arXiv subjects

Mingyu Derek Ma

Publications and source records attributed to Mingyu Derek Ma.

At least 19 recordsLinked to original sources

arXiv2026

MatSciBench: Benchmarking the Reasoning Ability of Large Language Models in Materials Science

Large Language Models have shown strong scientific reasoning ability, but their performance on materials science problems remains less studied. To fill this gap, we introduce MatSciBench, a comprehensive college-level benchmark comprising 1340 problems that span the essential subdisciplines of materials science. MatSciBench features a structured and fine-grained taxonomy that categorizes materials science questions into 6 primary fields and 31 subfields, together with a three-tier difficulty classification based on the reasoning length needed to solve each problem. MatSciBench includes detailed reference solutions for 946 questions, supports process-level error analysis, and contains 315 questions with images for evaluating multimodal reasoning. We evaluate leading thinking and non-thinking LLMs on MatSciBench, and further test three reasoning methods for non-thinking models: basic chain-of-thought prompting, tool augmentation, and self-correction. The results show that current models still face clear limits in college-level materials science reasoning. DeepSeek-R1 achieves the highest score on text-only questions at 75.22% accuracy, and GPT-5 performs the best on questions with images at 53.02%. Our analysis shows that tool augmentation improves many non-thinking models in a token-efficient way, while self-correction often fails to provide reliable gains and can revise correct answers into incorrect ones. We further analyze performance across difficulty levels, reasoning efficiency, multimodal reasoning, and failure patterns, and find that current models are mainly limited by domain knowledge gaps, calculation errors, problem comprehension failures, and difficulty in extracting precise information from scientific figures. Overall, MatSciBench provides a clear testbed for measuring current LLM limitations and guiding future work on scientific reasoning in materials science.

cs.AI↗

arXiv2026

iSeal: Encrypted Fingerprinting for Reliable LLM Ownership Verification

Given the high cost of large language model (LLM) training from scratch, safeguarding LLM intellectual property (IP) has become increasingly crucial. As the standard paradigm for IP ownership verification, LLM fingerprinting thus plays a vital role in addressing this challenge. Existing LLM fingerprinting methods verify ownership by extracting or injecting model-specific features. However, they overlook potential attacks during the verification process, leaving them ineffective when the model thief fully controls the LLM's inference process. In such settings, attackers may share prompt-response pairs to enable fingerprint unlearning or manipulate outputs to evade exact-match verification. We propose iSeal, the first fingerprinting method designed for reliable verification when the model thief controls the suspected LLM in an end-to-end manner. It injects unique features into both the model and an external module, reinforced by an error-correction mechanism and a similarity-based verification strategy. These components are resistant to verification-time attacks, including collusion-based fingerprint unlearning and response manipulation, backed by both theoretical analysis and empirical results. iSeal achieves 100 percent Fingerprint Success Rate (FSR) on 12 LLMs against more than 10 attacks, while baselines fail under unlearning and response manipulations.

cs.CR↗

arXiv2026

TwinWeaver: An LLM-Based Foundation Model Framework for Pan-Cancer Digital Twins

Precision oncology requires forecasting clinical events and trajectories, yet modeling sparse, multi-modal clinical time series remains a critical challenge. We introduce TwinWeaver, an open-source framework that serializes longitudinal patient histories into text, enabling unified event prediction as well as forecasting with large language models, and use it to build Genie Digital Twin (GDT) on 93,054 patients across 20 cancer types. In benchmarks, GDT significantly reduces forecasting error, achieving a median Mean Absolute Scaled Error (MASE) of 0.87 compared to 0.97 for the strongest time-series baseline (p<0.001). Furthermore, GDT improves risk stratification, achieving an average concordance index (C-index) of 0.703 across survival, progression, and therapy switching tasks, surpassing the best baseline of 0.662. GDT also generalizes to out-of-distribution clinical trials, matching trained baselines at zero-shot and surpassing them with fine-tuning, achieving a median MASE of 0.75-0.88 and outperforming the strongest baseline in event prediction with an average C-index of 0.672 versus 0.648. Finally, TwinWeaver enables an interpretable clinical reasoning extension, providing a scalable and transparent foundation for longitudinal clinical modeling.

