arXiv subjects

Dongwoo Kim

Publications and source records attributed to Dongwoo Kim.

At least 37 records · Page 2Linked to original sources

arXiv2026

Mind the Rarities: Can Rare Skin Diseases Be Reliably Diagnosed via Diagnostic Reasoning?

Large vision-language models (LVLMs) demonstrate strong performance in dermatology; however, evaluating diagnostic reasoning for rare conditions remains largely unexplored. Existing benchmarks focus on common diseases and assess only final accuracy, overlooking the clinical reasoning process, which is critical for complex cases. We address this gap by constructing DermCase, a long-context benchmark derived from peer-reviewed case reports. Our dataset contains 26,030 multi-modal image-text pairs and 6,354 clinically challenging cases, each annotated with comprehensive clinical information and step-by-step reasoning chains. To enable reliable evaluation, we establish DermLIP-based similarity metrics that achieve stronger alignment with dermatologists for assessing differential diagnosis quality. Benchmarking 22 leading LVLMs exposes significant deficiencies across diagnosis accuracy, differential diagnosis, and clinical reasoning. Fine-tuning experiments demonstrate that instruction tuning substantially improves performance while Direct Preference Optimization (DPO) yields minimal gains. Systematic error analysis further reveals critical limitations in current models' reasoning capabilities.

cs.CV↗

arXiv2026

Transductive Generalization via Optimal Transport and Its Application to Graph Node Classification

Many existing transductive bounds rely on classical complexity measures that are computationally intractable and often misaligned with empirical behavior. In this work, we establish new representation-based generalization bounds in a distribution-free transductive setting, where learned representations are dependent, and test features are accessible during training. We derive global and class-wise bounds via optimal transport, expressed in terms of Wasserstein distances between encoded feature distributions. We demonstrate that our bounds are efficiently computable and strongly correlate with empirical generalization in graph node classification, improving upon classical complexity measures. Additionally, our analysis reveals how the GNN aggregation process transforms the representation distributions, inducing a trade-off between intra-class concentration and inter-class separation. This yields depth-dependent characterizations that capture the non-monotonic relationship between depth and generalization error observed in practice. The code is available at https://github.com/ml-postech/Transductive-OT-Gen-Bound.

cs.LG↗

arXiv2026

Posterior Label Smoothing for Node Classification

Label smoothing is a widely studied regularization technique in machine learning. However, its potential for node classification in graph-structured data, spanning homophilic to heterophilic graphs, remains largely unexplored. We introduce posterior label smoothing, a novel method for transductive node classification that derives soft labels from a posterior distribution conditioned on neighborhood labels. The likelihood and prior distributions are estimated from the global statistics of the graph structure, allowing our approach to adapt naturally to various graph properties. We evaluate our method on 10 benchmark datasets using eight baseline models, demonstrating consistent improvements in classification accuracy. The following analysis demonstrates that soft labels mitigate overfitting during training, leading to better generalization performance, and that pseudo-labeling effectively refines the global label statistics of the graph. Our code is available at https://github.com/ml-postech/PosteL.

cs.LG↗

arXiv2026

Influence Functions for Edge Edits in Non-Convex Graph Neural Networks

Understanding how individual edges influence the behavior of graph neural networks (GNNs) is essential for improving their interpretability and robustness. Graph influence functions have emerged as promising tools to efficiently estimate the effects of edge deletions without retraining. However, existing influence prediction methods rely on strict convexity assumptions, exclusively consider the influence of edge deletions while disregarding edge insertions, and fail to capture changes in message propagation caused by these modifications. In this work, we propose a proximal Bregman response function specifically tailored for GNNs, relaxing the convexity requirement and enabling accurate influence prediction for standard neural network architectures. Furthermore, our method explicitly accounts for message propagation effects and extends influence prediction to both edge deletions and insertions in a principled way. Experiments with real-world datasets demonstrate accurate influence predictions for different characteristics of GNNs. We further demonstrate that the influence function is versatile in applications such as graph rewiring and adversarial attacks.

