MALAY BHATTACHARYYA - Indian Statistical Institute

MALAY BHATTACHARYYA
Current
Position
Contact
Information
Date of Birth
Citizenship
Research
Interests
Education
Senior Research Fellow August 2009 to present
Machine Intelligence Unit, Indian Statistical Institute, Kolkata – 700108, India
• Supervisor: Prof. Sanghamitra Bandyopadhyay, Fellow of NASI, Fellow of INAE, Humboldt
Fellow as Senior Researcher, Shanti Swarup Bhatnagar Awardee in Engineering Sciences, 2010.
Machine Intelligence Unit Voice: (+91) (33) 2575 3112
Indian Statistical Institute Fax: (+91) (33) 2578 3357
203 B. T. Road E-mail: malay r@isical.ac.in
Kolkata – 700108, India Web: http://www.isical.ac.in/∼malay r
February 02, 1983.
India.
Graph Theory, Soft Computing, Computational Biology and Bioinformatics.
Working towards the degree of Doctor of Philosophy (Ph.D.) August 2007 to present
Indian Statistical Institute, Kolkata – 700108, India
• In Computer Science.
• Tentative Dissertation Title: Mining Co-expression Graphs: Applications to MicroRNA Regulation
and Disease Analysis.
• Supervisor: Prof. Sanghamitra Bandyopadhyay.
Master of Engineering (M.E.) July 2005 to June 2007
Jadavpur University, Kolkata – 700032, India
• In Electronics & Telecommunication Engineering with GPA 9.24/10 (University rank 5).
• Dissertation Title: Solving Single Courier Problem Using Genetic Algorithms.
• Supervisor: Prof. Anup Kumar Bandyopadhyay.
Bachelor of Technology (B.Tech.) August 2001 to July 2005
Government College of Engineering and Textile Technology (formerly College of Textile Technology),
Berhampore – 742101, India
• In Computer Science & Engineering with GPA 8.35/10 (College rank 3).
• Dissertation Title: Implementing Fragmentation in Distributed Database.
• Supervisor (External): Prof. Parama Bhaumik, IT Department, Jadavpur University.
Editorial
Activities • Editorial Board Member for Journal of Digital Information Management (ISSN# 0972-7272) since
January 2012.
• Issue Editor, Feature Editor, Editor, Associate Editor, Assistant Editor and Web Editor for XRDS:
Crossroads – The ACM Magazine for Students (ISSN# 1528-4981) during January 2009 to June
2012.
• AssociatetoTechnicalEditorforSankhya–TheIndianJournalofStatistics[A(ISSN# 0976-836X)
& B (ISSN# 0976-8386)] in July 2009.
Organizing
Activities • Founding Chair of ACM Student Chapter ISI Kolkata, India during June 2011 to June 2012.
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• Committee Member in IEEE Computational Intelligence Society (CIS) Calcutta Chapter since October
2010.
• Program Committee Member in the conferences ICDIM 2012 (Macau, China), EEML 2012 (Leuven,
Belgium), NDT 2012 (Dubai, UAE), INCT 2011 (Tehran, Iran), ICDIM 2011 (Melbourne,
Australia), and NDT 2011 (Macau, China),
Refereeing
Activities • Reviewer for the Young Investigator Grant, HFSP in 2011.
• Reviewer for the journals Nucleic Acids Research, IEEE/ACM Transactions on Computational Biology
and Bioinformatics, Recent Patents on DNA & Gene Sequences, Journal of Digital Information
Management,EngineeringLetters, InternationalJournalofWebApplications,Current Bioinformatics,
Bioinformatics, and XRDS: Crossroads – The ACM Magazine for Students.
• Reviewer for the conferences ICDIM 2012 (Macau, China), NDT 2012 (Dubai, UAE), IDCTA 2011
(Busan, Korea), ICMiA 2010 (Seoul, Korea), ICCIT 2010 (Seoul, Korea), SEAL 2010 (Kanpur,
India), IACIS 2010 (Las Vegas, USA), CSCBCE 2010 (Ontario, Canada), NDT 2010 (Prague,
Czech Republic), and ICADIWT 2009 (London, United Kingdom).
