Xikun Zhang

Michihiro Yasunaga, Antoine Bosselut, Hongyu Ren et al. · stanford

Pretraining a language model (LM) on text has been shown to help various downstream NLP tasks. Recent works show that a knowledge graph (KG) can complement text data, offering structured background knowledge that provides a useful scaffold for reasoning. However, these works are not pretrained to learn a deep fusion of the two modalities at scale, limiting the potential to acquire fully joint representations of text and KG. Here we propose DRAGON (Deep Bidirectional Language-Knowledge Graph Pretraining), a self-supervised approach to pretraining a deeply joint language-knowledge foundation model from text and KG at scale. Specifically, our model takes pairs of text segments and relevant KG subgraphs as input and bidirectionally fuses information from both modalities. We pretrain this model by unifying two self-supervised reasoning tasks, masked language modeling and KG link prediction. DRAGON outperforms existing LM and LM+KG models on diverse downstream tasks including question answering across general and biomedical domains, with +5% absolute gain on average. In particular, DRAGON achieves notable performance on complex reasoning about language and knowledge (+10% on questions involving long contexts or multi-step reasoning) and low-resource QA (+8% on OBQA and RiddleSense), and new state-of-the-art results on various BioNLP tasks. Our code and trained models are available at https://github.com/michiyasunaga/dragon.

Haoyu Zhou, Qing Qing, Caichong Li et al.

Recent advancements in Vision-Language Models (VLMs) have significantly enhanced their ability to interpret complex visual semantics, yet their capacity for chronological reasoning remains under-explored. In this paper, we introduce a novel benchmark specifically designed to evaluate how VLMs perceive and reason about chronological information within and across images. Unlike existing video-based benchmarks that focus on frame sequencing, our work delves into the underlying logic of chronological judgment and the expansion toward multimodal integration. To facilitate this, we construct three specialized datasets: one containing visually similar objects spanning long historical durations, another categorized by diverse event and object types, and a third pairing images with time-sensitive news text for cross-modal alignment. Through extensive experiments, we analyze whether models exhibit performance disparities across categories and, crucially, explore whether they rely on ``incorrect shortcuts'', such as image color rather than genuine chronological features. Our results reveal that while VLMs show promise, they frequently exploit superficial cues like grayscale versus color filters to bypass authentic chronological reasoning. By providing these high-quality datasets and a rigorous evaluation framework, we offer a diagnostic tool to identify current limitations and guide the development of more robust, logically grounded multimodal models. The source code is shown in https://github.com/LuoRenqiang/ChronoVision.

Jiayuan Mao, Xuelin Yang, Xikun Zhang et al. · stanford

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.

Charlotte Bunne, Yusuf Roohani, Yanay Rosen et al.

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.

Hudi He, Fukun Wang, Zhe Wang et al.

Evaluating fairness in Spiking Neural Networks (SNNs) demands rigorous benchmarks that reflect real-world complexities, yet existing assessments remain limited by superficial dataset diversity and idealized hardware assumptions. This work introduces the first systematic fairness benchmark for SNNs, addressing three critical dimensions of realism: (1) demographic coverage gaps in training data, (2) spurious feature leakage (e.g., skin tone as a proxy for class labels), and (3) deployment-environment mismatches (e.g., edge devices with constrained spike encoding). Our framework integrates four cross-demographic datasets with controlled bias injections and three neuromorphic hardware simulators (Loihi 2, SpiNNaker), enabling isolated analysis of fairness-performance trade-offs under resource constraints. Standardized evaluations of 12 state-of-the-art SNNs reveal stark disparities: models trained on biased data exhibit 23\% higher false positive rates for underrepresented groups, while hardware limitations (e.g., reduced spike precision) further amplify accuracy gaps by up to 41\% in edge deployments. Critically, bias mitigation strategies developed for cloud-based SNNs often degrade under resource constraints, highlighting the need for co-design principles that jointly optimize fairness and hardware efficiency. By bridging algorithmic fairness research with neuromorphic engineering, our benchmark provides a foundation for trustworthy SNNs in socially critical applications such as healthcare and autonomous systems. Our code is available at: https://anonymous.4open.science/r/SNN-Benchmarks-8017.

