arXiv subjects

Youngseung Jeon

Publications and source records attributed to Youngseung Jeon.

7 recordsLinked to original sources

arXiv2026

HALO: Interactive Co-abductive Reasoning in Scientific Hypothesis Generation

Scientific discovery is essential yet inefficient, primarily because generating hypotheses within a vast search space hinders breakthroughs. While current AI systems assist in generating new hypothesis candidates, they lack interactive support for the reasoning process by which users develop these outputs into promising hypotheses, resulting in surface-level hypotheses. To address this issue, we present co-abduction, a human-AI collaborative framework for abductive reasoning in scientific hypothesis generation. To operationalize co-abduction, we build HALO, a human-AI collaborative system for molecular hypothesis generation in drug discovery, enabling improved candidate clustering, strategy identification, and multi-strategy synthesis. In expert studies involving 10 medicinal chemists, HALO significantly facilitated abductive reasoning for hypothesis generation -- efficient candidate observation, systematic strategy identification, and coherent multi-strategy composition -- and enabled participants to produce higher-quality, more diverse candidate molecules.

cs.HC↗

arXiv2026

RAGPPI: RAG Benchmark for Protein-Protein Interactions in Drug Discovery

Retrieving the biological impacts of protein-protein interactions (PPIs) is essential for target identification (Target ID) in drug development. Given the vast number of proteins involved, this process remains time-consuming and challenging. Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) frameworks have supported Target ID; however, no benchmark currently exists for identifying the biological impacts of PPIs. To bridge this gap, we introduce the RAG Benchmark for PPIs (RAGPPI), a factual question-answer benchmark of 4,420 question-answer pairs that focus on the potential biological impacts of PPIs. Through interviews with experts, we identified criteria for a benchmark dataset, such as a type of QA and source. We built a gold-standard dataset (500 QA pairs) through expert-driven data annotation. We developed an ensemble auto-evaluation LLM that incorporates expert labeling characteristics, average fact-abstract similarity (F1), and low-similarity fact counts (F2), enabling the construction of a silver-standard dataset (3,720 QA pairs). We are committed to maintaining RAGPPI as a resource to support the research community in advancing RAG systems for drug discovery QA solutions.

cs.CL↗

arXiv2026

C-MORAL: Controllable Multi-Objective Molecular Optimization with Reinforcement Alignment for LLMs

Large language models (LLMs) show promise for molecular optimization, but aligning them with selective and competing drug-design constraints remains challenging. We propose C-Moral, a reinforcement learning post-training framework for controllable multi-objective molecular optimization. C-Moral combines group-based relative optimization, property score alignment for heterogeneous objectives, and bottleneck-sensitive non-linear reward aggregation to improve stability across competing molecular properties. Experiments on C-MuMOInstruct and S$^2$-Bench MolOpt show that C-Moral achieves the best performance among compared methods on both benchmarks. On C-MuMOInstruct, C-Moral achieves the best Success Optimized Rate (SOR) of 48.9\% on in-domain tasks and 39.5\% on out-of-domain tasks while preserving scaffold similarity. On S$^2$-Bench MolOpt, it also achieves the strongest results across LogP, MR, and QED optimization tasks. These results suggest that C-Moral is an effective way to align molecular LLMs with continuous and constrained molecular design objectives. Our code and models are publicly available at https://github.com/Rwigie/C-MORAL.

cs.LG↗

arXiv2025

Supporting Medicinal Chemists in Iterative Hypothesis Generation for Drug Target Identification

While drug discovery is vital for human health, the process remains inefficient. Medicinal chemists must navigate a vast protein space to identify target proteins that meet three criteria: physical and functional interactions, therapeutic impact, and docking potential. Prior approaches have provided fragmented support for each criterion, limiting the generation of promising hypotheses for wet-lab experiments. We present HAPPIER, an AI-powered tool that supports hypothesis generation with integrated multi-criteria support for target identification. HAPPIER enables medicinal chemists to 1) efficiently explore and verify proteins in a single integrated graph component showing multi-criteria satisfaction and 2) validate AI suggestions with domain knowledge. These capabilities facilitate iterative cycles of divergent and convergent thinking, essential for hypothesis generation. We evaluated HAPPIER with ten medicinal chemists, finding that it increased the number of high-confidence hypotheses and support for the iterative cycle, and further demonstrated the relationship between engaging in such cycles and confidence in outputs.