cs.LG↗

arXiv2026

Exploring Iterative Controllable Summarization with Large Language Models

Large language models (LLMs) have demonstrated remarkable performance in abstractive summarization tasks. However, their ability to precisely control summary attributes (e.g., length or topic) remains underexplored, limiting their adaptability to specific user preferences. In this paper, we systematically explore the controllability of LLMs. To this end, we revisit summary attribute measurements and introduce iterative evaluation metrics, failure rate and average iteration count to precisely evaluate controllability of LLMs, rather than merely assessing errors. Our findings show that LLMs struggle more with numerical attributes than with linguistic attributes. To address this challenge, we propose a guide-to-explain framework (GTE) for controllable summarization. Our GTE framework enables the model to identify misaligned attributes in the initial draft and guides it in self-explaining errors in the previous output. By allowing the model to reflect on its misalignment, GTE generates well-adjusted summaries that satisfy the desired attributes with robust effectiveness, requiring surprisingly fewer iterations than other iterative approaches.

cs.CL↗

arXiv2025

Holistic Unlearning Benchmark: A Multi-Faceted Evaluation for Text-to-Image Diffusion Model Unlearning

As text-to-image diffusion models gain widespread commercial applications, there are increasing concerns about unethical or harmful use, including the unauthorized generation of copyrighted or sensitive content. Concept unlearning has emerged as a promising solution to these challenges by removing undesired and harmful information from the pre-trained model. However, the previous evaluations primarily focus on whether target concepts are removed while preserving image quality, neglecting the broader impacts such as unintended side effects. In this work, we propose Holistic Unlearning Benchmark (HUB), a comprehensive framework for evaluating unlearning methods across six key dimensions: faithfulness, alignment, pinpoint-ness, multilingual robustness, attack robustness, and efficiency. Our benchmark covers 33 target concepts, including 16,000 prompts per concept, spanning four categories: Celebrity, Style, Intellectual Property, and NSFW. Our investigation reveals that no single method excels across all evaluation criteria. By releasing our evaluation code and dataset, we hope to inspire further research in this area, leading to more reliable and effective unlearning methods.

cs.CV↗

arXiv2025

High-order Equivariant Flow Matching for Density Functional Theory Hamiltonian Prediction

Density functional theory (DFT) is a fundamental method for simulating quantum chemical properties, but it remains expensive due to the iterative self-consistent field (SCF) process required to solve the Kohn-Sham equations. Recently, deep learning methods are gaining attention as a way to bypass this step by directly predicting the Hamiltonian. However, they rely on deterministic regression and do not consider the highly structured nature of Hamiltonians. In this work, we propose QHFlow, a high-order equivariant flow matching framework that generates Hamiltonian matrices conditioned on molecular geometry. Flow matching models continuous-time trajectories between simple priors and complex targets, learning the structured distributions over Hamiltonians instead of direct regression. To further incorporate symmetry, we use a neural architecture that predicts SE(3)-equivariant vector fields, improving accuracy and generalization across diverse geometries. To further enhance physical fidelity, we additionally introduce a fine-tuning scheme to align predicted orbital energies with the target. QHFlow achieves state-of-the-art performance, reducing Hamiltonian error by 71% on MD17 and 53% on QH9. Moreover, we further show that QHFlow accelerates the DFT process without trading off the solution quality when initializing SCF iterations with the predicted Hamiltonian, significantly reducing the number of iterations and runtime.