cs.LG↗

arXiv2025

BioVerge: A Comprehensive Benchmark and Study of Self-Evaluating Agents for Biomedical Hypothesis Generation

Hypothesis generation in biomedical research has traditionally centered on uncovering hidden relationships within vast scientific literature, often using methods like Literature-Based Discovery (LBD). Despite progress, current approaches typically depend on single data types or predefined extraction patterns, which restricts the discovery of novel and complex connections. Recent advances in Large Language Model (LLM) agents show significant potential, with capabilities in information retrieval, reasoning, and generation. However, their application to biomedical hypothesis generation has been limited by the absence of standardized datasets and execution environments. To address this, we introduce BioVerge, a comprehensive benchmark, and BioVerge Agent, an LLM-based agent framework, to create a standardized environment for exploring biomedical hypothesis generation at the frontier of existing scientific knowledge. Our dataset includes structured and textual data derived from historical biomedical hypotheses and PubMed literature, organized to support exploration by LLM agents. BioVerge Agent utilizes a ReAct-based approach with distinct Generation and Evaluation modules that iteratively produce and self-assess hypothesis proposals. Through extensive experimentation, we uncover key insights: 1) different architectures of BioVerge Agent influence exploration diversity and reasoning strategies; 2) structured and textual information sources each provide unique, critical contexts that enhance hypothesis generation; and 3) self-evaluation significantly improves the novelty and relevance of proposed hypotheses.

cs.CL↗

arXiv2025

GIVE: Structured Reasoning of Large Language Models with Knowledge Graph Inspired Veracity Extrapolation

Existing approaches based on context prompting or reinforcement learning (RL) to improve the reasoning capacities of large language models (LLMs) depend on the LLMs' internal knowledge to produce reliable Chain-Of-Thought (CoT). However, no matter the size of LLMs, certain problems cannot be resolved in a single forward pass. Meanwhile, agent-based reasoning systems require access to a comprehensive nonparametric knowledge base, which is often costly or not feasible for use in scientific and niche domains. We present Graph Inspired Veracity Extrapolation (GIVE), a novel reasoning method that merges parametric and non-parametric memories to improve accurate reasoning with minimal external input. GIVE guides the LLM agent to select the most pertinent expert data (observe), engage in query-specific divergent thinking (reflect), and then synthesize this information to produce the final output (speak). Extensive experiments demonstrated the following benefits of our framework: (1) GIVE boosts the performance of LLMs across various sizes. (2) In some scenarios, GIVE allows smaller LLMs to surpass larger, more sophisticated ones in scientific tasks (GPT3.5T + GIVE > GPT4). (3) GIVE is effective on scientific and open-domain assessments. (4) GIVE is a training-free method that enables LLMs to tackle new problems that extend beyond their training data (up to 43.5% -> 88.2%} accuracy improvement). (5) GIVE allows LLM agents to reason using both restricted (very small) and noisy (very large) knowledge sources, accommodating knowledge graphs (KG) ranging from 135 to more than 840k nodes. (6) The reasoning process involved in GIVE is fully interpretable.

cs.AI↗

arXiv2025

BIASINSPECTOR: Detecting Bias in Structured Data through LLM Agents

Detecting biases in structured data is a complex and time-consuming task. Existing automated techniques are limited in diversity of data types and heavily reliant on human case-by-case handling, resulting in a lack of generalizability. Currently, large language model (LLM)-based agents have made significant progress in data science, but their ability to detect data biases is still insufficiently explored. To address this gap, we introduce the first end-to-end, multi-agent synergy framework, BIASINSPECTOR, designed for automatic bias detection in structured data based on specific user requirements. It first develops a multi-stage plan to analyze user-specified bias detection tasks and then implements it with a diverse and well-suited set of tools. It delivers detailed results that include explanations and visualizations. To address the lack of a standardized framework for evaluating the capability of LLM agents to detect biases in data, we further propose a comprehensive benchmark that includes multiple evaluation metrics and a large set of test cases. Extensive experiments demonstrate that our framework achieves exceptional overall performance in structured data bias detection, setting a new milestone for fairer data applications.

