I am thrilled about an opportunity to co-edit a research topic on single-cell data analytics, resources, challenges and perspectives for Frontiers in Genetics! With this research topic, we aim to provide a broad coverage of single-cell data analytic...

Also labeled: Bioinformatics, Computer Science, Factorization, Machine Learning, Network Science, Stanford University

I am excited to announce that our tutorial on Representation learning for network biology is accepted at ISMB 2018. I will present the tutorial at ISMB 2018 conference in Chicago, IL. Stay tuned for more information and tutorial materials. Networks...

Also labeled: Factorized Models, Machine Learning, Network Science, Neural Embeddings, Stanford University, Data Mining

I am 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 machine ...

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...

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...

Also labeled: Baylor College of Medicine, Bioinformatics, Computer Science, Data Fusion, Factorization, Factorized Models, Machine Learning

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 ...

Also labeled: Bioinformatics, Computer Science, Data Fusion, Data Mining, Factorization, Factorized Models, Orange, Visualization

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...

Also labeled: Association for Computing Machinery, Bioinformatics, Computer Science, Factorization, Factorized Models, Data Mining

Our paper at ISMB 2015 addresses a challenging task of inferring gene networks by taking into consideration potentially many data sets. Importantly, these data sets might be nonidentically distributed and can follow any combination of exponential...

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...

Also labeled: Bioinformatics, Computer Science, Data Fusion, Data Mining, Factorization, Factorized Models, Maths, Numerical Analysis

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...

Our paper on Gene network inference by fusing data from diverse distributions has been published in Bioinformatics. We will present it at ISMB 2015 in Dublin. In the paper we describe FuseNet, a Markov network formulation that infers networks from a...

Also labeled: Bioinformatics, Cancer Genomes Analysis, Data Fusion, Probabilistic Numerics, Network Science, Maths

Our poster on Gene prioritization by compressive data fusion and chaining got best poster award at the Basel Computational Biology Conference ([BC]^2). The poster highlights our recent computational method that prioritizes genes by fusing ...

Also labeled: Baylor College of Medicine, Bioinformatics, Data Fusion, Factorization, Machine Learning

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...

Also labeled: Bioinformatics, Data Fusion, Factorization, Factorized Models, Machine Learning, Orange, Visualization, Computer Science

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,...

Also labeled: Cancer Genomes Analysis, Computer Science, Data Fusion, Factorization, Factorized Models, Machine Learning, Maths, Survival Regression, Bioinformatics

Our recent paper in Journal of Computational Biology introduces an interaction data imputation method called network-guided matrix completion (NG-MC). The core part of NG-MC is low-rank probabilistic matrix completion that incorporates prior knowledge...

Also labeled: Bioinformatics, Computer Science, Data Fusion, Factorization, Factorized Models, Machine Learning, Matrix Completion, Network Science, Maths

We recently published a paper on a new data fusion method in IEEE Transactions on Pattern Analysis and Machine Intelligence. For most problems in science and engineering we can obtain data sets that describe the observed system from various ...

Also labeled: Bioinformatics, Data Fusion, Factorization, Factorized Models, Machine Learning, Maths, Optimization

I am visiting the Department of Computer Science at Stanford University, CA, USA in Summer and Fall 2014. During my stay we will study the interplay between network analysis, data integration and biology. There are many exciting challenges one can...

I have presented at CAMDA 2014 an extension of our recent matrix factorization-based data fusion approach that couples data fusion with survival regression. CAMDA 2014 runs as a satellite meeting at ISMB 2014, Boston, MA, USA. Our presentation got ...

Also labeled: Bioinformatics, Cancer Genomes Analysis, Computer Science, Data Fusion, Factorization, Factorized Models, Maths, Numerical Analysis, Optimization, Survival Regression

We are presenting a poster about our recent data fusion methodology (ArXiv preprint) at RECOMB Conference. Thanks to Prof. Blaz Zupan for the storyline and Prof. Richard H. Kessin for valuable comments. xkcd.com served as an inspiration of poster...

Also labeled: Bioinformatics, Computer Science, Data Fusion, Factorization, Factorized Models, Maths, Baylor College of Medicine

We got accepted a paper on Imputation of Quantitative Genetic Interactions in Epistatic MAPs by Interaction Propagation Matrix Completion to RECOMB 2014. Epistatic Miniarray Profile (E-MAP) is a popular large-scale gene interaction discovery...

Also labeled: Bioinformatics, Computer Science, Data Mining, Factorization, Maths, Machine Learning, Data Fusion, Matrix Completion, Factorized Models