Research areas
We develop machine learning methods that reflect the structure of biological data. The 5 areas below are what 33 publications since 2017 add up to.
Single-cell representation learning
10 papers · 2025–2026We learn representations of cells from scRNA-seq data so that clustering, cell type annotation, and batch effect correction can be addressed together rather than as separate steps. Recent work pairs a dual-encoder cross-attention architecture with large language models for annotation.
Publications 10
- Integrative evidence-knowledge marker selection enhances LLM-based cell type annotation in single-cell RNA-seq analysisBioData Mining2026International journalSCIEIF 7.9
- scFANCL: Dual contrastive learning with false-negative correction at cell level for single-cell RNA-seq clusteringBMC Genomics2026International journalSCIEIF 3.9
- Annotation-free phenotype prediction using knowledge-augmented clustering from single-cell RNA sequencing dataBriefings in Bioinformatics2026International journalSCIEIF 7.3
- CMAgent: 단일세포 RNA-seq 주석을 위한 LLM 기반 세포 유형–마커 관계 큐레이션 에이전트Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2026Domestic conference
- HetDrugKG: 이종 지식 그래프 기반 단일세포 약물 유도 유전자 발현 변화 예측Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2026Domestic conference
- scRNA-seq 기반 표현형 예측을 위한 사전 학습 임베딩을 활용한 환자 단위 메타셀 구성Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2026Domestic conference
- LLM 기반 세포 유형 특이적 마커 유전자 추출을 위한 자동화 접근법Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2025Domestic conference
- scRNA-seq 데이터 축소 기법을 이용한 환자 표현형 예측의 연산 경량화 분석Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2025Domestic conference
- AMIL: Automated cell grouping framework for phenotype prediction with multiple instance learningProceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2025Domestic conference
- GPT-4를 활용한 마커 유전자 기반 단일세포 세포 유형 자동 주석화 모델Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2025Domestic conference
Spatial transcriptomics
5 papers · 2025–2026We work with transcriptomes measured alongside positional information in tissue: predicting expression from histology images, imputing unmeasured spots, and identifying spatial domains.
Publications 5
- 국소 유전자 맥락과 Spot과 유전자 간 교차 어텐션을 이용한 공간 전사체 표현 학습Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2026Domestic conference
- 전역·지역 매칭 기반 공간 전사체와 조직 이미지 정렬 자동화 프레임워크Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2026Domestic conference
- 클라이언트 기반 GeoMx DSP 공간 전사체 데이터 분석 플랫폼Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2025Domestic conference
- Spatial Transcript와 H&E Whole Slide Image의 정렬 자동화 프레임워크Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2025Domestic conference
- DeepSpot-VAE: H&E 이미지 기반 Xenium 유전자 발현 복원 프레임워크Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2025Domestic conference
Multi-omics integration for drug response and phenotype
8 papers · 2020–2026We integrate transcriptome, methylome, and other omics layers to explain how cells respond to drug treatment and how patient phenotypes differ, using autoencoders, tensor decomposition, and graph attention networks.
Publications 8
- Ferroptosis-based therapeutic strategy targeting iron metabolism and SLC7A11 overcomes oxaliplatin resistance in patient-derived pancreatic cancer organoidsJournal of Experimental & Clinical Cancer Research2026International journalSCIEIF 14.3
- Machine learning based plasma proteomic analysis identifies disease differentiating biomarkers in atopic dermatitisJournal of Korean Medical Science2026Domestic journalSCIEIF 3.2
- Integrative multi-omic profiling in blood reveals distinct immune and metabolic signatures between ACPA-negative and ACPA-positive rheumatoid arthritisFrontiers in Immunology2025International journalSCIEIF 7.0
- LassoNet을 활용한 Olink 프로테오믹스 데이터 기반 질병 분류 및 바이오마커 탐지Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2025Domestic conference
- XGBoost와 SHAP을 이용한 RNA-seq 기반 유방암 서브타입 예측 및 주요 유전자 분석Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2024Domestic conference
- GOAT: Gene-level biomarker discovery from multi-omics data using graph ATtention neural network for eosinophilic asthma subtypeBioinformatics2023International journalSCIEIF 5.5
- Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulationsBriefings in Bioinformatics2021International journalSCIEIF 7.3
- DRIM: A web-based system for investigating drug response at the molecular level by condition-specific multi-omics data integrationFrontiers in Genetics2020International journalSCIEIF 3.0
Condition-specific regulatory networks
7 papers · 2017–2026We reconstruct gene regulatory relationships that hold under a specific condition rather than on average — through transcription factor network propagation, kernel canonical correlation analysis, Gaussian process models for time-series data, and literature mining for miRNA-mRNA targets.