Wen Shi, Zhe Wang, Huafei Huang et al.

Graph Anomaly Detection (GAD) aims to identify atypical graph entities, such as nodes, edges, or substructures, that deviate significantly from the majority. While existing text-rich approaches typically integrate structural context into the data representation pipeline using raw textual features, they often neglect the structural context of nodes. This limitation hinders their ability to detect sophisticated anomalies arising from inconsistencies between a node's inherent content and its topological role. To bridge this gap, we propose TERGAD (Structure-aware Text-enhanced Representations for Graph Anomaly Detection), A novel data augmentation framework that enriches structural semantics for GAD via the semantic reasoning capabilities of Large Language Models (LLMs). Specifically, TERGAD translates node-level topological properties into descriptive natural language narratives, which are subsequently processed by an LLM to derive high-level semantic embeddings. These embeddings are then adaptively fused with original node attributes through a gated dual-branch autoencoder to jointly reconstruct both graph structure and node features. The anomaly score is computed based on the integrated reconstruction error, effectively capturing deviations in both observable attributes and LLM-informed semantic expectations. Extensive experiments on six real-world datasets demonstrate that TERGAD consistently outperforms state-of-the-art baselines. Furthermore, our ablation studies validate the indispensable role of structural semantic guidance and the efficacy of the gated fusion mechanism. Code is available at https://github.com/Kantorakitty/TERGAD-main.

Guiquan Sun, Xikun Zhang, Jingchao Ni et al.

Continual graph learning (CGL) aims to learn from dynamically evolving graphs while mitigating catastrophic forgetting. Existing CGL approaches typically adopt a task-based formulation, where the data stream is partitioned into a sequence of discrete tasks with pre-defined boundaries. However, such assumptions rarely hold in real-world environments, where data distributions evolve continuously and task identity is often unavailable. To better reflect realistic non-stationary environments, we revisit continual graph learning from a task-free perspective. We propose a unified formulation that models the data stream as a time-varying mixture of latent task distributions, enabling continuous modeling of distribution drift. Based on this formulation, we construct DRIFT, a benchmark that spans a spectrum of transition dynamics ranging from hard task switches to smooth distributional drift through a Gaussian parameterization. We evaluate representative continual learning methods under this task-free setting and observe substantial performance degradation compared to traditional task-based protocols. Our findings indicate that many existing approaches implicitly rely on task boundary information and struggle under realistic task-free graph streams. This work highlights the importance of studying continual graph learning under realistic non-stationary conditions and provides a benchmark for future research in this direction. Our code is available at https://github.com/gqBond/DRIFT.

Yihan Gao, Chenxi Huang, Wen Shi et al.

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.

Yao Li, Xikun Zhang, Xiaotao Shen et al.

Epigenetic clocks based on DNA methylation have emerged as powerful tools for estimating biological age, with broad applications in aging research, age-related disease studies, and longevity science. Despite advances across machine learning approaches to epigenetic age prediction, spanning penalised linear regression, deep feedforward networks, residual architectures, and graph neural networks, no existing method jointly models co-methylation graph structure and site-specific DNA sequence context within a unified framework. We propose a unified sequence--graph integration framework for epigenetic age prediction that addresses this gap, integrating eight-dimensional DNA sequence statistical features through a lightweight gated modulation mechanism that adaptively scales each site's methylation signal according to its sequence-determined biological relevance prior to graph convolution. Evaluated on 3,707 blood methylation samples against a comprehensive set of baselines, our method achieves a test MAE of 3.149 years, a 12.8\% improvement over the strongest graph-based baseline. Biologically informed statistical features outperform CNN-based sequence encoding, demonstrating that handcrafted sequence features are more effective than end-to-end learned representations in this data regime. Post-hoc interpretability analysis identifies CpG density and local adenine frequency as features with age-dependent importance shifts, consistent with known mechanisms of age-related hypermethylation at CpG-dense promoter regions. Our code is at https://github.com/yaoli2022/graphage-seq.

Yousef A. Radwan, Yao Li, Qing Qing et al.