Teaching
Experience
SQC & OR Unit, Indian Statistical Institute, Kolkata – 700108, India
Teaching Assistant July 2011 to December 2011
• TaughtProgrammingTechniquesandDataStructurestothe2011-13BatchofM.Tech. (QROR).
Awards and
Honors • Best Reviewer Award in the 7 th International Conference on Digital Information Management
(ICDIM) held in Macau, China during August 22-24, 2012.
• Travel Fellowship for Developing Nations from International Society for Computational Biology
(ISCB) for attending the 8 th ISCB Student Council Symposium 2012 (SCS8) held in Long Beach,
California, USA on July 13, 2012.
• Co-runner Up Award from NextBio for the Research Travel Grant 2012.
• Erdős number is 4 (P. Erdős → M. M. Klawe → R. E. Tarjan → T. Lengauer) since 2012.
• Travel Grant from Association for Computing Machinery (ACM) for attending the XRDS Annual
Editorial Board Meeting held at the ACM Headquarters, New York, USA on November 18, 2011.
• Travel Grant Award from Federation of European Neuroscience Societies (FENS) for attending the
SiNAPSA Neuroscience Conference held in Ljubljana, Slovenia during September 22-25, 2011.
• International Travel Grant from Indian Statistical Institute, Kolkata, India for attending the 4 th
International Conference on Pattern Recognitionand Machine Intelligence, Moscow, Russia, during
June 27-July 01, 2011.
• Third Best Paper Award for the work “Modeling the Co-expression Differentiability of Oncogenes”
in the PG category of IEEE M. V. Chauhan Students’ Paper Contest 2010 organized by IEEE India
Council.
• Received International rank 769 (within top 51%) as a team (R10 CodeTigers) in the 24 hour
online IEEEXtreme 5.0 programming competition held on October 22, 2011.
• Received International Top 500 certificate as a team (R10 CodeTigers) in the 24 hour online
IEEEXtreme 4.0 programming competition held on October 23, 2010.
• Received International rank 145 (within top 21%) as a single-member team (R10 MIU) in the 24
hour online IEEEXtreme 3.0 programming competition held on October 24, 2009.
• ReceivedNationalrank899(withintop4%)intheComputerSciencecategoryofGraduateAptitude
Test in Engineering, held on February 13, 2005.
Fellowships and
Grants Received • Senior Research Fellowship during the study of Ph.D. in Indian Statistical Institute, Kolkata, India
from August 2009 to present (on the basis of the SRF Evaluation held in July 2009).
• Junior Research Fellowship during the study of Ph.D. in Indian Statistical Institute, Kolkata, India
from August 2007to August 2009(on the basis ofthe JRF Entrance Examinationheld in May-June
2007).
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• GATE Fellowship during the study of M.E. in Jadavpur University, Kolkata, India from July 2005
to June 2007 (on the basis of the GATE (CS) percentile score 96.66 earned in March 2005).
Membership of International Society for Computational Biology (ISCB)
Professional
Bodies Student Member April 2012 to present
International Association of Engineers (IAENG)
Member (Membership No. - 102987) June 2009 to present
• SocietyMembership: IAENG SocietyofArtificialIntelligence, IAENGSocietyofBioinformatics,
IAENG Society of Computer Science and IAENG Society of Data Mining.
Association for Computing Machinery (ACM)
Student Member (Membership No. - 4705595) August 2008 to present
• SIG Membership: Student Member, ACM SIGAPP.
Institute of Electrical and Electronics Engineers (IEEE)
Student Member (Membership No. - 90462219) August 2008 to present
• Society Membership: Student Member, IEEE CIS.
Invited Talks
and Tutorials • Identifying the Transcription Start Sites of Human MicroRNAs, In Department of Molecular, Cell
and Developmental Biology, University of California, Los Angeles, California, USA, July 12, 2012.
• Regulation of MicroRNAs, In Microbiology & Immunology Department, Stanford University, Stanford,
California, USA, July 09, 2012.
