arXiv subjects

Kaize Ding

Publications and source records attributed to Kaize Ding.

At least 55 records · Page 3Linked to original sources

arXiv2025

POLO: Preference-Guided Multi-Turn Reinforcement Learning for Lead Optimization

Lead optimization in drug discovery requires efficiently navigating vast chemical space through iterative cycles to enhance molecular properties while preserving structural similarity to the original lead compound. Despite recent advances, traditional optimization methods struggle with sample efficiency-achieving good optimization performance with limited oracle evaluations. Large Language Models (LLMs) provide a promising approach through their in-context learning and instruction following capabilities, which align naturally with these iterative processes. However, existing LLM-based methods fail to leverage this strength, treating each optimization step independently. To address this, we present POLO (Preference-guided multi-turn Optimization for Lead Optimization), which enables LLMs to learn from complete optimization trajectories rather than isolated steps. At its core, POLO introduces Preference-Guided Policy Optimization (PGPO), a novel reinforcement learning algorithm that extracts learning signals at two complementary levels: trajectory-level optimization reinforces successful strategies, while turn-level preference learning provides dense comparative feedback by ranking intermediate molecules within each trajectory. Through this dual-level learning from intermediate evaluation, POLO achieves superior sample efficiency by fully exploiting each costly oracle call. Extensive experiments demonstrate that POLO achieves 84% average success rate on single-property tasks (2.3x better than baselines) and 50% on multi-property tasks using only 500 oracle evaluations, significantly advancing the state-of-the-art in sample-efficient molecular optimization.

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arXiv2025

AMANDA: Agentic Medical Knowledge Augmentation for Data-Efficient Medical Visual Question Answering

Medical Multimodal Large Language Models (Med-MLLMs) have shown great promise in medical visual question answering (Med-VQA). However, when deployed in low-resource settings where abundant labeled data are unavailable, existing Med-MLLMs commonly fail due to their medical reasoning capability bottlenecks: (i) the intrinsic reasoning bottleneck that ignores the details from the medical image; (ii) the extrinsic reasoning bottleneck that fails to incorporate specialized medical knowledge. To address those limitations, we propose AMANDA, a training-free agentic framework that performs medical knowledge augmentation via LLM agents. Specifically, our intrinsic medical knowledge augmentation focuses on coarse-to-fine question decomposition for comprehensive diagnosis, while extrinsic medical knowledge augmentation grounds the reasoning process via biomedical knowledge graph retrieval. Extensive experiments across eight Med-VQA benchmarks demonstrate substantial improvements in both zero-shot and few-shot Med-VQA settings. The code is available at https://github.com/REAL-Lab-NU/AMANDA.

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arXiv2025

Explaining Length Bias in LLM-Based Preference Evaluations

The use of large language models (LLMs) as judges, particularly in preference comparisons, has become widespread, but this reveals a notable bias towards longer responses, undermining the reliability of such evaluations. To better understand such bias, we propose to decompose the preference evaluation metric, specifically the win rate, into two key components: desirability and information mass, where the former is length-independent and related to trustworthiness such as correctness, toxicity, and consistency, and the latter is length-dependent and represents the amount of information in the response. We empirically demonstrated the decomposition through controlled experiments and found that response length impacts evaluations by influencing information mass. To derive a reliable evaluation metric that assesses content quality without being confounded by response length, we propose AdapAlpaca, a simple yet effective adjustment to win rate measurement. Specifically, AdapAlpaca ensures a fair comparison of response quality by aligning the lengths of reference and test model responses under equivalent length intervals.

