arXiv subjects

Dawei Zhou

Publications and source records attributed to Dawei Zhou.

At least 37 records · Page 2Linked to original sources

arXiv2025

GENUINE: Graph Enhanced Multi-level Uncertainty Estimation for Large Language Models

Uncertainty estimation is essential for enhancing the reliability of Large Language Models (LLMs), particularly in high-stakes applications. Existing methods often overlook semantic dependencies, relying on token-level probability measures that fail to capture structural relationships within the generated text. We propose GENUINE: Graph ENhanced mUlti-level uncertaINty Estimation for Large Language Models, a structure-aware framework that leverages dependency parse trees and hierarchical graph pooling to refine uncertainty quantification. By incorporating supervised learning, GENUINE effectively models semantic and structural relationships, improving confidence assessments. Extensive experiments across NLP tasks show that GENUINE achieves up to 29% higher AUROC than semantic entropy-based approaches and reduces calibration errors by over 15%, demonstrating the effectiveness of graph-based uncertainty modeling. The code is available at https://github.com/ODYSSEYWT/GUQ.

cs.CL↗

arXiv2025

Non-exchangeable Conformal Prediction for Temporal Graph Neural Networks

Conformal prediction for graph neural networks (GNNs) offers a promising framework for quantifying uncertainty, enhancing GNN reliability in high-stakes applications. However, existing methods predominantly focus on static graphs, neglecting the evolving nature of real-world graphs. Temporal dependencies in graph structure, node attributes, and ground truth labels violate the fundamental exchangeability assumption of standard conformal prediction methods, limiting their applicability. To address these challenges, in this paper, we introduce NCPNET, a novel end-to-end conformal prediction framework tailored for temporal graphs. Our approach extends conformal prediction to dynamic settings, mitigating statistical coverage violations induced by temporal dependencies. To achieve this, we propose a diffusion-based non-conformity score that captures both topological and temporal uncertainties within evolving networks. Additionally, we develop an efficiency-aware optimization algorithm that improves the conformal prediction process, enhancing computational efficiency and reducing coverage violations. Extensive experiments on diverse real-world temporal graphs, including WIKI, REDDIT, DBLP, and IBM Anti-Money Laundering dataset, demonstrate NCPNET's capability to ensure guaranteed coverage in temporal graphs, achieving up to a 31% reduction in prediction set size on the WIKI dataset, significantly improving efficiency compared to state-of-the-art methods. Our data and code are available at https://github.com/ODYSSEYWT/NCPNET.

cs.LG↗

arXiv2025

DISPROTBENCH: Uncovering the Functional Limits of Protein Structure Prediction Models in Intrinsically Disordered Regions

Intrinsically disordered regions (IDRs) play central roles in cellular function, yet remain poorly evaluated by existing protein structure prediction benchmarks. Current evaluations largely focus on well-folded domains, overlooking three fundamental challenges in realistic biological settings: the structural complexity of proteins, the resulting low availability of reliable ground truth, and prediction uncertainty that can propagate into high-risk downstream failures, such as in drug discovery, protein-protein interaction modeling, and functional annotation. We present DisProtBench, an IDR-centric benchmark that explicitly incorporates prediction uncertainty into the evaluation of protein structure prediction models (PSPMs). To address structural complexity and ground-truth scarcity, we curate and unify a large-scale, multi-modal dataset spanning disease-relevant IDRs, GPCR-ligand interactions, and multimeric protein complexes. To assess predictive uncertainty, we introduce Functional Uncertainty Sensitivity (FUS), a novel prediction uncertainty-stratified metric that quantifies downstream task performance under prediction uncertainty. Using this benchmark, we conduct a systematic evaluation of state-of-the-art PSPMs and reveal clear, task-dependent failure modes. Protein-protein interaction prediction degrades sharply in IDRs, while structure-based drug discovery remains comparatively robust. These effects are largely invisible to standard global accuracy metrics, which overestimate functional reliability under prediction uncertainty. We have open-sourced our benchmark and the codebase at https://github.com/Susan571/DisProtBench.

