Gaotang Li

Gaotang Li, Marlena Duda, Xiang Zhang et al.

Brain graphs, which model the structural and functional relationships between brain regions, are crucial in neuroscientific and clinical applications involving graph classification. However, dense brain graphs pose computational challenges including high runtime and memory usage and limited interpretability. In this paper, we investigate effective designs in Graph Neural Networks (GNNs) to sparsify brain graphs by eliminating noisy edges. While prior works remove noisy edges based on explainability or task-irrelevant properties, their effectiveness in enhancing performance with sparsified graphs is not guaranteed. Moreover, existing approaches often overlook collective edge removal across multiple graphs. To address these issues, we introduce an iterative framework to analyze different sparsification models. Our findings are as follows: (i) methods prioritizing interpretability may not be suitable for graph sparsification as they can degrade GNNs' performance in graph classification tasks; (ii) simultaneously learning edge selection with GNN training is more beneficial than post-training; (iii) a shared edge selection across graphs outperforms separate selection for each graph; and (iv) task-relevant gradient information aids in edge selection. Based on these insights, we propose a new model, Interpretable Graph Sparsification (IGS), which enhances graph classification performance by up to 5.1% with 55.0% fewer edges. The retained edges identified by IGS provide neuroscientific interpretations and are supported by well-established literature.

Jiong Zhu, Gaotang Li, Yao-An Yang et al.

Heterophily, or the tendency of connected nodes in networks to have different class labels or dissimilar features, has been identified as challenging for many Graph Neural Network (GNN) models. While the challenges of applying GNNs for node classification when class labels display strong heterophily are well understood, it is unclear how heterophily affects GNN performance in other important graph learning tasks where class labels are not available. In this work, we focus on the link prediction task and systematically analyze the impact of heterophily in node features on GNN performance. Theoretically, we first introduce formal definitions of homophilic and heterophilic link prediction tasks, and present a theoretical framework that highlights the different optimizations needed for the respective tasks. We then analyze how different link prediction encoders and decoders adapt to varying levels of feature homophily and introduce designs for improved performance. Our empirical analysis on a variety of synthetic and real-world datasets confirms our theoretical insights and highlights the importance of adopting learnable decoders and GNN encoders with ego- and neighbor-embedding separation in message passing for link prediction tasks beyond homophily.

Xiusi Chen, Gaotang Li, Ziqi Wang et al.

Reward modeling is essential for aligning large language models with human preferences through reinforcement learning from human feedback. To provide accurate reward signals, a reward model (RM) should stimulate deep thinking and conduct interpretable reasoning before assigning a score or a judgment. Inspired by recent advances of long chain-of-thought on reasoning-intensive tasks, we hypothesize and validate that integrating reasoning capabilities into reward modeling significantly enhances RMs interpretability and performance. To this end, we introduce a new class of generative reward models - Reasoning Reward Models (ReasRMs) - which formulate reward modeling as a reasoning task. We propose a reasoning-oriented training pipeline and train a family of ReasRMs, RM-R1. RM-R1 features a chain-of-rubrics (CoR) mechanism - self-generating sample-level chat rubrics or math/code solutions, and evaluating candidate responses against them. The training of RM-R1 consists of two key stages: (1) distillation of high-quality reasoning chains and (2) reinforcement learning with verifiable rewards. Empirically, our models achieve state-of-the-art performance across three reward model benchmarks on average, outperforming much larger open-weight models (e.g., INF-ORM-Llama3.1-70B) and proprietary ones (e.g., GPT-4o) by up to 4.9%. Beyond final performance, we perform thorough empirical analyses to understand the key ingredients of successful ReasRM training. To facilitate future research, we release six REASRM models along with code and data at https://github.com/RM-R1-UIUC/RM-R1.

Xuying Ning, Katherine Tieu, Dongqi Fu et al.