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arXiv2025

Fact or Facsimile? Evaluating the Factual Robustness of Modern Retrievers

Dense retrievers and rerankers are central to retrieval-augmented generation (RAG) pipelines, where accurately retrieving factual information is crucial for maintaining system trustworthiness and defending against RAG poisoning. However, little is known about how much factual competence these components inherit or lose from the large language models (LLMs) they are based on. We pair 12 publicly released embedding checkpoints with their original base LLMs and evaluate both sets on a factuality benchmark. Across every model evaluated, the embedding variants achieve markedly lower accuracy than their bases, with absolute drops ranging from 12 to 43 percentage points (median 28 pts) and typical retriever accuracies collapsing into the 25-35 % band versus the 60-70 % attained by the generative models. This degradation intensifies under a more demanding condition: when the candidate pool per question is expanded from four options to one thousand, the strongest retriever's top-1 accuracy falls from 33 % to 26 %, revealing acute sensitivity to distractor volume. Statistical tests further show that, for every embedding model, cosine-similarity scores between queries and correct completions are significantly higher than those for incorrect ones (p < 0.01), indicating decisions driven largely by surface-level semantic proximity rather than factual reasoning. To probe this weakness, we employed GPT-4.1 to paraphrase each correct completion, creating a rewritten test set that preserved factual truth while masking lexical cues, and observed that over two-thirds of previously correct predictions flipped to wrong, reducing overall accuracy to roughly one-third of its original level. Taken together, these findings reveal a systematic trade-off introduced by contrastive learning for retrievers: gains in semantic retrieval are paid for with losses in parametric factual knowledge......

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arXiv2025

A Systematic Survey of Model Extraction Attacks and Defenses: State-of-the-Art and Perspectives

Machine learning (ML) models have significantly grown in complexity and utility, driving advances across multiple domains. However, substantial computational resources and specialized expertise have historically restricted their wide adoption. Machine-Learning-as-a-Service (MLaaS) platforms have addressed these barriers by providing scalable, convenient, and affordable access to sophisticated ML models through user-friendly APIs. While this accessibility promotes widespread use of advanced ML capabilities, it also introduces vulnerabilities exploited through Model Extraction Attacks (MEAs). Recent studies have demonstrated that adversaries can systematically replicate a target model's functionality by interacting with publicly exposed interfaces, posing threats to intellectual property, privacy, and system security. In this paper, we offer a comprehensive survey of MEAs and corresponding defense strategies. We propose a novel taxonomy that classifies MEAs according to attack mechanisms, defense approaches, and computing environments. Our analysis covers various attack techniques, evaluates their effectiveness, and highlights challenges faced by existing defenses, particularly the critical trade-off between preserving model utility and ensuring security. We further assess MEAs within different computing paradigms and discuss their technical, ethical, legal, and societal implications, along with promising directions for future research. This systematic survey aims to serve as a valuable reference for researchers, practitioners, and policymakers engaged in AI security and privacy. Additionally, we maintain an online repository continuously updated with related literature at https://github.com/kzhao5/ModelExtractionPapers.

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arXiv2025

A Survey on Model Extraction Attacks and Defenses for Large Language Models

Model extraction attacks pose significant security threats to deployed language models, potentially compromising intellectual property and user privacy. This survey provides a comprehensive taxonomy of LLM-specific extraction attacks and defenses, categorizing attacks into functionality extraction, training data extraction, and prompt-targeted attacks. We analyze various attack methodologies including API-based knowledge distillation, direct querying, parameter recovery, and prompt stealing techniques that exploit transformer architectures. We then examine defense mechanisms organized into model protection, data privacy protection, and prompt-targeted strategies, evaluating their effectiveness across different deployment scenarios. We propose specialized metrics for evaluating both attack effectiveness and defense performance, addressing the specific challenges of generative language models. Through our analysis, we identify critical limitations in current approaches and propose promising research directions, including integrated attack methodologies and adaptive defense mechanisms that balance security with model utility. This work serves NLP researchers, ML engineers, and security professionals seeking to protect language models in production environments.

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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.

