arXiv subjects

Jaewoo Kang

Publications and source records attributed to Jaewoo Kang.

At least 37 records · Page 2Linked to original sources

arXiv2026

ToxReason: A Benchmark for Mechanistic Chemical Toxicity Reasoning via Adverse Outcome Pathway

Recent advances in large language models (LLMs) have enabled molecular reasoning for property prediction. However, toxicity arises from complex biological mechanisms beyond chemical structure, necessitating mechanistic reasoning for reliable prediction. Despite its importance, current benchmarks fail to systematically evaluate this capability. LLMs can generate fluent but biologically unfaithful explanations, making it difficult to assess whether predicted toxicities are grounded invalid mechanisms. To bridge this gap, we introduce ToxReason, a benchmark grounded in the Adverse Outcome Pathway (AOP) that evaluates organ-level toxicity reasoning across multiple organs. ToxReason integrates experimental drug-target interaction evidence with toxicity labels, requiring models to infer both toxic outcomes and their underlying mechanisms from Molecular Initiating Event (MIE) to Adverse Outcome (AO). Using ToxReason, we evaluate toxicity prediction performance and reasoning quality across diverse LLMs. We find that strong predictive performance does not necessarily imply reliable reasoning. Furthermore, we show that reasoning-aware training improves mechanistic reasoning and, consequently, toxicity prediction performance. Together, these results underscore the necessity of integrating reasoning into both evaluation and training for trustworthy toxicity modeling.

q-bio.QM↗

arXiv2026

ATTNSOM: Learning Cross-Isoform Attention for Cytochrome P450 Site-of-Metabolism

Identifying metabolic sites where cytochrome P450 enzymes metabolize small-molecule drugs is essential for drug discovery. Although existing computational approaches have been proposed for site-of-metabolism prediction, they typically ignore cytochrome P450 isoform identity or model isoforms independently, thereby failing to fully capture inherent cross-isoform metabolic patterns. In addition, prior evaluations often rely on top-k metrics, where false positive atoms may be included among the top predictions, underscoring the need for complementary metrics that more directly assess binary atom-level discrimination under severe class imbalance. We propose ATTNSOM, an atom-level site-of-metabolism prediction framework that integrates intrinsic molecular reactivity with cross-isoform relationships. The model combines a shared graph encoder, molecule-conditioned atom representations, and a cross-attention mechanism to capture correlated metabolic patterns across cytochrome P450 isoforms. The model is evaluated on two benchmark datasets annotated with site-of-metabolism labels at atom resolution. Across these benchmarks, the model achieves consistently strong top-k performance across multiple cytochrome P450 isoforms. Relative to ablated variants, the model yields higher Matthews correlation coefficient, indicating improved discrimination of true metabolic sites. These results support the importance of explicitly modeling cross-isoform relationships for site-of-metabolism prediction. The code and datasets are available at https://github.com/dmis-lab/ATTNSOM.

q-bio.QM↗

arXiv2026

Benchmarking Direct Preference Optimization for Medical Large Vision-Language Models

Large Vision-Language Models (LVLMs) hold significant promise for medical applications, yet their deployment is often constrained by insufficient alignment and reliability. While Direct Preference Optimization (DPO) has emerged as a potent framework for refining model responses, its efficacy in high-stakes medical contexts remains underexplored, lacking the rigorous empirical groundwork necessary to guide future methodological advances. To bridge this gap, we present the first comprehensive examination of diverse DPO variants within the medical domain, evaluating nine distinct formulations across two medical LVLMs: LLaVA-Med and HuatuoGPT-Vision. Our results reveal several critical limitations: current DPO approaches often yield inconsistent gains over supervised fine-tuning, with their efficacy varying significantly across different tasks and backbones. Furthermore, they frequently fail to resolve fundamental visual misinterpretation errors. Building on these insights, we present a targeted preference construction strategy as a proof-of-concept that explicitly addresses visual misinterpretation errors frequently observed in existing DPO models. This design yields a 3.6% improvement over the strongest existing DPO baseline on visual question-answering tasks. To support future research, we release our complete framework, including all training data, model checkpoints, and our codebase at https://github.com/dmis-lab/med-vlm-dpo.

cs.CV↗

arXiv2026

SCRIPTMIND: Crime Script Inference and Cognitive Evaluation for LLM-based Social Engineering Scam Detection System

