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{
"pub_grouping": {
"conference": "conference/workshop",
"workshop": "conference/workshop",
"journal": "journal/chapter",
"dissertation": "journal/chapter",
"chapter": "journal/chapter",
"poster": "other",
"article": "other",
"demo": "other",
"tech report": "other"
},
"publications": [
{
"key": "submission23a",
"author": ["Hanchen Wang*", "Tianfan Fu*", "Yuanqi Du*", "Wenhao Gao", "Kexin Huang", "Ziming Liu", "Payal Chandak", "Shengchao Liu", "Peter Van Katwyk", "Andreea Deac", "Anima Anandkumar", "Karianne Bergen", "Carla P. Gomez", "Shirley Ho", "Pushmeet Kohli", "Joan Lasenby", "Jure Leskovec", "Tie-Yan Liu", "Arjun Manrai", "Debora Marks", "Bharath Ramsundar", "Le Song", "Jimeng Sun", "Jian Tang", "Petar Velickovic", "Max Welling", "Connor W. Coley", "Yoshua Bengio", "Marinka Zitnik"],
"title": "Scientific Discovery in the Age of Artificial Intelligence",
"venue": "Nature",
"year": "2023",
"thumbnail": "AI4Science-Nature23.png",
"type": "journal",
"pdf": "https://rdcu.be/dinBA",
"url": "https://www.nature.com/articles/s41586-023-06221-2",
"supp":
{
"AI4Science Initiative": "https://ai4sciencecommunity.github.io/",
"Harvard Medicine News": "https://dbmi.hms.harvard.edu/news/artificial-intelligence-beyond-clinic",
"The Economist": "https://www.economist.com/leaders/2023/09/14/how-artificial-intelligence-can-revolutionise-science",
"Chemical and Engineering News": "https://cen.acs.org/business/informatics/tricky-ethics-AI-lab/101/i31",
"Kempner Institute": "https://www.harvard.edu/kempner-institute/2023/09/15/zitnik-nature-publications/",
"ChatGPT and Science in Nature": "https://www.nature.com/articles/d41586-023-03930-6"
}
},
{
"key": "submission24f",
"author": ["Shanghua Gao", "Ada Fang*", "Yepeng Huang*", "Valentina Giunchiglia*", "Ayush Noori*", "Jonathan Richard Schwarz", "Yasha Ektefaie", "Jovana Kondic", "Marinka Zitnik"],
"title": "Empowering Biomedical Discovery with AI Agents",
"venue": "Cell",
"year": "2024",
"thumbnail": "AIAgents.png",
"pdf": "https://www.cell.com/cell/fulltext/S0092-8674(24)01070-5",
"url": "https://www.cell.com/cell/fulltext/S0092-8674(24)01070-5",
"type": "journal",
"supp":
{
"arXiv": "https://arxiv.org/abs/2404.02831"
}
},
{
"key": "submission24u",
"author": ["Owen Queen*", "Yepeng Huang*", "Robert Calef*", "Valentina Giunchiglia", "Tianlong Chen", "George Dasoulas", "LeAnn Tai", "Yasha Ektefaie", "Ayush Noori", "Joseph Brown", "Tom Cobley", "Karin Hrovatin", "Tom Hartvigsen", "Fabian J. Theis", "Bradley L. Pentelute", "Vikram Khurana", "Manolis Kellis", "Marinka Zitnik"],
"title": "ProCyon: A Multimodal Foundation Model for Protein Phenotypes",
"venue": "In Review",
"year": "2025",
"thumbnail": "ProCyon25.png",
"pdf": "",
"url": "https://www.biorxiv.org/content/10.1101/2024.12.10.627665",
"type": "journal",
"supp":
{
"bioRxiv": "https://www.biorxiv.org/content/10.1101/2024.12.10.627665",
"project website": "https://zitniklab.hms.harvard.edu/ProCyon/",
"code": "https://github.com/mims-harvard/ProCyon",
"Kempner Institute": "https://kempnerinstitute.harvard.edu/research/deeper-learning/procyon-a-multimodal-foundation-model-for-protein-phenotypes/"
}
},
{
"key": "submission25d",
"author": ["Michelle M. Li", "Kevin Li", "Yasha Ektefaie", "Shvat Messica", "Marinka Zitnik"],
"title": "Controllable Sequence Editing for Counterfactual Generation",
"venue": "In Review",
"year": "2025",
"thumbnail": "clef25.png",
"pdf": "",
"url": "https://arxiv.org/abs/2502.03569",
"type": "journal",
"supp":
{
"arXiv": "https://arxiv.org/abs/2502.03569"
}
},
{
"key": "submission25c",
