Suleiman Ali Khan

Doctor of Science (Technology)  (khan 'DOT' suleiman -AT- gmail [DOT] COM)

Ph.D. Thesis: Bayesian multi-view models for data-driven drug response analysis
Press Release

Update [Aug 2014]: I have joined FIMM Institute of Molecular Medicine Finland at University of Helsinki where I am working on feature selection on high-dimensional biological data using using integrative models. My updated contact and publications can allways be found on the Google Scholar page, and profile on LinkedIn.

I did my PhD at Statistical Machine Learning and Bioinformatics Group (MI), where I worked on multi-view learning and its application to new problems in Bioinformatics. During my PhD, I have been a member of the Helsinki Institute for Information Technology, FICS graduate school and the Finnish Centre of Excellence in Computational Inference Research (COIN).

Challenges and Fundings

• We (Team FIMM-UTU) won the NCI-DREAM Prostate Cancer Prediction Challenge (Dream9.5)!


• We (TeamFAT) won the NCI-DREAM Gene Essentiality Prediction Challenge (Dream9)!


• We (TeamMI) won upto the Consortium Phase of NCI-DREAM Cytotoxicity Prediction Challenge (Dream8)!


• We (TeamFin) won the NCI-DREAM Drug Sensitivity Prediction Challenge (Dream7)! published in Nautre Biotechnology.


• BCH Biocentrum Grant received for "Analysing Cell Stress Response in Breast Cancer Cells" with Mamun Majumder (University of Helsinki)


• TES Grant received for "Identifying biomarkers from high dimensional responses" (University of Helsinki)

Publications

Google Scholar Profile


• Suleiman A. Khan, Eemeli Leppäaho, Samuel Kaski, Multi Tensor Factorization, 2015 PDF , CODE


• Suleiman A. Khan Bayesian multi-view models for data-driven drug response analysis, Ph.D. Thesis, Aalto University, 2015 PDF, Press Release


• J. C. Costello, L. M. Heiser, E. Georgii, M. Gonen, M. P. Menden, N. J. Wang, M. Bansal, M. Ammad-ud-din, P. Hintsanen, Suleiman A. Khan, J.P. Mpindi, NCI Dream Community, O. Kallioniemi, A. Honkela, T. Aittokallio, K. Wennerberg, J. J. Collins, D. Gallahan, D. Singer, J. Saez-Rodriguez, S. Kaski, J. W. Gray, and G. Stolovitzky A Community Effort to Assess and Improve Drug Sensitivity Prediction Algorithms, Nature Biotechnology, 2014 PDF , CODE, Press Release


• Suleiman A. Khan, Seppo Virtanen, Olli P. Kallioniemi, Krister Wennerberg, Antti Poso, and Samuel Kaski. Identification of structural features in chemicals associated with cancer drug response: A systematic data-driven analysis, Bioinformatics 30 (17), pp 497-504 2014, ECCB. PDF , CODE


• Suleiman A. Khan, Samuel Kaski, Bayesian Multi-view Tensor Factorization, European Conference on Machine Learning (ECML 2014), Machine Learning and Knowledge Discovery in Databases, 8724: pp 656-671, Nancy, France, 2014. PDF , CODE


• M. Gonen Suleiman A. Khan, S Kaski, Kernelized Bayesian Matrix Factorization, In Proceedings of the 30th International Conference on Machine Learning (ICML 2013), Atlanta, Georgia, USA, 2013 PDF , CODE


• Suleiman 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., BMC Bioinformatics 2012. Volume 13:112. PDF


• Seppo Virtanen, Arto Klami, Suleiman A. Khan, Samuel Kaski, Bayesian Group Factor Analysis, AISTATS 2012 JMLR W&CP 22: 1269-1277, 2012. PDF , CODE


• AB Dunkley, M Costa, H Hielkema, Suleiman A. Khan, E Litvinova, K Visala, NV Hoang, T Kiravuo, V Looga, Håkan Mitts, GR Moktan, O Mäkinen, M Kuikka Book Chapters in Future of Internet Yrjö Neuvo & E Karvonen Edition BitBang4: 1) Are We All Criminals? 2) Internet, Find me a Job! and 3) Internet, Find me a Cure. Online Version: PDF


