arXiv subjects

Yikun Han

Publications and source records attributed to Yikun Han.

11 recordsLinked to original sources

arXiv2026

A General-Purpose Molecular Foundation Model Transfers Across Diverse Olfactory Tasks

Foundation models have transformed molecular property prediction, yet it remains unclear whether a molecular foundation model, fine-tuned on a single canonical olfactory prediction task, can learn representations that transfer across diverse machine olfaction problems. We investigate this question by fine-tuning Uni-Mol2 on the GS-LF benchmark for multi-label odor descriptor prediction and evaluating the resulting model, without additional deep-learning training, on four complementary downstream settings: cross-dataset odor descriptor prediction, odorous-versus-odorless classification, enantiomer evaluation, and odor mixture discriminability. The fine-tuned model matches or exceeds the performance of the state-of-the-art olfaction-specific baseline on the primary GS-LF benchmark and consistently transfers across these downstream evaluations. The enantiomer analysis further shows that three-dimensional molecular representations distinguish mirror-image molecules in a way that two-dimensional graph models fundamentally cannot, although accurately predicting the perceptual consequences of stereochemistry remains an open challenge. Together, these results support a train-once, transfer-across-tasks paradigm for machine olfaction and suggest that chemically pretrained molecular representations provide a strong foundation for transferable olfactory prediction.

cs.LG↗

arXiv2026

ANCHOR-RE: An Agentic Neuro-Symbolic Framework for Grounded Biomedical Relation Extraction

Biomedical relation extraction (BioRE) extracts structured knowledge from biomedical literature for applications such as knowledge base construction and hypothesis generation. Traditional symbolic systems such as SemRep provide high precision but limited recall, while large language models (LLMs) offer stronger contextual reasoning but remain prone to false-positive predictions. We developed ANCHOR-RE, a framework that integrates ontology-guided reasoning, external knowledge grounding, and data-driven verification rules into LLM inference. We evaluated it on three BioRE benchmarks (SemRepGS, DDI, and ChemProt) using both proprietary and open-weight LLMs. To assess generalizability beyond benchmark datasets while reducing potential evaluation bias from LLM pretraining contamination, we conducted a temporal evaluation using 100 biomedical articles published in 2026. With the proprietary backbone, ANCHOR-RE outperformed direct LLM prompting, improving micro-F1 from 0.654 to 0.676 on SemRepGS, from 0.769 to 0.872 on DDI, and from 0.939 to 0.941 on ChemProt. On DDI and ChemProt, it also outperformed previously reported inference-only methods and approached fine-tuned or instruction-tuned systems without parameter updates. Similar performance gains observed with open-weight LLMs indicate that the benefits were not limited to the proprietary backbone. On the post-cutoff set, manual assessment of 500 randomly sampled predictions yielded a precision of 69%, maintaining consistent precision on previously unseen biomedical literature. Neuro-symbolic reasoning can improve the reliability of LLM-based BioRE without fine-tuning. Results across multiple benchmarks, model families, and post-cutoff literature support ANCHOR-RE as a practical training-free approach to biomedical literature mining.

cs.CL↗

arXiv2026

When Evidence Conflicts: Uncertainty and Order Effects in Retrieval-Augmented Biomedical Question Answering

Biomedical retrieval-augmented large language models (LLMs) often face evidence that is incomplete, misleading, or internally contradictory, yet evaluation usually emphasizes answer accuracy under helpful context rather than reliability under conflict. Using HealthContradict, we evaluate six open-weight LLMs under five controlled evidence conditions: no retrieved context, correct-only context, incorrect-only context, and two mixed conditions containing both correct and contradictory documents in opposite orders. In this conflicting-evidence order contrast, where the same two documents are both present and only their order is reversed, accuracy drops for every model and 11.4%--25.2% of predictions flip. To support abstention in these difficult cases, we also evaluate a conflict-aware abstention score that combines model confidence with a detector of evidence conflict. In the two hardest conditions, this score improves selective accuracy over confidence-only, with mean gains of 7.2--33.4 points in incorrect-only (`IC') and 3.6--14.4 points in incorrect-first conflicting (`ICC') conditions across 75%, 50%, and 25% coverage. These results show that conflicting biomedical evidence is both an uncertainty and robustness problem and motivate evaluation and abstention methods that explicitly account for evidence disagreement.

cs.CL↗

arXiv2026

ReLay: Personalized LLM-Generated Plain-Language Summaries for Better Understanding, but at What Cost?