Biomedical knowledge graphs underwrite drug repurposing and clinical decision support, yet the upstream ontologies they depend on update on independent cycles that add millions of edges and deprecate hundreds of thousands more between releases. Yet existing continual graph learning has been studied almost exclusively on synthetic random splits of static, generic KGs, a regime that cannot reproduce the asynchronous, structured evolution real biomedical KGs undergo. To this end, we introduce PrimeKG-CL, a CGL benchmark built from nine authoritative biomedical databases (129K+ nodes, 8.1M+ edges, 10 node types, 30 relation types) with two genuine temporal snapshots (June 2021, July 2023; 5.83M edges added, 889K removed, 7.21M persistent), 10 entity-type-grouped tasks, multimodal node features, and a per-task persistent/added/removed test stratification. On three tasks (biomedical relationship prediction, entity classification, KGQA), we evaluate six CL strategies across four KGE decoders, plus LKGE, an LLM-RAG agent, and CMKL. We find that decoder choice and continual learning strategy interact strongly: no single strategy performs best across all decoders, and mismatched combinations can significantly degrade performance. Moreover, only DistMult exhibits a clear separation between persistent and deprecated knowledge, indicating that standard metrics conflate retention of still-valid facts with failure to forget outdated ones; this effect is absent under RotatE. In addition, multimodal features improve entity-level tasks by up to 60%, and a recent CKGE framework (IncDE) failed to scale to our 5.67M-triple base task across five attempts up to 350GB RAM. Data, pipeline, baselines, and the stratified split are released openly. Dataset:huggingface.co/datasets/yradwan147/PrimeKGCL|Code:github.com/yradwan147/primekg-cl-neurips2026

Yousef A. Radwan, Yao Li, Qing Qing et al.

Biomedical knowledge graphs are increasingly large, dynamic, and multimodal, driven by rapid advances in biotechnology such as high-throughput sequencing. Machine learning models can infer previously unobserved biomedical relationships and characterize biomedical entities in these graphs, but existing knowledge graph embedding methods and their continual learning extensions either assume static graph structure or fail to exploit multimodal information under evolving data distributions. They also apply uniform regularization across all model parameters, ignoring that different modalities may exhibit distinct forgetting dynamics as the graph evolves. We propose the Continual Multimodal Knowledge Graph Learner (CMKL), a CL framework for biomedical KGs that natively encodes structure, text, and molecules, fuses them through a Mixture-of-Experts (MoE) router, and protects previously learned knowledge with standard EWC regularization and a K-means-diverse multimodal replay buffer. We evaluate CMKL on a 129K-entity biomedical continual benchmark with 10 tasks. On continual biomedical entity classification, CMKL reaches AP 0.591 versus 0.370 for the strongest structural baseline, a 60% gain that is driven by access to multimodal features and preserved across the sequence with near-zero forgetting (AF 0.008). On continual relationship prediction, CMKL reaches AP $0.062$, matching Naive Sequential and EWC (0.058) within seed noise and outperforming Joint Training (0.047, p=0.045) and LKGE (0.039). A frozen-text ablation reaches AP 0.136, more than double any jointly trained model, yet that signal is unreachable by margin-ranking gradients: the greedy-modality asymmetry lives at the representation level, not the fusion level, and MoE routing manages it by suppressing the unreachable modality without forcing it through a learned bottleneck. Code: github.com/yradwan147/cmkl-neurips2026

Danhui Zhang, Zhe Wang, Qing Qing et al.

Graph learning research has increasingly shifted toward continual graph learning (CGL), which better reflects real-world scenarios where graphs evolve over time. However, existing CGL methods largely assume clean supervision and overlook a critical challenge: the newly arriving portions of the graph are often noisy, due to annotation errors or adversarial corruption. This mismatch limits their applicability in practice. In this work, we study robust continual graph learning, where models must simultaneously handle catastrophic forgetting and noisy supervision in evolving graph data. We show that label noise introduces a new failure mode, catastrophic remembering, where models persistently reinforce corrupted knowledge across tasks. To address these challenges, we propose a Unified Flow-Oriented framework (UFO). First, UFO models conditional feature distributions via flow-based generative modeling and produces replay representations, mitigating forgetting without storing historical data. Second, UFO estimates instance-level reliability scores to distinguish clean from noisy nodes, reducing the impact of corrupted supervision and alleviating catastrophic remembering. Extensive experiments on four benchmark graph datasets under varying noise ratios demonstrate that UFO consistently outperforms existing methods in both accuracy and forgetting metrics. Code is available at: https://anonymous.4open.science/r/UFO.