q-bio.BM↗

arXiv2025

Cross-Domain Conditional Diffusion Models for Time Series Imputation

Cross-domain time series imputation is an underexplored data-centric research task that presents significant challenges, particularly when the target domain suffers from high missing rates and domain shifts in temporal dynamics. Existing time series imputation approaches primarily focus on the single-domain setting, which cannot effectively adapt to a new domain with domain shifts. Meanwhile, conventional domain adaptation techniques struggle with data incompleteness, as they typically assume the data from both source and target domains are fully observed to enable adaptation. For the problem of cross-domain time series imputation, missing values introduce high uncertainty that hinders distribution alignment, making existing adaptation strategies ineffective. Specifically, our proposed solution tackles this problem from three perspectives: (i) Data: We introduce a frequency-based time series interpolation strategy that integrates shared spectral components from both domains while retaining domain-specific temporal structures, constructing informative priors for imputation. (ii) Model: We design a diffusion-based imputation model that effectively learns domain-shared representations and captures domain-specific temporal dependencies with dedicated denoising networks. (iii) Algorithm: We further propose a cross-domain consistency alignment strategy that selectively regularizes output-level domain discrepancies, enabling effective knowledge transfer while preserving domain-specific characteristics. Extensive experiments on three real-world datasets demonstrate the superiority of our proposed approach. Our code implementation is available here.

cs.LG↗

arXiv2025

EVINET: Towards Open-World Graph Learning via Evidential Reasoning Network

Graph learning has been crucial to many real-world tasks, but they are often studied with a closed-world assumption, with all possible labels of data known a priori. To enable effective graph learning in an open and noisy environment, it is critical to inform the model users when the model makes a wrong prediction to in-distribution data of a known class, i.e., misclassification detection or when the model encounters out-of-distribution from novel classes, i.e., out-of-distribution detection. This paper introduces Evidential Reasoning Network (EVINET), a framework that addresses these two challenges by integrating Beta embedding within a subjective logic framework. EVINET includes two key modules: Dissonance Reasoning for misclassification detection and Vacuity Reasoning for out-of-distribution detection. Extensive experiments demonstrate that EVINET outperforms state-of-the-art methods across multiple metrics in the tasks of in-distribution classification, misclassification detection, and out-of-distribution detection. EVINET demonstrates the necessity of uncertainty estimation and logical reasoning for misclassification detection and out-of-distribution detection and paves the way for open-world graph learning. Our code and data are available at https://github.com/SSSKJ/EviNET.

cs.LG↗

arXiv2025

UniMate: A Unified Model for Mechanical Metamaterial Generation, Property Prediction, and Condition Confirmation

Metamaterials are artificial materials that are designed to meet unseen properties in nature, such as ultra-stiffness and negative materials indices. In mechanical metamaterial design, three key modalities are typically involved, i.e., 3D topology, density condition, and mechanical property. Real-world complex application scenarios place the demanding requirements on machine learning models to consider all three modalities together. However, a comprehensive literature review indicates that most existing works only consider two modalities, e.g., predicting mechanical properties given the 3D topology or generating 3D topology given the required properties. Therefore, there is still a significant gap for the state-of-the-art machine learning models capturing the whole. Hence, we propose a unified model named UNIMATE, which consists of a modality alignment module and a synergetic diffusion generation module. Experiments indicate that UNIMATE outperforms the other baseline models in topology generation task, property prediction task, and condition confirmation task by up to 80.2%, 5.1%, and 50.2%, respectively. We opensource our proposed UNIMATE model and corresponding results at https://github.com/wzhan24/UniMate.

cs.LG↗

arXiv2025

Towards Generalized Proactive Defense against Face Swapping with Contour-Hybrid Watermark

Face swapping, recognized as a privacy and security concern, has prompted considerable defensive research. With the advancements in AI-generated content, the discrepancies between the real and swapped faces have become nuanced. Considering the difficulty of forged traces detection, we shift the focus to the face swapping purpose and proactively embed elaborate watermarks against unknown face swapping techniques. Given that the constant purpose is to swap the original face identity while preserving the background, we concentrate on the regions surrounding the face to ensure robust watermark generation, while embedding the contour texture and face identity information to achieve progressive image determination. The watermark is located in the facial contour and contains hybrid messages, dubbed the contour-hybrid watermark (CMark). Our approach generalizes face swapping detection without requiring any swapping techniques during training and the storage of large-scale messages in advance. Experiments conducted across 8 face swapping techniques demonstrate the superiority of our approach compared with state-of-the-art passive and proactive detectors while achieving a favorable balance between the image quality and watermark robustness.

cs.CV↗

arXiv2025

Plan and Budget: Effective and Efficient Test-Time Scaling on Reasoning Large Language Models