Plain Language Summaries (PLS) aim to make research accessible to lay readers, but they are typically written in a one-size-fits-all style that ignores differences in readers' information needs and comprehension. In health contexts, this limitation is particularly important because misunderstanding scientific information can affect real-world decisions. Large language models (LLMs) offer new opportunities for personalizing PLS, but it remains unclear whether personalization helps, which strategies are most effective, and how to balance personalization with safety. We introduce ReLay, a dataset of 300 participant--PLS pairs from 50 lay participants in both static (expert-written) and interactive (LLM-personalized) settings. ReLay includes user characteristics, health information needs, information-seeking behavior, comprehension outcomes, interaction logs, and quality ratings. We use ReLay to evaluate five LLMs across two personalization methods. Personalization improves comprehension and perceived quality, but it also raises the risk of reinforcing user biases and introducing hallucinations, revealing a trade-off between personalization and safety. These findings highlight the need for personalization methods that are both effective and trustworthy for diverse lay audiences.

cs.CL↗

arXiv2026

MedConceal: A Benchmark for Clinical Hidden-Concern Reasoning Under Partial Observability

Patient-clinician communication is an asymmetric-information problem: patients often do not disclose fears, misconceptions, or practical barriers unless clinicians elicit them skillfully. Effective medical dialogue therefore requires reasoning under partial observability: clinicians must elicit latent concerns, confirm them through interaction, and respond in ways that guide patients toward appropriate care. However, existing medical dialogue benchmarks largely sidestep this challenge by exposing hidden patient state, collapsing elicitation into extraction, or evaluating responses without modeling what remains hidden. We present MedConceal, a benchmark with an interactive patient simulator for evaluating hidden-concern reasoning in medical dialogue, comprising 300 curated cases and 600 clinician-LLM interactions. Built from clinician-answered online health discussions, each case pairing clinician-visible context with simulator-internal hidden concerns derived from prior literature and structured using an expert-developed taxonomy. The simulator withholds these concerns from the dialogue agent, tracks whether they have been revealed and addressed via theory-grounded turn-level communication signals, and is clinician-reviewed for clinical plausibility. This enables process-aware evaluation of both task success and the interaction process that leads to it. We study two abilities: confirmation, surfacing hidden concerns through multi-turn dialogue, and intervention, addressing the primary concern and guiding the patient toward a target plan. Results show that no single system dominates: frontier models lead on different confirmation metrics, while human clinicians (N=159) remain strongest on intervention success. Together, these results identify hidden-concern reasoning under partial observability as a key unresolved challenge for medical dialogue systems.

cs.CL↗

arXiv2025

Mapping from Meaning: Addressing the Miscalibration of Prompt-Sensitive Language Models

An interesting behavior in large language models (LLMs) is prompt sensitivity. When provided with different but semantically equivalent versions of the same prompt, models may produce very different distributions of answers. This suggests that the uncertainty reflected in a model's output distribution for one prompt may not reflect the model's uncertainty about the meaning of the prompt. We model prompt sensitivity as a type of generalization error, and show that sampling across the semantic ``concept space'' with paraphrasing perturbations improves uncertainty calibration without compromising accuracy. Additionally, we introduce a new metric for uncertainty decomposition in black-box LLMs that improves upon entropy-based decomposition by modeling semantic continuities in natural language generation. We show that this decomposition metric can be used to quantify how much LLM uncertainty is attributed to prompt sensitivity. Our work introduces a new way to improve uncertainty calibration in prompt-sensitive language models, and provides evidence that some LLMs fail to exhibit consistent general reasoning about the meanings of their inputs.

cs.CL↗

arXiv2024

Large Language Models on Fine-grained Emotion Detection Dataset with Data Augmentation and Transfer Learning

This paper delves into enhancing the classification performance on the GoEmotions dataset, a large, manually annotated dataset for emotion detection in text. The primary goal of this paper is to address the challenges of detecting subtle emotions in text, a complex issue in Natural Language Processing (NLP) with significant practical applications. The findings offer valuable insights into addressing the challenges of emotion detection in text and suggest directions for future research, including the potential for a survey paper that synthesizes methods and performances across various datasets in this domain.

