Marinka Zitnik

Fusing bits and DNA

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Numerical Analysis of Matrix Functions

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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 thorough overview of current theoretical results on matrix functions and several efficient numerical methods for computing them. Another well written text is by Rajendra Bhatia on matrix analysis (graduate texts in mathematics), which includes topics such as the theory of majorization, variational principles for eigenvalues, operator monotone and convex functions, matrix inequalities and perturbation of matrix functions. Bhatia's book is more functional analytic in spirit, whereas Higham's book focuses more on numerical linear algebra.

Below you will find a report that I produced and which contains a few interesting (some are elementary) proofs and implementations of algorithms. Interested reader should check the literature above to be able to follow the text.

Last Updated on Sunday, 25 August 2013 21:36

Topological Concepts in Machine Learning @ACAT Summer School

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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 requires alternative approaches to understand large and complex data sets in order to turn data into useful knowledge. Topological methods are making an increasing contribution in revealing patterns and shapes of high-dimensional data sets. Ideas, such as studying the shapes in a coordinate free ways, compressed representations and invariance to data deformations are important when one is dealing with large data sets. In this talk we consider which key concepts make topological methods appropriate for data analysis and survey some machine learning techniques proposed in the literature, which exploit them. We illustrate their utility with examples from computational biology, text classification and data visualization.

Slides (in English).

Last Updated on Thursday, 25 June 2015 14:41

BioDay: Trends in Bioinformatics @Hekovnik

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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, bioinformaticians, mathematicians and physicists.

The first event focused on recent trends in bioinformatics, specifically on experimental methods in systems biology (by Spela Baebler, PhD) and biomedical data fusion. I presented the latter topic and discussed how heterogeneous data sources in biology can be collectively mined by data fusion. The video of the event is available at (in Slovene). Enjoy!

Last Updated on Sunday, 25 August 2013 21:33

Winning BioNLP Challenge 2013: Extracting Gene Regulation Network

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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 systems to extract a gene regulation network of a specific cellular function in Bacillus Subutilis. This function was sporulation and is related to the adaptation of bacteria to scarce resource conditions. The automatic reconstruction of gene regulation networks is of great importance in biology, because it furthers the understanding of cellular regulation systems.

We were provided a manually curated annotation of the training corpus including entities, events and relations with gene interactions. Also, the regulation network that can be reconstructed with interactions mentioned in sentences of training data was provided (picture on the right). The task required to estimate gene regulation network from test data by specifying a directed graph where vertices represent genes, and arcs represent interactions between genes extracted from the text. The arcs were labeled with an interaction type (e.g., inhibition, activation, binding, transcription).

We hope to describe our approach using conditional random fields and rules in a paper but the details are not public yet (stay tuned).


P.S. I have been accepted to Machine Learning Summer School (MLSS) 2013 (acceptance rate 26%) that will take place at Max Planck Institute for Intelligent Systems, Tubingen, Germany late in August this year. There is a list of highly acclaimed speakers and I am looking forward to it!

Last Updated on Sunday, 25 August 2013 21:40

ACM HQ, NY, XRDS Editorial Meeting

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Some of the ACM XRDS Editors are participating these days in a meeting to discuss the magazine's future direction in print and online. We will do our best to further promote the XRDS, enhance its departments, improve web presence, build a community of readers, and provide high quality content from various CS disciplines.

See the current ACM XRDS issue on Information and Communication Technologies and Development (ICTD). The Spring issue is coming very soon! It will be on Scientific Computing. And, the Summer issue will be on Computer Science and Creativity.

If you are interested in submitting an article or have some crazy good ideas, please share them with us (contact the editorial staff). Or, share with your colleagues any interesting columns/featured articles you read in ACM XRDS.

XRDS is the ACM's flagship magazine for students, established in 1994. It is published quarterly and invites submissions of high quality articles of interest to computer science students (from Editorial Calendar).


Last Updated on Thursday, 09 July 2015 15:09

Preseren Award of U of Ljubljana, 2012

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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 and Preseren Award of U of Ljubljana for thesis "A Matrix Factorization Approach for Inference of Prediction Models from Heterogeneous Data Sources" (slo: univerzitetna Prešernova nagrada za delo "Pristop matrične faktorizacije za gradnjo napovednih modelov iz heterogenih podatkovnih virov"). I would like to thank my supervisor and mentor Prof. dr. Blaž Zupan for encouragement and advice he provides throughout my time as his student. I am lucky to have a supervisor who cares so much about my work and responds to my questions promptly. I could not have won the award without his support and mentoring.

Last Updated on Sunday, 30 March 2014 16:37

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

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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. More about Google Chrome Web Lab experiment.

