arXiv subjects

Seonghyun Park

Publications and source records attributed to Seonghyun Park.

9 recordsLinked to original sources

arXiv2026

DA-Flow: Degradation-Aware Optical Flow Estimation with Diffusion Models

Optical flow models trained on high-quality data often degrade severely when confronted with real-world corruptions such as blur, noise, and compression artifacts. To overcome this limitation, we formulate Degradation-Aware Optical Flow, a new task targeting accurate dense correspondence estimation from real-world corrupted videos. Our key insight is that the intermediate representations of image restoration diffusion models are inherently corruption-aware but lack temporal awareness. To address this limitation, we lift the model to attend across adjacent frames via full spatio-temporal attention, and empirically demonstrate that the resulting features exhibit zero-shot correspondence capabilities. Based on this finding, we present DA-Flow, a hybrid architecture that fuses these diffusion features with convolutional features within an iterative refinement framework. DA-Flow substantially outperforms existing optical flow methods under severe degradation across multiple benchmarks.

cs.CV↗

arXiv2026

Riemannian MeanFlow

Diffusion and flow models have become the dominant paradigm for generative modeling on Riemannian manifolds, with successful applications in protein backbone generation and DNA sequence design. However, these methods require tens to hundreds of neural network evaluations at inference time, which can become a computational bottleneck in large-scale scientific sampling workflows. We introduce Riemannian MeanFlow~(RMF), a framework for learning flow maps directly on manifolds, enabling high-quality generations with as few as one forward pass. We derive three equivalent characterizations of the manifold average velocity (Eulerian, Lagrangian, and semigroup identities), and analyze parameterizations and stabilization techniques to improve training on high-dimensional manifolds. In promoter DNA design and protein backbone generation settings, RMF achieves comparable sample quality to prior methods while requiring up to 10$\times$ fewer function evaluations. Finally, we show that few-step flow maps enable efficient reward-guided design through reward look-ahead, where terminal states can be predicted from intermediate steps at minimal additional cost.

cs.LG↗

arXiv2026

INDIBATOR: Diverse and Fact-Grounded Individuality for Multi-Agent Debate in Molecular Discovery

Multi-agent systems have emerged as a powerful paradigm for automating scientific discovery. To differentiate agent behavior in the multi-agent system, current frameworks typically assign generic role-based personas such as ''reviewer'' or ''writer'' or rely on coarse grained keyword-based personas. While functional, this approach oversimplifies how human scientists operate, whose contributions are shaped by their unique research trajectories. In response, we propose INDIBATOR, a framework for molecular discovery that grounds agents in individualized scientist profiles constructed from two modalities: publication history for literature-derived knowledge and molecular history for structural priors. These agents engage in multi-turn debate through proposal, critique, and voting phases. Our evaluation demonstrates that these fine-grained individuality-grounded agents consistently outperform systems relying on coarse-grained personas, achieving competitive or state-of-the-art performance. These results validate that capturing the ``scientific DNA'' of individual agents is essential for high-quality discovery.

cs.AI↗

arXiv2026

A Systematic Evaluation of Co-folding Model Representations for Small-Molecule Learning

Small-molecule foundation models are typically pretrained on standalone molecular data, unlike vision and language models that often benefit from cross-modal or relational supervision. Protein-ligand co-folding provides a molecular analogue of such supervision by exposing models to atom-level ligand-protein interactions, raising the question of whether co-folding models can yield strong small-molecule representations. We study this question using Boltz2, a modern co-folding model, by transferring its atom-level ligand representations to standalone small-molecule tasks. Through systematic probing and distillation, we show that Boltz2 representations match or outperform existing models on the ADMET benchmark, accelerate molecular generative modeling, and improve sample efficiency in structure-guided ligand optimization. We further find that Boltz2 representations are complementary to those learned from conventional standalone molecular supervision, including 3D conformers, bioassay labels, and quantum-chemical properties. Finally, we extend representation alignment to reinforcement learning, showing that dense representation-level supervision can complement scalar rewards in molecular discovery. These results identify protein-ligand co-folding as a promising pretraining paradigm for small-molecule representation learning and position Boltz2 as a strong, off-the-shelf molecular foundation model.

q-bio.BM↗

arXiv2025

Learning Collective Variables from BioEmu with Time-Lagged Generation

Molecular dynamics is crucial for understanding molecular systems but its applicability is often limited by the vast timescales of rare events like protein folding. Enhanced sampling techniques overcome this by accelerating the simulation along key reaction pathways, which are defined by collective variables (CVs). However, identifying effective CVs that capture the slow, macroscopic dynamics of a system remains a major bottleneck. This work proposes a novel framework coined BioEmu-CV that learns these essential CVs automatically from BioEmu, a recently proposed foundation model for generating protein equilibrium samples. In particular, we re-purpose BioEmu to learn time-lagged generation conditioned on the learned CV, i.e., predict the distribution of molecular states after a certain amount of time. This training process promotes the CV to encode only the slow, long-term information while disregarding fast, random fluctuations. We validate our learned CV on fast-folding proteins with two key applications: (1) estimating free energy differences using on-the-fly probability enhanced sampling and (2) sampling transition paths with steered molecular dynamics. Our empirical study also serves as a new systematic and comprehensive benchmark for MLCVs on fast-folding proteins larger than Alanine Dipeptide.