"author": ["Xiaorui Su", "Shvat Messica", "Yepeng Huang", "Ruth Johnson", "Lukas Fesser", "Shanghua Gao", "Faryad Sahneh", "Marinka Zitnik"],
"title": "Multimodal Medical Code Tokenizer",
"venue": "In Review",
"year": "2025",
"thumbnail": "medtok25.png",
"pdf": "",
"url": "https://arxiv.org/abs/2502.04397",
"type": "journal",
"supp":
{
"arXiv": "https://arxiv.org/abs/2502.04397"
}
},
{
"key": "submission24p",
"author": ["Xiaorui Su", "Yibo Wang", "Shanghua Gao", "Xiaolong Liu", "Valentina Giunchiglia", "Djork-Arné Clevert", "Marinka Zitnik"],
"title": "Knowledge Graph Based Agent for Complex, Knowledge-Intensive QA in Medicine",
"venue": "International Conference on Learning Representations, ICLR",
"year": "2025",
"thumbnail": "KGARevion.png",
"pdf": "https://openreview.net/pdf?id=tnB94WQGrn",
"url": "https://arxiv.org/abs/2410.04660",
"type": "journal",
"supp":
{
"arXiv": "https://arxiv.org/abs/2410.04660",
"project website": "https://zitniklab.hms.harvard.edu/projects/KGARevion",
"code": "https://github.com/mims-harvard/KGARevion"
}
},
{
"key": "submission25b",
"author": ["Andrew Shen*", "Yasha Ektefaie*", "Lavik Jain", "Maha Farhat*", "Marinka Zitnik*"],
"title": "Phyla: Towards a Foundation Model for Phylogenetic Inference",
"venue": "In Review",
"year": "2025",
"thumbnail": "phyla.png",
"pdf": "",
"url": "https://www.biorxiv.org/content/10.1101/2025.01.17.633626",
"type": "journal",
"supp":
{
"bioRxiv": "https://www.biorxiv.org/content/10.1101/2025.01.17.633626",
"code": "https://github.com/mims-harvard/Phyla"
}
},
{
"key": "submission24a",
"author": ["Guadalupe Gonzalez", "Isuru Herath", "Kirill Veselkov", "Michael Bronstein", "Marinka Zitnik"],
"title": "Combinatorial Prediction of Therapeutic Perturbations Using Causally-Inspired Neural Networks",
"venue": "In Review",
"year": "2025",
"thumbnail": "PDGrapher24.png",
"pdf": "",
"url": "https://www.biorxiv.org/content/10.1101/2024.01.03.573985",
"type": "journal",
"supp":
{
"bioRxiv": "https://www.biorxiv.org/content/10.1101/2024.01.03.573985",
"project website": "https://zitniklab.hms.harvard.edu/projects/PDGrapher/",
"code": "https://github.com/mims-harvard/PDGrapher"
}
},
{
"key": "submission24t",
"author": ["Ruth Johnson", "Uri Gottlieb", "Galit Shaham", "Lihi Eisen", "Jacob Waxman", "Stav Devons-Sberro", "Curtis R. Ginder", "Peter Hong", "Raheel Sayeed", "Ben Y. Reis", "Ran D. Balicer", "Noa Dagan", "Marinka Zitnik"],
"title": "Unified Clinical Vocabulary Embeddings for Advancing Precision Medicine",
"venue": "In Review",
"year": "2025",
"thumbnail": "clinical-knowledge-embeddings.png",
"pdf": "",
"url": "https://www.medrxiv.org/content/10.1101/2024.12.03.24318322",
"type": "journal",
"supp":
{
"medRxiv": "https://www.medrxiv.org/content/10.1101/2024.12.03.24318322",
"code": "https://github.com/mims-harvard/Clinical-knowledge-embeddings",
"project website": "https://zitniklab.hms.harvard.edu/projects/Clinical-knowledge-embeddings"
}
},
{
"key": "submission25a",
"author": ["Charlotte Bunne", "Yusuf Roohani", "Yanay Rosen", "and others", "Marinka Zitnik", "Theofanis Karaletsos", "Aviv Regev", "Emma Lundberg", "Jure Leskovec", "Stephen R Quake"],
"title": "How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities",
"venue": "Cell",
"year": "2024",
"thumbnail": "AIAgents.png",
"pdf": "https://www.cell.com/cell/fulltext/S0092-8674(24)01332-1",
"url": "https://www.cell.com/cell/fulltext/S0092-8674(24)01332-1",
"type": "journal",
"supp":
{
"arXiv": "https://arxiv.org/abs/2409.11654"
}
},
{
"key": "submission23g",
"author": ["Michelle M Li", "Yepeng Huang", "Marissa Sumathipala", "Man Qing Liang", "Alberto Valdeolivas", "Ashwin N Ananthakrishnan", "Katherine Liao", "Daniel Marbach", "Marinka Zitnik"],