Large Language Models (LLMs) have achieved remarkable success in complex reasoning tasks, but their inference remains computationally inefficient. We observe a common failure mode in many prevalent LLMs, overthinking, where models generate verbose and tangential reasoning traces even for simple queries. Recent work has tried to mitigate this by enforcing fixed token budgets, however, this can lead to underthinking, especially on harder problems. Through empirical analysis, we identify that this inefficiency often stems from unclear problem-solving strategies. To formalize this, we develop a theoretical model, BAM (Budget Allocation Model), which models reasoning as a sequence of sub-questions with varying uncertainty, and introduce the E3 metric to capture the trade-off between correctness and computation efficiency. Building on theoretical results from BAM, we propose Plan-and-Budget, a model-agnostic, test-time framework that decomposes complex queries into sub-questions and allocates token budgets based on estimated complexity using adaptive scheduling. Plan-and-Budget improves reasoning efficiency across a range of tasks and models, achieving up to 70% accuracy gains, 39% token reduction, and 193.8% improvement in E3. Notably, it improves the efficiency of a smaller model (DS-Qwen-32B) to match the efficiency of a larger model (DS-LLaMA-70B), demonstrating Plan-and-Budget's ability to close performance gaps without retraining. Our code is available at https://github.com/junhongmit/P-and-B.

cs.LG↗

arXiv2025

MetamatBench: Integrating Heterogeneous Data, Computational Tools, and Visual Interface for Metamaterial Discovery

Metamaterials, engineered materials with architected structures across multiple length scales, offer unprecedented and tunable mechanical properties that surpass those of conventional materials. However, leveraging advanced machine learning (ML) for metamaterial discovery is hindered by three fundamental challenges: (C1) Data Heterogeneity Challenge arises from heterogeneous data sources, heterogeneous composition scales, and heterogeneous structure categories; (C2) Model Complexity Challenge stems from the intricate geometric constraints of ML models, which complicate their adaptation to metamaterial structures; and (C3) Human-AI Collaboration Challenge comes from the "dual black-box'' nature of sophisticated ML models and the need for intuitive user interfaces. To tackle these challenges, we introduce a unified framework, named MetamatBench, that operates on three levels. (1) At the data level, we integrate and standardize 5 heterogeneous, multi-modal metamaterial datasets. (2) The ML level provides a comprehensive toolkit that adapts 17 state-of-the-art ML methods for metamaterial discovery. It also includes a comprehensive evaluation suite with 12 novel performance metrics with finite element-based assessments to ensure accurate and reliable model validation. (3) The user level features a visual-interactive interface that bridges the gap between complex ML techniques and non-ML researchers, advancing property prediction and inverse design of metamaterials for research and applications. MetamatBench offers a unified platform deployed at http://zhoulab-1.cs.vt.edu:5550 that enables machine learning researchers and practitioners to develop and evaluate new methodologies in metamaterial discovery. For accessibility and reproducibility, we open-source our benchmark and the codebase at https://github.com/cjpcool/Metamaterial-Benchmark.

physics.optics↗

arXiv2025

Scientific Hypothesis Generation and Validation: Methods, Datasets, and Future Directions

Large Language Models (LLMs) are transforming scientific hypothesis generation and validation by enabling information synthesis, latent relationship discovery, and reasoning augmentation. This survey provides a structured overview of LLM-driven approaches, including symbolic frameworks, generative models, hybrid systems, and multi-agent architectures. We examine techniques such as retrieval-augmented generation, knowledge-graph completion, simulation, causal inference, and tool-assisted reasoning, highlighting trade-offs in interpretability, novelty, and domain alignment. We contrast early symbolic discovery systems (e.g., BACON, KEKADA) with modern LLM pipelines that leverage in-context learning and domain adaptation via fine-tuning, retrieval, and symbolic grounding. For validation, we review simulation, human-AI collaboration, causal modeling, and uncertainty quantification, emphasizing iterative assessment in open-world contexts. The survey maps datasets across biomedicine, materials science, environmental science, and social science, introducing new resources like AHTech and CSKG-600. Finally, we outline a roadmap emphasizing novelty-aware generation, multimodal-symbolic integration, human-in-the-loop systems, and ethical safeguards, positioning LLMs as agents for principled, scalable scientific discovery.