Social engineering scams increasingly employ personalized, multi-turn deception, exposing the limits of traditional detection methods. While Large Language Models (LLMs) show promise in identifying deception, their cognitive assistance potential remains underexplored. We propose ScriptMind, an integrated framework for LLM-based scam detection that bridges automated reasoning and human cognition. It comprises three components: the Crime Script Inference Task (CSIT) for scam reasoning, the Crime Script-Aware Inference Dataset (CSID) for fine-tuning small LLMs, and the Cognitive Simulation-based Evaluation of Social Engineering Defense (CSED) for assessing real-time cognitive impact. Using 571 Korean phone scam cases, we built 22,712 structured scammer-sequence training instances. Experimental results show that the 11B small LLM fine-tuned with ScriptMind outperformed GPT-4o by 13%, achieving superior performance over commercial models in detection accuracy, false-positive reduction, scammer utterance prediction, and rationale quality. Moreover, in phone scam simulation experiments, it significantly enhanced and sustained users' suspicion levels, improving their cognitive awareness of scams. ScriptMind represents a step toward human-centered, cognitively adaptive LLMs for scam defense.

cs.AI↗

arXiv2025

The Curious Case of Analogies: Investigating Analogical Reasoning in Large Language Models

Analogical reasoning is at the core of human cognition, serving as an important foundation for a variety of intellectual activities. While prior work has shown that LLMs can represent task patterns and surface-level concepts, it remains unclear whether these models can encode high-level relational concepts and apply them to novel situations through structured comparisons. In this work, we explore this fundamental aspect using proportional and story analogies, and identify three key findings. First, LLMs effectively encode the underlying relationships between analogous entities; both attributive and relational information propagate through mid-upper layers in correct cases, whereas reasoning failures reflect missing relational information within these layers. Second, unlike humans, LLMs often struggle not only when relational information is missing, but also when attempting to apply it to new entities. In such cases, strategically patching hidden representations at critical token positions can facilitate information transfer to a certain extent. Lastly, successful analogical reasoning in LLMs is marked by strong structural alignment between analogous situations, whereas failures often reflect degraded or misplaced alignment. Overall, our findings reveal that LLMs exhibit emerging but limited capabilities in encoding and applying high-level relational concepts, highlighting both parallels and gaps with human cognition.

cs.CL↗

arXiv2025

CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Prediction

Drug toxicity remains a major challenge in pharmaceutical development. Recent machine learning models have improved in silico toxicity prediction, but their reliance on annotated data and lack of interpretability limit their applicability. This limits their ability to capture organ-specific toxicities driven by complex biological mechanisms. Large language models (LLMs) offer a promising alternative through step-by-step reasoning and integration of textual data, yet prior approaches lack biological context and transparent rationale. To address this issue, we propose CoTox, a novel framework that integrates LLM with chain-of-thought (CoT) reasoning for multi-toxicity prediction. CoTox combines chemical structure data, biological pathways, and gene ontology (GO) terms to generate interpretable toxicity predictions through step-by-step reasoning. Using GPT-4o, we show that CoTox outperforms both traditional machine learning and deep learning model. We further examine its performance across various LLMs to identify where CoTox is most effective. Additionally, we find that representing chemical structures with IUPAC names, which are easier for LLMs to understand than SMILES, enhances the model's reasoning ability and improves predictive performance. To demonstrate its practical utility in drug development, we simulate the treatment of relevant cell types with drug and incorporated the resulting biological context into the CoTox framework. This approach allow CoTox to generate toxicity predictions aligned with physiological responses, as shown in case study. This result highlights the potential of LLM-based frameworks to improve interpretability and support early-stage drug safety assessment. The code and prompt used in this work are available at https://github.com/dmis-lab/CoTox.

cs.LG↗

arXiv2025

Assessing LLM Reasoning Steps via Principal Knowledge Grounding

Step-by-step reasoning has become a standard approach for large language models (LLMs) to tackle complex tasks. While this paradigm has proven effective, it raises a fundamental question: How can we verify that an LLM's reasoning is accurately grounded in knowledge? To address this question, we introduce a novel evaluation suite that systematically assesses the knowledge grounding of intermediate reasoning. Our framework comprises three key components. (1) Principal Knowledge Collection, a large-scale repository of atomic knowledge essential for reasoning. Based on the collection, we propose (2) knowledge-grounded evaluation metrics designed to measure how well models recall and apply prerequisite knowledge in reasoning. These metrics are computed by our (3) evaluator LLM, a lightweight model optimized for cost-effective and reliable metric computation. Our evaluation suite demonstrates remarkable effectiveness in identifying missing or misapplied knowledge elements, providing crucial insights for uncovering fundamental reasoning deficiencies in LLMs. Beyond evaluation, we demonstrate how these metrics can be integrated into preference optimization, showcasing further applications of knowledge-grounded evaluation.

