Marinka Zitnik

Fusing bits and DNA

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Article: Jozef Stefan Golden Emblem Prize

Last month, I was honored to receive Jozef Stefan Golden Emblem for winning PhD dissertation in the fields of natural sciences, medicine and biotechnology. The prize is awarded by Jozef Stefan Institute. I look forward to making further progress on...

Article: Submit to AIME 2017 Workshop on Advanced Healthcare Analytics

You are cordially invited to submit a paper to the Workshop on Advanced Predictive Models in Healthcare that will take place during the AIME 2017 conference. This workshop will focus on topics related to advanced predictive models, capable of ...

Article: Submit to ECML PKDD 2017

You are cordially invited to submit a paper to the upcoming 2017 ECML PKDD conference. ECML PKDD is the European Conference on Machine Learning and Knowledge Discovery. It is the largest European conference in these areas that has developed from the...

Article: ACM XRDS: The Infinite Mixtures of Food Products

The Fall issue of ACM XRDS is here! In this issue of XRDS, we take a closer look at the marriage of physics and computer science through quantum computing. Quantum computing is a model of computation that breaks with the tradition of digital computers...

Article: ISMB 2016: Connecting Gene-Disease Contexts

We presented our recent approach for disease module detection at the ISMB 2016. Slides are available. The method is capable of making inference over heterogeneous data collections in new interesting ways! One of them, an approach we call jumping ac...

Article: Bioinformatics: Jumping Across Contexts Using Compressive Fusion

Our paper on Jumping across biomedical contexts using compressive data fusion has just appeared in Bioinformatics. We will present the paper at ISMB 2016 in July 2016. The rapid growth of diverse biological data allows us to consider interactions...

Article: ACM XRDS: Cultures of Computing

The Summer issue of ACM XRDS is here! The issue is centered around computing, culture, postcoloniality and questions of power. In it, many fascinating authors ask whether an Anglo-European culture of computing could be made more aware of its politics...

Article: ACM XRDS: The Brownian Wanderlust of Things

The Spring issue of ACM XRDS is here! This issue is centered around digital fabrication, which in many ways highlights the expanded role of computer in today's society. Digital fabrication is not merely about 3D printing knickknacks, rather it enables...

Article: ACM XRDS: Activities of Daily Living in the Era of Internet of Things

The Winter issue of ACM XRDS is here! This issue discusses Internet of Things (IoT), a collection of emerging technologies that promise to seamlessly expand our sensing capabilities across the globe with imagination as our only limit. In the issue you...

Article: PSB 2016: Collective Pairwise Classification for Multi-Way Analysis

Our paper on Collective Pairwise Classification for Multi-Way Analysis has been published in the Proceedings of the 21st Pacific Symposium on Biocomputing. We will present the work at the PSB conference in January 2016. In the paper, we develop a...

Article: ACM XRDS: The Marvel Comic Book Universe

The Fall issue of ACM XRDS is here! In this issue we write about virtual reality. Among others, you can read about the virtual reality revolution and ways to bring virtual reality home. The issue also discusses how to use your own muscles to achieve...

Article: BMC Bioinformatics: Extracting Gene Regulatory Networks from Text

Our paper on Sieve-based relation extraction of gene regulatory networks from biological literature has been published in BMC Bioinformatics. In the paper, we describe a network extraction algorithm, which is an improvement on our winning submission...

Article: PLoS CompBio: Gene Prioritization by Compressive Data Fusion

Our paper on Gene prioritization by compressive data fusion and chaining has been published in PLoS Computational Biology. In the paper, we present Collage, a new data fusion approach to gene prioritization. Together with collaborators from Baylor...

Article: Data Fusion Tutorial at the IEEE Engineering in Medicine and Biology

Together with Blaz Zupan we organize a tutorial on data fusion at the International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). In the tutorial, we will explore latent factor models, a popular class of approaches that ...

Article: ACM XRDS: Understanding Cancer with Matrix Factorization

The Summer issue of ACM XRDS is here! In this issue we write about computational biology. Our features and interviews present different perspectives about some of the most recent advances of computational biology. You can read about personalized...

Article: ISMB 2015: Integrate Everything but the Kitchen Sink

Our poster at ISMB 2015 is concerned with data set selection and sensitivity estimation in collective factor models. Molecular biology data is rich in volume as well as heterogeneity. We can view individual data sets as relations between objects of...

Article: Compressive Data Fusion and Persistent Homology

My talk at the Summer School on Computational Topology in Ljubljana, Slovenia was about coupling compressive data fusion methods with algebraic topology, in particular persistent homology. There, I discussed how the latent data space obtained by f...

Article: Invited Talk on Learning Latent Factor Models by Data Fusion

Our invited talk at the Workshop on Matrix Computations for Biomedical Informatics at the 15th Conference on Artificial Intelligence in Medicine, AIME in Pavia, Italy, discussed the use of collective latent factor models for various predictive...

Article: Data Fusion Tutorial at the Basel Computational Biology Conference

Together with Blaz Zupan we organize a tutorial on data fusion at the Basel Computational Biology Conference ([BC]^2). The tutorial is targeted at computational scientists, data mining researchers and molecular biologists interested in large-scale...

Article: Syst Biomed: Survival Regression by Data Fusion

Our recent paper in Systems Biomedicine describes a new computational approach that predicts patient’s survival time from a collection of heterogeneous data sets. This is the full paper of our award winning entry at CAMDA meeting at ISMB 2014, Boston,...

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