Marinka Zitnik

Fusing bits and DNA

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Deep networks

Article: To Embed or Not: Network Embedding as a Paradigm in Computational Biology

Current technology is producing high throughput biomedical data at an ever-growing rate. A common approach to interpreting such data is through network-based analyses. Since biological networks are notoriously complex and hard to decipher, a growing...

Article: Submit to ICLR 2019 Workshop on Representation Learning on Graphs and Manifolds

Many scientific fields study data with an underlying graph or manifold structure—such as protein networks, sensor networks, and biomedical knowledge graphs. The need for new optimization methods and neural network architectures that can accommodate...

Article: ICLR 2019 Workshop: Representation Learning on Graphs and Manifolds

I am very excited to be co-organizing an ICLR 2019 workshop on Representation Learning on Graphs and Manifolds. We will be having an amazing lineup of invited speakers on a variety of methods and problems in this area! Also, stay tuned for the...

Article: Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities

My review of machine learning for biomedical data integration is now available online in Information Fusion. This paper is intended for computer scientists and biomedical researchers who are curious about recent developments and applications of...

Article: ISMB 2018: Polypharmacy Side Effects

We presented our work on predicting polypharmacy side effects at ISMB/ECCB in Chicago, IL, USA. Here are the slides. This work has been highlighted in Stanford News, covered by several other news outlets, and is the most read paper in Bioinformati...

Article: Tutorial on Deep Learning for Network Biology at ISMB

We just presented a tutorial on Deep Learning for Network Biology at ISMB 2018 in Chicago, IL, USA. If you are interested in these topics and would like to learn more about graph neural networks and/or their biomedical applications but could not...

Article: Bioinformatics: What side effects to expect if taking multiple drugs?

Many patients take multiple drugs at the same time to treat complex diseases, such as heart failure, or co-occurring diseases, such as diabetes and epilepsy. The use of combinations of drugs is a common practice. In fact, 25 percent of people ages 65...