cs.CL↗

arXiv2025

LENSLLM: Unveiling Fine-Tuning Dynamics for LLM Selection

The proliferation of open-sourced Large Language Models (LLMs) and diverse downstream tasks necessitates efficient model selection, given the impracticality of fine-tuning all candidates due to computational constraints. Despite the recent advances in LLM selection, a fundamental research question largely remains nascent: how can we model the dynamic behaviors of LLMs during fine-tuning, thereby enhancing our understanding of their generalization performance across diverse downstream tasks? In this work, we propose a novel theoretical framework that provides a proper lens to assess the generalization capabilities of LLMs, thereby enabling accurate and efficient LLM selection for downstream applications. In particular, we first derive a PAC-Bayesian Generalization Bound that unveils fine-tuning dynamics of LLMs and then introduce LENSLLM, a Neural Tangent Kernel (NTK)-based Rectified Scaling Model that enables accurate performance predictions across diverse tasks while maintaining computational efficiency. Extensive empirical results on 3 large-scale benchmarks demonstrate that our model achieves up to 91.1% accuracy and reduces up to 88.5% computational cost in LLM selection, outperforming 5 state-of-the-art methods. We open-source our proposed LENSLLM model and corresponding results at LensLLM.io.

cs.LG↗

arXiv2025

Are Vision LLMs Road-Ready? A Comprehensive Benchmark for Safety-Critical Driving Video Understanding

Vision Large Language Models (VLLMs) have demonstrated impressive capabilities in general visual tasks such as image captioning and visual question answering. However, their effectiveness in specialized, safety-critical domains like autonomous driving remains largely unexplored. Autonomous driving systems require sophisticated scene understanding in complex environments, yet existing multimodal benchmarks primarily focus on normal driving conditions, failing to adequately assess VLLMs' performance in safety-critical scenarios. To address this, we introduce DVBench, a pioneering benchmark designed to evaluate the performance of VLLMs in understanding safety-critical driving videos. Built around a hierarchical ability taxonomy that aligns with widely adopted frameworks for describing driving scenarios used in assessing highly automated driving systems, DVBench features 10,000 multiple-choice questions with human-annotated ground-truth answers, enabling a comprehensive evaluation of VLLMs' capabilities in perception and reasoning. Experiments on 14 SOTA VLLMs, ranging from 0.5B to 72B parameters, reveal significant performance gaps, with no model achieving over 40% accuracy, highlighting critical limitations in understanding complex driving scenarios. To probe adaptability, we fine-tuned selected models using domain-specific data from DVBench, achieving accuracy gains ranging from 5.24 to 10.94 percentage points, with relative improvements of up to 43.59%. This improvement underscores the necessity of targeted adaptation to bridge the gap between general-purpose VLLMs and mission-critical driving applications. DVBench establishes an essential evaluation framework and research roadmap for developing VLLMs that meet the safety and robustness requirements for real-world autonomous systems. We released the benchmark toolbox and the fine-tuned model at: https://github.com/tong-zeng/DVBench.git.

cs.CV↗

arXiv2025

Structure-Accurate Medical Image Translation via Dynamic Frequency Balance and Knowledge Guidance

Multimodal medical images play a crucial role in the precise and comprehensive clinical diagnosis. Diffusion model is a powerful strategy to synthesize the required medical images. However, existing approaches still suffer from the problem of anatomical structure distortion due to the overfitting of high-frequency information and the weakening of low-frequency information. Thus, we propose a novel method based on dynamic frequency balance and knowledge guidance. Specifically, we first extract the low-frequency and high-frequency components by decomposing the critical features of the model using wavelet transform. Then, a dynamic frequency balance module is designed to adaptively adjust frequency for enhancing global low-frequency features and effective high-frequency details as well as suppressing high-frequency noise. To further overcome the challenges posed by the large differences between different medical modalities, we construct a knowledge-guided mechanism that fuses the prior clinical knowledge from a visual language model with visual features, to facilitate the generation of accurate anatomical structures. Experimental evaluations on multiple datasets show the proposed method achieves significant improvements in qualitative and quantitative assessments, verifying its effectiveness and superiority.

cs.CV↗

arXiv2025

A Knowledge-guided Adversarial Defense for Resisting Malicious Visual Manipulation

Malicious applications of visual manipulation have raised serious threats to the security and reputation of users in many fields. To alleviate these issues, adversarial noise-based defenses have been enthusiastically studied in recent years. However, ``data-only" methods tend to distort fake samples in the low-level feature space rather than the high-level semantic space, leading to limitations in resisting malicious manipulation. Frontier research has shown that integrating knowledge in deep learning can produce reliable and generalizable solutions. Inspired by these, we propose a knowledge-guided adversarial defense (KGAD) to actively force malicious manipulation models to output semantically confusing samples. Specifically, in the process of generating adversarial noise, we focus on constructing significant semantic confusions at the domain-specific knowledge level, and exploit a metric closely related to visual perception to replace the general pixel-wise metrics. The generated adversarial noise can actively interfere with the malicious manipulation model by triggering knowledge-guided and perception-related disruptions in the fake samples. To validate the effectiveness of the proposed method, we conduct qualitative and quantitative experiments on human perception and visual quality assessment. The results on two different tasks both show that our defense provides better protection compared to state-of-the-art methods and achieves great generalizability.