"title": "Contextual AI Models for Single-Cell Protein Biology",
"venue": "Nature Methods",
"year": "2024",
"thumbnail": "PINNACLE23.png",
"pdf": "https://www.nature.com/articles/s41592-024-02341-3",
"url": "https://www.nature.com/articles/s41592-024-02341-3",
"type": "journal",
"supp":
{
"bioRxiv": "https://www.biorxiv.org/content/10.1101/2023.07.18.549602",
"Research Briefing in Nature Methods": "https://www.nature.com/articles/s41592-024-02342-2",
"project website": "https://zitniklab.hms.harvard.edu/projects/PINNACLE/",
"code": "https://github.com/mims-harvard/PINNACLE",
"Harvard Medicine News": "https://hms.harvard.edu/news/new-ai-tool-captures-how-proteins-behave-context",
"Kempner Institute": "https://kempnerinstitute.harvard.edu/research/deeper-learning/context-matters-for-foundation-models-in-biology/"
}
},
{
"key": "submission23d",
"author": ["Kexin Huang*", "Payal Chandak*", "Qianwen Wang", "Shreyas Havaldar", "Akhil Vaid", "Jure Leskovec", "Girish Nadkarni", "Benjamin S. Glicksberg", "Nils Gehlenborg", "Marinka Zitnik"],
"title": "A Foundation Model for Clinician Centered Drug Repurposing",
"venue": "Nature Medicine",
"year": "2024",
"thumbnail": "txgnn.png",
"pdf": "https://www.nature.com/articles/s41591-024-03233-x",
"url": "https://www.nature.com/articles/s41591-024-03233-x",
"type": "journal",
"supp":
{
"medRxiv": "https://www.medrxiv.org/content/10.1101/2023.03.19.23287458",
"code": "https://github.com/mims-harvard/TxGNN",
"project website": "/projects/TxGNN",
"TxGNN Explorer": "http://txgnn.org",
"Harvard Gazette": "https://news.harvard.edu/gazette/story/2024/09/using-ai-to-repurpose-existing-drugs-for-treatment-of-rare-diseases/",
"Harvard Medicine News": "https://hms.harvard.edu/news/researchers-harness-ai-repurpose-existing-drugs-treatment-rare-diseases",
"Forbes": "https://www.forbes.com/sites/greglicholai/2024/09/26/ai-tool-speeds-drug-repurposing-and-its-free/",
"NVIDIA": "https://developer.nvidia.com/blog/ai-uses-zero-shot-learning-to-find-existing-drugs-for-treating-rare-diseases/",
"Kempner Institute": "https://kempnerinstitute.harvard.edu/news/txgnn-ai-dr-house-for-disease-treatment/",
"Harvard Crimson": "https://www.thecrimson.com/article/2024/10/9/drug-repurposing-ai-model/"
}
},
{
"key": "submission24d",
"author": ["Zaixi Zhang", "Wanxiang Shen", "Qi Liu", "Marinka Zitnik"],
"title": "Efficient Generation of Protein Pockets with PocketGen",
"venue": "Nature Machine Intelligence",
"year": "2024",
"thumbnail": "PocketGen.png",
"pdf": "https://www.nature.com/articles/s42256-024-00920-9",
"url": "https://www.nature.com/articles/s42256-024-00920-9",
"type": "journal",
"supp":
{
"bioRxiv": "https://www.biorxiv.org/content/10.1101/2024.02.25.581968",
"project website": "https://zitniklab.hms.harvard.edu/projects/PocketGen/",
"code": "https://github.com/zaixizhang/PocketGen"
}
},
{
"key": "submission24c",
"author": ["Yasha Ektefaie", "Andrew Shen", "Daria Bykova", "Maximillian Marin", "Marinka Zitnik*", "Maha R Farhat*"],
"title": "Evaluating Generalizability of Artificial Intelligence Models for Molecular Datasets",
"venue": "Nature Machine Intelligence",
"year": "2024",
"thumbnail": "SPECTRA.png",
"pdf": "https://rdcu.be/d2D0z",
"url": "https://www.nature.com/articles/s42256-024-00931-6",
"type": "journal",
"supp":
{
"bioRxiv": "https://www.biorxiv.org/content/10.1101/2024.02.25.581982",
"project website": "https://zitniklab.hms.harvard.edu/projects/SPECTRA/",
"code": "https://github.com/mims-harvard/SPECTRA"
}
},
{
"key": "submission24l",
