Zitnik, Marinka

42 publications

TMLR 2026 Beyond Affinity: A Benchmark of 1d, 2D, and 3D Methods Reveals Critical Trade-Offs in Structure-Based Drug Design Kangyu Zheng, Kai Zhang, Jiale Tan, Xuehan Chen, Yingzhou Lu, Zaixi Zhang, Lichao Sun, Marinka Zitnik, Tianfan Fu, Zhiding Liang

FnTML 2025 Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems Xuan Zhang, Limei Wang, Jacob Helwig, Youzhi Luo, Cong Fu, Yaochen Xie, Meng Liu, Yuchao Lin, Zhao Xu, Keqiang Yan, Keir Adams, Maurice Weiler, Xiner Li, Tianfan Fu, Yucheng Wang, Alex Strasser, Haiyang Yu, Yuqing Xie, Xiang Fu, Shenglong Xu, Yi Liu, Yuanqi Du, Alexandra Saxton, Hongyi Ling, Hannah Lawrence, Hannes Stärk, Shurui Gui, Carl Edwards, Nicholas Gao, Adriana Ladera, Tailin Wu, Elyssa F. Hofgard, Aria Mansouri Tehrani, Rui Wang, Ameya Daigavane, Montgomery Bohde, Jerry Kurtin, Qian Huang, Tuong Phung, Minkai Xu, Chaitanya K. Joshi, Simon V. Mathis, Kamyar Azizzadenesheli, Ada Fang, Alán Aspuru-Guzik, Erik J. Bekkers, Michael M. Bronstein, Marinka Zitnik, Anima Anandkumar, Stefano Ermon, Pietro Liò, Rose Yu, Stephan Günnemann, Jure Leskovec, Heng Ji, Jimeng Sun, Regina Barzilay, Tommi S. Jaakkola, Connor W. Coley, Xiaoning Qian, Xiaofeng Qian, Tess E. Smidt, Shuiwang Ji

ICLR 2025 Composable Interventions for Language Models Arinbjörn Kolbeinsson, Kyle O'Brien, Tianjin Huang, Shanghua Gao, Shiwei Liu, Jonathan Richard Schwarz, Anurag Jayant Vaidya, Faisal Mahmood, Marinka Zitnik, Tianlong Chen, Thomas Hartvigsen

NeurIPS 2025 DQVis Dataset: Natural Language to Biomedical Visualization Devin Lange, Pengwei Sui, Shanghua Gao, Marinka Zitnik, Nils Gehlenborg

NeurIPS 2025 Evolutionary Reasoning Does Not Arise in Standard Usage of Protein Language Models Yasha Ektefaie, Andrew Shen, Lavik Jain, Maha Farhat, Marinka Zitnik

ICLR 2025 KGARevion: An AI Agent for Knowledge-Intensive Biomedical QA Xiaorui Su, Yibo Wang, Shanghua Gao, Xiaolong Liu, Valentina Giunchiglia, Djork-Arné Clevert, Marinka Zitnik

ICML 2025 Multimodal Medical Code Tokenizer Xiaorui Su, Shvat Messica, Yepeng Huang, Ruth Johnson, Lukas Fesser, Shanghua Gao, Faryad Sahneh, Marinka Zitnik

ICLRW 2025 Phyla: Towards a Foundation Model for Phylogenetic Inference Andrew Shen, Yasha Ektefaie, Lavik Jain, Maha Farhat, Marinka Zitnik

ICML 2025 PyTDC: A Multimodal Machine Learning Training, Evaluation, and Inference Platform for Biomedical Foundation Models Alejandro Velez-Arce, Marinka Zitnik

ICLRW 2024 Composing Knowledge and Compression Interventions for Language Models Arinbjörn Kolbeinsson, Tianjin Huang, Shanghua Gao, Shiwei Liu, Jonathan Richard Schwarz, Anurag Jayant Vaidya, Faisal Mahmood, Marinka Zitnik, Tianlong Chen, Thomas Hartvigsen

ICLRW 2024 Expanding Genomic Discovery: Causally-Inspired Neural Networks for Predicting Therapeutic Targets Guadalupe Gonzalez, Isuru Herath, Kirill Veselkov, Michael M. Bronstein, Marinka Zitnik