cs.CL↗

arXiv2025

Rationale-Guided Retrieval Augmented Generation for Medical Question Answering

Large language models (LLM) hold significant potential for applications in biomedicine, but they struggle with hallucinations and outdated knowledge. While retrieval-augmented generation (RAG) is generally employed to address these issues, it also has its own set of challenges: (1) LLMs are vulnerable to irrelevant or incorrect context, (2) medical queries are often not well-targeted for helpful information, and (3) retrievers are prone to bias toward the specific source corpus they were trained on. In this study, we present RAG$^2$ (RAtionale-Guided RAG), a new framework for enhancing the reliability of RAG in biomedical contexts. RAG$^2$ incorporates three key innovations: a small filtering model trained on perplexity-based labels of rationales, which selectively augments informative snippets of documents while filtering out distractors; LLM-generated rationales as queries to improve the utility of retrieved snippets; a structure designed to retrieve snippets evenly from a comprehensive set of four biomedical corpora, effectively mitigating retriever bias. Our experiments demonstrate that RAG$^2$ improves the state-of-the-art LLMs of varying sizes, with improvements of up to 6.1\%, and it outperforms the previous best medical RAG model by up to 5.6\% across three medical question-answering benchmarks. Our code is available at https://github.com/dmis-lab/RAG2.

cs.CL↗

arXiv2025

Med-PRM: Medical Reasoning Models with Stepwise, Guideline-verified Process Rewards

Large language models have shown promise in clinical decision making, but current approaches struggle to localize and correct errors at specific steps of the reasoning process. This limitation is critical in medicine, where identifying and addressing reasoning errors is essential for accurate diagnosis and effective patient care. We introduce Med-PRM, a process reward modeling framework that leverages retrieval-augmented generation to verify each reasoning step against established medical knowledge bases. By verifying intermediate reasoning steps with evidence retrieved from clinical guidelines and literature, our model can precisely assess the reasoning quality in a fine-grained manner. Evaluations on five medical QA benchmarks and two open-ended diagnostic tasks demonstrate that Med-PRM achieves state-of-the-art performance, with improving the performance of base models by up to 13.50% using Med-PRM. Moreover, we demonstrate the generality of Med-PRM by integrating it in a plug-and-play fashion with strong policy models such as Meerkat, achieving over 80\% accuracy on MedQA for the first time using small-scale models of 8 billion parameters. Our code and data are available at: https://med-prm.github.io/

cs.CL↗

arXiv2025

DeepAries: Adaptive Rebalancing Interval Selection for Enhanced Portfolio Selection

We propose DeepAries , a novel deep reinforcement learning framework for dynamic portfolio management that jointly optimizes the timing and allocation of rebalancing decisions. Unlike prior reinforcement learning methods that employ fixed rebalancing intervals regardless of market conditions, DeepAries adaptively selects optimal rebalancing intervals along with portfolio weights to reduce unnecessary transaction costs and maximize risk-adjusted returns. Our framework integrates a Transformer-based state encoder, which effectively captures complex long-term market dependencies, with Proximal Policy Optimization (PPO) to generate simultaneous discrete (rebalancing intervals) and continuous (asset allocations) actions. Extensive experiments on multiple real-world financial markets demonstrate that DeepAries significantly outperforms traditional fixed-frequency and full-rebalancing strategies in terms of risk-adjusted returns, transaction costs, and drawdowns. Additionally, we provide a live demo of DeepAries at https://deep-aries.github.io/, along with the source code and dataset at https://github.com/dmis-lab/DeepAries, illustrating DeepAries' capability to produce interpretable rebalancing and allocation decisions aligned with shifting market regimes. Overall, DeepAries introduces an innovative paradigm for adaptive and practical portfolio management by integrating both timing and allocation into a unified decision-making process.