Recent large language models (LLMs) have demonstrated strong capabilities in understanding and generating code, from competitive programming to repository-level software engineering. In emerging agentic systems, code is no longer only a target output. It increasingly serves as an operational substrate for agent reasoning, acting, environment modeling, and execution-based verification. We frame this shift through the lens of agent harnesses and introduce code as agent harness: a unified view that centers code as the basis for agent infrastructure. To systematically study this perspective, we organize the survey around three connected layers. First, we study the harness interface, where code connects agents to reasoning, action, and environment modeling. Second, we examine harness mechanisms: planning, memory, and tool use for long-horizon execution, together with feedback-driven control and optimization that make harness reliable and adaptive. Third, we discuss scaling the harness from single-agent systems to multi-agent settings, where shared code artifacts support multi-agent coordination, review, and verification. Across these layers, we summarize representative methods and practical applications of code as agent harness, spanning coding assistants, GUI/OS automation, embodied agents, scientific discovery, personalization and recommendation, DevOps, and enterprise workflows. We further outline open challenges for harness engineering, including evaluation beyond final task success, verification under incomplete feedback, regression-free harness improvement, consistent shared state across multiple agents, human oversight for safety-critical actions, and extensions to multimodal environments. By centering code as the harness of agentic AI, this survey provides a unified roadmap toward executable, verifiable, and stateful AI agent systems.

Ruizhong Qiu, Ting-Wei Li, Gaotang Li et al.

Graph neural networks (GNNs) have emerged as a powerful tool for modeling graph-structured data. However, existing GNNs often struggle with heterophilic graphs, where connected nodes tend to have dissimilar features or labels. While numerous methods have been proposed to address this challenge, they primarily focus on architectural designs without directly targeting the root cause of the heterophily problem. These approaches still perform even worse than the simplest MLPs on challenging heterophilic datasets. For instance, our experiments show that 21 latest GNNs still fall behind the MLP on the Actor dataset. This critical challenge calls for an innovative approach to addressing graph heterophily beyond architectural designs. To bridge this gap, we propose and study a new and unexplored paradigm: directly increasing the graph homophily via a carefully designed graph transformation. In this work, we present a simple yet effective framework called GRAPHITE to address graph heterophily. To the best of our knowledge, this work is the first method that explicitly transforms the graph to directly improve the graph homophily. Stemmed from the exact definition of homophily, our proposed GRAPHITE creates feature nodes to facilitate homophilic message passing between nodes that share similar features. Furthermore, we both theoretically and empirically show that our proposed GRAPHITE significantly increases the homophily of originally heterophilic graphs, with only a slight increase in the graph size. Extensive experiments on challenging datasets demonstrate that our proposed GRAPHITE significantly outperforms state-of-the-art methods on heterophilic graphs while achieving comparable accuracy with state-of-the-art methods on homophilic graphs.

Jiarui Liu, Kaustubh Dhole, Yingheng Wang et al.

Reinforcement learning with verifiable rewards (RLVR) has recently emerged as a promising framework for aligning language models with complex reasoning objectives. However, most existing methods optimize only for final task outcomes, leaving models vulnerable to collapse when negative rewards dominate early training. This challenge is especially pronounced in honesty alignment, where models must not only solve answerable queries but also identify when conclusions cannot be drawn from the given premises. Deductive reasoning provides an ideal testbed because it isolates reasoning capability from reliance on external factual knowledge. To investigate honesty alignment, we curate two multi-step deductive reasoning datasets from graph structures, one for linear algebra and one for logical inference, and introduce unanswerable cases by randomly perturbing an edge in half of the instances. We find that GRPO, with or without supervised fine tuning initialization, struggles on these tasks. Through extensive experiments across three models, we evaluate stabilization strategies and show that curriculum learning provides some benefit but requires carefully designed in distribution datasets with controllable difficulty. To address these limitations, we propose Anchor, a reinforcement learning method that injects ground truth trajectories into rollouts, preventing early training collapse. Our results demonstrate that this method stabilizes learning and significantly improves the overall reasoning performance, underscoring the importance of training dynamics for enabling reliable deductive reasoning in aligned language models.

