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Dohoon Lee

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3 papers

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ICML Conference 2025 Conference Paper

Multidimensional Adaptive Coefficient for Inference Trajectory Optimization in Flow and Diffusion

Dohoon Lee
Jaehyun Park
Hyunwoo J. Kim
Kyogu Lee

Flow and diffusion models have demonstrated strong performance and training stability across various tasks but lack two critical properties of simulation-based methods: freedom of dimensionality and adaptability to different inference trajectories. To address this limitation, we propose the Multidimensional Adaptive Coefficient (MAC), a plug-in module for flow and diffusion models that extends conventional unidimensional coefficients to multidimensional ones and enables inference trajectory-wise adaptation. MAC is trained via simulation-based feedback through adversarial refinement. Empirical results across diverse frameworks and datasets demonstrate that MAC enhances generative quality with high training efficiency. Consequently, our work offers a new perspective on inference trajectory optimality, encouraging future research to move beyond vector field design and to leverage training-efficient, simulation-based optimization.

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AAAI Conference 2024 Conference Paper

DiSCO: Diffusion Schrödinger Bridge for Molecular Conformer Optimization

Danyeong Lee
Dohoon Lee
Dongmin Bang
Sun Kim

The generation of energetically optimal 3D molecular conformers is crucial in cheminformatics and drug discovery. While deep generative models have been utilized for direct generation in Euclidean space, this approach encounters challenges, including the complexity of navigating a vast search space. Recent generative models that implement simplifications to circumvent these challenges have achieved state-of-the-art results, but this simplified approach unavoidably creates a gap between the generated conformers and the ground-truth conformational landscape. To bridge this gap, we introduce DiSCO: Diffusion Schrödinger Bridge for Molecular Conformer Optimization, a novel diffusion framework that enables direct learning of nonlinear diffusion processes in prior-constrained Euclidean space for the optimization of 3D molecular conformers. Through the incorporation of an SE(3)-equivariant Schrödinger bridge, we establish the roto-translational equivariance of the generated conformers. Our framework is model-agnostic and offers an easily implementable solution for the post hoc optimization of conformers produced by any generation method. Through comprehensive evaluations and analyses, we establish the strengths of our framework, substantiating the application of the Schrödinger bridge for molecular conformer optimization. First, our approach consistently outperforms four baseline approaches, producing conformers with higher diversity and improved quality. Then, we show that the intermediate conformers generated during our diffusion process exhibit valid and chemically meaningful characteristics. We also demonstrate the robustness of our method when starting from conformers of diverse quality, including those unseen during training. Lastly, we show that the precise generation of low-energy conformers via our framework helps in enhancing the downstream prediction of molecular properties. The code is available at https://github.com/Danyeong-Lee/DiSCO.

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AAAI Conference 2022 Conference Paper

Sparse Structure Learning via Graph Neural Networks for Inductive Document Classification

Yinhua Piao
Sangseon Lee
Dohoon Lee
Sun Kim

Recently, graph neural networks (GNNs) have been widely used for document classification. However, most existing methods are based on static word co-occurrence graphs without sentence-level information, which poses three challenges: (1) word ambiguity, (2) word synonymity, and (3) dynamic contextual dependency. To address these challenges, we propose a novel GNN-based sparse structure learning model for inductive document classification. Specifically, a document-level graph is initially generated by a disjoint union of sentence-level word co-occurrence graphs. Our model collects a set of trainable edges connecting disjoint words between sentences, and employs structure learning to sparsely select edges with dynamic contextual dependencies. Graphs with sparse structures can jointly exploit local and global contextual information in documents through GNNs. For inductive learning, the refined document graph is further fed into a general readout function for graph-level classification and optimization in an end-to-end manner. Extensive experiments on several real-world datasets demonstrate that the proposed model outperforms most state-of-the-art results, and reveal the necessity to learn sparse structures for each document.

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