cs.HC↗

arXiv2025

GraPPI: A Retrieve-Divide-Solve GraphRAG Framework for Large-scale Protein-protein Interaction Exploration

Drug discovery (DD) has tremendously contributed to maintaining and improving public health. Hypothesizing that inhibiting protein misfolding can slow disease progression, researchers focus on target identification (Target ID) to find protein structures for drug binding. While Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) frameworks have accelerated drug discovery, integrating models into cohesive workflows remains challenging. We conducted a user study with drug discovery researchers to identify the applicability of LLMs and RAGs in Target ID. We identified two main findings: 1) an LLM should provide multiple Protein-Protein Interactions (PPIs) based on an initial protein and protein candidates that have a therapeutic impact; 2) the model must provide the PPI and relevant explanations for better understanding. Based on these observations, we identified three limitations in previous approaches for Target ID: 1) semantic ambiguity, 2) lack of explainability, and 3) short retrieval units. To address these issues, we propose GraPPI, a large-scale knowledge graph (KG)-based retrieve-divide-solve agent pipeline RAG framework to support large-scale PPI signaling pathway exploration in understanding therapeutic impacts by decomposing the analysis of entire PPI pathways into sub-tasks focused on the analysis of PPI edges.

q-bio.QM↗

arXiv2024

HearHere: Mitigating Echo Chambers in News Consumption through an AI-based Web System

Considerable efforts are currently underway to mitigate the negative impacts of echo chambers, such as increased susceptibility to fake news and resistance towards accepting scientific evidence. Prior research has presented the development of computer systems that support the consumption of news information from diverse political perspectives to mitigate the echo chamber effect. However, existing studies still lack the ability to effectively support the key processes of news information consumption and quantitatively identify a political stance towards the information. In this paper, we present HearHere, an AI-based web system designed to help users accommodate information and opinions from diverse perspectives. HearHere facilitates the key processes of news information consumption through two visualizations. Visualization 1 provides political news with quantitative political stance information, derived from our graph-based political classification model, and users can experience diverse perspectives (Hear). Visualization 2 allows users to express their opinions on specific political issues in a comment form and observe the position of their own opinions relative to pro-liberal and pro-conservative comments presented on a map interface (Here). Through a user study with 94 participants, we demonstrate the feasibility of HearHere in supporting the consumption of information from various perspectives. Our findings highlight the importance of providing political stance information and quantifying users' political status as a means to mitigate political polarization. In addition, we propose design implications for system development, including the consideration of demographics such as political interest and providing users with initiatives.

cs.HC↗

arXiv2023

KHAN: Knowledge-Aware Hierarchical Attention Networks for Accurate Political Stance Prediction

The political stance prediction for news articles has been widely studied to mitigate the echo chamber effect -- people fall into their thoughts and reinforce their pre-existing beliefs. The previous works for the political stance problem focus on (1) identifying political factors that could reflect the political stance of a news article and (2) capturing those factors effectively. Despite their empirical successes, they are not sufficiently justified in terms of how effective their identified factors are in the political stance prediction. Motivated by this, in this work, we conduct a user study to investigate important factors in political stance prediction, and observe that the context and tone of a news article (implicit) and external knowledge for real-world entities appearing in the article (explicit) are important in determining its political stance. Based on this observation, we propose a novel knowledge-aware approach to political stance prediction (KHAN), employing (1) hierarchical attention networks (HAN) to learn the relationships among words and sentences in three different levels and (2) knowledge encoding (KE) to incorporate external knowledge for real-world entities into the process of political stance prediction. Also, to take into account the subtle and important difference between opposite political stances, we build two independent political knowledge graphs (KG) (i.e., KG-lib and KG-con) by ourselves and learn to fuse the different political knowledge. Through extensive evaluations on three real-world datasets, we demonstrate the superiority of DASH in terms of (1) accuracy, (2) efficiency, and (3) effectiveness.

cs.CL↗