cs.AI↗

arXiv2025

Entropy-Based Adaptive Weighting for Self-Training

The mathematical problem-solving capabilities of large language models have become a focal point of research, with growing interests in leveraging self-generated reasoning paths as a promising way to refine and enhance these models. These paths capture step-by-step logical processes while requiring only the correct answer for supervision. The self-training method has been shown to be effective in reasoning tasks while eliminating the need for external models and manual annotations. However, optimizing the use of self-generated data for model training remains an open challenge. In this work, we propose Entropy-Based Adaptive Weighting for Self-Training (EAST), an adaptive weighting strategy designed to prioritize uncertain data during self-training. Specifically, EAST employs a mapping function with a tunable parameter that controls the sharpness of the weighting, assigning higher weights to data where the model exhibits greater uncertainty. This approach guides the model to focus on more informative and challenging examples, thereby enhancing its reasoning ability. We evaluate our approach on GSM8K and MATH benchmarks. Empirical results show that, while the vanilla method yields virtually no improvement (0%) on MATH, EAST achieves around a 1% gain over backbone model. On GSM8K, EAST attains a further 1-2% performance boost compared to the vanilla method.

cs.CL↗

arXiv2025

Memorize and Rank: Elevating Large Language Models for Clinical Diagnosis Prediction

Clinical diagnosis prediction models, when provided with a patient's medical history, aim to detect potential diseases early, facilitating timely intervention and improving prognostic outcomes. However, the inherent scarcity of patient data and large disease candidate space often pose challenges in developing satisfactory models for this intricate task. The exploration of leveraging Large Language Models (LLMs) for encapsulating clinical decision processes has been limited. We introduce MERA, a clinical diagnosis prediction model that bridges pertaining natural language knowledge with medical practice. We apply hierarchical contrastive learning on a disease candidate ranking list to alleviate the large decision space issue. With concept memorization through fine-tuning, we bridge the natural language clinical knowledge with medical codes. Experimental results on MIMIC-III and IV datasets show that MERA achieves the state-of-the-art diagnosis prediction performance and dramatically elevates the diagnosis prediction capabilities of generative LMs.

cs.CL↗

arXiv2025

Inferring from Logits: Exploring Best Practices for Decoding-Free Generative Candidate Selection

Generative Language Models rely on autoregressive decoding to produce the output sequence token by token. Many tasks such as preference optimization, require the model to produce task-level output consisting of multiple tokens directly by selecting candidates from a pool as predictions. Determining a task-level prediction from candidates using the ordinary token-level decoding mechanism is constrained by time-consuming decoding and interrupted gradients by discrete token selection. Existing works have been using decoding-free candidate selection methods to obtain candidate probability from initial output logits over vocabulary. Though these estimation methods are widely used, they are not systematically evaluated, especially on end tasks. We introduce an evaluation of a comprehensive collection of decoding-free candidate selection approaches on a comprehensive set of tasks, including five multiple-choice QA tasks with a small candidate pool and four clinical decision tasks with a massive amount of candidates, some with 10k+ options. We evaluate the estimation methods paired with a wide spectrum of foundation LMs covering different architectures, sizes and training paradigms. The results and insights from our analysis inform the future model design.

cs.CL↗

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

CLIMB: A Benchmark of Clinical Bias in Large Language Models

Large language models (LLMs) are increasingly applied to clinical decision-making. However, their potential to exhibit bias poses significant risks to clinical equity. Currently, there is a lack of benchmarks that systematically evaluate such clinical bias in LLMs. While in downstream tasks, some biases of LLMs can be avoided such as by instructing the model to answer "I'm not sure...", the internal bias hidden within the model still lacks deep studies. We introduce CLIMB (shorthand for A Benchmark of Clinical Bias in Large Language Models), a pioneering comprehensive benchmark to evaluate both intrinsic (within LLMs) and extrinsic (on downstream tasks) bias in LLMs for clinical decision tasks. Notably, for intrinsic bias, we introduce a novel metric, AssocMAD, to assess the disparities of LLMs across multiple demographic groups. Additionally, we leverage counterfactual intervention to evaluate extrinsic bias in a task of clinical diagnosis prediction. Our experiments across popular and medically adapted LLMs, particularly from the Mistral and LLaMA families, unveil prevalent behaviors with both intrinsic and extrinsic bias. This work underscores the critical need to mitigate clinical bias and sets a new standard for future evaluations of LLMs' clinical bias.

cs.CL↗

arXiv2024

Are Large-Language Models Graph Algorithmic Reasoners?