Qing Qing, Xikun Zhang, Zhongyuan Zhang et al.

Aging clocks aim to estimate biological age, a measure of physiological state distinct from chronological age, from observable biomarkers, and are widely used for health assessment and disease analysis. DNA methylation is a particularly informative biomarker due to its stability and strong association with aging, and recent learning-based approaches have improved predictive performance. However, most existing methods treat CpG sites as independent features, overlooking the complex and heterogeneous biological relationships among them. We propose RelAge-GNN, a multi-relational graph neural network framework for DNA methylation-based age prediction. Our method constructs three complementary graphs capturing co-methylation patterns, genomic co-localization, and gene-level associations among CpG sites. Each graph is modeled by an independent GNN branch, and a learnable gating mechanism adaptively fuses the resulting representations. Experiments on large-scale datasets show that RelAge-GNN achieves competitive accuracy and stronger correlation with chronological age compared to state-of-the-art methods. Moreover, the model exhibits improved sensitivity in detecting age acceleration across diverse disease cohorts, highlighting its potential utility for disease characterization. Finally, through post hoc interpretability analyses, we quantify the contributions of different relational structures and CpG sites, providing biologically meaningful insights and suggesting potential directions for aging-related research. Our code is available at: https://anonymous.4open.science/r/RelAge-GNN-F1E3/.

Jingjing Zhou, Shiyu Huang, Qing Qing et al.

Graph Anomaly Detection (GAD) is a critical task in graph machine learning with vital applications in financial fraud detection and social platform governance. However, existing GAD benchmarks are often restricted to small-scale, curated graphs with relatively balanced anomaly ratios, leaving a substantial gap between academic evaluation and real-world deployment. To bridge this gap, we present a multi-dimensional benchmark that systematically evaluates GAD models under three deployment-relevant challenges: million-scale graphs, extreme anomaly scarcity, and missing node attributes. We derive a family of controlled benchmark variants from five diverse graphs, including two native industrial-scale datasets with over 3.7 million nodes. Our extensive evaluation of nine representative GAD models reveals three major limitations: (1) most GNN-based methods fail to scale to million-node graphs due to prohibitive memory requirements; (2) detection performance drops sharply under realistic anomaly ratios (e.g., 0.1\%), often resulting in zero recall; and (3) reconstruction-based models are highly sensitive to attribute imputation strategies. Our findings suggest that strong performance in laboratory settings does not guarantee robustness in production environments. We release this benchmark and empirical evaluation as a diagnostic testbed to promote the development of robust and scalable GAD systems for large-scale, imperfect graphs encountered in practice. Code is available at https://anonymous.4open.science/r/Benchmark_GAD-E7A3.

Yangmei Chen, Zhongyuan Zhang, Xikun Zhang et al.

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.

Xikun Zhang, Dongjin Song, Dacheng Tao

Continual learning on graph data has recently attracted paramount attention for its aim to resolve the catastrophic forgetting problem on existing tasks while adapting the sequentially updated model to newly emerged graph tasks. While there have been efforts to summarize progress on continual learning research over Euclidean data, e.g., images and texts, a systematic review of progress in continual learning on graphs, a.k.a, continual graph learning (CGL) or lifelong graph learning, is still demanding. Graph data are far more complex in terms of data structures and application scenarios, making CGL task settings, model designs, and applications extremely challenging. To bridge the gap, we provide a comprehensive review of existing continual graph learning (CGL) algorithms by elucidating the different task settings and categorizing the existing methods based on their characteristics. We compare the CGL methods with traditional continual learning techniques and analyze the applicability of the traditional continual learning techniques to CGL tasks. Additionally, we review the benchmark works that are crucial to CGL research. Finally, we discuss the remaining challenges and propose several future directions. We will maintain an up-to-date GitHub repository featuring a comprehensive list of CGL algorithms, accessible at https://github.com/UConn-DSIS/Survey-of-Continual-Learning-on-Graphs.