• From Machine Learning to Learning Machines – A Perspective toward Personalized Medicine, In
Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA,
November 17, 2011.
• Mining Co-expression Graphs: Applications to MicroRNA Regulation and Disease Analysis, In
Faculty of Computer and Information Science, University of Ljubljana, Slovenia, September 21,
2011.
• Neural Networks for Machine Learning Problems: Hands-on – Neural Networks using MATLAB,
In Workshop on Neural Networks and Applications, Gauhati University, Guwahati, Assam, India,
December 17, 2009.
• Implementing Neural Networks using MATLAB: Hands-on – Neural Networks using MATLAB,
In Workshop on Neural Networks and Applications, Gauhati University, Guwahati, Assam, India,
December 16, 2009.
• Correlation, Co-expression and Co-functionality of Genes, In Seminar Series 2009, MIU, Indian
Statistical Institute, Kolkata, India, August 27, 2009.
• Mining the Largest N-vertexlet in a Fuzzy Scale-free Graph, In Seminar Series 2008, MIU, Indian
Statistical Institute, Kolkata, India, July 23, 2008.
Contributed
Talks • Finding Bicliques in Digraphs: Application into Viral-host Protein Interactome, In 4 th International
Conference on Pattern Recognition and Machine Intelligence (PReMI), Moscow, Russia, June 29,
2011.
• Integration of Co-expression Networks for Gene Clustering, In 7 th International Conference on
Advances in Pattern Recognition (ICAPR), Kolkata, India, February 06, 2009.
• On Heuristics in Population Initialization to Control the Time Factor of a Class of Evolutionary
Algorithms for Real-life Problems, In 1 st International Conference on Information Technology
(INTL-INFOTECH), Haldia, India, March 19, 2007.
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Attended
Programs • 23 rd International Workshop on Combinatorial Algorithms (IWOCA), Tamil Nadu, India, July
19-21, 2012.
• 20 th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Long
Beach, California, USA, July 15-17, 2012.
• 8 th ISCB Student Council Symposium 2012 (SCS8), Long Beach, California, USA, July 13, 2012.
• Educational Workshop on Affective Neuroscience, Ljubljana, Slovenia, September 24, 2011.
• SiNAPSA Neuroscience Conference (SNC), Ljubljana, Slovenia, September 22-25, 2011.
• Young Neuroscientists Forum Ljubljana, Faculty of Medicine, Ljubljana, Slovenia, September 22,
2011.
• 4 th International Conference on Pattern Recognition and Machine Intelligence (PReMI), Moscow,
Russia, June 26-June 30, 2011.
• 13 th International Conference on Rough Sets, Fuzzy Sets, Data Mining and Granular Computing
(RSFDGrC), Moscow, Russia, June 25-June 27, 2011.
• Workshop on Data-Intensive Scientific Computing Using DryadLINQ, Microsoft Research India,
Bangalore, India, December 13-14, 2010.
• 2 nd International Conference on Pattern Recognition and Machine Intelligence (PReMI), Indian
Statistical Institute, Kolkata, India, December 20-22, 2007.
• 1 st InternationalConferenceonInformationTechnology(INTL-INFOTECH), Haldia,India,March
19, 2007.
• CalcuttaConference ofIEEECalcuttaSection(CALCON), PeerlessInn, Kolkata, India, December
02-03, 2005.
Academic Visits
Abroad
Microbiology & Immunology Department, Stanford University, USA
Visiting Researcher invited by Prof. Chang-Zheng Chen July 2012
Center for Computational Biology and Bioinformatics, Columbia University, USA
Visiting Fellow invited by Prof. Dana Pe’er November 2011
Faculty of Computer and Information Science, University of Ljubljana, Slovenia
Visiting Researcher invited by Prof. Blaˇz Zupan September 2011 to October 2011
Citation ISI Web of Knowledge: 19 (h-index: 2), Scopus: 23 (h-index: 2) and Google Scholar: 27 (h-index: 3)
Statistics [excluding self-citations].