q-fin.PM↗

arXiv2025

Understanding and Tackling Over-Dilution in Graph Neural Networks

Message Passing Neural Networks (MPNNs) hold a key position in machine learning on graphs, but they struggle with unintended behaviors, such as over-smoothing and over-squashing, due to irregular data structures. The observation and formulation of these limitations have become foundational in constructing more informative graph representations. In this paper, we delve into the limitations of MPNNs, focusing on aspects that have previously been overlooked. Our observations reveal that even within a single layer, the information specific to an individual node can become significantly diluted. To delve into this phenomenon in depth, we present the concept of Over-dilution and formulate it with two dilution factors: intra-node dilution for attribute-level and inter-node dilution for node-level representations. We also introduce a transformer-based solution that alleviates over-dilution and complements existing node embedding methods like MPNNs. Our findings provide new insights and contribute to the development of informative representations. The implementation and supplementary materials are publicly available at https://github.com/LeeJunHyun/NATR.

cs.LG↗

arXiv2025

HiRef: Leveraging Hierarchical Ontology and Network Refinement for Robust Medication Recommendation

Medication recommendation is a crucial task for assisting physicians in making timely decisions from longitudinal patient medical records. However, real-world EHR data present significant challenges due to the presence of rarely observed medical entities and incomplete records that may not fully capture the clinical ground truth. While data-driven models trained on longitudinal Electronic Health Records often achieve strong empirical performance, they struggle to generalize under missing or novel conditions, largely due to their reliance on observed co-occurrence patterns. To address these issues, we propose Hierarchical Ontology and Network Refinement for Robust Medication Recommendation (HiRef), a unified framework that combines two complementary structures: (i) the hierarchical semantics encoded in curated medical ontologies, and (ii) refined co-occurrence patterns derived from real-world EHRs. We embed ontology entities in hyperbolic space, which naturally captures tree-like relationships and enables knowledge transfer through shared ancestors, thereby improving generalizability to unseen codes. To further improve robustness, we introduce a prior-guided sparse regularization scheme that refines the EHR co-occurrence graph by suppressing spurious edges while preserving clinically meaningful associations. Our model achieves strong performance on EHR benchmarks (MIMIC-III and MIMIC-IV) and maintains high accuracy under simulated unseen-code settings. Extensive experiments with comprehensive ablation studies demonstrate HiRef's resilience to unseen medical codes, supported by in-depth analyses of the learned sparsified graph structure and medical code embeddings.

cs.AI↗

arXiv2025

Learning from Negative Samples in Biomedical Generative Entity Linking

Generative models have become widely used in biomedical entity linking (BioEL) due to their excellent performance and efficient memory usage. However, these models are usually trained only with positive samples, i.e., entities that match the input mention's identifier, and do not explicitly learn from hard negative samples, which are entities that look similar but have different meanings. To address this limitation, we introduce ANGEL (Learning from Negative Samples in Biomedical Generative Entity Linking), the first framework that trains generative BioEL models using negative samples. Specifically, a generative model is initially trained to generate positive entity names from the knowledge base for given input entities. Subsequently, both correct and incorrect outputs are gathered from the model's top-k predictions. Finally, the model is updated to prioritize the correct predictions through preference optimization. Our models outperform the previous best baseline models by up to an average top-1 accuracy of 1.4% on five benchmarks. When incorporating our framework into pre-training, the performance improvement increases further to 1.7%, demonstrating its effectiveness in both the pre-training and fine-tuning stages. The code and model weights are available at https://github.com/dmis-lab/ANGEL.

cs.CL↗

arXiv2025

Outlier-Safe Pre-Training for Robust 4-Bit Quantization of Large Language Models

Extreme activation outliers in Large Language Models (LLMs) critically degrade quantization performance, hindering efficient on-device deployment. While channel-wise operations and adaptive gradient scaling are recognized causes, practical mitigation remains challenging. We introduce Outlier-Safe Pre-Training (OSP), a practical guideline that proactively prevents outlier formation rather than relying on post-hoc mitigation. OSP combines three key innovations: (1) the Muon optimizer, eliminating privileged bases while maintaining training efficiency; (2) Single-Scale RMSNorm, preventing channel-wise amplification; and (3) a learnable embedding projection, redistributing activation magnitudes originating from embedding matrices. We validate OSP by training a 1.4B-parameter model on 1 trillion tokens, which is the first production-scale LLM trained without such outliers. Under aggressive 4-bit quantization, our OSP model achieves a 35.7 average score across 10 benchmarks (compared to 26.5 for an Adam-trained model), with only a 2% training overhead. Remarkably, OSP models exhibit near-zero excess kurtosis (0.04) compared to extreme values (1818.56) in standard models, fundamentally altering LLM quantization behavior. Our work demonstrates that outliers are not inherent to LLMs but are consequences of training strategies, paving the way for more efficient LLM deployment. The source code and pretrained checkpoints are available at https://github.com/dmis-lab/Outlier-Safe-Pre-Training.