Publications 7
- HetDrugKG: 이종 지식 그래프 기반 단일세포 약물 유도 유전자 발현 변화 예측Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2026Domestic conference
- TFNetPropX: A web-based comprehensive analysis tool for exploring condition-specific RNA-seq data using transcription factor network propagationApplied Sciences2023International journalSCIEIF 2.9
- Adipocyte HIF2α functions as a thermostat via PKA Cα regulation in beige adipocytesNature Communications2022International journalSCIEIF 18.1
- mirTime: identifying condition-specific targets of microRNA in time-series transcript data using Gaussian process model and spherical vector clusteringBioinformatics2021International journalSCIEIF 5.5
- Construction of condition-specific gene regulatory network using kernel canonical correlation analysisFrontiers in Genetics2021International journalSCIEIF 3.0
- miRTarVis+: Web-based interactive visual analytics tool for microRNA target predictionsMethods2017International journalSCIEIF 3.6
- Literature-based condition-specific miRNA-mRNA target predictionPLOS ONE2017International journalSCIEIF 2.8
Machine learning methods for biological data
4 papers · 2018–2025Method development that is not tied to a single omics modality: alignment-free protein family modeling with convolutional networks, hierarchical clustering for arbitrary-shaped data, and algorithms for quantifying genome editing outcomes.
Publications 4
- Large DNA deletions occur during DNA repair at 20-fold lower frequency for base editors and prime editors than for Cas9 nucleasesNature Biomedical Engineering2025International journalSCIEIF 26.3
- MIMIC-III 데이터를 이용한 급성호흡곤란증후군 환자의 병원 내 사망 예측: 다양한 결측 데이터 처리 전략을 적용한 머신러닝 모델의 비교 연구Proceedings of the KIISE Conference (한국정보과학회 학술발표논문집)2023Domestic conference
- IDEA: Integrating divisive and ensemble-agglomerate hierarchical clustering framework for arbitrary shape dataIEEE International Conference on Big Data2021International conference
- DeepFam: deep learning based alignment-free method for protein family modeling and predictionBioinformatics2018International journalSCIEIF 5.5
R&D projects
4 ongoing · 2 completed- Ongoing2026.04–2029.12Development of AI-based game content rating technology for efficient rating classification and post-release managementKorea Creative Content Agency (KOCCA) · Co-investigator
- Ongoing2024.04–2028.12Development of CAR-Treg cell therapeutics for chronic inflammatory diseases through an AI-based target discovery platformKorea Health Industry Development Institute (KHIDI) · Co-investigator
- Ongoing2026.09–2027.08Development of an evidence-grounded AI agent for automated cell type–marker relation curation in single-cell transcriptome analysisNational Research Foundation of Korea (NRF) · PI
- Ongoing2022.07–2026.12IoMT artificial intelligence and NFT interface standard development for the metaverseKorea Planning & Evaluation Institute of Industrial Technology (KEIT) · Co-PI
- —Deep reinforcement learning-based combination optimization for identifying patient-specific multi-omics regulatory networks
- Completed2025.09–2026.08Development of a client-side, high-speed and high-precision web-based analysis platform for detecting and quantifying CRISPR-Cas9-induced large DNA deletionsNational Research Foundation of Korea (NRF) · PI
- Completed2022.09–2025.02Graph neural network based multi-omics integrative method for drug response predictionNational Research Foundation of Korea (NRF) · PI