Sumeet Agarwal
Department of Physics
University of Oxford
Clarendon Laboratory
Parks Road
Oxford OX1 3PU

Merton College
Merton Street
Oxford OX1 4JD
Oxfordshire, United Kingdom

sumeet.agarwal@physics.ox.ac.uk
sumeet.agarwal@merton.ox.ac.uk

I am a D.Phil. student, working on the analysis of large-scale biological networks (see below for details). Broadly speaking, my interests lie at the interface of machine learning, statistical physics, and biology. My supervisors are Nick Jones, Charlotte Deane, and Mason Porter; I thus have the good fortune of being associated with their respective impressive-sounding groups: Systems and Signals, Protein Informatics, and Chaotic Dynamics (don't ask me what any of those mean).
I was initially at the Systems Biology Doctoral Training Centre, which is linked to the Oxford Centre for Integrative Systems Biology.

D.Phil. Stuff

• Research proposal
• Thesis abstract
• Thesis (submitted 21-02-2012; 5.25 MB)

Publications

Journal

• Sumeet Agarwal, Charlotte M. Deane, Mason A. Porter, and Nick S. Jones. Revisiting Date and Party Hubs: Novel Approaches to Role Assignment in Protein Interaction Networks. PLoS Computational Biology 6(6):e1000817 (2010) [preprint] [blog post] [slides] [arXiv:0911.0408] .
• Sumeet Agarwal, Candida Vaz, Alok Bhattacharya, and Ashwin Srinivasan. Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM). BMC Bioinformatics 11(Suppl 1):S29 (2010) [preprint] [slides] [website].
• Sumeet Agarwal, V. Vijaya Saradhi, and Harish Karnick. Kernel-based online machine learning and support vector reduction. Neurocomputing 71:1230-1237 (2008) [preprint].

Conference Proceedings

• Sumeet Agarwal, Shantanu Godbole, Diwakar Punjani, and Shourya Roy. How Much Noise in Text is too Much: A Study in Automatic Document Classification. In Proceedings of the 7^th IEEE International Conference on Data Mining (ICDM), Omaha, Nebraska, USA, October 2007 [preprint].
• Sumeet Agarwal, V. Vijaya Saradhi, and Harish Karnick. Kernel-based online machine learning and support vector reduction. In Proceedings of the 15^th European Symposium on Artificial Neural Networks (ESANN), Bruges, Belgium, April 2007 [preprint].

Workshop Proceedings

• Gabriel Villar, Sumeet Agarwal, and Nick S. Jones. High Throughput Network Analysis (extended abstract). In Proceedings of the Workshop on Analysis of Complex NEtworks (ACNE), ECML PKDD, Barcelona, Spain, September 2010 [preprint] [slides].
• Sumeet Agarwal, Gabriel Villar, and Nick S. Jones. High Throughput Network Analysis (extended abstract). In Machine Learning in Systems Biology (MLSB), Proceedings of the Fourth International Workshop, Edinburgh, Scotland, October 2010 [preprint] [slides] [talk].

Academic Reports

• Sumeet Agarwal. Revisiting date and party hubs: Novel approaches to role assignment in protein interaction networks (first year D.Phil. research) [report] [slides].
• Sumeet Agarwal. Dynamically organised modularity in protein interaction networks (10-week research project) [report] [slides].
• Sumeet Agarwal. Mathematical Modeling of T-Cell Receptor Triggering and Activation (10-week research project) [report].
• Sumeet Agarwal. Spatio-Temporal Evolution of Grammars (course project) [report] [slides].

Other Presentations

• Learning Predictive Models of Gene Dynamics (given at the School of Computational and Integrative Sciences, Jawaharlal Nehru University, Delhi, 5 August 2009) [slides].
• Dynamics and Inference on Biological Networks (given to M.Sc. in Biology (Integrative Bioscience) students, Department of Zoology, University of Oxford, 28 October 2009 and 26 October 2010) [slides].
• The Oxford Systems Biology Doctoral Training Centre (given at the EPSRC Inter-DTC Conference, University of Warwick, 23 July 2010) [slides].
• Evolvability as Learnability (given to Doctoral Training Centre students, University of Oxford, 21 March 2011) [slides].

Miscellanea

• Genetics and Evolution through the Ages
• Some Brief Thoughts on Philosophical Questions in Systems Biology
• Fastest trains in India

Blog