cs.LG↗

arXiv2025

PubMed knowledge graph 2.0: Connecting papers, patents, and clinical trials in biomedical science

Papers, patents, and clinical trials are essential scientific resources in biomedicine, crucial for knowledge sharing and dissemination. However, these documents are often stored in disparate databases with varying management standards and data formats, making it challenging to form systematic and fine-grained connections among them. To address this issue, we construct PKG 2.0, a comprehensive knowledge graph dataset encompassing over 36 million papers, 1.3 million patents, and 0.48 million clinical trials in the biomedical field. PKG 2.0 integrates these dispersed resources through 482 million biomedical entity linkages, 19 million citation linkages, and 7 million project linkages. The construction of PKG 2.0 wove together fine-grained biomedical entity extraction, high-performance author name disambiguation, multi-source citation integration, and high-quality project data from the NIH Exporter. Data validation demonstrates that PKG 2.0 excels in key tasks such as author disambiguation and biomedical entity recognition. This dataset provides valuable resources for biomedical researchers, bibliometric scholars, and those engaged in literature mining.

cs.DL↗

arXiv2025

Ask Optimal Questions: Aligning Large Language Models with Retriever's Preference in Conversation

Conversational search, unlike single-turn retrieval tasks, requires understanding the current question within a dialogue context. The common approach of rewrite-then-retrieve aims to decontextualize questions to be self-sufficient for off-the-shelf retrievers, but most existing methods produce sub-optimal query rewrites due to the limited ability to incorporate signals from the retrieval results. To overcome this limitation, we present a novel framework RetPO (Retriever's Preference Optimization), which is designed to optimize a language model (LM) for reformulating search queries in line with the preferences of the target retrieval systems. The process begins by prompting a large LM to produce various potential rewrites and then collects retrieval performance for these rewrites as the retrievers' preferences. Through the process, we construct a large-scale dataset called RF collection, containing Retrievers' Feedback on over 410K query rewrites across 12K conversations. Furthermore, we fine-tune a smaller LM on this dataset to align it with the retrievers' feedback. Our resulting model demonstrates superiority on two benchmarks, surpassing the previous state-of-the-art performance of rewrite-then-retrieve approaches.

cs.IR↗

arXiv2025

Monet: Mixture of Monosemantic Experts for Transformers

Understanding the internal computations of large language models (LLMs) is crucial for aligning them with human values and preventing undesirable behaviors like toxic content generation. However, mechanistic interpretability is hindered by polysemanticity -- where individual neurons respond to multiple, unrelated concepts. While Sparse Autoencoders (SAEs) have attempted to disentangle these features through sparse dictionary learning, they have compromised LLM performance due to reliance on post-hoc reconstruction loss. To address this issue, we introduce Mixture of Monosemantic Experts for Transformers (Monet) architecture, which incorporates sparse dictionary learning directly into end-to-end Mixture-of-Experts pretraining. Our novel expert decomposition method enables scaling the expert count to 262,144 per layer while total parameters scale proportionally to the square root of the number of experts. Our analyses demonstrate mutual exclusivity of knowledge across experts and showcase the parametric knowledge encapsulated within individual experts. Moreover, Monet allows knowledge manipulation over domains, languages, and toxicity mitigation without degrading general performance. Our pursuit of transparent LLMs highlights the potential of scaling expert counts to enhance mechanistic interpretability and directly resect the internal knowledge to fundamentally adjust model behavior. The source code and pretrained checkpoints are available at https://github.com/dmis-lab/Monet.

cs.AI↗

arXiv2025

Does Time Have Its Place? Temporal Heads: Where Language Models Recall Time-specific Information

While the ability of language models to elicit facts has been widely investigated, how they handle temporally changing facts remains underexplored. We discover Temporal Heads, specific attention heads that primarily handle temporal knowledge, through circuit analysis. We confirm that these heads are present across multiple models, though their specific locations may vary, and their responses differ depending on the type of knowledge and its corresponding years. Disabling these heads degrades the model's ability to recall time-specific knowledge while maintaining its general capabilities without compromising time-invariant and question-answering performances. Moreover, the heads are activated not only numeric conditions ("In 2004") but also textual aliases ("In the year ..."), indicating that they encode a temporal dimension beyond simple numerical representation. Furthermore, we expand the potential of our findings by demonstrating how temporal knowledge can be edited by adjusting the values of these heads.

cs.CL↗