cs.LG↗

arXiv2025

Transition Path Sampling with Improved Off-Policy Training of Diffusion Path Samplers

Understanding transition pathways between two meta-stable states of a molecular system is crucial to advance drug discovery and material design. However, unbiased molecular dynamics (MD) simulations are computationally infeasible because of the high energy barriers that separate these states. Although recent machine learning techniques are proposed to sample rare events, they are often limited to simple systems and rely on collective variables (CVs) derived from costly domain expertise. In this paper, we introduce a novel approach that trains diffusion path samplers (DPS) to address the transition path sampling (TPS) problem without requiring CVs. We reformulate the problem as an amortized sampling from the transition path distribution by minimizing the log-variance divergence between the path distribution induced by DPS and the transition path distribution. Based on the log-variance divergence, we propose learnable control variates to reduce the variance of gradient estimators and the off-policy training objective with replay buffers and simulated annealing techniques to improve sample efficiency and diversity. We also propose a scale-based equivariant parameterization of the bias forces to ensure scalability for large systems. We extensively evaluate our approach, termed TPS-DPS, on a synthetic system, small peptide, and challenging fast-folding proteins, demonstrating that it produces more realistic and diverse transition pathways than existing baselines.

cs.LG↗

arXiv2024

Non-backtracking Graph Neural Networks

The celebrated message-passing updates for graph neural networks allow representing large-scale graphs with local and computationally tractable updates. However, the updates suffer from backtracking, i.e., a message flowing through the same edge twice and revisiting the previously visited node. Since the number of message flows increases exponentially with the number of updates, the redundancy in local updates prevents the graph neural network from accurately recognizing a particular message flow relevant for downstream tasks. In this work, we propose to resolve such a redundancy issue via the non-backtracking graph neural network (NBA-GNN) that updates a message without incorporating the message from the previously visited node. We theoretically investigate how NBA-GNN alleviates the over-squashing of GNNs, and establish a connection between NBA-GNN and the impressive performance of non-backtracking updates for stochastic block model recovery. Furthermore, we empirically verify the effectiveness of our NBA-GNN on the long-range graph benchmark and transductive node classification problems.

cs.LG↗

arXiv2023

Diffusion Probabilistic Models for Structured Node Classification

This paper studies structured node classification on graphs, where the predictions should consider dependencies between the node labels. In particular, we focus on solving the problem for partially labeled graphs where it is essential to incorporate the information in the known label for predicting the unknown labels. To address this issue, we propose a novel framework leveraging the diffusion probabilistic model for structured node classification (DPM-SNC). At the heart of our framework is the extraordinary capability of DPM-SNC to (a) learn a joint distribution over the labels with an expressive reverse diffusion process and (b) make predictions conditioned on the known labels utilizing manifold-constrained sampling. Since the DPMs lack training algorithms for partially labeled data, we design a novel training algorithm to apply DPMs, maximizing a new variational lower bound. We also theoretically analyze how DPMs benefit node classification by enhancing the expressive power of GNNs based on proposing AGG-WL, which is strictly more powerful than the classic 1-WL test. We extensively verify the superiority of our DPM-SNC in diverse scenarios, which include not only the transductive setting on partially labeled graphs but also the inductive setting and unlabeled graphs.

cs.LG↗

arXiv2022

NTIRE 2022 Challenge on High Dynamic Range Imaging: Methods and Results

This paper reviews the challenge on constrained high dynamic range (HDR) imaging that was part of the New Trends in Image Restoration and Enhancement (NTIRE) workshop, held in conjunction with CVPR 2022. This manuscript focuses on the competition set-up, datasets, the proposed methods and their results. The challenge aims at estimating an HDR image from multiple respective low dynamic range (LDR) observations, which might suffer from under- or over-exposed regions and different sources of noise. The challenge is composed of two tracks with an emphasis on fidelity and complexity constraints: In Track 1, participants are asked to optimize objective fidelity scores while imposing a low-complexity constraint (i.e. solutions can not exceed a given number of operations). In Track 2, participants are asked to minimize the complexity of their solutions while imposing a constraint on fidelity scores (i.e. solutions are required to obtain a higher fidelity score than the prescribed baseline). Both tracks use the same data and metrics: Fidelity is measured by means of PSNR with respect to a ground-truth HDR image (computed both directly and with a canonical tonemapping operation), while complexity metrics include the number of Multiply-Accumulate (MAC) operations and runtime (in seconds).

cs.CV↗