physics.comp-ph↗

arXiv2025

Retrieval-Augmented Generation with Estimation of Source Reliability

Retrieval-Augmented Generation (RAG) is an effective approach to enhance the factual accuracy of large language models (LLMs) by retrieving information from external databases, which are typically composed of diverse sources, to supplement the limited internal knowledge of LLMs. However, the standard RAG often risks retrieving incorrect information, as it relies solely on relevance between a query and a document, overlooking the heterogeneous reliability of these sources. To address this issue, we propose Reliability-Aware RAG (RA-RAG), a new multi-source RAG framework that estimates the reliability of sources and leverages this information to prioritize highly reliable and relevant documents, ensuring more robust and accurate response generation. Specifically, RA-RAG first estimates source reliability by cross-checking information across multiple sources. It then retrieves documents from the top-$κ$ reliable and relevant sources and aggregates their information using weighted majority voting (WMV), where the selective retrieval ensures scalability while not compromising the performance. Comprehensive experiments show that RA-RAG consistently outperforms baselines in scenarios with heterogeneous source reliability while scaling efficiently as the number of sources increases. Furthermore, we demonstrate the ability of RA-RAG to estimate real-world sources' reliability, highlighting its practical applicability. \jy{Our code and data are available at \href{https://github.com/ml-postech/RA-RAG}{RA-RAG}.}

cs.LG↗

arXiv2025

GeoDANO: Geometric VLM with Domain Agnostic Vision Encoder

We introduce GeoDANO, a geometric vision-language model (VLM) with a domain-agnostic vision encoder, for solving plane geometry problems. Although VLMs have been employed for solving geometry problems, their ability to recognize geometric features remains insufficiently analyzed. To address this gap, we propose a benchmark that evaluates the recognition of visual geometric features, including primitives such as dots and lines, and relations such as orthogonality. Our preliminary study shows that vision encoders often used in general-purpose VLMs, e.g., OpenCLIP, fail to detect these features and struggle to generalize across domains. To overcome the limitation, we develop GeoCLIP, a CLIP-based model trained on synthetic geometric diagram--caption pairs. Benchmark results show that GeoCLIP outperforms existing vision encoders in recognizing geometric features. We then propose our VLM, GeoDANO, which augments GeoCLIP with a domain adaptation strategy for unseen diagram styles. GeoDANO outperforms specialized methods for plane geometry problems and GPT-4o on MathVerse. The implementation is available at https://github.com/ml-postech/GeoDANO.

cs.CV↗

arXiv2025

CoPL: Collaborative Preference Learning for Personalizing LLMs

Personalizing large language models (LLMs) is important for aligning outputs with diverse user preferences, yet existing methods struggle with flexibility and generalization. We propose CoPL (Collaborative Preference Learning), a graph-based collaborative filtering framework that models user-response relationships to enhance preference estimation, particularly in sparse annotation settings. By integrating a mixture of LoRA experts, CoPL efficiently fine-tunes LLMs while dynamically balancing shared and user-specific preferences. Additionally, an optimization-free adaptation strategy enables generalization to unseen users without fine-tuning. Experiments on UltraFeedback-P demonstrate that CoPL outperforms existing personalized reward models, effectively capturing both common and controversial preferences, making it a scalable solution for personalized LLM alignment. The code is available at https://github.com/ml-postech/CoPL.

cs.LG↗

arXiv2025

Delving into Instance-Dependent Label Noise in Graph Data: A Comprehensive Study and Benchmark

Graph Neural Networks (GNNs) have achieved state-of-the-art performance in node classification tasks but struggle with label noise in real-world data. Existing studies on graph learning with label noise commonly rely on class-dependent label noise, overlooking the complexities of instance-dependent noise and falling short of capturing real-world corruption patterns. We introduce BeGIN (Benchmarking for Graphs with Instance-dependent Noise), a new benchmark that provides realistic graph datasets with various noise types and comprehensively evaluates noise-handling strategies across GNN architectures, noisy label detection, and noise-robust learning. To simulate instance-dependent corruptions, BeGIN introduces algorithmic methods and LLM-based simulations. Our experiments reveal the challenges of instance-dependent noise, particularly LLM-based corruption, and underscore the importance of node-specific parameterization to enhance GNN robustness. By comprehensively evaluating noise-handling strategies, BeGIN provides insights into their effectiveness, efficiency, and key performance factors. We expect that BeGIN will serve as a valuable resource for advancing research on label noise in graphs and fostering the development of robust GNN training methods. The code is available at https://github.com/kimsu55/BeGIN.

