Ramanuja Simha

    PhD student in Computer Science
    Computational Biomedicine and Machine Learning Lab
    Department of Computer and Information Sciences
    University of Delaware

    Email: rsimha<at>udel<dot>edu
    DBLP; Google Scholar; LinkedIn; Kaggle

Ramanuja Simha is a PhD student in Computer Science at the University of Delaware. His research interests lie in machine-learning, data-mining, and bioinformatics. Before joining the PhD program, he received his Masters in Computer Science at the University of South Florida (GPA 4.0/4.0). His professional experience include internships at LinkedIn (2014) and National Center for Atmospheric Research (2010), summer research at Carnegie Mellon University (2011), and work at Tesco as a Senior Software Engineer (2005-08).

Research Areas

Machine learning, data mining, multi-label classification, probabilistic data modeling, bioinformatics, computational biology, protein subcellular multi-localization, social networks.

Experience

Applied Data Mining Intern, LinkedIn, June 2014 - August 2014
Research Assistant, University of Delaware, June 2011 - August 2013
Visiting Graduate Student, Carnegie Mellon University, June 2011 - July 2011
SIParCS Intern, National Center for Atmospheric Research, May 2010 - August 2011
Research/Teaching Assistant, University of South Florida, 2008 - 2011
Senior Software Engineer, Tesco HSC, July 2005 - August 2008

Honors and Awards

University of Delaware Graduate Fellowship, 2013-15
Tony B. academic travel award for SLAS 2015, February 2015
Machine Learning Summer School 2012 scholarship, July 2012
NSF ICDE (International Conference in Data Engineering) 2012 scholarship, April 2012
HPDC (High-Performance Parallel and Distributed Computing) 2011 student travel grant, June 2011
HPDC/SIGMETRICS 2011 Best Student Poster Award, June 2011
Petascale Programing Environments and Tools, June 2010
Appreciation award, IT Innovation Summit, Tesco HSC, 2008
Quarterly awards for stellar performance, Tesco HSC, November 2006, May 2007

Publications

Peer-Reviewed Journal Papers

R. Simha and H. Shatkay. Protein (Multi-)Location Prediction: Using Location Inter-Dependencies in a Probabilistic Framework. Algorithms for Molecular Biology 9(8), 2014.

L. Coelho, J. Kangas, A. Naik, E. Osuna-Highley, E. Glory-Afshar, M. Fuhrman, R. Simha, P. Berget, J. Jarvik, R. Murphy. Determining the subcellular location of new proteins from microscope images using local features. Bioinformatics 29(18), 2013.

N. Kourtellis, T. Alahakoon, R. Simha, A. Iamnitchi, R. Tripathi. Identifying High Betweenness Centrality Nodes in Large Social Networks. Social Network Analysis and Mining 3(4), 2013.

Peer-Reviewed Conference Papers, Workshop Papers, and Posters

R. Simha and H. Shatkay. Protein (Multi-)Location Prediction: Using Bayesian Networks for Location Inter-dependencies, and a Mixture Model. Abstract accepted for Podium Presentation, Society for Laboratory Automation and Screening (SLAS), February 2015.

R. Simha and H. Shatkay. Protein (Multi-)Location Prediction: Using Location Inter-Dependencies in a Probabilistic Framework. Proceedings of the International Workshop on Algorithms for Bioinformatics (WABI), September 2013.

R. Simha, R. Tripathi, M. Thakur. Mining Associations Using Directed Hypergraphs. Proceedings of the Workshop on Graph Data Management (GDM) at the International Conference on Data Engineering (ICDE), April 2012.

J. Blackburn, R. Simha, N. Kourtellis, X. Zuo, M. Ripeanu, J. Skvoretz, A. Iamnitchi. Branded with a Scarlet C: Cheaters in a Gaming Social Network. Proceedings of the International World Wide Web Conference (WWW), April 2012. (Acceptance Rate: 12%)

J. Blackburn, R. Simha, C. Long, X. Zuo, J. Skvoretz, A. Iamnitchi. Cheaters in a Gaming Metanetwork. HPDC/SIGMETRICS Student Posters, June 2011. SIGMETRICS Performance Evaluation Review 39(3), 2011. (Best Student Poster Award)

T. Alahakoon, R. Tripathi, N. Kourtellis, R. Simha, and A. Iamnitchi. K-Path Centrality: A New Centrality Measure in Social Networks. Proceedings of the Workshop in Social Network Systems (SNS), April 2011.

Thesis

R. Simha. Mining Associations Using Directed Hypergraphs. Masters Thesis, University of South Florida, March 2011.

Professional Activites

Reviewer. Journal of Computational Biology.
PC Member. Mid-Atlantic Student Colloquium on Speech, Language and Learning 2012.
Reviewer. SC11 International Conf. for High Perf. Comp., N/w, Storage and Analysis.
Reviewer. International Conference on Information Systems 2009.

Graduate Courses

Computational Biomedicine, Spring 2012, Prof. Hagit Shatkay
Machine Learning, Spring 2012, Prof. Vijay Shanker
Theory of Computation, Fall 2011, Prof. John Case
Artificial Intelligence, Fall 2011, Prof. Sandra Carberry
Bioinformatics, Fall 2011, Prof. Hagit Shatkay
Parallel and Distributed Computing, Spring 2011, Prof. Adriana Iamnitchi
Intro to Computer Graphics I, Fall 2010, Prof. Les Piegl
Data Mining, Spring 2010, Prof. Lawrence Hall
Foundations of Software Security, Spring 2010, Prof. Jay Ligatti
Compiler Design, Fall 2009, Prof. Jay Ligatti
Operating Systems, Spring 2009, Prof. Adriana Iamnitchi
Advanced Algorithms, Spring 2009, Prof. Rahul Tripathi
Intro to Theory of Algorithms, Fall 2008, Prof. Rahul Tripathi
Princ of Computer Architecture, Fall 2008, Prof. Nagarajan Ranganathan

Courses as a Teaching Assistant

Analysis of Algorithms, Spring 2011, Prof. Rahul Tripathi
Intro to Theory of Algorithms, Fall 2010, Prof. Rahul Tripathi
Operating Systems, Spring 2010, Prof. Adriana Iamnitchi
Intro to Theory of Algorithms, Fall 2009, Prof. Rahul Tripathi
Automata Theory, Fall 2008, Prof. Rahul Tripathi