cs.CV↗

arXiv2025

TransNet: Transfer Knowledge for Few-shot Knowledge Graph Completion

Knowledge graphs (KGs) are ubiquitous and widely used in various applications. However, most real-world knowledge graphs are incomplete, which significantly degrades their performance on downstream tasks. Additionally, the relationships in real-world knowledge graphs often follow a long-tail distribution, meaning that most relations are represented by only a few training triplets. To address these challenges, few-shot learning has been introduced. Few-shot KG completion aims to make accurate predictions for triplets involving novel relations when only a limited number of training triplets are available. Although many methods have been proposed, they typically learn each relation individually, overlooking the correlations between different tasks and the relevant information in previously trained tasks. In this paper, we propose a transfer learning-based few-shot KG completion method (TransNet). By learning the relationships between different tasks, TransNet effectively transfers knowledge from similar tasks to improve the current task's performance. Furthermore, by employing meta-learning, TransNet can generalize effectively to new, unseen relations. Extensive experiments on benchmark datasets demonstrate the superiority of TransNet over state-of-the-art methods. Code can be found at https://github.com/lihuiliullh/TransNet/tree/main

cs.AI↗

arXiv2025

Improving Adversarial Robustness via Phase and Amplitude-aware Prompting

Deep neural networks are found to be vulnerable to adversarial perturbations. The prompt-based defense has been increasingly studied due to its high efficiency. However, existing prompt-based defenses mainly exploited mixed prompt patterns, where critical patterns closely related to object semantics lack sufficient focus. The phase and amplitude spectra have been proven to be highly related to specific semantic patterns and crucial for robustness. To this end, in this paper, we propose a Phase and Amplitude-aware Prompting (PAP) defense. Specifically, we construct phase-level and amplitude-level prompts for each class, and adjust weights for prompting according to the model's robust performance under these prompts during training. During testing, we select prompts for each image using its predicted label to obtain the prompted image, which is inputted to the model to get the final prediction. Experimental results demonstrate the effectiveness of our method.

cs.CV↗

arXiv2024

MetaScientist: A Human-AI Synergistic Framework for Automated Mechanical Metamaterial Design

The discovery of novel mechanical metamaterials, whose properties are dominated by their engineered structures rather than chemical composition, is a knowledge-intensive and resource-demanding process. To accelerate the design of novel metamaterials, we present MetaScientist, a human-in-the-loop system that integrates advanced AI capabilities with expert oversight with two primary phases: (1) hypothesis generation, where the system performs complex reasoning to generate novel and scientifically sound hypotheses, supported with domain-specific foundation models and inductive biases retrieved from existing literature; (2) 3D structure synthesis, where a 3D structure is synthesized with a novel 3D diffusion model based on the textual hypothesis and refined it with a LLM-based refinement model to achieve better structure properties. At each phase, domain experts iteratively validate the system outputs, and provide feedback and supplementary materials to ensure the alignment of the outputs with scientific principles and human preferences. Through extensive evaluation from human scientists, MetaScientist is able to deliver novel and valid mechanical metamaterial designs that have the potential to be highly impactful in the metamaterial field.

cs.AI↗

arXiv2024

Enhancing Temporal Link Prediction with HierTKG: A Hierarchical Temporal Knowledge Graph Framework

The rapid spread of misinformation on social media, especially during crises, challenges public decision-making. To address this, we propose HierTKG, a framework combining Temporal Graph Networks (TGN) and hierarchical pooling (DiffPool) to model rumor dynamics across temporal and structural scales. HierTKG captures key propagation phases, enabling improved temporal link prediction and actionable insights for misinformation control. Experiments demonstrate its effectiveness, achieving an MRR of 0.9845 on ICEWS14 and 0.9312 on WikiData, with competitive performance on noisy datasets like PHEME (MRR: 0.8802). By modeling structured event sequences and dynamic social interactions, HierTKG adapts to diverse propagation patterns, offering a scalable and robust solution for real-time analysis and prediction of rumor spread, aiding proactive intervention strategies.

cs.SI↗