we curate challenging questions requiring multi-step reasoning from various fields (i.e., 6 disciplines) and multiple difficulty levels (i.e., from pre-university to university, and from foundational to competition tiers). Second, these questions are reformulated into an open-ended format and filtered using a multi-model voting technique to eliminate shortcut cases related to guessing and memorization, ensuring robust reasoning evaluations. Third, we annotate the questions with detailed step-by-step solutions, and design a reference-based ternary scoring mechanism to reliably assess intermediate reasoning steps. With MMReason, we benchmark popular leading MLLMs and provide an in-depth analysis of their reasoning capabilities. We hope MMReason will serve as a valuable resource for advancing MLLM reasoning research. Code will be available at https://github.com/HJYao00/MMReason.

cs.AI↗

arXiv2025

Improving Large Language Models with Concept-Aware Fine-Tuning

Large language models (LLMs) have become the cornerstone of modern AI. However, the existing paradigm of next-token prediction fundamentally limits their ability to form coherent, high-level concepts, making it a critical barrier to human-like understanding and reasoning. Take the phrase "ribonucleic acid" as an example: an LLM will first decompose it into tokens, i.e., artificial text fragments ("rib", "on", ...), then learn each token sequentially, rather than grasping the phrase as a unified, coherent semantic entity. This fragmented representation hinders deeper conceptual understanding and, ultimately, the development of truly intelligent systems. In response, we introduce Concept-Aware Fine-Tuning (CAFT), a novel multi-token training method that redefines how LLMs are fine-tuned. By enabling the learning of sequences that span multiple tokens, this method fosters stronger concept-aware learning. Our experiments demonstrate significant improvements compared to conventional next-token finetuning methods across diverse tasks, including traditional applications like text summarization and domain-specific ones like de novo protein design. Multi-token prediction was previously only possible in the prohibitively expensive pretraining phase; CAFT, to our knowledge, is the first to bring the multi-token setting to the post-training phase, thus effectively democratizing its benefits for the broader community of practitioners and researchers. Finally, the unexpected effectiveness of our proposed method suggests wider implications for the machine learning research community. All code and data are available at https://github.com/michaelchen-lab/caft-llm

cs.LG↗

arXiv2025

CLEVRER-Humans: Describing Physical and Causal Events the Human Way

Building machines that can reason about physical events and their causal relationships is crucial for flexible interaction with the physical world. However, most existing physical and causal reasoning benchmarks are exclusively based on synthetically generated events and synthetic natural language descriptions of causal relationships. This design brings up two issues. First, there is a lack of diversity in both event types and natural language descriptions; second, causal relationships based on manually-defined heuristics are different from human judgments. To address both shortcomings, we present the CLEVRER-Humans benchmark, a video reasoning dataset for causal judgment of physical events with human labels. We employ two techniques to improve data collection efficiency: first, a novel iterative event cloze task to elicit a new representation of events in videos, which we term Causal Event Graphs (CEGs); second, a data augmentation technique based on neural language generative models. We convert the collected CEGs into questions and answers to be consistent with prior work. Finally, we study a collection of baseline approaches for CLEVRER-Humans question-answering, highlighting the great challenges set forth by our benchmark.

cs.AI↗

arXiv2025

JustLogic: A Comprehensive Benchmark for Evaluating Deductive Reasoning in Large Language Models

Logical reasoning is a critical component of Large Language Models (LLMs), and substantial research efforts in recent years have aimed to enhance their deductive reasoning capabilities. However, existing deductive reasoning benchmarks, which are crucial for evaluating and advancing LLMs, are inadequate due to their lack of task complexity, presence of prior knowledge as a confounder, and superficial error analysis. To address these deficiencies, we introduce JustLogic, a synthetically generated deductive reasoning benchmark designed for rigorous evaluation of LLMs. JustLogic is (i) highly complex, capable of generating a diverse range of linguistic patterns, vocabulary, and argument structures; (ii) prior knowledge independent, eliminating the advantage of models possessing prior knowledge and ensuring that only deductive reasoning is used to answer questions; and (iii) capable of in-depth error analysis on the heterogeneous effects of reasoning depth and argument form on model accuracy. Our experimental results on JustLogic reveal that (i) state-of-the-art (SOTA) reasoning LLMs perform on par or better than the human average but significantly worse than the human ceiling, and (ii) SOTA non-reasoning models still underperform the human average. All code and data are available at https://github.com/michaelchen-lab/JustLogic

cs.CL↗

arXiv2025

Crisp: Cognitive Restructuring of Negative Thoughts through Multi-turn Supportive Dialogues