cs.CL↗

arXiv2024

Beyond Answers: Transferring Reasoning Capabilities to Smaller LLMs Using Multi-Teacher Knowledge Distillation

Transferring the reasoning capability from stronger large language models (LLMs) to smaller ones has been quite appealing, as smaller LLMs are more flexible to deploy with less expense. Among the existing solutions, knowledge distillation stands out due to its outstanding efficiency and generalization. However, existing methods suffer from several drawbacks, including limited knowledge diversity and the lack of rich contextual information. To solve the problems and facilitate the learning of compact language models, we propose TinyLLM, a new knowledge distillation paradigm to learn a small student LLM from multiple large teacher LLMs. In particular, we encourage the student LLM to not only generate the correct answers but also understand the rationales behind these answers. Given that different LLMs possess diverse reasoning skills, we guide the student model to assimilate knowledge from various teacher LLMs. We further introduce an in-context example generator and a teacher-forcing Chain-of-Thought strategy to ensure that the rationales are accurate and grounded in contextually appropriate scenarios. Extensive experiments on six datasets across two reasoning tasks demonstrate the superiority of our method. Results show that TinyLLM can outperform large teacher LLMs significantly, despite a considerably smaller model size. The source code is available at: https://github.com/YikunHan42/TinyLLM.

cs.CL↗

arXiv2024

When Large Language Models Meet Vector Databases: A Survey

This survey explores the synergistic potential of Large Language Models (LLMs) and Vector Databases (VecDBs), a burgeoning but rapidly evolving research area. With the proliferation of LLMs comes a host of challenges, including hallucinations, outdated knowledge, prohibitive commercial application costs, and memory issues. VecDBs emerge as a compelling solution to these issues by offering an efficient means to store, retrieve, and manage the high-dimensional vector representations intrinsic to LLM operations. Through this nuanced review, we delineate the foundational principles of LLMs and VecDBs and critically analyze their integration's impact on enhancing LLM functionalities. This discourse extends into a discussion on the speculative future developments in this domain, aiming to catalyze further research into optimizing the confluence of LLMs and VecDBs for advanced data handling and knowledge extraction capabilities.

cs.DB↗

arXiv2024

A Community Detection and Graph Neural Network Based Link Prediction Approach for Scientific Literature

This study presents a novel approach that synergizes community detection algorithms with various Graph Neural Network (GNN) models to bolster link prediction in scientific literature networks. By integrating the Louvain community detection algorithm into our GNN frameworks, we consistently enhance performance across all models tested. For example, integrating Louvain with the GAT model resulted in an AUC score increase from 0.777 to 0.823, exemplifying the typical improvements observed. Similar gains are noted when Louvain is paired with other GNN architectures, confirming the robustness and effectiveness of incorporating community-level insights. This consistent uplift in performance reflected in our extensive experimentation on bipartite graphs of scientific collaborations and citations highlights the synergistic potential of combining community detection with GNNs to overcome common link prediction challenges such as scalability and resolution limits. Our findings advocate for the integration of community structures as a significant step forward in the predictive accuracy of network science models, offering a comprehensive understanding of scientific collaboration patterns through the lens of advanced machine learning techniques.

cs.SI↗

arXiv2023

A Comprehensive Survey on Vector Database: Storage and Retrieval Technique, Challenge

As high-dimensional vector data increasingly surpasses the processing capabilities of traditional database management systems, Vector Databases (VDBs) have emerged and become tightly integrated with large language models, being widely applied in modern artificial intelligence systems. However, existing research has primarily focused on underlying technologies such as approximate nearest neighbor search, with relatively few studies providing a systematic architectural-level review of VDBs or analyzing how these core technologies collectively support the overall capacity of VDBs. This survey aims to offer a comprehensive overview of the core designs and algorithms of VDBs, establishing a holistic understanding of this rapidly evolving field. First, we systematically review the key technologies and design principles of VDBs from the two core dimensions of storage and retrieval, tracing their technological evolution. Next, we conduct an in-depth comparison of several mainstream VDB architectures, summarizing their strengths, limitations, and typical application scenarios. Finally, we explore emerging directions for integrating VDBs with large language models, including open research challenges and trends such as novel indexing strategies. This survey serves as a systematic reference guide for researchers and practitioners, helping readers quickly grasp the technological landscape and development trends in the field of vector databases, and promoting further innovation in both theoretical and applied aspects.

cs.DB↗