"author": ["Arinbjorn Kolbeinsson", "Kyle O'Brien", "Tianjin Huang", "Shanghua Gao", "Shiwei Liu", "Jonathan Richard Schwarz", "Anurag Vaidya", "Faisal Mahmood", "Marinka Zitnik", "Tianlong Chen", "Thomas Hartvigsen"],
"title": "Composable Interventions for Language Models",
"venue": "International Conference on Learning Representations, ICLR",
"year": "2025",
"thumbnail": "test-time-interventionsLLM.png",
"pdf": "https://openreview.net/pdf?id=tu3qwNjrtw",
"url": "https://arxiv.org/abs/2407.06483",
"type": "journal",
"supp":
{
"arXiv": "https://arxiv.org/abs/2407.06483"
}
},
{
"key": "submission24j",
"author": ["Xinxiu Li", "Joseph Loscalzo", "AKM Firoj Mahmud", "Dina Mansour Aly Aly", "Andrey Rzhetsky", "Marinka Zitnik", "Mikael Benson"],
"title": "Digital Twins as Global Learning Health and Disease Models for Preventive and Personalized Medicine",
"venue": "Genome Medicine",
"year": "2025",
"thumbnail": "digitaltwins25.png",
"pdf": "https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-025-01435-7",
"url": "https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-025-01435-7",
"type": "journal",
"supp":
{
"arXiv": "https://www.preprints.org/manuscript/202406.0357"
}
},
{
"key": "submission24z",
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"venue": "In Review",
"year": "2025",
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"title": "Multi Scale Graph Neural Network for Alzheimer's Disease",
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"title": "UniTS: A Unified Multi-Task Time Series Model",
"venue": "NeurIPS",
"year": "2024",
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"author": ["Zaixi Zhang", "Marinka Zitnik*", "Qi Liu*"],
"title": "Generalized Protein Pocket Generation with Prior-Informed Flow Matching",
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"year": "2024",
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"title": "Invariant Tokenization for Language Model Enabled Crystal Materials Generation",
"venue": "NeurIPS",
"year": "2024",
"thumbnail": "InvariantCrystals.png",
"pdf": "https://openreview.net/pdf?id=18FGRNd0wZ",
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"author": ["Wanxiang Shen", "Chao Cui", "Xiaorui Su", "Zaixi Zhang", "Alejandro Velez-Arce", "Jianming Wang", "Xiangcheng Shi", "Yanbing Zhang", "Jie Wu", "Yu Zong Chen", "Marinka Zitnik"],
"title": "Activity Cliff-Informed Contrastive Learning for Molecular Property Prediction",
"venue": "In Review",
"year": "2025",
"thumbnail": "MoExtend.png",
"pdf": "",
"url": "https://chemrxiv.org/engage/chemrxiv/article-details/6470c963be16ad5c57f5526c",
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"title": "TDC-2: Multimodal Foundation for Therapeutic Science",
"venue": "In Review",
"year": "2025",
"thumbnail": "tdc2.png",
"pdf": "",
"url": "https://www.biorxiv.org/content/10.1101/2024.06.12.598655",
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"author": ["Shanshan Zhong", "Shanghua Gao", "Zhongzhan Huang", "Wushao Wen", "Marinka Zitnik", "Pan Zhou"],
"title": "MoExtend: Tuning New Experts for Modality and Task Extension",
"venue": "Association for Computational Linguistics, ACL SRW",
"year": "2024",
"thumbnail": "MoExtend.png",
"pdf": "",
"url": "https://arxiv.org/abs/2408.03511",
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"key": "submission23j",
"author": ["Ruth Johnson", "Michelle M. Li", "Ayush Noori", "Owen Queen", "Marinka Zitnik"],
"title": "Graph Artificial Intelligence in Medicine",
"venue": "Annual Review of Biomedical Data Science",
"year": "2024",
"thumbnail": "GraphAIMedicine23.png",
"pdf": "papers/graphAIMedicine24.pdf",
"url": "https://www.annualreviews.org/content/journals/10.1146/annurev-biodatasci-110723-024625",