Gaotang Li, Jiarui Liu, Wei Hu

Neural networks produced by standard training are known to suffer from poor accuracy on rare subgroups despite achieving high accuracy on average, due to the correlations between certain spurious features and labels. Previous approaches based on worst-group loss minimization (e.g. Group-DRO) are effective in improving worse-group accuracy but require expensive group annotations for all the training samples. In this paper, we focus on the more challenging and realistic setting where group annotations are only available on a small validation set or are not available at all. We propose BAM, a novel two-stage training algorithm: in the first stage, the model is trained using a bias amplification scheme via introducing a learnable auxiliary variable for each training sample; in the second stage, we upweight the samples that the bias-amplified model misclassifies, and then continue training the same model on the reweighted dataset. Empirically, BAM achieves competitive performance compared with existing methods evaluated on spurious correlation benchmarks in computer vision and natural language processing. Moreover, we find a simple stopping criterion based on minimum class accuracy difference that can remove the need for group annotations, with little or no loss in worst-group accuracy. We perform extensive analyses and ablations to verify the effectiveness and robustness of our algorithm in varying class and group imbalance ratios.

Xiao Lin, Philip Li, Zhichen Zeng et al.

Despite rich safety alignment strategies, large language models (LLMs) remain highly susceptible to jailbreak attacks, which compromise safety guardrails and pose serious security risks. Existing detection methods mainly detect jailbreak status relying on jailbreak templates present in the training data. However, few studies address the more realistic and challenging zero-shot jailbreak detection setting, where no jailbreak templates are available during training. This setting better reflects real-world scenarios where new attacks continually emerge and evolve. To address this challenge, we propose a layer-wise, module-wise, and token-wise amplification framework that progressively magnifies internal feature discrepancies between benign and jailbreak prompts. We uncover safety-relevant layers, identify specific modules that inherently encode zero-shot discriminative signals, and localize informative safety tokens. Building upon these insights, we introduce ALERT (Amplification-based Jailbreak Detector), an efficient and effective zero-shot jailbreak detector that introduces two independent yet complementary classifiers on amplified representations. Extensive experiments on three safety benchmarks demonstrate that ALERT achieves consistently strong zero-shot detection performance. Specifically, (i) across all datasets and attack strategies, ALERT reliably ranks among the top two methods, and (ii) it outperforms the second-best baseline by at least 10% in average Accuracy and F1-score, and sometimes by up to 40%.

Gaotang Li, Yuzhong Chen, Hanghang Tong

Language Models (LMs) often encounter knowledge conflicts when parametric memory contradicts contextual knowledge. Previous works attribute this conflict to the interplay between "memory heads" and "context heads", attention heads assumed to promote either memory or context exclusively. In this study, we go beyond this fundamental assumption by uncovering a critical phenomenon we term the superposition of contextual information and parametric memory, where highly influential attention heads simultaneously contribute to both memory and context. Building upon this insight, we propose Just Run Twice (JuICE), a test-time attention intervention method that steers LMs toward either parametric beliefs or contextual knowledge without requiring fine-tuning. JuICE identifies a set of reliable attention heads and leverages a dual-run approach to mitigate the superposition effects. Extensive experiments across 11 datasets and 6 model architectures demonstrate that JuICE sets the new state-of-the-art performance and robust generalization, achieving significant and consistent improvement across different domains under various conflict types. Finally, we theoretically analyze knowledge conflict and the superposition of contextual information and parametric memory in attention heads, which further elucidates the effectiveness of JuICE in these settings. Our code is available at https://github.com/GaotangLi/JUICE.

Xiao Lin, Zhining Liu, Ze Yang et al.