Cognitive Restructuring (CR) is a psychotherapeutic process aimed at identifying and restructuring an individual's negative thoughts, arising from mental health challenges, into more helpful and positive ones via multi-turn dialogues. Clinician shortage and stigma urge the development of human-LLM interactive psychotherapy for CR. Yet, existing efforts implement CR via simple text rewriting, fixed-pattern dialogues, or a one-shot CR workflow, failing to align with the psychotherapeutic process for effective CR. To address this gap, we propose CRDial, a novel framework for CR, which creates multi-turn dialogues with specifically designed identification and restructuring stages of negative thoughts, integrates sentence-level supportive conversation strategies, and adopts a multi-channel loop mechanism to enable iterative CR. With CRDial, we distill Crisp, a large-scale and high-quality bilingual dialogue dataset, from LLM. We then train Crispers, Crisp-based conversational LLMs for CR, at 7B and 14B scales. Extensive human studies show the superiority of Crispers in pointwise, pairwise, and intervention evaluations.

cs.CL↗

arXiv2025

Benchmarking Reasoning Robustness in Large Language Models

Despite the recent success of large language models (LLMs) in reasoning such as DeepSeek, we for the first time identify a key dilemma in reasoning robustness and generalization: significant performance degradation on novel or incomplete data, suggesting a reliance on memorized patterns rather than systematic reasoning. Our closer examination reveals four key unique limitations underlying this issue:(1) Positional bias--models favor earlier queries in multi-query inputs but answering the wrong one in the latter (e.g., GPT-4o's accuracy drops from 75.8 percent to 72.8 percent); (2) Instruction sensitivity--performance declines by 5.0 to 7.5 percent in the Qwen2.5 Series and by 5.0 percent in DeepSeek-V3 with auxiliary guidance; (3) Numerical fragility--value substitution sharply reduces accuracy (e.g., GPT-4o drops from 97.5 percent to 82.5 percent, GPT-o1-mini drops from 97.5 percent to 92.5 percent); and (4) Memory dependence--models resort to guesswork when missing critical data. These findings further highlight the reliance on heuristic recall over rigorous logical inference, demonstrating challenges in reasoning robustness. To comprehensively investigate these robustness challenges, this paper introduces a novel benchmark, termed as Math-RoB, that exploits hallucinations triggered by missing information to expose reasoning gaps. This is achieved by an instruction-based approach to generate diverse datasets that closely resemble training distributions, facilitating a holistic robustness assessment and advancing the development of more robust reasoning frameworks. Bad character(s) in field Abstract.

cs.AI↗

arXiv2025

Learning System Dynamics without Forgetting

Observation-based trajectory prediction for systems with unknown dynamics is essential in fields such as physics and biology. Most existing approaches are limited to learning within a single system with fixed dynamics patterns. However, many real-world applications require learning across systems with evolving dynamics patterns, a challenge that has been largely overlooked. To address this, we systematically investigate the problem of Continual Dynamics Learning (CDL), examining task configurations and evaluating the applicability of existing techniques, while identifying key challenges. In response, we propose the Mode-switching Graph ODE (MS-GODE) model, which integrates the strengths LG-ODE and sub-network learning with a mode-switching module, enabling efficient learning over varying dynamics. Moreover, we construct a novel benchmark of biological dynamic systems for CDL, Bio-CDL, featuring diverse systems with disparate dynamics and significantly enriching the research field of machine learning for dynamic systems. Our code available at https://github.com/QueuQ/MS-GODE.

cs.LG↗

arXiv2024

How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities

The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in artificial intelligence (AI), combined with the ability to generate large-scale experimental data, present novel opportunities to model cells. Here we propose a vision of leveraging advances in AI to construct virtual cells, high-fidelity simulations of cells and cellular systems under different conditions that are directly learned from biological data across measurements and scales. We discuss desired capabilities of such AI Virtual Cells, including generating universal representations of biological entities across scales, and facilitating interpretable in silico experiments to predict and understand their behavior using virtual instruments. We further address the challenges, opportunities and requirements to realize this vision including data needs, evaluation strategies, and community standards and engagement to ensure biological accuracy and broad utility. We envision a future where AI Virtual Cells help identify new drug targets, predict cellular responses to perturbations, as well as scale hypothesis exploration. With open science collaborations across the biomedical ecosystem that includes academia, philanthropy, and the biopharma and AI industries, a comprehensive predictive understanding of cell mechanisms and interactions has come into reach.

q-bio.QM↗