Marinka Zitnik

Fusing bits and DNA

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Marinka Zitnik

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 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).

 

Chairing the PhD Forum at ECML-PKDD 2020

I am excited to be co-chairing the PhD Forum at the 18th European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD) in 2020. Stay tuned for our call for submissions and more details soon!

 

Named a Rising Star in Biomedicine

I am honored to be named a Rising Star in Biomedicine by The Broad Institute of Harvard and MIT! I am thrilled to present my research at the Next Generation in Biomedicine Symposium at the Broad.

 

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 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!

 

ACM HQ, NY, XRDS Editorial Meeting

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).

See http://xrds.acm.org.

 


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