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"author": ["Jason J. Kwon*", "Joshua Pan*", "Guadalupe Gonzalez", "William C. Hahn", "Marinka Zitnik"],
"title": "On Knowing a Gene: A Distributional Hypothesis of Gene Function",
"venue": "Cell Systems",
"year": "2024",
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"pdf": "papers/DistributedGeneFunction-CellSystems24.pdf",
"url": "https://www.sciencedirect.com/science/article/pii/S2405471224001236",
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"author": ["Lichao Sun", "Yue Huang", "Haoran Wang", "et al."],
"title": "TrustLLM: Trustworthiness in Large Language Models",
"venue": "International Conference on Machine Learning, ICML",
"year": "2024",
"thumbnail": "trustLLM24.png",
"pdf": "papers/TrustLLM-ICML24.pdf",
"url": "https://arxiv.org/abs/2401.05561",
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"key": "submission24g",
"author": ["Songtao Liu", "Jinghui Chen", "Tianfan Fu", "Lu Lin", "Marinka Zitnik", "Dinghao Wu"],
"title": "Graph Adversarial Diffusion Convolution",
"venue": "International Conference on Machine Learning, ICML",
"year": "2024",
"thumbnail": "GADC24.png",
"pdf": "papers/GADC-ICML24.pdf",
"url": "https://arxiv.org/abs/2406.02059v1",
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"author": ["Kangyu Zheng", "Yingzhou Lu", "Zaixi Zhang", "Zhongwei Wan", "Yao Ma", "Marinka Zitnik", "Tianfan Fu"],
"title": "Structure-based Drug Design Benchmark: Do 3D Methods Really Dominate?",
"venue": "In Review",
"year": "2025",
"thumbnail": "GADC24.png",
"pdf": "",
"url": "https://arxiv.org/abs/2406.03403",
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"title": "TrialBench: Multi-Modal Artificial Intelligence-Ready Clinical Trial Datasets",
"venue": "In Review",
"year": "2025",
"thumbnail": "GADC24.png",
"pdf": "",
"url": "https://arxiv.org/abs/2407.00631",
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"author": ["Shanshan Zhong", "Shanghua Gao", "Zhongzhan Huang", "Wushao Wen", "Marinka Zitnik", "Pan Zhou"],
"title": "MoExtend: Tuning New Experts for Modality and Task Extension",
"venue": "ACL",
"year": "2024",
"thumbnail": "MoExtend.png",
"pdf": "https://aclanthology.org/2024.acl-srw.8.pdf",
"url": "https://aclanthology.org/2024.acl-srw.8.pdf",
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"author": ["Zaixi Zhang", "Jiaxian Yan", "Qi Liu", "Enhong Chen", "Marinka Zitnik"],
"title": "Geometric Deep Learning for Structure-Based Drug Design: A Survey",
"venue": "In Review",
"year": "2025",
"thumbnail": "SBDD23.png",
"pdf": "",
"url": "https://arxiv.org/abs/2306.11768",
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"title": "Let's Think Outside the Box: Exploring Leap-of-Thought in Large Language Models with Creative Humor Generation",
"venue": "Computer Vision and Pattern Recognition Conference, CVPR",
"year": "2024",
"thumbnail": "Image-Graph-ML4H23.png",
"pdf": "papers/CLoT-CVPR24.pdf",
"url": "https://arxiv.org/abs/2312.02439",
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"key": "submission23h",
"author": ["Marinka Zitnik*", "Michelle M. Li*", "Aydin Wells*", "Kimberly Glass", "Deisy Morselli Gysi", "Arjun Krishnan", "T. M. Murali", "Predrag Radivojac", "Sushmita Roy", "Anaïs Baudot", "Serdar Bozdag", "Danny Z. Chen", "Lenore Cowen", "Kapil Devkota", "Anthony Gitter", "Sara Gosline", "Pengfei Gu", "Pietro H. Guzzi", "Heng Huang", "Meng Jiang", "Ziynet Nesibe Kesimoglu", "Mehmet Koyuturk", "Jian Ma", "Alexander R. Pico", "Natasa Przulj", "Teresa M. Przytycka", "Benjamin J. Raphael", "Anna Ritz", "Roded Sharan", "Yang Shen", "Mona Singh", "Donna K. Slonim", "Hanghang Tong", "Xinan Holly Yang", "Byung-Jun Yoon", "Haiyuan Yu", "Tijana Milenkovic"],