We seek to address a core challenge facing current Large Language Models (LLMs). LLMs have demonstrated superior performance in many tasks, yet continue to struggle with reasoning problems on explicit graphs that require multiple steps. To address this gap, we introduce a novel benchmark designed to evaluate LLM performance on classical algorithmic reasoning tasks on explicit graphs. Our benchmark encompasses five fundamental algorithms: Breadth-First Search (BFS) and Depth-First Search (DFS) for connectivity, Dijkstra's algorithm and Floyd-Warshall algorithm for all nodes shortest path, and Prim's Minimum Spanning Tree (MST-Prim's) algorithm. Through extensive experimentation, we assess the capabilities of state-of-the-art LLMs in executing these algorithms step-by-step and systematically evaluate their performance at each stage. Our findings highlight the persistent challenges LLMs face in this domain and underscore the necessity for advanced prompting techniques and algorithmic instruction to enhance their graph reasoning abilities. This work presents MAGMA, the first comprehensive benchmark focused on LLMs completing classical graph algorithms, and provides a critical step toward understanding and improving their structured problem-solving skills.

cs.LG↗

arXiv2024

Decoding Susceptibility: Modeling Misbelief to Misinformation Through a Computational Approach

Susceptibility to misinformation describes the degree of belief in unverifiable claims, a latent aspect of individuals' mental processes that is not observable. Existing susceptibility studies heavily rely on self-reported beliefs, which can be subject to bias, expensive to collect, and challenging to scale for downstream applications. To address these limitations, in this work, we propose a computational approach to model users' latent susceptibility levels. As shown in previous research, susceptibility is influenced by various factors (e.g., demographic factors, political ideology), and directly influences people's reposting behavior on social media. To represent the underlying mental process, our susceptibility modeling incorporates these factors as inputs, guided by the supervision of people's sharing behavior. Using COVID-19 as a testbed domain, our experiments demonstrate a significant alignment between the susceptibility scores estimated by our computational modeling and human judgments, confirming the effectiveness of this latent modeling approach. Furthermore, we apply our model to annotate susceptibility scores on a large-scale dataset and analyze the relationships between susceptibility with various factors. Our analysis reveals that political leanings and psychological factors exhibit varying degrees of association with susceptibility to COVID-19 misinformation.

cs.CL↗

arXiv2024

CliBench: A Multifaceted and Multigranular Evaluation of Large Language Models for Clinical Decision Making

The integration of Artificial Intelligence (AI), especially Large Language Models (LLMs), into the clinical diagnosis process offers significant potential to improve the efficiency and accessibility of medical care. While LLMs have shown some promise in the medical domain, their application in clinical diagnosis remains underexplored, especially in real-world clinical practice, where highly sophisticated, patient-specific decisions need to be made. Current evaluations of LLMs in this field are often narrow in scope, focusing on specific diseases or specialties and employing simplified diagnostic tasks. To bridge this gap, we introduce CliBench, a novel benchmark developed from the MIMIC IV dataset, offering a comprehensive and realistic assessment of LLMs' capabilities in clinical diagnosis. This benchmark not only covers diagnoses from a diverse range of medical cases across various specialties but also incorporates tasks of clinical significance: treatment procedure identification, lab test ordering and medication prescriptions. Supported by structured output ontologies, CliBench enables a precise and multi-granular evaluation, offering an in-depth understanding of LLM's capability on diverse clinical tasks of desired granularity. We conduct a zero-shot evaluation of leading LLMs to assess their proficiency in clinical decision-making. Our preliminary results shed light on the potential and limitations of current LLMs in clinical settings, providing valuable insights for future advancements in LLM-powered healthcare.