NeurIPS 2024 Generalized Protein Pocket Generation with Prior-Informed Flow Matching Zaixi Zhang, Marinka Zitnik, Qi Liu

ICML 2024 Graph Adversarial Diffusion Convolution Songtao Liu, Jinghui Chen, Tianfan Fu, Lu Lin, Marinka Zitnik, Dinghao Wu

NeurIPS 2024 Invariant Tokenization of Crystalline Materials for Language Model Enabled Generation Keqiang Yan, Xiner Li, Hongyi Ling, Kenna Ashen, Carl Edwards, Raymundo Arróyave, Marinka Zitnik, Heng Ji, Xiaofeng Qian, Xiaoning Qian, Shuiwang Ji

CVPR 2024 Let's Think Outside the Box: Exploring Leap-of-Thought in Large Language Models with Creative Humor Generation Shanshan Zhong, Zhongzhan Huang, Shanghua Gao, Wushao Wen, Liang Lin, Marinka Zitnik, Pan Zhou

ICML 2024 Position: TrustLLM: Trustworthiness in Large Language Models Yue Huang, Lichao Sun, Haoran Wang, Siyuan Wu, Qihui Zhang, Yuan Li, Chujie Gao, Yixin Huang, Wenhan Lyu, Yixuan Zhang, Xiner Li, Hanchi Sun, Zhengliang Liu, Yixin Liu, Yijue Wang, Zhikun Zhang, Bertie Vidgen, Bhavya Kailkhura, Caiming Xiong, Chaowei Xiao, Chunyuan Li, Eric P. Xing, Furong Huang, Hao Liu, Heng Ji, Hongyi Wang, Huan Zhang, Huaxiu Yao, Manolis Kellis, Marinka Zitnik, Meng Jiang, Mohit Bansal, James Zou, Jian Pei, Jian Liu, Jianfeng Gao, Jiawei Han, Jieyu Zhao, Jiliang Tang, Jindong Wang, Joaquin Vanschoren, John Mitchell, Kai Shu, Kaidi Xu, Kai-Wei Chang, Lifang He, Lifu Huang, Michael Backes, Neil Zhenqiang Gong, Philip S. Yu, Pin-Yu Chen, Quanquan Gu, Ran Xu, Rex Ying, Shuiwang Ji, Suman Jana, Tianlong Chen, Tianming Liu, Tianyi Zhou, William Yang Wang, Xiang Li, Xiangliang Zhang, Xiao Wang, Xing Xie, Xun Chen, Xuyu Wang, Yan Liu, Yanfang Ye, Yinzhi Cao, Yong Chen, Yue Zhao

ICMLW 2024 Pre-Training of Single-Cell Language Models Through Genetic Pathway Learning Xuxi Chen, Zhangyang Wang, Marinka Zitnik, Manolis Kellis, Tianlong Chen

NeurIPSW 2024 Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics Alejandro Velez-Arce, Kexin Huang, Michelle M Li, Xiang Lin, Wenhao Gao, Bradley Pentelute, Tianfan Fu, Manolis Kellis, Marinka Zitnik

ICMLW 2024 Structure-Based Drug Design Benchmark: Do 3D Methods Really Dominate? Kangyu Zheng, Yingzhou Lu, Zaixi Zhang, Zhongwei Wan, Yao Ma, Marinka Zitnik, Tianfan Fu

NeurIPS 2024 UniTS: A Unified Multi-Task Time Series Model Shanghua Gao, Teddy Koker, Owen Queen, Thomas Hartvigsen, Theodoros Tsiligkaridis, Marinka Zitnik

ICML 2023 Domain Adaptation for Time Series Under Feature and Label Shifts Huan He, Owen Queen, Teddy Koker, Consuelo Cuevas, Theodoros Tsiligkaridis, Marinka Zitnik

NeurIPS 2023 Encoding Time-Series Explanations Through Self-Supervised Model Behavior Consistency Owen Queen, Tom Hartvigsen, Teddy Koker, Huan He, Theodoros Tsiligkaridis, Marinka Zitnik

NeurIPS 2023 Full-Atom Protein Pocket Design via Iterative Refinement Zaixi Zhang, Zepu Lu, Hao Zhongkai, Marinka Zitnik, Qi Liu

