Ali Faisal MSc.Machine Learning @ Edinburgh(UK) & Trento(Italy) I was a post-graduate researcher at the Statistical Machine Learning and Bioinformatics research group. My research interests include probabilistic generative and latent variable models. In my work I developed these methods for information retreival and data integration for biological and textual data. Doctoral dissertation (electronic copy): Retrieval of gene expression measurements with probabilistic models Update (Mar. 2013): I have joined the Brain research unit of Aalto, where I continue to develop computational models that help understand semantic processing of language using the high-dimensional neuroimaging data. An updated webpage at LinkedIn .

Publications

Journal articles

• A Faisal, J Peltonen, E Georgii, J Rung, S Kaski. Toward computational cumulative biology by combining models of biological datasets. [PDF] arXiv preprint 2014. arXiv:1404.0329


• A Faisal, J Gillberg, G Leen, J Peltonen. Transfer Learning using a Nonparameteric Sparse Topic Model. [PDF], [Neurocomputing] Neurocomputing 2013. Volume 112, Issue 18, Pg 124-137


• Riku Louhimo, Viljami Aittomaki, Ali Faisal,Marko Laakso, Ping Chen, Kristian Ovaska, Erkka Valo, Leo Lahti, Vladimir Rogojin, Samuel Kaski, Sampsa Hautaniemi Systematic use of computational methods allows stratification of treatment responders in glioblastoma multiforme. [PDF], [Website and Supplementary material], [Code]. Systems Biomedicine 2013 Volume 1, Issue 2, Pg 130-136


• S A Khan, A Faisal, J P Mpindi, J A Parkkinen, T Kalliokoski, A Poso, O P Kallioniemi, K Wennerberg, S Kaski Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs. [PDF] BMC Bioinformatics 2012. Volume 13:112


• J Caldas, N Gehlenborg, E Kettunen, A Faisal, M Ronty, AG Nicholson, S Knuutila, A Brazma and S Kaski Data-Driven Information Retrieval in Heterogeneous Collections of Transcriptomics Data Links SIM2s to Malignant Pleural Mesothelioma. [PDF], [Supplementary material] Bioinformatics 2012.Volume 28, Issue 2, Pp. i246-i253


• Penny Nymark, Mohamed Guled, Ioana Borze, Ali Faisal, Leo Lahti, Kaisa Salmenkivi, Eeva Kettunen, Sisko Anttila and Sakari Knuutila Integrative Analysis of microRNA, mRNA and aCGH Data Reveals Asbestos- and Histology-Related Changes in Lung Cancer. [PDF]. Genes, Chromosomes and Cancer 2011. Volumne 50. doi: 10.1002/gcc.20880


• A. Faisal, F. Dondelinger, D. Husmeier and C. M. Beale Inferring species interaction networks from species abundance data: A comparative evaluation of various statistical and machine learning methods [Eco. inf. version], [PDF], [Supplementary Material], [Code]. Ecological Informatics 2010. Volume 5, Issue 6, Pg 451-464


• J. Caldas, N. Gehlenborg, A. Faisal, A. Brazma, S. Kaski Probabilistic retrieval and visualization of biologically relevant microarray experiments [PDF], [Code]. Bioinformatics 2009. Volume 25, Issue 12, Pp. i145-i153 (Best poster award at the 5th ISCB Student Council Symposium, ISMB/ECCB 2009).

Conference Proceedings and Book Chapters

• A Faisal, J Gillberg, J Peltonen, G Leen, S Kaski. Sparse Nonparametric Topic Model for Transfer Learning [PDF] In Proceedings of ESANN 2012: European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning, Bruges, Norway 2012


• A Faisal, R Louhimo, L Lahti, S Hautaniemi, S Kaski Biomarker discovery via dependency analysis of multi-view functional genomics data. [PDF], [Code]. In Proceedings of NIPS 2011 Workshop: From Statistical Genetics to Predictive Models in Personalized Medicine, Sierra Nevada, Spain 2011.


• Riku Louhimo, Viljami Aittomaki, Ali Faisal,Marko Laakso, Ping Chen, Kristian Ovaska, Erkka Valo, Leo Lahti, Vladimir Rogojin, Samuel Kaski, Sampsa Hautaniemi Systematic Use of Computational Methods Allows Stratifying Treatment Responders in Glioblastoma Multiforme. [PDF], [Website and Supplementary material] In Proceedings of CAMDA 2011 conference, Critical Assessment of Massive Data Analysis, Vienna, Austria 2011


• A. Faisal, A. Karilainen, M. Li, P. Ramkumar, P. Salminen and M. Turunen. Book Chapter: Creating a Flourishing Innovation Climate., In Bit Bang - Energising Innovation, Innovating Energy. Eds. Yrjo Neuvo and Sami Ylonen. Helsinki University: Helsinki [PDF], ISBN 978-952-60-3152-1, Helsinki University Print, 2010


• A. Amogpai, X. Chen, A. Faisal, V. Lozano, T. Saarelainen, P. Salminen and A. Temmes Book Chapter: A Sustainable Helsinki Metropolitan Area., In Bit Bang - Energising Innovation, Innovating Energy. Eds. Yrjo Neuvo and Sami Ylonen. Helsinki University: Helsinki [PDF], ISBN 978-952-60-3152-1, Helsinki University Print, 2010

Non-refereed publications

• A. Faisal Europe survival against production outsourcing, Bright 2007, Karolinka Institute, Sweden, The work was presented as representative of Edinburgh University.
  
  

For an updated publication list, see Google scholar profile.

Talks

• "Sparse Nonparametric Topic Model for Transfer Learning" European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning, Bruges, Norway, 26th Apr. 2012
  


• "Retrieval of relevant experiments using topic models" FICS Winter Meeting, Helsinki, 13th Jan. 2012
  


• "Biomarker discovery via dependency analysis of multi-view functional genomics data" NIPS 2011 Workshop: From Statistical Genetics to Predictive Models in Personalized Medicine, Sierra Nevada, Spain, 16th Dec. 2011
  


• "Retreival of relevant experiments" Machine Learning Summer School, ANU, Canberra, Australia, 27-06 Sept-Oct 2010
  


• "Creating a Flourishing Innovation Climate" MIDE Workshop Tongji University, Shanghai, China, 3rd March 2010
  


• "A hybrid model for protein translation" FEBS-SysBio, Alpbach, Austria, 7-13 March 2009
  


• "Modeling Ecological Networks" EMA Climate Change Conference, CEU, Budapest, Hungary, 26-27 February 2009
  

Teaching

• T-61.5050 High-Throughput Bioinformatics, Exercise sessions (Spring 2014)


• T-61.3050 Machine Learning: Basic Principles, Exercise sessions (Autumn 2011)


• euSYSBIO: Masters Programme in Systems Biology (Tutor, 2011-12)


• T-61.5110 Modeling biological networks, Programming sessions (Autumn 2009 and 2010)


• T-61.6070 Special Course in Bioinformatics I: Information retreival from biological databases (Spring 2010)

Contact information