{"type":"ScholarlyArticle","title":"SPARK: Harnessing Human-Centered Workflows with Biomedical Foundation Models for Drug Discovery","authors":[{"name":"Bum Chul Kwon","slug":"bum-chul-kwon","given":"Bum Chul","family":"Kwon","affiliation":"IBM Research"},{"name":"Simona Rabinovici-Cohen","slug":"simona-rabinovici-cohen","given":"Simona","family":"Rabinovici-Cohen","affiliation":"IBM Research"},{"name":"Beldine Moturi","slug":"beldine-moturi","given":"Beldine","family":"Moturi","affiliation":"IBM Research"},{"name":"Ruth Mwaura","slug":"ruth-mwaura","given":"Ruth","family":"Mwaura","affiliation":"IBM Research"},{"name":"Kezia Wahome","slug":"kezia-wahome","given":"Kezia","family":"Wahome","affiliation":"IBM Research"},{"name":"Oliver Njeru","slug":"oliver-njeru","given":"Oliver","family":"Njeru","affiliation":"IBM Research"},{"name":"Miguel Shinyenyi","slug":"miguel-shinyenyi","given":"Miguel","family":"Shinyenyi","affiliation":"IBM Research"},{"name":"Catherine Wanjiru","slug":"catherine-wanjiru","given":"Catherine","family":"Wanjiru","affiliation":"IBM Research"},{"name":"Sekou Remy","slug":"sekou-remy","given":"Sekou","family":"Remy","affiliation":"IBM Research"},{"name":"William Ogallo","slug":"william-ogallo","given":"William","family":"Ogallo","affiliation":"IBM Research"},{"name":"Itai Guez","slug":"itai-guez","given":"Itai","family":"Guez","affiliation":"IBM Research"},{"name":"Partha Suryanarayanan","slug":"partha-suryanarayanan","given":"Partha","family":"Suryanarayanan","affiliation":"IBM Research"},{"name":"Joseph Morrone","slug":"joseph-morrone","given":"Joseph","family":"Morrone","affiliation":"IBM Research"},{"name":"Shreyans Sethi","slug":"shreyans-sethi","given":"Shreyans","family":"Sethi","affiliation":"IBM Research"},{"name":"Seung-Gu Kang","slug":"seung-gu-kang","given":"Seung-Gu","family":"Kang","affiliation":"IBM Research"},{"name":"Tien Huynh","slug":"tien-huynh","given":"Tien","family":"Huynh","affiliation":"IBM Research"},{"name":"Kenney Ng","slug":"kenney-ng","given":"Kenney","family":"Ng","affiliation":"IBM Research"},{"name":"Diwakar Mahajan","slug":"diwakar-mahajan","given":"Diwakar","family":"Mahajan","affiliation":"IBM Research"},{"name":"Hongyang Li","slug":"hongyang-li","given":"Hongyang","family":"Li","affiliation":"IBM Research"},{"name":"Matan Ninio","slug":"matan-ninio","given":"Matan","family":"Ninio","affiliation":"IBM Research"},{"name":"Shervin Ayati","slug":"shervin-ayati","given":"Shervin","family":"Ayati","affiliation":"IBM Research"},{"name":"Efrat Hexter","slug":"efrat-hexter","given":"Efrat","family":"Hexter","affiliation":"IBM Research"},{"name":"Wendy Cornell","slug":"wendy-cornell","given":"Wendy","family":"Cornell","affiliation":"IBM Research"}],"abstract":"Biomedical foundation models, trained on diverse sources of small molecule data, hold great potential for accelerating drug discovery. However, their complex nature often presents a barrier for researchers seeking scientific insights and drug candidate generation. SPARK addresses this challenge by providing a user-friendly, web-based interface that empowers researchers to leverage these powerful models in their scientific workflows. Through SPARK, users can specify target proteins and desired molecule properties, adjust pre-trained models for tailored inferences, generate lists of potential drug candidates, analyze and compare molecules through interactive visualizations, and filter candidates based on key metrics (e.g., toxicity). By seamlessly integrating human knowledge and biomedical AI models' capabilities through an interactive web-based system, SPARK can improve the efficiency of collaboration between human experts and AI, thereby accelerating drug candidate discovery and ultimately leading to breakthroughs in finding cures for various diseases.","doi":"10.24963/ijcai.2024/1015","url":"https://ijcai.org/proceedings/2024/1015","pdf":"https://ijcai.org/proceedings/2024/1015.pdf","markdown":"https://ijcai.org/proceedings/2024/1015.md","bibtex":"https://ijcai.org/proceedings/2024/bibtex/1015","volume":{"slug":"2024","title":"Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence","short_title":"IJCAI 2024","url":"https://ijcai.org/proceedings/2024/","year":2024,"location":"Jeju, Korea","dates":"3-9 August 2024","editors":"Kate Larson","isbn":"978-1-956792-04-1","publisher":"International Joint Conferences on Artificial Intelligence Organization","doi_prefix":"10.24963/ijcai.2024"},"section":"Demo Track","track":"Demo Track","number":1015,"pages":{"first":8713,"last":8716},"keywords":["Multidisciplinary Topics and Applications: MDA: Health and medicine","Data Mining: DM: Data visualization","Humans and AI: HAI: Human-AI collaboration","Multidisciplinary Topics and Applications: MDA: Bioinformatics"],"videos":[],"references":[{"position":1,"raw":"[Belgodere et al., 2022] Brian Belgodere, Vijil Chenthama- rakshan, Payel Das, Pierre Dognin, Toby Kurien, Igor Melnyk, Youssef Mroueh, Inkit