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arXiv2025

A Survey of Large Language Models for Text-Guided Molecular Discovery: from Molecule Generation to Optimization

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal inputs. To advance the new field of LLM for molecular discovery, this survey provides an up-to-date and forward-looking review of the emerging use of LLMs for two central tasks: molecule generation and molecule optimization. Based on our proposed taxonomy for both problems, we analyze representative techniques in each category, highlighting how LLM capabilities are leveraged across different learning settings. In addition, we include the commonly used datasets and evaluation protocols. We conclude by discussing key challenges and future directions, positioning this survey as a resource for researchers working at the intersection of LLMs and molecular science. A continuously updated reading list is available at https://github.com/REAL-Lab-NU/Awesome-LLM-Centric-Molecular-Discovery.

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arXiv2025

LEGO-Learn: Label-Efficient Graph Open-Set Learning

How can we train graph-based models to recognize unseen classes while keeping labeling costs low? Graph open-set learning (GOL) and out-of-distribution (OOD) detection aim to address this challenge by training models that can accurately classify known, in-distribution (ID) classes while identifying and handling previously unseen classes during inference. It is critical for high-stakes, real-world applications where models frequently encounter unexpected data, including finance, security, and healthcare. However, current GOL methods assume access to many labeled ID samples, which is unrealistic for large-scale graphs due to high annotation costs. In this paper, we propose LEGO-Learn (Label-Efficient Graph Open-set Learning), a novel framework that tackles open-set node classification on graphs within a given label budget by selecting the most informative ID nodes. LEGO-Learn employs a GNN-based filter to identify and exclude potential OOD nodes and then select highly informative ID nodes for labeling using the K-Medoids algorithm. To prevent the filter from discarding valuable ID examples, we introduce a classifier that differentiates between the C known ID classes and an additional class representing OOD nodes (hence, a C+1 classifier). This classifier uses a weighted cross-entropy loss to balance the removal of OOD nodes while retaining informative ID nodes. Experimental results on four real-world datasets demonstrate that LEGO-Learn significantly outperforms leading methods, with up to a 6.62% improvement in ID classification accuracy and a 7.49% increase in AUROC for OOD detection.

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arXiv2025

Let's Ask GNN: Empowering Large Language Model for Graph In-Context Learning

Textual Attributed Graphs (TAGs) are crucial for modeling complex real-world systems, yet leveraging large language models (LLMs) for TAGs presents unique challenges due to the gap between sequential text processing and graph-structured data. We introduce AskGNN, a novel approach that bridges this gap by leveraging In-Context Learning (ICL) to integrate graph data and task-specific information into LLMs. AskGNN employs a Graph Neural Network (GNN)-powered structure-enhanced retriever to select labeled nodes across graphs, incorporating complex graph structures and their supervision signals. Our learning-to-retrieve algorithm optimizes the retriever to select example nodes that maximize LLM performance on graph. Experiments across three tasks and seven LLMs demonstrate AskGNN's superior effectiveness in graph task performance, opening new avenues for applying LLMs to graph-structured data without extensive fine-tuning.

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arXiv2025

Unifying Unsupervised Graph-Level Anomaly Detection and Out-of-Distribution Detection: A Benchmark

To build safe and reliable graph machine learning systems, unsupervised graph-level anomaly detection (GLAD) and unsupervised graph-level out-of-distribution (OOD) detection (GLOD) have received significant attention in recent years. Though those two lines of research indeed share the same objective, they have been studied independently in the community due to distinct evaluation setups, creating a gap that hinders the application and evaluation of methods from one to the other. To bridge the gap, in this work, we present a \underline{\textbf{U}}nified \underline{\textbf{B}}enchmark for unsupervised \underline{\textbf{G}}raph-level \underline{\textbf{O}}OD and anoma\underline{\textbf{L}}y \underline{\textbf{D}}etection (\ourmethod), a comprehensive evaluation framework that unifies GLAD and GLOD under the concept of generalized graph-level OOD detection. Our benchmark encompasses 35 datasets spanning four practical anomaly and OOD detection scenarios, facilitating the comparison of 18 representative GLAD/GLOD methods. We conduct multi-dimensional analyses to explore the effectiveness, OOD sensitivity spectrum, robustness, and efficiency of existing methods, shedding light on their strengths and limitations. Furthermore, we provide an open-source codebase (https://github.com/UB-GOLD/UB-GOLD) of \ourmethod to foster reproducible research and outline potential directions for future investigations based on our insights.

