Publications

Pre-prints

• Seungheun Baek*, Soyon Park*, Yan Ting Chok, Junhyun Lee, Jueon Park, Mogan Gim**, Jaewoo Kang**, "Cradle-VAE: Enhancing Single-Cell Gene Perturbation Modeling with Counterfactual Reasoning-based Artifact Disentanglement", arxiv, https://arxiv.org/abs/2409.05484

International Conference

• Heedou Kim, Dain Kim, Jiwoo Lee, Chanwoong Yoon, Donghee Choi, Mogan Gim**, Jaewoo Kang**, "LAPIS: Language Model-Augmented Police Investigation System", CIKM 2024, October 21--25, 2024, Boise, ID, USA, (Full Paper Accepted, Oral Presentation, https://dl.acm.org/doi/10.1145/3627673.3680044)

• Donghee Choi*, Jinkyu Kim*, Mogan Gim, Jinho Lee, Jaewoo Kang, "DeepClair: Utilizing Market Forecasts for Effective Portfolio Selection", CIKM 2024, October 21--25, 2024, Boise, ID, USA, (Full Paper Accepted, Oral Presentation, https://dl.acm.org/doi/abs/10.1145/3627673.3680008)

• Mogan Gim*, Jueon Park*, Soyon Park, Sanghoon Lee, Seungheun Baek, Junhyun Lee, Ngoc-Quang Nguyen and Jaewoo Kang. "MolPLA: A Molecular Pretraining Framework for Learning Cores, R-Groups and their Linker Joints", ISMB 2024, July 12--16, 2024, Montreal, Canada, (Full Paper Accepted, Oral Presentation, Bioinformatics, vol. 40, https://doi.org/10.1093/bioinformatics/btae256)

• Donghee Choi, Mogan Gim, Donghyeon Park, Mujeen Sung, Hyunjae Kim, Jaewoo Kang and Jihun Kim. "CookingSense: A Culinary Knowledgebase with Multidisciplinary Assertions", LREC-COLING 2024, May 20--25, 2024, Torino, Italy,  https://doi.org/10.48550/arXiv.2405.00523 (in press)

• Mogan Gim, Junseok Choi, Seungheun Baek, Jueon Park, Chaeeun Lee, Minjae Ju, Sumin Lee and Jaewoo Kang. "ArkDTA: Attention Regularization guided by non-Covalent Interactions for Explainable Drug-Target Binding Affinity Prediction", ISMB/ECCB 2023, July 23--27, 2023, Lyon, France, (Full Paper Accepted, Oral Presentation, Bioinformatics, vol. 39,  https://doi.org/10.1093/bioinformatics/btad207)

• Mogan Gim*, Donghee Choi*, Kana Maruyama, Jihun Choi, Hajung Kim, Donghyeon Park and Jaewoo Kang. "RecipeMind: Guiding Ingredient Choices from Food Pairing to Recipe Completion using Cascaded Set Transformer", CIKM '22: Proceedings of the 31st ACM International Conference on Information and Knowledge Management, October 17--21, 2022, Atlanta, GA, USA, https://doi.org/10.1145/3511808.3557092 (Full Paper Accepted, Oral Presentation)

• Junseok Choe, Mogan Gim, Minjae Ju, Sumin Lee, and Jaewoo Kang. "Improved Binding Affinity Prediction Using Non-Covalent Interactions and Graph Integration", 2022  IEEE International Conference on Big Data and Smart Computing (BigComp), January 17--21, 2022, Daegu, South Korea, https://doi.org/10.1109/BigComp54360.2022.00079 (Short Paper Accepted)

• Donghyeon Park, Mogan Gim, Yonggyu Park, Jungwoon Shin and Jaewoo Kang. "KitcheNette: Predicting and Recommending Food Ingredient Pairings using Siamese Neural Networks", The 28th International Joint Conference on Artificial Intelligence (IJCAI 2019), August 10-16, 2019, Macau, China, https://doi.org/10.24963/ijcai.2019/822  (Full Paper Accepted, Oral Presentation)

International Journal

• Jonathan L. Golob, Tomiko T. Oskotsky,  Alice S. Tang, Alennie Roldan, Verena Chung, Connie W.Y. Ha, Ronald J. Wong,  Kaitlin J. Flynn, Antonio Parraga-Leo, Camilla Wibrand, Samuel S. Minot, Boris Oskotsky, Gaia Andreoletti, Idit Kosti, Julie Bletz, Amber Nelson, Jifan Gao, Zhoujingpeng Wei, Guanhua Chen, Zheng-Zheng Tang, Pierfrancesco Novielli, Donato Romano, Ester Pantaleo, Nicola Amoroso, Alfonso Monaco, Mirco Vacca, Maria De Angelis, Roberto Bellotti, Sabina Tangaro, Abigail Kuntzleman, Isaac Bigcraft, Stephen Techtmann, Daehun Bae, Eunyoung Kim, Jongbum Jeon, Soobok Joe,  The Preterm Birth DREAM Community, Kevin R. Theis, Sherrianne Ng,  Yun S. Lee, Patricia Diaz-Gimeno, Phillip R. Bennett, David A. MacIntyre, Gustavo Stolovitzky, Susan V. Lynch, Jake Albrecht, Nardhy Gomez-Lopez, Roberto Romero, David K. Stevenson, Nima Aghaeepour, Adi L. Tarca, James C. Costello and Marina Sirota. "Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research", Cell Reports Medicine, Jan 2024, https://doi.org/10.1016/j.xcrm.2023.101350

