publications

2025

1. ISMB

   MixingDTA: Improved Drug-Target Affinity Prediction by Extending Mixup with Guilt-By-Association.

   Youngoh Kim^*, Dongmin Bang^*, Bonil Koo, and 4 more authors

   Bioinformatics, 2025

   DOI Bib

   @article{kim2025mixingtda,
     title = {MixingDTA: Improved Drug-Target Affinity Prediction by Extending Mixup with Guilt-By-Association. },
     author = {Kim, Youngoh and Bang, Dongmin and Koo, Bonil and Yi, Jungseob and Cho, Changyun and Choi, Jeonguk and Kim, Sun},
     journal = {Bioinformatics},
     volume = {Accepted},
     year = {2025},
     doi = {https://doi.org/10.1093/bioinformatics/btaf238},
   }

2. ISMB

   ADME-Drug-Likeness: Enriching Molecular Foundation Models via Pharmacokinetics-Guided Multi-Task Learning for Drug-likeness Prediction

   Dongmin Bang^*, Juyeon Kim^*, Haerin Song, and 1 more author

   Bioinformatics, 2025

   DOI Bib

   @article{bang2025admedl,
     title = {ADME-Drug-Likeness: Enriching Molecular Foundation Models via Pharmacokinetics-Guided Multi-Task Learning for Drug-likeness Prediction},
     author = {Bang, Dongmin and Kim, Juyeon and Song, Haerin and Kim, Sun},
     journal = {Bioinformatics},
     volume = {Accepted},
     year = {2025},
     doi = {https://doi.org/10.1093/bioinformatics/btaf259},
   }

3. ICML

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

   Dongmin Bang, Inyoung Sung, Yinhua Piao, and 2 more authors

   In Forty-second International Conference on Machine Learning, 2025

   Bib HTML PDF

   @inproceedings{bang2025boundre,
     title = {BounDr.E: Predicting Drug-likeness via Biomedical Knowledge Alignment and {EM}-like One-Class Boundary Optimization},
     author = {Bang, Dongmin and Sung, Inyoung and Piao, Yinhua and Lee, Sangseon and Kim, Sun},
     booktitle = {Forty-second International Conference on Machine Learning},
     year = {2025},
     url = {https://openreview.net/forum?id=Z9Xugry05b},
   }

4. Survey on AI-Drug Discovery with Knowledge Graphs: Data, Algorithm, and Application

   Daeun Kong^*, Yoojin Ha^*, HaEun Yoo^*, and 2 more authors

   Journal of Computing Science and Engineering, 2025

   DOI Bib PDF

   @article{kong2025survey,
     title = {Survey on AI-Drug Discovery with Knowledge Graphs: Data, Algorithm, and Application},
     author = {Kong, Daeun and Ha, Yoojin and Yoo, HaEun and Bang, Dongmin and Kim, Sun},
     journal = {Journal of Computing Science and Engineering},
     volume = {19},
     number = {1},
     pages = {1--15},
     year = {2025},
     doi = {http://dx.doi.org/10.5626/JCSE.2025.19.1.1},
   }

5. JCI

   Fate-tox: fragment attention transformer for E (3)-equivariant multi-organ toxicity prediction

   Sumin Ha^*, Dongmin Bang^*, and Sun Kim

   Journal of Cheminformatics, 2025

   Bib

   @article{ha2025fate,
     title = {Fate-tox: fragment attention transformer for E (3)-equivariant multi-organ toxicity prediction},
     author = {Ha, Sumin and Bang, Dongmin and Kim, Sun},
     journal = {Journal of Cheminformatics},
     volume = {17},
     number = {1},
     pages = {1--16},
     year = {2025},
     publisher = {Springer},
   }

6. Transferring Preclinical Drug Response to Patient via Tumor Heterogeneity-Aware Alignment and Perturbation Modeling

   Inyoung Sung, Dongmin Bang, Sun Kim, and 1 more author

   In ICLR 2025 Workshop on Machine Learning for Genomics Explorations, 2025

   Bib HTML PDF

   @inproceedings{sung2025transferring,
     title = {Transferring Preclinical Drug Response to Patient via Tumor Heterogeneity-Aware Alignment and Perturbation Modeling},
     author = {Sung, Inyoung and Bang, Dongmin and Kim, Sun and Lee, Sangseon},
     booktitle = {ICLR 2025 Workshop on Machine Learning for Genomics Explorations},
     year = {2025},
     url = {https://openreview.net/forum?id=prYPSWtKCC},
   }