Warning: This paper contains examples of harmful language and images. Reader discretion is advised. Recently, vision-language models have demonstrated increasing influence in morally sensitive domains such as autonomous driving and medical analysis, owing to their powerful multimodal reasoning capabilities. As these models are deployed in high-stakes real-world applications, it is of paramount importance to ensure that their outputs align with human moral values and remain within moral boundaries. However, existing work on moral alignment either focuses solely on textual modalities or relies heavily on AI-generated images, leading to distributional biases and reduced realism. To overcome these limitations, we introduce MORALISE, a comprehensive benchmark for evaluating the moral alignment of vision-language models (VLMs) using diverse, expert-verified real-world data. We begin by proposing a comprehensive taxonomy of 13 moral topics grounded in Turiel's Domain Theory, spanning the personal, interpersonal, and societal moral domains encountered in everyday life. Built on this framework, we manually curate 2,481 high-quality image-text pairs, each annotated with two fine-grained labels: (1) topic annotation, identifying the violated moral topic(s), and (2) modality annotation, indicating whether the violation arises from the image or the text. For evaluation, we encompass two tasks, \textit{moral judgment} and \textit{moral norm attribution}, to assess models' awareness of moral violations and their reasoning ability on morally salient content. Extensive experiments on 19 popular open- and closed-source VLMs show that MORALISE poses a significant challenge, revealing persistent moral limitations in current state-of-the-art models. The full benchmark is publicly available at https://huggingface.co/datasets/Ze1025/MORALISE.

Zhining Liu, Tianyi Wang, Xiao Lin et al.

Despite substantial efforts toward improving the moral alignment of Vision-Language Models (VLMs), it remains unclear whether their ethical judgments are stable in realistic settings. This work studies moral robustness in VLMs, defined as the ability to preserve moral judgments under textual and visual perturbations that do not alter the underlying moral context. We systematically probe VLMs with a diverse set of model-agnostic multimodal perturbations and find that their moral stances are highly fragile, frequently flipping under simple manipulations. Our analysis reveals systematic vulnerabilities across perturbation types, moral domains, and model scales, including a sycophancy trade-off where stronger instruction-following models are more susceptible to persuasion. We further show that lightweight inference-time interventions can partially restore moral stability. These results demonstrate that moral alignment alone is insufficient and that moral robustness is a necessary criterion for the responsible deployment of VLMs.

Gaotang Li, Bhavana Dalvi Mishra, Zifeng Wang et al.

Training deep research agents, namely systems that plan, search, evaluate evidence, and synthesize long-form reports, pushes reinforcement learning beyond the regime of verifiable rewards. Their outputs lack ground-truth answers, their trajectories span many tool-augmented decisions, and standard post-training offers little mechanism for turning past attempts into reusable experience. In this work, we argue that rubrics should serve not merely as final-answer evaluators, but as the shared interface that structures policy execution, judge feedback, and agent memory. Based on this view, we introduce RubricEM, a rubric-guided reinforcement learning framework that combines stagewise policy decomposition with reflection-based meta-policy evolution. RubricEM first makes research trajectories stage-aware by conditioning planning, evidence gathering, review, and synthesis on self-generated rubrics. It then assigns credit with Stage-Structured GRPO, which uses stagewise rubric judgments to provide denser semantic feedback for long-horizon optimization. In parallel, RubricEM trains a shared-backbone reflection meta-policy that distills judged trajectories into reusable rubric-grounded guidance for future attempts. The resulting RubricEM-8B achieves strong performance across four long-form research benchmarks, outperforming comparable open models and approaching proprietary deep-research systems. Beyond final performance, we perform thorough analyses to understand the key ingredients of RubricEM.

Jiaru Zou, Xiyuan Yang, Ruizhong Qiu et al.

Multi-agent systems (MAS) extend large language models (LLMs) from independent single-model reasoning to coordinative system-level intelligence. While existing LLM agents depend on text-based mediation for reasoning and communication, we take a step forward by enabling models to collaborate directly within the continuous latent space. We introduce LatentMAS, an end-to-end training-free framework that enables pure latent collaboration among LLM agents. In LatentMAS, each agent first performs auto-regressive latent thoughts generation through last-layer hidden embeddings. A shared latent working memory then preserves and transfers each agent's internal representations, ensuring lossless information exchange. We provide theoretical analyses establishing that LatentMAS attains higher expressiveness and lossless information preservation with substantially lower complexity than vanilla text-based MAS. In addition, empirical evaluations across 9 comprehensive benchmarks spanning math and science reasoning, commonsense understanding, and code generation show that LatentMAS consistently outperforms strong single-model and text-based MAS baselines, achieving up to 14.6% higher accuracy, reducing output token usage by 70.8%-83.7%, and providing 4x-4.3x faster end-to-end inference. These results demonstrate that our new latent collaboration framework enhances system-level reasoning quality while offering substantial efficiency gains without any additional training. Code and data are fully open-sourced at https://github.com/Gen-Verse/LatentMAS.