Padhi, Mattia Rigotti, Jar- ret Ross, et al. Cloud-based real-time molecular screen- ing platform with molformer. In Joint European Confer- ence on Machine Learning and Knowledge Discovery in Databases, pages 641-644. Springer, 2022.","title":"Cloud-based real-time molecular screening platform with molformer","authors":"Brian Belgodere, Payel Vijil Chenthamarakshan, Pierre Das, Toby Dognin, Igor Kurien, Youssef Melnyk, Inkit Mroueh, Mattia Padhi, Jarret Rigotti, Ross","year":"2022","venue":"Joint European Conference on Machine Learning and Knowledge Discovery in Databases","doi":null,"url":null,"internal_url":null},{"position":2,"raw":"[Cadow et al., 2020] Joris Cadow, Jannis Born, Matteo Man- ica, Ali Oskooei, and María Rodríguez Martínez. Pac- cmann: a web service for interpretable anticancer com- pound sensitivity prediction. Nucleic acids research, 48(W1):W502-W508, 2020.","title":"Paccmann: a web service for interpretable anticancer compound sensitivity prediction","authors":"Joris Cadow, Jannis Born, Matteo Manica, Ali Oskooei, María Rodríguez, Martínez","year":"2020","venue":"Nucleic acids research","doi":null,"url":null,"internal_url":null},{"position":3,"raw":"[Dey et al., 2022] Sanjoy Dey, Prithwish Chakraborty, Bum Chul Kwon, Amit Dhurandhar, Mohamed Ghal- wash, Fernando J. Suarez Saiz, Kenney Ng, Daby Sow, Kush R. Varshney, and Pablo Meyer. Human-centered explainability for life sciences, healthcare, and medical informatics. Patterns, 3(5), May 2022.","title":"Human-centered explainability for life sciences, healthcare, and medical informatics","authors":"Sanjoy Dey, Prithwish Chakraborty, Bum Chul Kwon, Amit Dhurandhar, Mohamed Ghalwash, Fernando J Suarez Saiz, Kenney Ng, Daby Sow, R Kush, Pablo Varshney, Meyer","year":"2022","venue":"Patterns","doi":null,"url":null,"internal_url":null},{"position":4,"raw":"[Manica et al., 2023] Matteo Manica, Jannis Born, Joris Cadow, Dimitrios Christofidellis, Ashish Dave, Dean Clarke, Yves Gaetan Nana Teukam, Giorgio Giannone, Samuel C Hoffman, Matthew Buchan, et al. Accelerat- ing material design with the generative toolkit for scientific discovery. npj Computational Materials, 9(1):69, 2023.","title":"Accelerating material design with the generative toolkit for scientific discovery","authors":"Matteo Manica, Jannis Born, Joris Cadow, Dimitrios Christofidellis, Ashish Dave, Dean Clarke, Yves Gaetan, Nana Teukam, Giorgio Giannone, Matthew Samuel C Hoffman, Buchan","year":"2023","venue":"npj Computational Materials","doi":null,"url":null,"internal_url":null},{"position":5,"raw":"[Pezza et al., 2022] Alejandro Pezza, Luis E. Tavernelli, Victoria L. Alonso, Virginia Perdomo, Raquel Gabarro, Rab Prinjha, Elvio Rodríguez Araya, Inmaculada Rioja, Roberto Docampo, Felix Calderón, Julio Martin, and Es- teban Serra. Essential Bromodomain TcBDF2 as a Drug Target against Chagas Disease. ACS Infectious Diseases, 8(5):1062-1074, May 2022.","title":"Essential Bromodomain TcBDF2 as a Drug Target against Chagas Disease","authors":"Alejandro Pezza, Luis E Tavernelli, Victoria L Alonso, Virginia Perdomo, Raquel Gabarro, Rab Prinjha, Elvio Rodríguez Araya, Inmaculada Rioja, Roberto Docampo, Felix Calderón, Julio Martin, Esteban Serra","year":"2022","venue":"ACS Infectious Diseases","doi":null,"url":null,"internal_url":null},{"position":6,"raw":"[Rose and Hildebrand, 2015] Alexander S. Rose and Pe- ter W. Hildebrand. NGL Viewer: a web application for molecular visualization. Nucleic Acids Research, 43(W1):W576-W579, 2015.","title":"NGL Viewer: a web application for molecular visualization","authors":"Alexander S Rose, Peter W Hildebrand","year":"2015","venue":"Nucleic Acids Research","doi":null,"url":null,"internal_url":null},{"position":7,"raw":"[Ross et al., 2022] Jerret Ross, Brian Belgodere, Vijil Chen- thamarakshan, Inkit Padhi, Youssef Mroueh, and Payel Das. Large-scale chemical language representations cap- ture molecular structure and properties. Nature Machine Intelligence, 4(12):1256-1264, 2022.","title":"Large-scale chemical language representations capture molecular structure and properties","authors":"Jerret Ross, Brian Belgodere, Inkit Vijil Chenthamarakshan, Youssef Padhi, Payel Mroueh, Das","year":"2022","venue":"Nature Machine Intelligence","doi":null,"url":null,"internal_url":null},{"position":8,"raw":"[Schneuing et al., 2022] Arne Schneuing, Yuanqi Du, Charles Harris, Arian Jamasb, Ilia Igashov, Weitao Du, Tom Blundell, Pietro Lió, Carla Gomes, Max Welling, et al. Structure-based drug design with equivariant diffusion models. arXiv preprint arXiv:2210.13695, 2022.","title":"Structure-based drug design with equivariant diffusion models","authors":"Arne Schneuing, Yuanqi Du, Charles Harris, Arian Jamasb, Ilia Igashov, Weitao Du, Tom Blundell, Pietro Lió, Carla Gomes, Max Welling","year":"2022","venue":null,"doi":null,"url":null,"internal_url":null}],"license_note":"Copyright International Joint Conferences on Artificial Intelligence."}