cs.LG↗

arXiv2025

The Oversmoothing Fallacy: A Misguided Narrative in GNN Research

Oversmoothing has been recognized as a main obstacle to building deep Graph Neural Networks (GNNs), limiting the performance. This position paper argues that the influence of oversmoothing has been overstated and advocates for a further exploration of deep GNN architectures. Given the three core operations of GNNs, aggregation, linear transformation, and non-linear activation, we show that prior studies have mistakenly confused oversmoothing with the vanishing gradient, caused by transformation and activation rather than aggregation. Our finding challenges prior beliefs about oversmoothing being unique to GNNs. Furthermore, we demonstrate that classical solutions such as skip connections and normalization enable the successful stacking of deep GNN layers without performance degradation. Our results clarify misconceptions about oversmoothing and shed new light on the potential of deep GNNs.

cs.LG↗

arXiv2025

EPIC: Graph Augmentation with Edit Path Interpolation via Learnable Cost

Data augmentation plays a critical role in improving model performance across various domains, but it becomes challenging with graph data due to their complex and irregular structure. To address this issue, we propose EPIC (Edit Path Interpolation via learnable Cost), a novel interpolation-based method for augmenting graph datasets. To interpolate between two graphs lying in an irregular domain, EPIC leverages the concept of graph edit distance, constructing an edit path that represents the transformation process between two graphs via edit operations. Moreover, our method introduces a context-sensitive cost model that accounts for the importance of specific edit operations formulated through a learning framework. This allows for a more nuanced transformation process, where the edit distance is not merely count-based but reflects meaningful graph attributes. With randomly sampled graphs from the edit path, we enrich the training set to enhance the generalization capability of classification models. Experimental evaluations across several benchmark datasets demonstrate that our approach outperforms existing augmentation techniques in many tasks.

cs.LG↗

arXiv2025

Plane Geometry Problem Solving with Multi-modal Reasoning: A Survey

Plane geometry problem solving (PGPS) has recently gained significant attention as a benchmark to assess the multi-modal reasoning capabilities of large vision-language models. Despite the growing interest in PGPS, the research community still lacks a comprehensive overview that systematically synthesizes recent work in PGPS. To fill this gap, we present a survey of existing PGPS studies. We first categorize PGPS methods into an encoder-decoder framework and summarize the corresponding output formats used by their encoders and decoders. Subsequently, we classify and analyze these encoders and decoders according to their architectural designs. Finally, we outline major challenges and promising directions for future research. In particular, we discuss the hallucination issues arising during the encoding phase within encoder-decoder architectures, as well as the problem of data leakage in current PGPS benchmarks.

cs.CV↗

arXiv2025

Chemical and Morphological Transformations of a Ag-Cu Nanocatalyst During CO2 Reduction Reaction

The conversion of CO2 into high-value chemicals through a photoreduction reaction in water is a promising route to reduce the dependence on fossil fuels. Ag nanoparticles can drive this reaction via localized surface plasmon resonance, but their low selectivity limits usage in industry. Enhancing selectivity toward hydrocarbons or alcohols requires addition of a co-catalyst such as Cu. However, the stabilized surface state created by Ag-Cu interactions is still poorly understood. In this work, soft x-ray Ambient-Pressure X-ray Photoelectron Spectroscopy (AP-XPS) and Grazing-Incidence X-ray Scattering (AP-GIXS) were used to investigate the evolution of Ag-Cu nanoparticles under CO2RR-like conditions. AP-XPS revealed Ag and Cu surface and sub-surface diffusion, while AP-GIXS tracked change of shape and size of nanoparticles induced by diffusion mechanics. Under 532 nm laser irradiation, further oxidation of Cu and Ag sub-surface diffusion were observed, providing invaluable insights into the dynamic restructuring of the catalyst under reaction conditions.

cond-mat.mtrl-sci↗

arXiv2025

Phi-4-Mini Technical Report: Compact yet Powerful Multimodal Language Models via Mixture-of-LoRAs