7. ICLRw

   Predicting Drug-likeness via Biomedical Knowledge Alignment and EM-like One-Class Boundary Optimization

   Dongmin Bang, Inyoung Sung, Yinhua Piao, and 2 more authors

   In ICLR 2025 Workshop on Machine Learning for Genomics Explorations, 2025

   Bib

   @inproceedings{bang2025predicting,
     title = {Predicting Drug-likeness via Biomedical Knowledge Alignment and {EM}-like One-Class Boundary Optimization},
     author = {Bang, Dongmin and Sung, Inyoung and Piao, Yinhua and Lee, Sangseon and Kim, Sun},
     booktitle = {ICLR 2025 Workshop on Machine Learning for Genomics Explorations},
     year = {2025},
     url = {https://openreview.net/forum?id=G2zzdbgKxl},
   }

8. MDTR: a knowledge-guided interpretable representation for quantifying liver toxicity at transcriptomic level

   Inyoung Sung, Sangseon Lee, Dongmin Bang, and 3 more authors

   Frontiers in Pharmacology, 2025

   Bib

   @article{sung2025mdtr,
     title = {MDTR: a knowledge-guided interpretable representation for quantifying liver toxicity at transcriptomic level},
     author = {Sung, Inyoung and Lee, Sangseon and Bang, Dongmin and Yi, Jungseob and Lee, Sunho and Kim, Sun},
     journal = {Frontiers in Pharmacology},
     volume = {15},
     pages = {1398370},
     year = {2025},
     publisher = {Frontiers Media SA},
   }

2024

1. JCIM

   Residue-Level Multiview Deep Learning for ATP Binding Site Prediction and Applications in Kinase Inhibitors

   Jaechan Lee^*, Dongmin Bang^*, and Sun Kim

   Journal of Chemical Information and Modeling, 2024

   Bib

   @article{lee2024residue,
     title = {Residue-Level Multiview Deep Learning for ATP Binding Site Prediction and Applications in Kinase Inhibitors},
     author = {Lee, Jaechan and Bang, Dongmin and Kim, Sun},
     journal = {Journal of Chemical Information and Modeling},
     volume = {65},
     number = {1},
     pages = {50--61},
     year = {2024},
     publisher = {ACS Publications},
   }

2. ChemAP: predicting drug approval with chemical structures before clinical trial phase by leveraging multi-modal embedding space and knowledge distillation

   Changyun Cho, Sangseon Lee, Dongmin Bang, and 2 more authors

   Scientific Reports, 2024

   Bib

   @article{cho2024chemap,
     title = {ChemAP: predicting drug approval with chemical structures before clinical trial phase by leveraging multi-modal embedding space and knowledge distillation},
     author = {Cho, Changyun and Lee, Sangseon and Bang, Dongmin and Piao, Yinhua and Kim, Sun},
     journal = {Scientific Reports},
     volume = {14},
     number = {1},
     pages = {23010},
     year = {2024},
     publisher = {Nature Publishing Group UK London},
   }

3. ISMB

   Transfer learning of condition-specific perturbation in gene interactions improves drug response prediction

   Dongmin Bang^*, Bonil Koo^*, and Sun Kim

   Bioinformatics, 2024

   Best Paper Award DOI Bib

   Received the Best Paper Award in BIOINFO’24, Korean Society for Bioinformatics (KSBi), Korea

   @article{bang2024transfer,
     title = {Transfer learning of condition-specific perturbation in gene interactions improves drug response prediction},
     author = {Bang, Dongmin and Koo, Bonil and Kim, Sun},
     journal = {Bioinformatics},
     volume = {40},
     number = {Supplement\_1},
     pages = {i130--i139},
     year = {2024},
     publisher = {Oxford University Press},
     doi = {https://doi.org/10.1093/bioinformatics/btae249}
   }

4. DGDRP: drug-specific gene selection for drug response prediction via re-ranking through propagating and learning biological network

