arXiv subjects

Dongki Kim

Publications and source records attributed to Dongki Kim.

9 recordsLinked to original sources

arXiv2026

AdaPath: Query-Adaptive Path-Finding via Path-Bank for Multi-Hop Implicit Biomedical KGQA

Path-finding over knowledge graphs has become an effective way to ground LLM reasoning on multi-hop questions. However, biomedical QA introduces two distinct challenges that general-domain methods are not designed for: (i) queries do not expose intermediate reasoning and can be answered through multiple valid pathways, and (ii) biomedical knowledge graphs are densely connected, so path-finding methods easily take wrong turns. To address these challenges, we propose AdaPath, a path-finding framework that retrieves query-adaptive meta-paths from Path-Bank, which captures both query semantics and biomedical knowledge graph structure. AdaPath provides the missing cues in biomedical queries while effectively pruning dense knowledge graph neighborhoods during multi-hop reasoning. We further release BioStrat-QA, a biomedical KGQA benchmark that stratifies multi-hop queries by how much intermediate reasoning they expose. Across biomedical KGQA benchmarks, AdaPath consistently outperforms baselines, sustaining meaningful path-finding even when multi-hop queries expose less surface information. The source code is available at https://github.com/Jun-Hyeong-Kim/AdaPath.

cs.AI↗

arXiv2026

ES-Merging: Biological MLLM Merging via Embedding Space Signals

Biological multimodal large language models (MLLMs) have emerged as powerful foundation models for scientific discovery. However, existing models are specialized to a single modality, limiting their ability to solve inherently cross-modal scientific problems. While model merging is an efficient method to combine the different modalities into a unified MLLM, existing methods rely on input-agnostic parameter space heuristics that fail to faithfully capture modality specialization. To overcome this limitation, we propose the Embedding-Signal-based MLLM Merging (ES-Merging), a framework that estimates merging coefficients from embedding space signals, moving the merging paradigm from the parameter signals to the embedding signals. ES-Merging exploits coarse-grained and fine-grained signals from embedding space to estimate the layer-wise and element-wise merging coefficients, respectively, which are jointly combined for complementary coefficient estimation. Through extensive experiments, we demonstrate that ES-Merging outperforms existing merging methods not only on the cross-modal reasoning but also on the single-modal knowledge preservation, establishing that embedding space signals provide a principled and effective foundation for MLLM merging.

cs.LG↗

arXiv2025

Multimodal Prompt Optimization: Why Not Leverage Multiple Modalities for MLLMs

Large Language Models (LLMs) have shown remarkable success, and their multimodal expansions (MLLMs) further unlock capabilities spanning images, videos, and other modalities beyond text. However, despite this shift, prompt optimization approaches, designed to reduce the burden of manual prompt crafting while maximizing performance, remain confined to text, ultimately limiting the full potential of MLLMs. Motivated by this gap, we introduce the new problem of multimodal prompt optimization, which expands the prior definition of prompt optimization to the multimodal space defined by the pairs of textual and non-textual prompts. To tackle this problem, we then propose the Multimodal Prompt Optimizer (MPO), a unified framework that not only performs the joint optimization of multimodal prompts through alignment-preserving updates but also guides the selection process of candidate prompts by leveraging earlier evaluations as priors in a Bayesian-based selection strategy. Through extensive experiments across diverse modalities that go beyond text, such as images, videos, and even molecules, we demonstrate that MPO outperforms leading text-only optimization methods, establishing multimodal prompt optimization as a crucial step to realizing the potential of MLLMs.

cs.LG↗

arXiv2025

Rethinking Reward Models for Multi-Domain Test-Time Scaling

The reliability of large language models (LLMs) during test-time scaling is often assessed with \emph{external verifiers} or \emph{reward models} that distinguish correct reasoning from flawed logic. Prior work has studied both outcome reward models (ORMs), which assess only the final answer, and process reward models (PRMs), which score intermediate reasoning steps. Although PRMs are often viewed as advantageous due to their finer-grained supervision, much of the supporting evidence comes from math-adjacent settings, and their relative benefits across broader domains remain unclear. We present the first unified evaluation of four reward model variants, discriminative ORM and PRM (dORM, dPRM) and generative ORM and PRM (gORM, gPRM), across 14 diverse domains. Contrary to conventional wisdom, we find that (i) dORM performs on par with dPRM, (ii) gPRM is not competitive, and (iii) overall, gORM is the most robust, yielding significant and consistent gains across every tested domain. We attribute the worse performance of gPRM to the stepwise scoring process, which inherits label noise from LLM-based automatic labeling, leading to difficulties in evaluating long reasoning trajectories, including those involving self-correcting reasoning. Both our theoretical analysis and empirical observations indicate that stepwise aggregation compounds errors as reasoning length increases. These findings challenge the common assumption that fine-grained supervision is always better and support generative outcome verification for multi-domain deployment. Our \href{https://github.com/db-Lee/Multi-RM}{\underline{code}} is publicly available to facilitate future research in multi-domain settings.

cs.AI↗

arXiv2025

Mol-LLaMA: Towards General Understanding of Molecules in Large Molecular Language Model