"title": "Current and Future Directions in Network Biology",
"venue": "Bioinformatics Advances",
"year": "2024",
"thumbnail": "Future-NetBio.png",
"pdf": "https://academic.oup.com/bioinformaticsadvances/article/4/1/vbae099/7732851",
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"author": ["Leonid Komissarov", "Nenad Manevski", "Katrin Groebke Zbinden", "Torsten Schindler", "Marinka Zitnik", "Lisa Sach-Peltason"],
"title": "Actionable Predictions of Human Pharmacokinetics at the Drug Design Stage",
"venue": "Molecular Pharmaceutics",
"year": "2024",
"thumbnail": "pharmacokinetics24.png",
"pdf": "https://pubs.acs.org/doi/abs/10.1021/acs.molpharmaceut.4c00311",
"url": "https://pubs.acs.org/doi/abs/10.1021/acs.molpharmaceut.4c00311",
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"author": ["Yasha Ektefaie*", "George Dasoulas*", "Ayush Noori", "Maha Farhat", "Marinka Zitnik"],
"title": "Multimodal Learning with Graphs",
"venue": "Nature Machine Intelligence",
"year": "2023",
"thumbnail": "MGL22.png",
"pdf": "https://www.nature.com/articles/s42256-023-00624-6",
"url": "https://www.nature.com/articles/s42256-023-00624-6",
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"author": ["Matthew B. A. McDermott", "Brendan Yap", "Peter Szolovits", "Marinka Zitnik"],
"title": "Structure Inducing Pre-Training",
"venue": "Nature Machine Intelligence",
"year": "2023",
"thumbnail": "NatureMachIntel-SIPT23.png",
"pdf": "https://www.nature.com/articles/s42256-023-00647-z",
"url": "https://www.nature.com/articles/s42256-023-00647-z",
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"author": ["Owen Queen", "Thomas Hartvigsen", "Teddy Koker", "Huan He", "Theodoros Tsiligkaridis", "Marinka Zitnik"],
"title": "Encoding Time-Series Explanations through Self-Supervised Model Behavior Consistency",
"venue": "Proceedings of Neural Information Processing Systems, NeurIPS",
"year": "2023",
"thumbnail": "TimeX23.png",
"pdf": "papers/TimeX-NeurIPS23.pdf",
"url": "https://arxiv.org/abs/2306.02109",
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"key": "submission23i",
"author": ["Zaixi Zhang", "Zepu Lu", "Zhongkai Hao", "Marinka Zitnik", "Qi Liu"],
"title": "Full-Atom Protein Pocket Design via Iterative Refinement",
"venue": "Proceedings of Neural Information Processing Systems, NeurIPS",
"year": "2023",
"thumbnail": "FAIR23.png",
"pdf": "papers/FAIR-NeurIPS23.pdf",
"url": "https://arxiv.org/abs/2310.02553",
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"key": "submission23l",
"author": ["Sameer Khanna", "Daniel Michael", "Marinka Zitnik", "Pranav Rajpurkar"],
"title": "Learning Generalized Medical Image Representations Through Image-Graph Contrastive Pretraining",
"venue": "Machine Learning for Health",
"year": "2023",
"thumbnail": "Image-Graph-ML4H23.png",
"pdf": "papers/Image-Graph-ML4H23.pdf",
"url": "https://proceedings.mlr.press/v225/khanna23a.html",
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"author": ["Huan He", "Owen Queen", "Teddy Koker", "Consuelo Cuevas", "Theodoros Tsiligkaridis", "Marinka Zitnik"],
"title": "Domain Adaptation for Time Series Under Feature and Label Shifts",
"venue": "International Conference on Machine Learning, ICML",
"year": "2023",
"thumbnail": "Raincoat-ICML23.png",
"pdf": "papers/Raincoat-ICML23.pdf",
"url": "https://arxiv.org/abs/2302.03133",
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"author": ["Jiali Cheng", "George Dasoulas", "Huan He", "Chirag Agarwal", "Marinka Zitnik"],
"title": "GNNDelete: A General Strategy for Unlearning in Graph Neural Networks ",