cs.CL↗

arXiv2024

MuirBench: A Comprehensive Benchmark for Robust Multi-image Understanding

We introduce MuirBench, a comprehensive benchmark that focuses on robust multi-image understanding capabilities of multimodal LLMs. MuirBench consists of 12 diverse multi-image tasks (e.g., scene understanding, ordering) that involve 10 categories of multi-image relations (e.g., multiview, temporal relations). Comprising 11,264 images and 2,600 multiple-choice questions, MuirBench is created in a pairwise manner, where each standard instance is paired with an unanswerable variant that has minimal semantic differences, in order for a reliable assessment. Evaluated upon 20 recent multi-modal LLMs, our results reveal that even the best-performing models like GPT-4o and Gemini Pro find it challenging to solve MuirBench, achieving 68.0% and 49.3% in accuracy. Open-source multimodal LLMs trained on single images can hardly generalize to multi-image questions, hovering below 33.3% in accuracy. These results highlight the importance of MuirBench in encouraging the community to develop multimodal LLMs that can look beyond a single image, suggesting potential pathways for future improvements.

cs.CV↗

arXiv2024

MIRAI: Evaluating LLM Agents for Event Forecasting

Recent advancements in Large Language Models (LLMs) have empowered LLM agents to autonomously collect world information, over which to conduct reasoning to solve complex problems. Given this capability, increasing interests have been put into employing LLM agents for predicting international events, which can influence decision-making and shape policy development on an international scale. Despite such a growing interest, there is a lack of a rigorous benchmark of LLM agents' forecasting capability and reliability. To address this gap, we introduce MIRAI, a novel benchmark designed to systematically evaluate LLM agents as temporal forecasters in the context of international events. Our benchmark features an agentic environment with tools for accessing an extensive database of historical, structured events and textual news articles. We refine the GDELT event database with careful cleaning and parsing to curate a series of relational prediction tasks with varying forecasting horizons, assessing LLM agents' abilities from short-term to long-term forecasting. We further implement APIs to enable LLM agents to utilize different tools via a code-based interface. In summary, MIRAI comprehensively evaluates the agents' capabilities in three dimensions: 1) autonomously source and integrate critical information from large global databases; 2) write codes using domain-specific APIs and libraries for tool-use; and 3) jointly reason over historical knowledge from diverse formats and time to accurately predict future events. Through comprehensive benchmarking, we aim to establish a reliable framework for assessing the capabilities of LLM agents in forecasting international events, thereby contributing to the development of more accurate and trustworthy models for international relation analysis.

cs.CL↗

arXiv2024

Mitigating Bias for Question Answering Models by Tracking Bias Influence

Models of various NLP tasks have been shown to exhibit stereotypes, and the bias in the question answering (QA) models is especially harmful as the output answers might be directly consumed by the end users. There have been datasets to evaluate bias in QA models, while bias mitigation technique for the QA models is still under-explored. In this work, we propose BMBI, an approach to mitigate the bias of multiple-choice QA models. Based on the intuition that a model would lean to be more biased if it learns from a biased example, we measure the bias level of a query instance by observing its influence on another instance. If the influenced instance is more biased, we derive that the query instance is biased. We then use the bias level detected as an optimization objective to form a multi-task learning setting in addition to the original QA task. We further introduce a new bias evaluation metric to quantify bias in a comprehensive and sensitive way. We show that our method could be applied to multiple QA formulations across multiple bias categories. It can significantly reduce the bias level in all 9 bias categories in the BBQ dataset while maintaining comparable QA accuracy.

cs.CL↗

arXiv2024

Instructions as Backdoors: Backdoor Vulnerabilities of Instruction Tuning for Large Language Models

We investigate security concerns of the emergent instruction tuning paradigm, that models are trained on crowdsourced datasets with task instructions to achieve superior performance. Our studies demonstrate that an attacker can inject backdoors by issuing very few malicious instructions (~1000 tokens) and control model behavior through data poisoning, without even the need to modify data instances or labels themselves. Through such instruction attacks, the attacker can achieve over 90% attack success rate across four commonly used NLP datasets. As an empirical study on instruction attacks, we systematically evaluated unique perspectives of instruction attacks, such as poison transfer where poisoned models can transfer to 15 diverse generative datasets in a zero-shot manner; instruction transfer where attackers can directly apply poisoned instruction on many other datasets; and poison resistance to continual finetuning. Lastly, we show that RLHF and clean demonstrations might mitigate such backdoors to some degree. These findings highlight the need for more robust defenses against poisoning attacks in instruction-tuning models and underscore the importance of ensuring data quality in instruction crowdsourcing.

cs.CL↗