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in task transfer, they often struggle to accurately analyze molecular features due to limited knowledge and reasoning capabilities. To address this issue, we present Mol-LLaMA, a large molecular language model that grasps the general knowledge centered on molecules and exhibits explainability and reasoning ability. To this end, we design key data types that encompass the fundamental molecular features, taking into account the essential abilities for molecular reasoning. Further, to improve molecular understanding, we propose a module that integrates complementary information from different molecular encoders, leveraging the distinct advantages of molecular representations. Our experimental results demonstrate that Mol-LLaMA is capable of comprehending the general features of molecules and providing informative responses, implying its potential as a general-purpose assistant for molecular analysis. Our project page is at https://mol-llama.github.io/.

cs.LG↗

arXiv2024

Graph Generation with Diffusion Mixture

Generation of graphs is a major challenge for real-world tasks that require understanding the complex nature of their non-Euclidean structures. Although diffusion models have achieved notable success in graph generation recently, they are ill-suited for modeling the topological properties of graphs since learning to denoise the noisy samples does not explicitly learn the graph structures to be generated. To tackle this limitation, we propose a generative framework that models the topology of graphs by explicitly learning the final graph structures of the diffusion process. Specifically, we design the generative process as a mixture of endpoint-conditioned diffusion processes which is driven toward the predicted graph that results in rapid convergence. We further introduce a simple parameterization of the mixture process and develop an objective for learning the final graph structure, which enables maximum likelihood training. Through extensive experimental validation on general graph and 2D/3D molecule generation tasks, we show that our method outperforms previous generative models, generating graphs with correct topology with both continuous (e.g. 3D coordinates) and discrete (e.g. atom types) features. Our code is available at https://github.com/harryjo97/GruM.

cs.LG↗

arXiv2024

Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship

The goal of protein representation learning is to extract knowledge from protein databases that can be applied to various protein-related downstream tasks. Although protein sequence, structure, and function are the three key modalities for a comprehensive understanding of proteins, existing methods for protein representation learning have utilized only one or two of these modalities due to the difficulty of capturing the asymmetric interrelationships between them. To account for this asymmetry, we introduce our novel asymmetric multi-modal masked autoencoder (AMMA). AMMA adopts (1) a unified multi-modal encoder to integrate all three modalities into a unified representation space and (2) asymmetric decoders to ensure that sequence latent features reflect structural and functional information. The experiments demonstrate that the proposed AMMA is highly effective in learning protein representations that exhibit well-aligned inter-modal relationships, which in turn makes it effective for various downstream protein-related tasks.

q-bio.BM↗

arXiv2022

Graph Self-supervised Learning with Accurate Discrepancy Learning

Self-supervised learning of graph neural networks (GNNs) aims to learn an accurate representation of the graphs in an unsupervised manner, to obtain transferable representations of them for diverse downstream tasks. Predictive learning and contrastive learning are the two most prevalent approaches for graph self-supervised learning. However, they have their own drawbacks. While the predictive learning methods can learn the contextual relationships between neighboring nodes and edges, they cannot learn global graph-level similarities. Contrastive learning, while it can learn global graph-level similarities, its objective to maximize the similarity between two differently perturbed graphs may result in representations that cannot discriminate two similar graphs with different properties. To tackle such limitations, we propose a framework that aims to learn the exact discrepancy between the original and the perturbed graphs, coined as Discrepancy-based Self-supervised LeArning (D-SLA). Specifically, we create multiple perturbations of the given graph with varying degrees of similarity, and train the model to predict whether each graph is the original graph or the perturbed one. Moreover, we further aim to accurately capture the amount of discrepancy for each perturbed graph using the graph edit distance. We validate our D-SLA on various graph-related downstream tasks, including molecular property prediction, protein function prediction, and link prediction tasks, on which ours largely outperforms relevant baselines.

cs.LG↗

arXiv2021

Edge Representation Learning with Hypergraphs

Graph neural networks have recently achieved remarkable success in representing graph-structured data, with rapid progress in both the node embedding and graph pooling methods. Yet, they mostly focus on capturing information from the nodes considering their connectivity, and not much work has been done in representing the edges, which are essential components of a graph. However, for tasks such as graph reconstruction and generation, as well as graph classification tasks for which the edges are important for discrimination, accurately representing edges of a given graph is crucial to the success of the graph representation learning. To this end, we propose a novel edge representation learning framework based on Dual Hypergraph Transformation (DHT), which transforms the edges of a graph into the nodes of a hypergraph. This dual hypergraph construction allows us to apply message-passing techniques for node representations to edges. After obtaining edge representations from the hypergraphs, we then cluster or drop edges to obtain holistic graph-level edge representations. We validate our edge representation learning method with hypergraphs on diverse graph datasets for graph representation and generation performance, on which our method largely outperforms existing graph representation learning methods. Moreover, our edge representation learning and pooling method also largely outperforms state-of-the-art graph pooling methods on graph classification, not only because of its accurate edge representation learning, but also due to its lossless compression of the nodes and removal of irrelevant edges for effective message-passing.

cs.LG↗