Marinka Zitnik

Fusing bits and DNA

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Article: ACM XRDS: Zero-Knowledge Proofs

The Fall 2013 issue of XRDS: Crossroads, the ACM magazine for students is about the complexities of privacy and anonymity. The issue is motivated by the current research problems and recent societal concerns about digital privacy. When real and...

Article: MLSS 2013, Max Planck Institute for Intelligent Systems, Tübingen

This year I am participating at Machine Learning Summer School (MLSS) that is held in Tübingen, Germany. The Summer School offers an opportunity to learn about fundamental and advanced aspects of machine learning, data analysis and inference, f...

Article: Extracting Gene Regulation Networks Using Linear-Chain Conditional Random Fields and Rules @ACL 2013, BioNLP Workshop

This week Slavko Zitnik will present our paper (he is the first author) at ACL, ACL BioNLP Workshop on extending linear-chain conditional random fields (CRF) with skip-mentions to extract gene regulatory networks from biomedical literature a...

Article: ISMB/ECCB 2013 - 21st International Conference on Intelligent Systems in Molecular Biology & 12th European Conference on Computational Biology

I participated in CAMDA Satellite Meeting on critical assessment of massive data analysis during 29th and 20th July at ISMB in Berlin, where I presented our matrix factorization-based data fusion approach to predicting drug-induced liver injury from...

Article: CAMDA 2013: Matrix Factorization-Based Data Fusion for Drug-Induced Liver Injury Prediction

This work was recognized as first prize winner for excellent research at ISMB/ECCB CAMDA 2013 Conference. I am giving a talk at CAMDA 2013 Conference, which runs as a satellite meeting of ISMB/ECCB 2013 Conference. CAMDA focuses on challenges in th...

Article: Numerical Analysis of Matrix Functions

I have spent some time recently studying matrix functions, both from theoretical and computational perspective. There is a nice book by Nick J. Higham on functions of matrices, which I highly recommend to interested reader and which provides a...

Article: Topological Concepts in Machine Learning @ACAT Summer School

I had a talk at ACAT Summer school on computational topology and topological data analysis held at University of Ljubljana. Abstract: Fast growth in the amount of data emerging from studies across various scientific disciplines and engineering...

Article: BioDay: Trends in Bioinformatics @Hekovnik

In May I participated at the first BioDay meeting organized by Hekovnik in Ljubljana, Slovenia. The aim of the BioDay events is the exchange of ideas, knowledge and fostering collaboration and networking between life scientists, computer scientists,...

Article: Winning BioNLP Challenge 2013: Extracting Gene Regulation Network

I have recently participated in BioNLP Shared Task 2013 Challenge together with Slavko Zitnik and won the first place in the task extracting gene regulation networks. The goal of the challenge was to assess the performance of information extraction...

Article: Preseren Award of U of Ljubljana, 2012

In first week of December U of Ljubljana celebrates traditional "Week of University" (Why?) during which numerous invited lectures, presentations and award ceremonies are organized. This year, I was awarded the faculty award for best students an...

Article: @Imperial College London, Department of Computing (Part II)

Recent days at Department of Computing, Imperial College London, were pleasant (though intense) and our efforts in data fusion produced some very good results. Below are images taken at Imperial and nearby Chrome Web Lab, located in Science Museum....

Article: @Imperial College London, Department of Computing (Part I)

I have just arrived to London, United Kingdom, where I will stay until the end of November this year. I will be working at Imperial College London, Department of Computing, Computational Network Biology Research Group led by Prof. Dr. Natasa Przulj....

Article: @University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research (Part III)

So what have I been up to in recent weeks here at Toronto? Highlights include my first ride with famous American yellow school bus to a reception at ICSB12 conference, some sightseeing in Toronto city and a trip to Niagara Falls. Besides, I hav...

Article: @University of Toronto, The 13th International Conference on Systems Biology (Part II)

The 13th international conference on systems biology was held in Toronto, 19th--23rd August 2012. Here is a list of talks from platform sessions which I found especially interesting: Modeling the regulatory diversity of human cancers (S....

Article: @University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research (Part I)

In the past few days I have settled in Toronto, Canada, where I will stay until October this year. As a graduate student I will be working at the University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research in the Charli...

Article: A Randomized Algorithm for Linear Equations over Prime Fields in Clojure

Professor of Computer Science Dick Lipton from Georgia Tech has a few days ago posted an interesting post on his blog about a new way of solving systems of linear equations over prime fields. Solving linear systems of equations is a very well explored...

Also labeled: Computer Science

Article: Undergraduate Thesis Defense

Yesterday I defended my undergraduate Thesis entitled A Matrix Factorization Approach for Inference of Prediction Models from Heterogeneous Data Sources (slo: Pristop matri?ne faktorizacije za gradnjo napovednih modelov iz heterogenih podatkovnih...

Article: CRY: Commitment Schemes

I have been following the Cryptography and Theory of Coding 2 course this semester (summer 12). During the course I have been working on the project about Commitment schemes. Please find below attached the final report produced and a short...

Also labeled: Computer Science

Article: ML: Reliable Calibrated Probability Estimation in Classification

I followed a Machine Learning course this semester at the university (along with the one, offered by Stanford Uni). I have been working on a seminar studying Reliable probability estimation in classification using calibration. The final report is in...

Article: Renaming: MF - Matrix Factorization Techniques for Data Mining

In this short post I would like to update you on some recent changes in the MF - Matrix Factorization Techniques for Data Mining Library. Recently, the library MF - Matrix Factorization Techniques for Data Mining has been moved and renamed. It is...