"venue": "International Conference on Learning Representations, ICLR",
"year": "2023",
"thumbnail": "GNNDelete23.png",
"pdf": "papers/GNNDelete-iclr23.pdf",
"url": "https://openreview.net/pdf?id=X9yCkmT5Qrl",
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"author": ["Emily Alsentzer*", "Michelle M. Li*", "Shilpa N. Kobren", "Ayush Noori", "Undiagnosed Diseases Network", "Isaac S. Kohane", "Marinka Zitnik"],
"title": "Few Shot Learning for Phenotype-Driven Diagnosis of Patients with Rare Genetic Diseases",
"venue": "In Review ",
"year": "2025",
"thumbnail": "SHEPHERD23.png",
"pdf": "",
"url": "https://www.medrxiv.org/content/10.1101/2022.12.07.22283238",
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"key": "submission22b",
"author": ["Payal Chandak*", "Kexin Huang*", "Marinka Zitnik"],
"title": "Building a Knowledge Graph to Enable Precision Medicine",
"venue": "Scientific Data",
"year": "2023",
"thumbnail": "PrimeKG22.png",
"pdf": "papers/PrimeKG-scientificdata23.pdf",
"url": "https://www.nature.com/articles/s41597-023-01960-3",
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"author": ["Sabri Eyuboglu*", "Marinka Zitnik*", "Jure Leskovec"],
"title": "Mutual Interactors as a Principle for Phenotype Discovery in Molecular Interaction Networks",
"venue": "Pacific Symposium on Biocomputing, PSB",
"year": "2023",
"thumbnail": "Milieu23.png",
"pdf": "papers/MutualInteractors-psb23.pdf",
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"author": ["Ayush Noori", "Amelia L. M. Tan", "Michelle M. Li", "Marinka Zitnik"],
"title": "metapaths: Similarity Search in Heterogeneous Knowledge Graphs via Meta Paths",
"venue": "Bioinformatics",
"year": "2023",
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"pdf": "papers/metapaths23.pdf",
"url": "https://doi.org/10.1093/bioinformatics/btad297",
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"author": ["Yucong Lin*", "Keming Lu*", "Sheng Yu", "Tianxi Cai", "Marinka Zitnik"],
"title": "Multimodal Learning on Graphs for Disease Relation Extraction",
"venue": "Journal of Biomedical Informatics",
"year": "2023",
"thumbnail": "raindrop22.png",
"pdf": "https://doi.org/10.1016/j.jbi.2023.104415",
"url": "https://doi.org/10.1016/j.jbi.2023.104415",
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"author": ["Chirag Agarwal", "Owen Queen", "Himabindu Lakkaraju", "Marinka Zitnik"],
"title": "Evaluating Explainability for Graph Neural Networks",
"venue": "Scientific Data",
"year": "2023",
"thumbnail": "GraphXAI23.png",
"pdf": "https://www.nature.com/articles/s41597-023-01974-x",
"url": "https://www.nature.com/articles/s41597-023-01974-x",
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"key": "submission21n",
"author": ["Ryan T. Scott", "...", "Marinka Zitnik", "Sylvain V. Costes"],
"title": "Biomonitoring and Precision Health in Deep Space Supported by Artificial Intelligence",
"venue": "Nature Machine Intelligence",
"year": "2023",
"thumbnail": "spacehealth23.png",
"pdf": "https://www.nature.com/articles/s42256-023-00617-5",
"url": "https://www.nature.com/articles/s42256-023-00617-5",
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"author": ["Lauren M. Sanders", "...", "Marinka Zitnik", "Sylvain V. Costes"],
"title": "Biological Research and Self-Driving Labs in Deep Space Supported by Artificial Intelligence",
"venue": "Nature Machine Intelligence",
"year": "2023",
"thumbnail": "spacebiology23.png",
"pdf": "https://www.nature.com/articles/s42256-023-00618-4",
"url": "https://www.nature.com/articles/s42256-023-00618-4",
"type": "journal",
"supp":
{
"arXiv": "https://arxiv.org/abs/2112.12582",