Gaotang Li, Ruizhong Qiu, Xiusi Chen et al.

Supervised fine-tuning (SFT) is the standard approach for post-training large language models (LLMs), yet it often shows limited generalization. We trace this limitation to its default training objective: negative log likelihood (NLL). While NLL is classically optimal when training from scratch, post-training operates in a different paradigm and could violate its optimality assumptions, where models already encode task-relevant priors and supervision can be long and noisy. To this end, we study a general family of probability-based objectives and characterize their effectiveness under different conditions. Through comprehensive experiments and extensive ablation studies across 7 model backbones, 14 benchmarks, and 3 domains, we uncover a critical dimension that governs objective behavior: the model-capability continuum. Near the model-strong end, prior-leaning objectives that downweight low-probability tokens (e.g., $-p$, $-p^{10}$, thresholded variants) consistently outperform NLL; toward the model-weak end, NLL dominates; in between, no single objective prevails. Our theoretical analysis further elucidates how objectives trade places across the continuum, providing a principled foundation for adapting objectives to model capability. Our code is available at https://github.com/GaotangLi/Beyond-Log-Likelihood.

Ruizhong Qiu, Ting-Wei Li, Gaotang Li et al.

Graph neural networks (GNNs) have emerged as a powerful tool for modeling graph-structured data. However, existing GNNs often struggle with heterophilic graphs, where connected nodes tend to have dissimilar features or labels. While numerous methods have been proposed to address this challenge, they primarily focus on architectural designs without directly targeting the root cause of the heterophily problem. These approaches still perform even worse than the simplest MLPs on challenging heterophilic datasets. For instance, our experiments show that 21 latest GNNs still fall behind the MLP on the Actor dataset. This critical challenge calls for an innovative approach to addressing graph heterophily beyond architectural designs. To bridge this gap, we propose and study a new and unexplored paradigm: directly increasing the graph homophily via a carefully designed graph transformation. In this work, we present a simple yet effective framework called GRAPHITE to address graph heterophily. To the best of our knowledge, this work is the first method that explicitly transforms the graph to directly improve the graph homophily. Stemmed from the exact definition of homophily, our proposed GRAPHITE creates feature nodes to facilitate homophilic message passing between nodes that share similar features. Furthermore, we both theoretically and empirically show that our proposed GRAPHITE significantly increases the homophily of originally heterophilic graphs, with only a slight increase in the graph size. Extensive experiments on challenging datasets demonstrate that our proposed GRAPHITE significantly outperforms state-of-the-art methods on heterophilic graphs while achieving comparable accuracy with state-of-the-art methods on homophilic graphs.

Gaotang Li, Danai Koutra, Yujun Yan

We address the key challenge of size-induced distribution shifts in graph neural networks (GNNs) and their impact on the generalization of GNNs to larger graphs. Existing literature operates under diverse assumptions about distribution shifts, resulting in varying conclusions about the generalizability of GNNs. In contrast to prior work, we adopt a data-driven approach to identify and characterize the types of size-induced distribution shifts and explore their impact on GNN performance from a spectral standpoint, a perspective that has been largely underexplored. Leveraging the significant variance in graph sizes in real biological datasets, we analyze biological graphs and find that spectral differences, driven by subgraph patterns (e.g., average cycle length), strongly correlate with GNN performance on larger, unseen graphs. Based on these insights, we propose three model-agnostic strategies to enhance GNNs' awareness of critical subgraph patterns, identifying size-intensive attention as the most effective approach. Extensive experiments with six GNN architectures and seven model-agnostic strategies across five datasets show that our size-intensive attention strategy significantly improves graph classification on test graphs 2 to 10 times larger than the training graphs, boosting F1 scores by up to 8% over strong baselines.