Michael K. Chen, Xikun Zhang, Dacheng Tao

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

Huanjin Yao, Jiaxing Huang, Yawen Qiu et al.

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.

Yan Sun, Qixin Zhang, Zhiyuan Yu et al.

The rapid scaling of large language models (LLMs) has made inference efficiency a primary bottleneck in the practical deployment. To address this, semi-structured sparsity offers a promising solution by strategically retaining $N$ elements out of every $M$ weights, thereby enabling hardware-friendly acceleration and reduced memory. However, existing (N:M)-compatible approaches typically fall into two categories: rule-based layerwise greedy search, which suffers from considerable errors, and gradient-driven combinatorial learning, which incurs prohibitive training costs. To tackle these challenges, we propose a novel linear-space probabilistic framework named MaskPro, which aims to learn a prior categorical distribution for every $M$ consecutive weights and subsequently leverages this distribution to generate the (N:M)-sparsity throughout an $N$-way sampling without replacement. Furthermore, to mitigate the training instability induced by the high variance of policy gradients in the super large combinatorial space, we propose a novel update method by introducing a moving average tracker of loss residuals instead of vanilla loss. Finally, we conduct comprehensive theoretical analysis and extensive experiments to validate the superior performance of MaskPro, as well as its excellent scalability in memory efficiency and exceptional robustness to data samples. Our code is available at https://github.com/woodenchild95/Maskpro.git.

Jingyi Zhang, Jiaxing Huang, Huanjin Yao et al.

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.

Michael K. Chen, Xikun Zhang, Jiaxing Huang et al.

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

Xikun Zhang, Dongjin Song, Yushan Jiang et al.

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.

Yushan Jiang, Zijie Pan, Xikun Zhang et al.

Recently, remarkable progress has been made over large language models (LLMs), demonstrating their unprecedented capability in varieties of natural language tasks. However, completely training a large general-purpose model from the scratch is challenging for time series analysis, due to the large volumes and varieties of time series data, as well as the non-stationarity that leads to concept drift impeding continuous model adaptation and re-training. Recent advances have shown that pre-trained LLMs can be exploited to capture complex dependencies in time series data and facilitate various applications. In this survey, we provide a systematic overview of existing methods that leverage LLMs for time series analysis. Specifically, we first state the challenges and motivations of applying language models in the context of time series as well as brief preliminaries of LLMs. Next, we summarize the general pipeline for LLM-based time series analysis, categorize existing methods into different groups (i.e., direct query, tokenization, prompt design, fine-tune, and model integration), and highlight the key ideas within each group. We also discuss the applications of LLMs for both general and spatial-temporal time series data, tailored to specific domains. Finally, we thoroughly discuss future research opportunities to empower time series analysis with LLMs.

Xingtong Yu, Zhongwei Kuai, Chang Zhou et al.

Reasoning-acting frameworks enhance large language models (LLMs) by interleaving reasoning with actions for dynamic information acquisition. However, extending this paradigm to graph learning remains underexplored. Graph data is inherently structured, with information distributed across nodes and edges and encoded through both topology and latent representations. As a result, effective reasoning over graphs requires not only retrieving informative evidence from the graph, but also progressively refining the accumulated context during multi-step inference. In this work, we propose GraphReAct, a graph reasoning-acting framework that enables step-by-step inference over graph-structured data. Specifically, we design a graph-based action space with two complementary retrieval actions: topological retrieval, which captures local structural dependencies, and semantic retrieval, which accesses non-local but relevant evidence in the representation space. These actions dynamically expand the reasoning context. To further support multi-step reasoning, we introduce another type of action, context refinement, which distills and reorganizes accumulated information into a compact representation. By interleaving reasoning with both retrieval and refinement actions, our framework enables a progressive transition from context expansion to compression. Extensive experiments on six benchmark datasets demonstrate that GraphReAct consistently outperforms state-of-the-art methods, validating the effectiveness of reasoning-acting for graph learning.