Papers in
communication
1. M. Bhattacharyyaand S. Bandyopadhyay, Unifying Metric and Non-metric Spaces for Effective
Mapping from Statistical to Biological Proximity, IEEE/ACM Transactions on Computational
Biology and Bioinformatics, under review, 2012. (Latest Impact Factor: 1.664)
2. U. Maulik, A. Mukhopadhyay, M. Bhattacharyya, S. Bandyopadhyay, R. Eils, B. Brors and L.
Kaderali, Mining Quasi-Bicliques from HIV-1–Human Protein Interaction Network: A Multiobjective
Biclustering Approach, IEEE/ACM Transactions on Computational Biology and Bioinformatics,
under major revision, 2013. (Latest Impact Factor: 1.664)
3. M. Bhattacharyya, M. Das and S. Bandyopadhyay, miRT: A Database of Transcription Start
Sites of Human MicroRNAs, Genomics, Proteomics & Bioinformatics, under major revision,
2012.
4. M. Bhattacharyya and S. Bandyopadhyay, Differentially Expressed MicroRNAs Reveal the Significant
Role of White Matter in Early Alzheimer’s Progression, Molecular Biosystems, revision
submitted, 2012. (Latest Impact Factor: 3.825)
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Papers in
Peer-reviewed
Journals
1. M. Bhattacharyya and S. Bandyopadhyay, In Silico Identification of OncomiRs in Different
Cancer Types, Journal of The Institution of Engineers (India): Series B, 93(1):15-23, 2012.
2. M. Bhattacharyya,M.BhattacharyyaandS.Bandyopadhyay, RecentDirectionsinCompressing
Next Generation Sequencing Data, Current Bioinformatics, 7(1):2-6, 2012. (Latest IF: 0.976)
3. M. Bhattacharyya, L. Feuerbach, T. Bhadra, T. Lengauer and S. Bandyopadhyay, MicroRNA
Transcription Start Site Prediction with Multi-objective Feature Selection, Statistical Applications
in Genetics and Molecular Biology, 11(1):6, 2012. (Latest IF: 1.842)
4. S. Bandyopadhyay and M. Bhattacharyya, A Biologically Inspired Measure for Co-expression
Analysis, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(4):929-942,
2011. (Latest IF: 1.664) [Cited by 1 in ISI Web of Knowledge]
5. U. Maulik, M. Bhattacharyya, A. Mukhopadhyay and S. Bandyopadhyay, Identifying the Immunodeficiency
Gateway Proteins in Human and their Involvement in MicroRNA Regulation,
Molecular Biosystems, 7(6):1842-1851, 2011. (Latest IF: 3.825) [Cited by 1 in ISI Web of
Knowledge]
6. S. Bandyopadhyay and M. Bhattacharyya, PuTmiR: A database for extracting neighboring
transcription factors of human microRNAs, BMC Bioinformatics, 11:190, 2010. (Latest IF:
3.028) [Cited by 6 in ISI Web of Knowledge]
7. M. BhattacharyyaandS.Bandyopadhyay, SolvingMaximumFuzzyCliqueProblemwithNeural
Networks and its Applications, Memetic Computing, Thematic Issue on “Adaptive Soft Computing
Techniques and Applications”, 1(4):281-290, 2009. (Latest IF: Due in 2012) [Cited by
1 in ISI Web of Knowledge]
8. S. Bandyopadhyay and M. Bhattacharyya, Mining the Largest Dense Vertexlet in a Weighted
Scale-free Graph, Fundamenta Informaticae, 96(1-2):1-25, 2009. (Latest IF: 0.522)
9. M. Bhattacharyya, S. Bandyopadhyay and U. Maulik, Non-primes are Recursively Divisible,
Acta Universitatis Apulensis, 19:147-151, 2009.