• Ngoc-Quang Nguyen, Sejeong Park, Mogan Gim and Jaewoo Kang. "MultinforCPI: Enhancing Precision of Compound-Protein Interaction Prediction through Novel Perspectives on Multi-level Information Integration", Briefings in Bioinformatics, Jan 2024, https://doi.org/10.1093/bib/bbad484

• Jinkyu Kim, Donghee Choi, Mogan Gim and Jaewoo Kang. "HADAPS: Hierarchical Adaptive Multi-Asset Portfolio Selection", IEEE Access, June 2023, https://doi.org/10.1109/ACCESS.2023.3285613

• Donghee Choi, Mogan Gim, Samy Badreddine, Hajung Kim, Donghyeon Park and Jaewoo Kang. "KitchenScale: Learning to Predict Ingredient Quantities from Recipe Contexts", Expert Systems With Applications, 2023, http://dx.doi.org/10.1016/j.eswa.2023.120041

• Mogan Gim*, Donghyeon Park*, Michael Spranger, Kana Maruyama and Jaewoo Kang. "RecipeBowl: A Cooking Recommender for Ingredients and Recipes using Set Transformer", IEEE Access, vol. 9, October 2021, https://doi.org/10.1109/ACCESS.2021.3120265

• Adi L. Tarca, Blint Armin Pataki, Roberto Romero, Marina Sirota, Yuanfang Guan, Rintu Kutum, Nardhy Gomez-Lopez, Bogdan Done, Gaurav Bhatti, Thomas Yu, Gaia Andreoletti, Tinnakorn Chaiworapongsa, The DREAM Preterm Birth Prediction Challenge Consortium, Sonia S. Hassan, Chaur-Dong Hsu, Nima Aghaeepour, Gustavo Stolovitzky, Istvan Csabai, James C. Costello, "Crowdsourcing Assessment of Maternal Blood Multi-omics for Predicting Gestational Age and Preterm Birth", Cell Reports Medicine, vol 2, issue 6, June 2021 (Finished 8th at the Preterm Birth Prediction: Transcriptomics DREAM Challenge) , https://doi.org/10.1016/j.xcrm.2021.100323

• Donghyeon Park, Mogan Gim, Seoyoon Kim, Michael Spranger and Jaewoo Kang. "FlavorGraph: A Large-scale Food-Chemical Graph for Generating Food Representations and Recommending Food Pairings", Scientific Reports, vol. 11, Article number: 931 (2021), https://doi.org/10.1038/s41598-020-79422-8 

• Junghoon Shin, Mogan Gim, Donghyeon Park, Sunkyu Kim and Jaewoo Kang. "Bipartite Link Prediction by Intra-class Connection based Triadic Closure", IEEE Access, vol. 8, July 2020, https://doi.org/10.1109/ACCESS.2020.3010223

• Sunkyu Kim, Mogan Gim, Junseok Choi, Inggeol Lee and Jaewoo Kang. "Improved Survival Analysis by Learning Shared Genomic Information from Pan-Cancer Data", Bioinformatics, Volume 36 Issue Supplement_1 (Presented at The 28th Conference on Intelligent Systems for Molecular Biology, ISMB 2020),  https://doi.org/10.1093/bioinformatics/btaa462

• Ye Eun Jang, Insu Jang, Sunkyu Kim, Subin Cho, Daehan Kim, Mogan Gim, Jaewon Kim, Jimin Hwang, Sangok Kim, Jaesang Kim, Jaewoo Kang, Byungwook Lee, Sanghyuk Lee. "ChimerDB 4.0: an updated and expanded database of fusion genes", Nucleic Acids Research, gkz1013, Nov. 2019, https://doi.org/10.1093/nar/gkz1013

• Sunkyu Kim*, Heewon Lee*, Mogan Gim and Jaewoo Kang. "Mut2Vec: Distributed Representation of Cancerous Mutation". BMC Medical Genomics vol. 11, no. 2, pages 33, April 2018 (Presented at The 28th Interantional Conference on Genome Informatics Workshop, GIW/BIOINFO 2017) , https://doi.org/10.1186/s12920-018-0349-7

(*: Equal Contributors, **: Co-corresponding Authors)