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Marinka Zitnik

Towards a Rigorous Theoretical Analysis and Evaluation of GNN Explanations


Jun 16, 2021
Chirag Agarwal, Marinka Zitnik, Himabindu Lakkaraju

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Deep Contextual Learners for Protein Networks


Jun 04, 2021
Michelle M. Li, Marinka Zitnik

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Representation Learning for Networks in Biology and Medicine: Advancements, Challenges, and Opportunities


Apr 11, 2021
Michelle M. Li, Kexin Huang, Marinka Zitnik

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Rethinking Relational Encoding in Language Model: Pre-Training for General Sequences


Mar 18, 2021
Matthew B. A. McDermott, Brendan Yap, Peter Szolovits, Marinka Zitnik

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Towards a Unified Framework for Fair and Stable Graph Representation Learning


Mar 01, 2021
Chirag Agarwal, Himabindu Lakkaraju, Marinka Zitnik

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Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics


Feb 18, 2021
Kexin Huang, Tianfan Fu, Wenhao Gao, Yue Zhao, Yusuf Roohani, Jure Leskovec, Connor W. Coley, Cao Xiao, Jimeng Sun, Marinka Zitnik

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Contrastive Learning Improves Critical Event Prediction in COVID-19 Patients


Jan 11, 2021
Tingyi Wanyan, Hossein Honarvar, Suraj K. Jaladanki, Chengxi Zang, Nidhi Naik, Sulaiman Somani, Jessica K. De Freitas, Ishan Paranjpe, Akhil Vaid, Riccardo Miotto, Girish N. Nadkarni, Marinka Zitnik, ArifulAzad, Fei Wang, Ying Ding, Benjamin S. Glicksberg

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MolDesigner: Interactive Design of Efficacious Drugs with Deep Learning


Oct 05, 2020
Kexin Huang, Tianfan Fu, Dawood Khan, Ali Abid, Ali Abdalla, Abubakar Abid, Lucas M. Glass, Marinka Zitnik, Cao Xiao, Jimeng Sun

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* NeurIPS 2020 Demonstration Track 
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Graph Meta Learning via Local Subgraphs


Jun 19, 2020
Kexin Huang, Marinka Zitnik

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Subgraph Neural Networks


Jun 19, 2020
Emily Alsentzer, Samuel G. Finlayson, Michelle M. Li, Marinka Zitnik

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* E.A. and S.G.F. contributed equally 
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GNNGuard: Defending Graph Neural Networks against Adversarial Attacks


Jun 16, 2020
Xiang Zhang, Marinka Zitnik

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Open Graph Benchmark: Datasets for Machine Learning on Graphs


May 02, 2020
Weihua Hu, Matthias Fey, Marinka Zitnik, Yuxiao Dong, Hongyu Ren, Bowen Liu, Michele Catasta, Jure Leskovec

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SkipGNN: Predicting Molecular Interactions with Skip-Graph Networks


Apr 30, 2020
Kexin Huang, Cao Xiao, Lucas Glass, Marinka Zitnik, Jimeng Sun

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Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19


Apr 15, 2020
Deisy Morselli Gysi, Ítalo Do Valle, Marinka Zitnik, Asher Ameli, Xiao Gan, Onur Varol, Helia Sanchez, Rebecca Marlene Baron, Dina Ghiassian, Joseph Loscalzo, Albert-László Barabási

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Interpretability of machine learning based prediction models in healthcare


Feb 20, 2020
Gregor Stiglic, Primoz Kocbek, Nino Fijacko, Marinka Zitnik, Katrien Verbert, Leona Cilar

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* 12 pages, 2 figures, submitted to Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery 
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Pre-training Graph Neural Networks


May 29, 2019
Weihua Hu, Bowen Liu, Joseph Gomes, Marinka Zitnik, Percy Liang, Vijay Pande, Jure Leskovec

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GNN Explainer: A Tool for Post-hoc Explanation of Graph Neural Networks


Mar 10, 2019
Rex Ying, Dylan Bourgeois, Jiaxuan You, Marinka Zitnik, Jure Leskovec

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Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities


Oct 10, 2018
Marinka Zitnik, Francis Nguyen, Bo Wang, Jure Leskovec, Anna Goldenberg, Michael M. Hoffman

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* Information Fusion 50 (2019) 71-91 
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Cross-type Biomedical Named Entity Recognition with Deep Multi-Task Learning


Oct 08, 2018
Xuan Wang, Yu Zhang, Xiang Ren, Yuhao Zhang, Marinka Zitnik, Jingbo Shang, Curtis Langlotz, Jiawei Han

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* 7 pages, 4 figures 
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Embedding Logical Queries on Knowledge Graphs


Sep 06, 2018
William L. Hamilton, Payal Bajaj, Marinka Zitnik, Dan Jurafsky, Jure Leskovec

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* To appear in NIPS 2018 
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NIMFA: A Python Library for Nonnegative Matrix Factorization


Aug 06, 2018
Marinka Zitnik, Blaz Zupan

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* Journal of Machine Learning Research 13 (2012) 849-853 
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Learning Structural Node Embeddings Via Diffusion Wavelets


Jun 20, 2018
Claire Donnat, Marinka Zitnik, David Hallac, Jure Leskovec

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* The 24th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining, August 19--23, 2018, London, United Kingdom 
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Network Enhancement: a general method to denoise weighted biological networks


Jun 01, 2018
Bo Wang, Armin Pourshafeie, Marinka Zitnik, Junjie Zhu, Carlos D. Bustamante, Serafim Batzoglou, Jure Leskovec

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* Nature Communications, 9:3108, 2018 
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Prioritizing network communities


May 28, 2018
Marinka Zitnik, Rok Sosic, Jure Leskovec

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* Nature Communications, 9:2544, 2018 
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Modeling polypharmacy side effects with graph convolutional networks


Apr 26, 2018
Marinka Zitnik, Monica Agrawal, Jure Leskovec

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* Bioinformatics, 34:13, 457-466, 2018 
 * Presented at ISMB 2018 
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Large-scale analysis of disease pathways in the human interactome


Dec 03, 2017
Monica Agrawal, Marinka Zitnik, Jure Leskovec

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* Pacific Symposium on Biocomputing 23:111-122(2018) 
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Jumping across biomedical contexts using compressive data fusion


Aug 10, 2017
Marinka Zitnik, Blaz Zupan

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* Bioinformatics, 32 (12): i90-i100 (2016) 
 * In Proceedings of the 24th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2016 
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