Bowen Li, Ziqi Xu, Jing Ren et al.

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.

Jingjing Zhou, Yongshuai Yang, Qing Qing et al.

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.

Tong Yu, Yongcheng Jing, Xikun Zhang et al.

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.

Jinfeng Zhou, Yuxuan Chen, Jianing Yin et al.

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.

Xiangru Jian, Hao Xu, Wei Pang et al.

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.

Qixin Zhang, Yan Sun, Can Jin et al.

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.

Tianyang Luo, Xikun Zhang, Dongjin Song

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.

Elizabeth Fahsbender, Alma Andersson, Jeremy Ash et al.

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.

Guiquan Sun, Xikun Zhang, Jingchao Ni et al.

Heterogeneous graph neural networks have seen rapid progress in web applications such as social networks, knowledge graphs, and recommendation systems, driven by the inherent heterogeneity of web data. However, existing methods typically assume static graphs, while real-world graphs are continuously evolving. This dynamic nature requires models to adapt to new data while preserving existing knowledge. To this end, this work introduces HERO (HEterogeneous continual gRaph learning via meta-knOwledge distillation), a unified framework for continual learning on heterogeneous graphs. HERO employs meta-adaptation, a gradient-based meta-learning strategy that provides directional guidance for rapid adaptation to new tasks with limited samples. To enable efficient and effective knowledge reuse, we propose DiSCo (Diversity Sampling with semantic Consistency), a heterogeneity-aware sampling method that maximizes target node diversity and expands subgraphs along metapaths, retaining critical semantic and structural information with minimal overhead. Furthermore, HERO incorporates heterogeneity-aware knowledge distillation, which aligns knowledge at both the node and semantic levels to balance adaptation and retention across tasks. Extensive experiments on four web-related heterogeneous graph benchmarks demonstrate that HERO substantially mitigates catastrophic forgetting while achieving efficient and consistent knowledge reuse in dynamic web environments.

Renqiang Luo, Ziqi Xu, Xikun Zhang et al.

Augmenting specialised machine learning techniques into traditional graph learning models has achieved notable success across various domains, including federated graph learning, dynamic graph learning, and graph transformers. However, the intricate mechanisms of these specialised techniques introduce significant challenges in maintaining model fairness, potentially resulting in discriminatory outcomes in high-stakes applications such as recommendation systems, disaster response, criminal justice, and loan approval. This paper systematically examines the unique fairness challenges posed by Graph Learning augmented with Machine Learning (GL-ML). It highlights the complex interplay between graph learning mechanisms and machine learning techniques, emphasising how the augmentation of machine learning both enhances and complicates fairness. Additionally, we explore four critical techniques frequently employed to improve fairness in GL-ML methods. By thoroughly investigating the root causes and broader implications of fairness challenges in this rapidly evolving field, this work establishes a robust foundation for future research and innovation in GL-ML fairness.

Xikun Zhang, Dongjin Song, Yixin Chen et al.

Memory replay based techniques have shown great success for continual learning with incrementally accumulated Euclidean data. Directly applying them to continually expanding networks, however, leads to the potential memory explosion problem due to the need to buffer representative nodes and their associated topological neighborhood structures. To this end, we systematically analyze the key challenges in the memory explosion problem, and present a general framework, \textit{i.e.}, Parameter Decoupled Graph Neural Networks (PDGNNs) with Topology-aware Embedding Memory (TEM), to tackle this issue. The proposed framework not only reduces the memory space complexity from $\mathcal{O}(nd^L)$ to $\mathcal{O}(n)$~\footnote{$n$: memory budget, $d$: average node degree, $L$: the radius of the GNN receptive field}, but also fully utilizes the topological information for memory replay. Specifically, PDGNNs decouple trainable parameters from the computation ego-subnetwork via \textit{Topology-aware Embeddings} (TEs), which compress ego-subnetworks into compact vectors (\textit{i.e.}, TEs) to reduce the memory consumption. Based on this framework, we discover a unique \textit{pseudo-training effect} in continual learning on expanding networks and this effect motivates us to develop a novel \textit{coverage maximization sampling} strategy that can enhance the performance with a tight memory budget. Thorough empirical studies demonstrate that, by tackling the memory explosion problem and incorporating topological information into memory replay, PDGNNs with TEM significantly outperform state-of-the-art techniques, especially in the challenging class-incremental setting.