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arXiv2025

A Survey of Deep Graph Learning under Distribution Shifts: from Graph Out-of-Distribution Generalization to Adaptation

Distribution shifts on graphs -- the discrepancies in data distribution between training and employing a graph machine learning model -- are ubiquitous and often unavoidable in real-world scenarios. These shifts may severely deteriorate model performance, posing significant challenges for reliable graph machine learning. Consequently, there has been a surge in research on graph machine learning under distribution shifts, aiming to train models to achieve satisfactory performance on out-of-distribution (OOD) test data. In our survey, we provide an up-to-date and forward-looking review of deep graph learning under distribution shifts. Specifically, we cover three primary scenarios: graph OOD generalization, training-time graph OOD adaptation, and test-time graph OOD adaptation. We begin by formally formulating the problems and discussing various types of distribution shifts that can affect graph learning, such as covariate shifts and concept shifts. To provide a better understanding of the literature, we introduce a systematic taxonomy that classifies existing methods into model-centric and data-centric approaches, investigating the techniques used in each category. We also summarize commonly used datasets in this research area to facilitate further investigation. Finally, we point out promising research directions and the corresponding challenges to encourage further study in this vital domain. We also provide a continuously updated reading list at https://github.com/kaize0409/Awesome-Graph-OOD.

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arXiv2025

Uncertainty-Aware Robust Learning on Noisy Graphs

Graph neural networks (GNNs) have excelled in various graph learning tasks, particularly node classification. However, their performance is often hampered by noisy measurements in real-world graphs, which can corrupt critical patterns in the data. To address this, we propose a novel uncertainty-aware graph learning framework inspired by distributionally robust optimization. Specifically, we use a graph neural network-based encoder to embed the node features and find the optimal node embeddings by minimizing the worst-case risk through a minimax formulation. Such an uncertainty-aware learning process leads to improved node representations and a more robust graph predictive model that effectively mitigates the impact of uncertainty arising from data noise. Our experimental results demonstrate superior predictive performance over baselines across noisy scenarios.

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arXiv2025

On Large Language Model Continual Unlearning

While large language models have demonstrated impressive performance across various domains and tasks, their security issues have become increasingly severe. Machine unlearning has emerged as a representative approach for model safety and security by removing the influence of undesired data on the target model. However, these methods do not sufficiently consider that unlearning requests in real-world scenarios are continuously emerging, especially in the context of LLMs, which may lead to accumulated model utility loss that eventually becomes unacceptable. Moreover, existing LLM unlearning methods often ignore previous data access limitations due to privacy concerns and copyright protection. Without previous data, the utility preservation during unlearning is much harder. To overcome these challenges, we propose the OOO framework that includes an Orthogonal low-rank adapter (LoRA) for continually unlearning requested data and an Out-Of-Distribution (OOD) detector to measure the similarity between input and unlearning data. The orthogonal LoRA achieves parameter disentanglement among continual unlearning requests. The OOD detector is trained with a novel contrastive entropy loss and utilizes a glocal-aware scoring mechanism. During inference, our OOO framework can decide whether and to what extent to load the unlearning LoRA based on the OOD detector's predicted similarity between the input and the unlearned knowledge. Notably, OOO's effectiveness does not rely on any retained data. We conducted extensive experiments on OOO and state-of-the-art LLM unlearning methods across three tasks and seven datasets. The results indicate that OOO consistently achieves the best unlearning effectiveness and utility preservation, especially when facing continuous unlearning requests. The source codes can be found at https://github.com/GCYZSL/O3-LLM-UNLEARNING.

