1.5k citations · 6.9k across the 102 of their papers we have counts for
7 papers · 1 filter
NIMFA: A Python Library for Nonnegative Matrix Factorization
Marinka Zitnik, Blaz Zupan
NIMFA is an open-source Python library that provides a unified interface to nonnegative matrix factorization algorithms. It includes implementations of state-of-the-art factorizati…
Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities
Marinka Zitnik, Francis Nguyen, Bo Wang +3
New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include a myriad of properties de…
Embedding Logical Queries on Knowledge Graphs
William L. Hamilton, Payal Bajaj, Marinka Zitnik +2
Learning low-dimensional embeddings of knowledge graphs is a powerful approach used to predict unobserved or missing edges between entities. However, an open challenge in this area…
Network Enhancement: a general method to denoise weighted biological networks
Bo Wang, Armin Pourshafeie, Marinka Zitnik +4
Networks are ubiquitous in biology where they encode connectivity patterns at all scales of organization, from molecular to the biome. However, biological networks are noisy due to…
Prioritizing network communities
Marinka Zitnik, Rok Sosic, Jure Leskovec
Uncovering modular structure in networks is fundamental for systems in biology, physics, and engineering. Community detection identifies candidate modules as hypotheses, which then…
Modeling polypharmacy side effects with graph convolutional networks
Marinka Zitnik, Monica Agrawal, Jure Leskovec
The use of drug combinations, termed polypharmacy, is common to treat patients with complex diseases and co-existing conditions. However, a major consequence of polypharmacy is a m…