Xikun Zhang, Antoine Bosselut, Michihiro Yasunaga et al.

Answering complex questions about textual narratives requires reasoning over both stated context and the world knowledge that underlies it. However, pretrained language models (LM), the foundation of most modern QA systems, do not robustly represent latent relationships between concepts, which is necessary for reasoning. While knowledge graphs (KG) are often used to augment LMs with structured representations of world knowledge, it remains an open question how to effectively fuse and reason over the KG representations and the language context, which provides situational constraints and nuances. In this work, we propose GreaseLM, a new model that fuses encoded representations from pretrained LMs and graph neural networks over multiple layers of modality interaction operations. Information from both modalities propagates to the other, allowing language context representations to be grounded by structured world knowledge, and allowing linguistic nuances (e.g., negation, hedging) in the context to inform the graph representations of knowledge. Our results on three benchmarks in the commonsense reasoning (i.e., CommonsenseQA, OpenbookQA) and medical question answering (i.e., MedQA-USMLE) domains demonstrate that GreaseLM can more reliably answer questions that require reasoning over both situational constraints and structured knowledge, even outperforming models 8x larger.

Xikun Zhang, Dongjin Song, Dacheng Tao

Despite significant advances in graph representation learning, little attention has been paid to the more practical continual learning scenario in which new categories of nodes (e.g., new research areas in citation networks, or new types of products in co-purchasing networks) and their associated edges are continuously emerging, causing catastrophic forgetting on previous categories. Existing methods either ignore the rich topological information or sacrifice plasticity for stability. To this end, we present Hierarchical Prototype Networks (HPNs) which extract different levels of abstract knowledge in the form of prototypes to represent the continuously expanded graphs. Specifically, we first leverage a set of Atomic Feature Extractors (AFEs) to encode both the elemental attribute information and the topological structure of the target node. Next, we develop HPNs to adaptively select relevant AFEs and represent each node with three levels of prototypes. In this way, whenever a new category of nodes is given, only the relevant AFEs and prototypes at each level will be activated and refined, while others remain uninterrupted to maintain the performance over existing nodes. Theoretically, we first demonstrate that the memory consumption of HPNs is bounded regardless of how many tasks are encountered. Then, we prove that under mild constraints, learning new tasks will not alter the prototypes matched to previous data, thereby eliminating the forgetting problem. The theoretical results are supported by experiments on five datasets, showing that HPNs not only outperform state-of-the-art baseline techniques but also consume relatively less memory.

Rishi Bommasani, Drew A. Hudson, Ehsan Adeli et al.

AI is undergoing a paradigm shift with the rise of models (e.g., BERT, DALL-E, GPT-3) that are trained on broad data at scale and are adaptable to a wide range of downstream tasks. We call these models foundation models to underscore their critically central yet incomplete character. This report provides a thorough account of the opportunities and risks of foundation models, ranging from their capabilities (e.g., language, vision, robotics, reasoning, human interaction) and technical principles(e.g., model architectures, training procedures, data, systems, security, evaluation, theory) to their applications (e.g., law, healthcare, education) and societal impact (e.g., inequity, misuse, economic and environmental impact, legal and ethical considerations). Though foundation models are based on standard deep learning and transfer learning, their scale results in new emergent capabilities,and their effectiveness across so many tasks incentivizes homogenization. Homogenization provides powerful leverage but demands caution, as the defects of the foundation model are inherited by all the adapted models downstream. Despite the impending widespread deployment of foundation models, we currently lack a clear understanding of how they work, when they fail, and what they are even capable of due to their emergent properties. To tackle these questions, we believe much of the critical research on foundation models will require deep interdisciplinary collaboration commensurate with their fundamentally sociotechnical nature.

Xikun Zhang, Deepak Ramachandran, Ian Tenney et al.