"NASA White Paper": "http://surveygizmoresponseuploads.s3.amazonaws.com/fileuploads/623127/6392490/153-51083399580a7b71d52378a0d6012a73_SandersLaurenM.pdf"
}
},
{
"key": "submission23c",
"author": ["Jun Wen", "Xiang Zhang", "Everett Rush", "Vidul A Panickan", "Xingyu Li", "Tianrun Cai", "Doudou Zhou", "Yuk-Lam Ho", "Lauren Costa", "Edmon Begoli", "Chuan Hong", "J Michael Gaziano", "Kelly Cho", "Junwei Lu", "Katherine P Liao", "Marinka Zitnik", "Tianxi Cai"],
"title": "Multimodal Representation Learning for Predicting Molecule–Disease Relations ",
"venue": "Bioinformatics",
"year": "2023",
"thumbnail": "M2REMAP23.png",
"pdf": "papers/M2REMAP23.pdf",
"url": "https://doi.org/10.1093/bioinformatics/btad085",
"type": "journal",
"supp":
{
"code": "https://github.com/celehs/M2REMAP",
"web server": "https://shiny.parse-health.org/drugs-diseases-dev/"
}
},
{
"key": "submission22m",
"author": ["Alexander Turchin", "Stanislav Masharsky", "Marinka Zitnik"],
"title": "Comparison of BERT Implementations for Natural Language Processing of Narrative Medical Documents",
"venue": "Informatics in Medicine Unlocked",
"year": "2023",
"thumbnail": "bert-comparison22.png",
"pdf": "papers/bert-comparison22.pdf",
"url": "https://doi.org/10.1016/j.imu.2022.101139",
"type": "journal",
"supp":
{
}
},
{
"key": "submission21f",
"author": ["Michelle M. Li", "Kexin Huang", "Marinka Zitnik"],
"title": "Graph Representation Learning in Biomedicine and Healthcare",
"venue": "Nature Biomedical Engineering",
"year": "2022",
"thumbnail": "grl22.png",
"pdf": "https://www.nature.com/articles/s41551-022-00942-x",
"url": "https://www.nature.com/articles/s41551-022-00942-x",
"type": "journal",
"supp":
{
"arXiv": "https://arxiv.org/abs/2104.04883"
}
},
{
"key": "submission22e",
"author": ["Kexin Huang*", "Tianfan Fu*", "Wenhao Gao*", "Yue Zhao", "Yusuf Roohani", "Jure Leskovec", "Connor W. Coley", "Cao Xiao", "Jimeng Sun", "Marinka Zitnik"],
"title": "Artificial Intelligence Foundation for Therapeutic Science",
"venue": "Nature Chemical Biology",
"year": "2022",
"thumbnail": "tdc22.png",
"pdf": "https://www.nature.com/articles/s41589-022-01131-2",
"url": "https://www.nature.com/articles/s41589-022-01131-2",
"type": "journal",
"supp":
{
"project website": "https://tdcommons.ai",
"code": "https://github.com/mims-harvard/TDC",
"Harvard Medicine News": "https://hms.harvard.edu/news/can-ai-transform-way-we-discover-new-drugs"
}
},
{
"key": "submission22c",
"author": ["Xiang Zhang*", "Ziyuan Zhao*", "Theodoros Tsiligkaridis", "Marinka Zitnik"],
"title": "Self-Supervised Contrastive Pre-Training For Time Series via Time-Frequency Consistency",
"venue": "Proceedings of Neural Information Processing Systems, NeurIPS",
"year": "2022",
"thumbnail": "TF-C22.png",
"pdf": "papers/TF-C-self_supervised_contrastive_main.pdf",
"url": "https://openreview.net/pdf?id=OJ4mMfGKLN",
"type": "journal",
"supp":
{
"supplementary": "papers/TF-C-self_supervised_contrastive_SI.pdf",
"arXiv": "https://arxiv.org/abs/2206.08496",
"code": "https://github.com/mims-harvard/TFC-pretraining",
"project website": "/projects/TF-C"
}
},
{
"key": "submission21k",
"author": ["Xiang Zhang", "Marko Zeman", "Theodoros Tsiligkaridis", "Marinka Zitnik"],
"title": "Graph-Guided Network for Irregularly Sampled Multivariate Time Series",
"venue": "International Conference on Learning Representations, ICLR",
"year": "2022",
"thumbnail": "raindrop22.png",
"pdf": "papers/raindrop-iclr22.pdf",
"url": "https://openreview.net/pdf?id=Kwm8I7dU-l5",
"type": "journal",
"supp":
{
"arXiv": "https://arxiv.org/abs/2110.05357",
"code": "https://github.com/mims-harvard/Raindrop",
"project website": "/projects/Raindrop",
"slides": "slides/raindrop-AAAI22.pdf"
}
},