• Alice Marascu, Suleiman A. Khan, Themis Palpanas, Scalable Similarity Matching in Streaming Time Series, PAKDD 2012, LNCS, Advances in Knowledge Discovery and Data Mining, Volume 7302:218-230. PDF


• Haleem H. Shah, Suleiman A. Khan, S. Ismail Shah, "Performance Analysis of Simultaneous 802.11g Wireless LANs: Efficient Utilization of Total Overlap" Second International Conference on Business & Technology ICBTE-2010.


• Asad W. Malik, Shoab A. Khan, Suleiman A. Khan, "Context Aware Network Enabled Distributed Modeling and Simulation Framework" First Asia International Conference on Modelling & Simulation, AMS apos2007.


• Suleiman A. Khan, U.Burki, H.Feroze, R. Kiani, T. Rana, Shoab A. Khan "Distributing the HLA RTI to manage Increasingly Complex Simulations" International Conference on HLA Methodology and Applications. Lerici - Italy (June 2005).


• Suleiman A. Khan, "Reusable Architecture for Interoperable Simulations" International Multi-Conference in Computer Science and Computer Engineering (IMCSE'05) Las Vegas-USA (June2005).

Posters and Talks

• "Kernalized Bayesian Matrix Factorization" in NIPS 2013 Machine Learning in Computational Biology Workshop. poster, talk.
• "Decomposing Drug Response Patterns with Bayesian Group Factor Analysis" in NIPS 2011 Machine Learning in Computational Biology Workshop. poster, talk.


• "Decomposing Drug Action Mechanisms into Relationships of Chemical Structure with Genome Wide Drug Responses" in Socbin Conference 2011. poster, talk.


• "Distributing the HLA RTI to manage Increasingly Complex Simulations" in First International Conference on HLA Methodology and Applications. Lerici - Italy (June 2005). poster, talk.

Teaching and Supervision

Aalto University

• Assistant: T.61-5050: High Throughput Bioinformatics, (Spring 2014)
• Assistant: T.61-5110: Modelling of Biological Networks, (Autumn 2013)
• Assistant: T.61-5050: High Throughput Bioinformatics, (Spring 2013)
• Assistant: T.61-5110: Modelling of Biological Networks, (Autumn 2012)
• Assistant: T.61-5050: High Throughput Bioinformatics, (Spring 2012)
• Assistant: T.61-5110: Modelling of Biological Networks, (Autumn 2011)
• Co-Supervisor: Data driven translation of Cell-lines to Patient samples. Muhammad Ammad, Summer Intern, 2011
• Tutor: MBI Masters in Bioinformatics 2010-2011

Iqra University

• Supervisor: Performance Analysis of Simultaneous 802.11g Wireless LANs, Haleem H. Shah, MS-Thesis, 2009
• Lecturer: Advanced Design and Analysis of Algorithms, (Spring 2009)
• Lecturer: Data Structures (Spring 2009)

Center for Advanced Studies in Engineering

• Lecturer: Data Structures and C-programming, (Summer, Autumn 2005 - Spring 2006)

Education

M.Sc. in Life Science Informatics. Erasmus Mundus - University of Edinburgh/Trento (2006-2008)

• Thesis: Real Time Pattern Matching in Streaming Time Series
• Supervisor: Themis Palpanas and Peter Buneman

B.Eng. in Computer Software. NUST(Pakistan) (2001-2005)

• Thesis: Reusable Architecture Development for Interoperable Universal Simulations [based on IEEE std HLA 1516]
• Supervisor: Shoab Ahmed Khan and Tauseef Rana

Contact

Office:

Room A323, Computer Science Building,
Konemiehentie 2, Otaniemi campus area, Espoo

Postal Address:

Aalto University School of Science,
Department of Information and Computer Science,
P.O. Box 15400, FI-00076 Aalto, Finland

Telephone:

Lab:+358-9470-23281
Cell+358-40197-1212
Fax:+358-9470-23277

Email:

firstname.lastname@aalto.fi