Pretrained Language Models (LMs) have been shown to possess significant linguistic, common sense, and factual knowledge. One form of knowledge that has not been studied yet in this context is information about the scalar magnitudes of objects. We show that pretrained language models capture a significant amount of this information but are short of the capability required for general common-sense reasoning. We identify contextual information in pre-training and numeracy as two key factors affecting their performance and show that a simple method of canonicalizing numbers can have a significant effect on the results.

Srijan Kumar, Xikun Zhang, Jure Leskovec

Modeling sequential interactions between users and items/products is crucial in domains such as e-commerce, social networking, and education. Representation learning presents an attractive opportunity to model the dynamic evolution of users and items, where each user/item can be embedded in a Euclidean space and its evolution can be modeled by an embedding trajectory in this space. However, existing dynamic embedding methods generate embeddings only when users take actions and do not explicitly model the future trajectory of the user/item in the embedding space. Here we propose JODIE, a coupled recurrent neural network model that learns the embedding trajectories of users and items. JODIE employs two recurrent neural networks to update the embedding of a user and an item at every interaction. Crucially, JODIE also models the future embedding trajectory of a user/item. To this end, it introduces a novel projection operator that learns to estimate the embedding of the user at any time in the future. These estimated embeddings are then used to predict future user-item interactions. To make the method scalable, we develop a t-Batch algorithm that creates time-consistent batches and leads to 9x faster training. We conduct six experiments to validate JODIE on two prediction tasks---future interaction prediction and state change prediction---using four real-world datasets. We show that JODIE outperforms six state-of-the-art algorithms in these tasks by at least 20% in predicting future interactions and 12% in state change prediction.

Srijan Kumar, Xikun Zhang, Jure Leskovec

Modeling a sequence of interactions between users and items (e.g., products, posts, or courses) is crucial in domains such as e-commerce, social networking, and education to predict future interactions. Representation learning presents an attractive solution to model the dynamic evolution of user and item properties, where each user/item can be embedded in a euclidean space and its evolution can be modeled by dynamic changes in embedding. However, existing embedding methods either generate static embeddings, treat users and items independently, or are not scalable. Here we present JODIE, a coupled recurrent model to jointly learn the dynamic embeddings of users and items from a sequence of user-item interactions. JODIE has three components. First, the update component updates the user and item embedding from each interaction using their previous embeddings with the two mutually-recursive Recurrent Neural Networks. Second, a novel projection component is trained to forecast the embedding of users at any future time. Finally, the prediction component directly predicts the embedding of the item in a future interaction. For models that learn from a sequence of interactions, traditional training data batching cannot be done due to complex user-user dependencies. Therefore, we present a novel batching algorithm called t-Batch that generates time-consistent batches of training data that can run in parallel, giving massive speed-up. We conduct six experiments on two prediction tasks---future interaction prediction and state change prediction---using four real-world datasets. We show that JODIE outperforms six state-of-the-art algorithms in these tasks by up to 22.4%. Moreover, we show that JODIE is highly scalable and up to 9.2x faster than comparable models. As an additional experiment, we illustrate that JODIE can predict student drop-out from courses five interactions in advance.

Xikun Zhang, Chang Xu, Xinmei Tian et al.

This paper investigates body bones from skeleton data for skeleton based action recognition. Body joints, as the direct result of mature pose estimation technologies, are always the key concerns of traditional action recognition methods. However, instead of joints, we humans naturally identify how the human body moves according to shapes, lengths and places of bones, which are more obvious and stable for observation. Hence given graphs generated from skeleton data, we propose to develop convolutions over graph edges that correspond to bones in human skeleton. We describe an edge by integrating its spatial neighboring edges to explore the cooperation between different bones, as well as its temporal neighboring edges to address the consistency of movements in an action. A graph edge convolutional neural network is then designed for skeleton based action recognition. Considering the complementarity between graph node convolution and graph edge convolution, we additionally construct two hybrid neural networks to combine graph node convolutional neural network and graph edge convolutional neural network using shared intermediate layers. Experimental results on Kinetics and NTU-RGB+D datasets demonstrate that our graph edge convolution is effective to capture characteristic of actions and our graph edge convolutional neural network significantly outperforms existing state-of-art skeleton based action recognition methods. Additionally, more performance improvements can be achieved by the hybrid networks.