ICLR 2023 GNNDelete: A General Strategy for Unlearning in Graph Neural Networks Jiali Cheng, George Dasoulas, Huan He, Chirag Agarwal, Marinka Zitnik

NeurIPSW 2023 Mapping the Intermolecular Interaction Universe Through Self-Supervised Learning on Molecular Crystals Ada Fang, Zaixi Zhang, Marinka Zitnik

AISTATS 2022 Probing GNN Explainers: A Rigorous Theoretical and Empirical Analysis of GNN Explanation Methods Chirag Agarwal, Marinka Zitnik, Himabindu Lakkaraju

ICLR 2022 Graph-Guided Network for Irregularly Sampled Multivariate Time Series Xiang Zhang, Marko Zeman, Theodoros Tsiligkaridis, Marinka Zitnik

NeurIPS 2022 OpenXAI: Towards a Transparent Evaluation of Model Explanations Chirag Agarwal, Satyapriya Krishna, Eshika Saxena, Martin Pawelczyk, Nari Johnson, Isha Puri, Marinka Zitnik, Himabindu Lakkaraju

ICLRW 2022 Rethinking Stability for Attribution-Based Explanations Chirag Agarwal, Nari Johnson, Martin Pawelczyk, Satyapriya Krishna, Eshika Saxena, Marinka Zitnik, Himabindu Lakkaraju

NeurIPS 2022 Self-Supervised Contrastive Pre-Training for Time Series via Time-Frequency Consistency Xiang Zhang, Ziyuan Zhao, Theodoros Tsiligkaridis, Marinka Zitnik

NeurIPSW 2022 Structure-Inducing Pre-Training Matthew B.A. McDermott, Brendan Yap, Peter Szolovits, Marinka Zitnik

UAI 2021 Towards a Unified Framework for Fair and Stable Graph Representation Learning Chirag Agarwal, Himabindu Lakkaraju, Marinka Zitnik

NeurIPS 2020 GNNGuard: Defending Graph Neural Networks Against Adversarial Attacks Xiang Zhang, Marinka Zitnik

NeurIPS 2020 Graph Meta Learning via Local Subgraphs Kexin Huang, Marinka Zitnik

NeurIPS 2020 Open Graph Benchmark: Datasets for Machine Learning on Graphs Weihua Hu, Matthias Fey, Marinka Zitnik, Yuxiao Dong, Hongyu Ren, Bowen Liu, Michele Catasta, Jure Leskovec

ICLR 2020 Strategies for Pre-Training Graph Neural Networks Weihua Hu, Bowen Liu, Joseph Gomes, Marinka Zitnik, Percy Liang, Vijay Pande, Jure Leskovec

NeurIPS 2020 Subgraph Neural Networks Emily Alsentzer, Samuel Finlayson, Michelle Li, Marinka Zitnik

NeurIPS 2019 GNNExplainer: Generating Explanations for Graph Neural Networks Zhitao Ying, Dylan Bourgeois, Jiaxuan You, Marinka Zitnik, Jure Leskovec

NeurIPS 2018 Embedding Logical Queries on Knowledge Graphs Will Hamilton, Payal Bajaj, Marinka Zitnik, Dan Jurafsky, Jure Leskovec

ECML-PKDD 2017 Machine Learning and Knowledge Discovery in Databases - European Conference, ECML PKDD 2017, Skopje, Macedonia, September 18-22, 2017, Proceedings, Part III Yasemin Altun, Kamalika Das, Taneli Mielikäinen, Donato Malerba, Jerzy Stefanowski, Jesse Read, Marinka Zitnik, Michelangelo Ceci, Saso Dzeroski

MLOSS 2013 Orange: Data Mining Toolbox in Python Janez Demšar, Tomaž Curk, Aleš Erjavec, Črt Gorup, Tomaž Hočevar, Mitar Milutinovič, Martin Možina, Matija Polajnar, Marko Toplak, Anže Starič, Miha Štajdohar, Lan Umek, Lan Žagar, Jure Žbontar, Marinka Žitnik, Blaž Zupan

MLOSS 2012 NIMFA : A Python Library for Nonnegative Matrix Factorization Marinka Žitnik, Blaž Zupan