Author name cluster

Sangseon Lee

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

4 papers

2 author rows

ICML Conference 2025 Conference Paper

BounDr. E: Predicting Drug-likeness via Biomedical Knowledge Alignment and EM-like One-Class Boundary Optimization

Dongmin Bang
Inyoung Sung
Yinhua Piao
Sangseon Lee
Sun Kim

The advent of generative AI now enables large-scale $\textit{de novo}$ design of molecules, but identifying viable drug candidates among them remains an open problem. Existing drug-likeness prediction methods often rely on ambiguous negative sets or purely structural features, limiting their ability to accurately classify drugs from non-drugs. In this work, we introduce BounDr. E: a novel modeling of drug-likeness as a compact space surrounding approved drugs through a dynamic one-class boundary approach. Specifically, we enrich the chemical space through biomedical knowledge alignment, and then iteratively tighten the drug-like boundary by pushing non-drug-like compounds outside via an Expectation-Maximization (EM)-like process. Empirically, BounDr. E achieves 10% F1-score improvement over the previous state-of-the-art and demonstrates robust cross-dataset performance, including zero-shot toxic compound filtering. Additionally, we showcase its effectiveness through comprehensive case studies in large-scale $\textit{in silico}$ screening. Our codes and constructed benchmark data under various schemes are provided at: https: //github. com/eugenebang/boundr_e.

Details

ICLR Conference 2025 Conference Paper

CheapNet: Cross-attention on Hierarchical representations for Efficient protein-ligand binding Affinity Prediction

Hyukjun Lim
Sun Kim
Sangseon Lee

Accurately predicting protein-ligand binding affinity is a critical challenge in drug discovery, crucial for understanding drug efficacy. While existing models typically rely on atom-level interactions, they often fail to capture the complex, higher-order interactions, resulting in noise and computational inefficiency. Transitioning to modeling these interactions at the cluster level is challenging because it is difficult to determine which atoms form meaningful clusters that drive the protein-ligand interactions. To address this, we propose CheapNet, a novel interaction-based model that integrates atom-level representations with hierarchical cluster-level interactions through a cross-attention mechanism. By employing differentiable pooling of atom-level embeddings, CheapNet efficiently captures essential higher-order molecular representations crucial for accurate binding predictions. Extensive evaluations demonstrate that CheapNet not only achieves state-of-the-art performance across multiple binding affinity prediction tasks but also maintains prediction accuracy with reasonable computational efficiency. The code of CheapNet is available at https://github.com/hyukjunlim/CheapNet.

Details

JBHI Journal 2025 Journal Article

Dual Representation Learning for Predicting Drug-Side Effect Frequency Using Protein Target Information

Sungjoon Park
Sangseon Lee
Minwoo Pak
Sun Kim

Knowledge of unintended effects of drugs is critical in assessing the risk of treatment and in drug repurposing. Although numerous existing studies predict drug-side effect presence, only four of them predict the frequency of the side effects. Unfortunately, current prediction methods 1) do not utilize drug targets, 2) do not predict well for unseen drugs, and 3) do not use multiple heterogeneous drug features. We propose a novel deep learning-based drug-side effect frequency prediction model. Our model utilized heterogeneous features such as target protein information as well as molecular graph, fingerprints, and chemical similarity to create drug embeddings simultaneously. Furthermore, the model represents drugs and side effects into a common vector space, learning the dual representation vectors of drugs and side effects, respectively. We also extended the predictive power of our model to compensate for the drugs without clear target proteins using the Adaboost method. We achieved state-of-the-art performance over the existing methods in predicting side effect frequencies, especially for unseen drugs. Ablation studies show that our model effectively combines and utilizes heterogeneous features of drugs. Moreover, we observed that, when the target information given, drugs with explicit targets resulted in better prediction than the drugs without explicit targets.

Details DOI

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.

PDF Details