Last Updated on Sunday, 25 August 2013 21:31

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

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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. For this great opportunity I need to thank to my supervisor Prof. Dr. Blaz Zupan, Head of Bioinformatics Laboratory at UofLj.

My work here will be about network integration for disease classification, specifically inferring prediction models from heterogenous data sources through matrix factorization. More about it in the next days. For now you can check the Interactive map of the Diseasome (Below is an image showing a part of diseasome. Interested reader is referred to Barabasi's paper The Human Disease Network.) linked from the NYTimes article Redefining Disease, Genes and All.

I am very much looking forward to it :)

Last Updated on Sunday, 25 August 2013 21:40

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

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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. Nelander)
  • Tissue specific modeling of functional genomics data: from networks to understanding human disease (O. Troyanskaya)
  • An evaluation of methods for the modeling of transcription factor sequence specificity (M. T. Weirauch)
  • SEEK and find: data management for systems biology projects (O. Krebs)
  • Excerbt: next-generation knowledge extraction and hypothesis generation from massive amounts of biomedical literature (B. Wachinger)
  • Combining multiple biological domains using patient network fusion (B. Wang)
  • Combining many interaction networks to predict gene function and analyze gene lists (Q. Morris)
  • Assembling global maps of cellular function through integrative analysis of physical and genetic networks (R. K. Srivas)
  • iCAVE: immersive 3d visualization of biomolecular interaction network (Z. Gumus)
  • Systems-level insights from the global yeast genetic interaction network (C. Myers)
  • Monopoly systems edition: advance to GO collect $200 (T. Idekar) (*actually about NeXO, a network extracted ontology and functional enrichment)
  • Genome-scale metabolic models: a bridge between bioinformatics and systems biology (J. Nielsen)

The organizers came up with a nice social program, parts of it is depicted on images below. At opening ceremony Tanja Tagaq, an Inuit woman, performed a unique style of traditional throat singing, Amanda and Rasmus from Sweden made performance at first poster session, Serena Ryder entertained us at conference reception dinner. Shonen Knife, a Japanese punk band that opened Nirvana, played at second poster session at Hart House.

I attended workshops on Designing experiments using state of the art Bayesian global parameter search methodology (M. Goldstein), Introduction to the statistical inference or regulatory networks (F. Emmert-Streib), Imaging flow cytometry: a new view on systems biology (R. DeMarco). In addition to parallel sessions I also enjoyed special lectures and plenary sessions. A few of them are: Reading and writing omes (G. Church), Towards unification of genetic and hierarchy models of tumor heterogeneity (J. Dick), Interactome networks and human disease (M. Vidal), The genetics of individuals (B. Lehner), Synthetic genetic interaction analysis by high-throughput imaging to map cellular networks, Unraveling principles of gene regulation using thousands of designed promotor sequences (E. Segal), Systems biology applications of imaging flow cytometry (T. Galitski).

Last Updated on Sunday, 25 August 2013 21:41

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

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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 have finished with data analysis of real-time yeast S. cerevisiae microscopy screens, an idea about it can be captured here. I am now starting with time series analysis and will probably have time to work on integration of phenomics data with genetic interaction and protein interaction data.

Recently a quantum optics research group here at UofT demonstrated a violation of Heisenberg's uncertainty principle and I was really excited about their work. "The quantum world is still full of uncertainty, but at least our attempts to look at it don't have to add as much uncertainty as we used to think!" ... and an easy reading to motivate you to learn more.

I have also come upon a nice real-world (I do not like this term) implementation of an argument based machine learning offered through classification module in CellProfiler Analyst package, participated in a discussion about Gaussian processes (intro, notes) at ccbr-stats meeting and much more. The Lab organized a farewell lunch for summer students only two weeks after my arrival to Toronto, as here and in US classes have already begun (after the Labour Day), I considered it as a welcome event :)

Below are images of Toronto CN Tower, Niagara Falls as seen from Skylon Tower and squirrels at UofT campus (Yes, one cannot miss numerous squirrels playing in parks at campus. A careful look should reveal four of them.), respectively.

Last Updated on Sunday, 25 August 2013 21:42

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

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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 Charlie Boone's Lab.

My work will be mostly data analysis of S. cerevisiae screens by employing various statistical and machine learning methods to gain new knowledge about identification of yeast mutant strains with non-WT phenotype. Possibly I will also work on time-series analysis of actin patches in yeast cells to differentiate them. First impressions are great, I have already met some great people and am looking forward to meet some at the International Conference on Systems Biology (ICSB12), which is held in Toronto in the next week and have a fortunate opportunity to attend.

Last Updated on Sunday, 30 March 2014 17:21

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