   Minwoo Pak, Dongmin Bang, Inyoung Sung, and 2 more authors

   Frontiers in Genetics, 2024

   Bib

   @article{pak2024dgdrp,
     title = {DGDRP: drug-specific gene selection for drug response prediction via re-ranking through propagating and learning biological network},
     author = {Pak, Minwoo and Bang, Dongmin and Sung, Inyoung and Kim, Sun and Lee, Sunho},
     journal = {Frontiers in Genetics},
     volume = {15},
     pages = {1441558},
     year = {2024},
     publisher = {Frontiers Media SA},
   }

5. DISCO: Diffusion Schrödinger bridge for molecular conformer optimization

   Danyeong Lee, Dohoon Lee, Dongmin Bang, and 1 more author

   Proceedings of the AAAI conference on artificial intelligence, 2024

   DOI Bib PDF

   @article{lee2024disco,
     title = {DISCO: Diffusion Schrödinger bridge for molecular conformer optimization},
     author = {Lee, Danyeong and Lee, Dohoon and Bang, Dongmin and Kim, Sun},
     journal = {Proceedings of the AAAI conference on artificial intelligence},
     doi = {10.1609/aaai.v38i12.29238},
     publisher = {Cold Spring Harbor Laboratory},
     year = {2024},
   }

2023

1. Brief Bioinform.

   A model-agnostic framework to enhance knowledge graph-based drug combination prediction with drug–drug interaction data and supervised contrastive learning

   Jeonghyeon Gu^*, Dongmin Bang^*, Jungseob Yi^*, and 3 more authors

   Briefings in Bioinformatics, 2023

   Bib

   @article{gu2023model,
     title = {A model-agnostic framework to enhance knowledge graph-based drug combination prediction with drug--drug interaction data and supervised contrastive learning},
     author = {Gu, Jeonghyeon and Bang, Dongmin and Yi, Jungseob and Lee, Sangseon and Kim, Dong Kyu and Kim, Sun},
     journal = {Briefings in Bioinformatics},
     volume = {24},
     number = {5},
     pages = {bbad285},
     year = {2023},
     publisher = {Oxford University Press},
   }

2. Nat Commun.

   Biomedical knowledge graph learning for drug repurposing by extending guilt-by-association to multiple layers

   Dongmin Bang, Sangsoo Lim, Sangseon Lee, and 1 more author

   Nature Communications, 2023

   Best Paper Award DOI Bib

   Received the Best Paper Award in BIOINFO’23, Korean Society for Bioinformatics (KSBi), Korea

   @article{bang2023biomedical,
     title = {Biomedical knowledge graph learning for drug repurposing by extending guilt-by-association to multiple layers},
     author = {Bang, Dongmin and Lim, Sangsoo and Lee, Sangseon and Kim, Sun},
     journal = {Nature Communications},
     volume = {14},
     number = {1},
     pages = {3570},
     year = {2023},
     publisher = {Nature Publishing Group UK London},
     doi = {https://doi.org/10.1038/s41467-023-39301-y}
   }

2022

1. DRPreter: interpretable anticancer drug response prediction using knowledge-guided graph neural networks and transformer

   Jihye Shin, Yinhua Piao, Dongmin Bang, and 2 more authors

   International Journal of Molecular Sciences, 2022

   Bib

   @article{shin2022drpreter,
     title = {DRPreter: interpretable anticancer drug response prediction using knowledge-guided graph neural networks and transformer},
     author = {Shin, Jihye and Piao, Yinhua and Bang, Dongmin and Kim, Sun and Jo, Kyuri},
     journal = {International Journal of Molecular Sciences},
     volume = {23},
     number = {22},
     pages = {13919},
     year = {2022},
     publisher = {MDPI},
   }

2. IJMS

   A survey on computational methods for investigation on ncRNA-disease association through the mode of action perspective

   Dongmin Bang^*, Jeonghyeon Gu^*, Joonhyeong Park, and 7 more authors

   International Journal of Molecular Sciences, 2022

   Bib

   @article{bang2022survey,
     title = {A survey on computational methods for investigation on ncRNA-disease association through the mode of action perspective},
     author = {Bang, Dongmin and Gu, Jeonghyeon and Park, Joonhyeong and Jeong, Dabin and Koo, Bonil and Yi, Jungseob and Shin, Jihye and Jung, Inuk and Kim, Sun and Lee, Sunho},
     journal = {International Journal of Molecular Sciences},
     volume = {23},
     number = {19},
     pages = {11498},
     year = {2022},
     publisher = {MDPI},
   }