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arXiv2025

A Survey of Model Extraction Attacks and Defenses in Distributed Computing Environments

Model Extraction Attacks (MEAs) threaten modern machine learning systems by enabling adversaries to steal models, exposing intellectual property and training data. With the increasing deployment of machine learning models in distributed computing environments, including cloud, edge, and federated learning settings, each paradigm introduces distinct vulnerabilities and challenges. Without a unified perspective on MEAs across these distributed environments, organizations risk fragmented defenses, inadequate risk assessments, and substantial economic and privacy losses. This survey is motivated by the urgent need to understand how the unique characteristics of cloud, edge, and federated deployments shape attack vectors and defense requirements. We systematically examine the evolution of attack methodologies and defense mechanisms across these environments, demonstrating how environmental factors influence security strategies in critical sectors such as autonomous vehicles, healthcare, and financial services. By synthesizing recent advances in MEAs research and discussing the limitations of current evaluation practices, this survey provides essential insights for developing robust and adaptive defense strategies. Our comprehensive approach highlights the importance of integrating protective measures across the entire distributed computing landscape to ensure the secure deployment of machine learning models.

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arXiv2025

Large Language Models for Anomaly and Out-of-Distribution Detection: A Survey

Detecting anomalies or out-of-distribution (OOD) samples is critical for maintaining the reliability and trustworthiness of machine learning systems. Recently, Large Language Models (LLMs) have demonstrated their effectiveness not only in natural language processing but also in broader applications due to their advanced comprehension and generative capabilities. The integration of LLMs into anomaly and OOD detection marks a significant shift from the traditional paradigm in the field. This survey focuses on the problem of anomaly and OOD detection under the context of LLMs. We propose a new taxonomy to categorize existing approaches into two classes based on the role played by LLMs. Following our proposed taxonomy, we further discuss the related work under each of the categories and finally discuss potential challenges and directions for future research in this field. We also provide an up-to-date reading list of relevant papers.

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arXiv2025

Avoiding Copyright Infringement via Large Language Model Unlearning

Pre-trained Large Language Models (LLMs) have demonstrated remarkable capabilities but also pose risks by learning and generating copyrighted material, leading to significant legal and ethical concerns. In real-world scenarios, model owners need to continuously address copyright infringement as new requests for content removal emerge at different time points. This leads to the need for sequential unlearning, where copyrighted content is removed sequentially as new requests arise. Despite its practical relevance, sequential unlearning in the context of copyright infringement has not been rigorously explored in existing literature. To address this gap, we propose Stable Sequential Unlearning (SSU), a novel framework designed to unlearn copyrighted content from LLMs over multiple time steps. Our approach works by identifying and removing specific weight updates in the model's parameters that correspond to copyrighted content. We improve unlearning efficacy by introducing random labeling loss and ensuring the model retains its general-purpose knowledge by adjusting targeted parameters. Experimental results show that SSU achieves an effective trade-off between unlearning efficacy and general-purpose language abilities, outperforming existing baselines.

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arXiv2025

Exploring Concept Depth: How Large Language Models Acquire Knowledge and Concept at Different Layers?

Large language models (LLMs) have shown remarkable performances across a wide range of tasks. However, the mechanisms by which these models encode tasks of varying complexities remain poorly understood. In this paper, we explore the hypothesis that LLMs process concepts of varying complexities in different layers, introducing the idea of "Concept Depth" to suggest that more complex concepts are typically acquired in deeper layers. Specifically, we categorize concepts based on their level of abstraction, defining them in the order of increasing complexity within factual, emotional, and inferential tasks. We conduct extensive probing experiments using layer-wise representations across various LLM families (Gemma, LLaMA, Qwen) on various datasets spanning the three domains of tasks. Our findings reveal that models could efficiently conduct probing for simpler tasks in shallow layers, and more complex tasks typically necessitate deeper layers for accurate understanding. Additionally, we examine how external factors, such as adding noise to the input and quantizing the model weights, might affect layer-wise representations. Our findings suggest that these factors can impede the development of a conceptual understanding of LLMs until deeper layers are explored. We hope that our proposed concept and experimental insights will enhance the understanding of the mechanisms underlying LLMs. Our codes are available at https://github.com/Luckfort/CD.

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