We introduce Phi-4-Mini and Phi-4-Multimodal, compact yet highly capable language and multimodal models. Phi-4-Mini is a 3.8-billion-parameter language model trained on high-quality web and synthetic data, significantly outperforming recent open-source models of similar size and matching the performance of models twice its size on math and coding tasks requiring complex reasoning. This achievement is driven by a carefully curated synthetic data recipe emphasizing high-quality math and coding datasets. Compared to its predecessor, Phi-3.5-Mini, Phi-4-Mini features an expanded vocabulary size of 200K tokens to better support multilingual applications, as well as group query attention for more efficient long-sequence generation. Phi-4-Multimodal is a multimodal model that integrates text, vision, and speech/audio input modalities into a single model. Its novel modality extension approach leverages LoRA adapters and modality-specific routers to allow multiple inference modes combining various modalities without interference. For example, it now ranks first in the OpenASR leaderboard to date, although the LoRA component of the speech/audio modality has just 460 million parameters. Phi-4-Multimodal supports scenarios involving (vision + language), (vision + speech), and (speech/audio) inputs, outperforming larger vision-language and speech-language models on a wide range of tasks. Additionally, we experiment to further train Phi-4-Mini to enhance its reasoning capabilities. Despite its compact 3.8-billion-parameter size, this experimental version achieves reasoning performance on par with or surpassing significantly larger models, including DeepSeek-R1-Distill-Qwen-7B and DeepSeek-R1-Distill-Llama-8B.

cs.CL↗

arXiv2024

Position-Sensing Graph Neural Networks: Proactively Learning Nodes Relative Positions

Most existing graph neural networks (GNNs) learn node embeddings using the framework of message passing and aggregation. Such GNNs are incapable of learning relative positions between graph nodes within a graph. To empower GNNs with the awareness of node positions, some nodes are set as anchors. Then, using the distances from a node to the anchors, GNNs can infer relative positions between nodes. However, P-GNNs arbitrarily select anchors, leading to compromising position-awareness and feature extraction. To eliminate this compromise, we demonstrate that selecting evenly distributed and asymmetric anchors is essential. On the other hand, we show that choosing anchors that can aggregate embeddings of all the nodes within a graph is NP-complete. Therefore, devising efficient optimal algorithms in a deterministic approach is practically not feasible. To ensure position-awareness and bypass NP-completeness, we propose Position-Sensing Graph Neural Networks (PSGNNs), learning how to choose anchors in a back-propagatable fashion. Experiments verify the effectiveness of PSGNNs against state-of-the-art GNNs, substantially improving performance on various synthetic and real-world graph datasets while enjoying stable scalability. Specifically, PSGNNs on average boost AUC more than 14% for pairwise node classification and 18% for link prediction over the existing state-of-the-art position-aware methods. Our source code is publicly available at: https://github.com/ZhenyueQin/PSGNN.

cs.LG↗

arXiv2024

Towards Bridging Generalization and Expressivity of Graph Neural Networks

Expressivity and generalization are two critical aspects of graph neural networks (GNNs). While significant progress has been made in studying the expressivity of GNNs, much less is known about their generalization capabilities, particularly when dealing with the inherent complexity of graph-structured data. In this work, we address the intricate relationship between expressivity and generalization in GNNs. Theoretical studies conjecture a trade-off between the two: highly expressive models risk overfitting, while those focused on generalization may sacrifice expressivity. However, empirical evidence often contradicts this assumption, with expressive GNNs frequently demonstrating strong generalization. We explore this contradiction by introducing a novel framework that connects GNN generalization to the variance in graph structures they can capture. This leads us to propose a $k$-variance margin-based generalization bound that characterizes the structural properties of graph embeddings in terms of their upper-bounded expressive power. Our analysis does not rely on specific GNN architectures, making it broadly applicable across GNN models. We further uncover a trade-off between intra-class concentration and inter-class separation, both of which are crucial for effective generalization. Through case studies and experiments on real-world datasets, we demonstrate that our theoretical findings align with empirical results, offering a deeper understanding of how expressivity can enhance GNN generalization.

cs.LG↗