10. S. Bandyopadhyayand M. Bhattacharyya,A Novel Method of Studying the Disease Regulatory
Activities of MicroRNAs, Current Bioinformatics, 4(3):234-241, 2009. (Latest IF: 0.976)
11. S. Bandyopadhyay and M. Bhattacharyya,Analyzing miRNA co-expression networks to explore
TF-miRNA regulation, BMC Bioinformatics, 10:163, 2009. (Latest IF: 3.028) [Cited by 8 in
ISI Web of Knowledge]
12. M. Bhattacharyya and A. K. Bandyopadhyay, Comparative Study of Some Solution Methods
forTravelingSalesmanProblem UsingGenetic Algorithms, Cybernetics and Systems, 40(1):1-24,
2009. (Latest IF: 0.662) [Cited by 2 in ISI Web of Knowledge]
13. M. Bhattacharyyaand A. K. Bandyopadhyay, On single courier problem, Optimization Letters,
2(4):535-541, 2008. (Latest IF: 1.01)
14. M. Bhattacharyya and M. Bhattacharyya, A Novel Design Approach of Boolean Functions
with 2-input Universal NAND Gates using µ-graph Method, Journal of Multiple-Valued Logic
and Soft Computing, 14(1-2):177-189, 2008. (Latest IF: 0.333)
Papers in
Peer-reviewed
Book Chapters 1. M. Bhattacharyya and S. Bandyopadhyay, Analyzing Topological Properties of Protein-protein
Interaction Networks: A Perspective towards Systems Biology, Computational Intelligence and
Pattern Analysis in Biological Informatics, U. Maulik, S. Bandyopadhyay and J. T. L. Wang
(Eds.), John Wiley & Sons, Inc., pp. 349-368, 2010 (ISBN: 978-0-470-58159-9).
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Invited Articles
in
Peer-reviewed
Magazines
Papers in
Peer-reviewed
Conference
Proceedings
2. S. Bandyopadhyay and M. Bhattacharyya, A Neuro-GA Approach for the Maximum Fuzzy
Clique Problem, Advances in Neuro-Information Processing, M. Köeppen, N. Kasabov and G.
Coghill (Eds.), Springer LNCS 5506, pp. 605-612, 2009 (ISBN: 978-3-642-02489-4). [Preliminary
version presented in the 15 th International Conference on Neural Information Processing
(ICONIP), Auckland, New Zealand, November 25-28, 2008]
1. M. Bhattacharyya, Simulating a Turing Machine, XRDS: Crossroads – The ACM Magazine for
Students, 18(3), pp. 43-45, 2012.
2. M. Bhattacharyya and V. Giannikas, Behold a Pail of Milk: The Future of Banking, Currency,
and E-commerce, XRDS: Crossroads – The ACM Magazine for Students, 17(3), pp. 5, 2011.
3. M. Bhattacharyya, Courier Problems, XRDS: Crossroads – The ACM Magazine for Students,
15(4), pp. 19-21, 2009.
4. M. Bhattacharyya and S. Bandyopadhyay, Information Fusion in Bioinformatics, Technorama,
The Institution of Engineers (India), 58(T), pp. 21-25, Summer-Winter 2008-09.
1. M. Bhattacharyya and S. Bandyopadhyay, Bounds on Quasi-completeness, In Proceedings of
the 23 rd International Workshop on Combinatorial Algorithms (IWOCA), Tamil Nadu, India,
July 19-21, Springer LNCS, in press, 2012. [Acceptance: 30%]
2. M. Bhattacharyya, S. Bandyopadhyay and U. Maulik, Finding Bicliques in Digraphs: Application
into Viral-host Protein Interactome, In Proceedings of the 4 th International Conference
on Pattern Recognition and Machine Intelligence (PReMI), Moscow, Russia, June 27-July 01,
Springer LNCS 6744, pp. 412-417, 2011. [Acceptance: 46%]
3. M. Bhattacharyya and S. Bandyopadhyay, Computational Discovery of Different Categories
of Human Oncogenic MicroRNAs, In Proceedings of the 1 st IFIP International Conference on
Bioinformatics (BIOINFO), Surat, India, March 25-28, no. 94, 2010. [Acceptance: 57%]
4. M. Bhattacharyya and S. Bandyopadhyay, A Combinatorial Counterpart of the Maximum
Quasi-clique Problem, In Proceedings of the International Conference on Discrete Mathematics,
Algebra and their Applications (DIMA), Minsk, Belarus, October 19-22, pp. 129-130, 2009
(ISBN: 985-6499-61-5).
5. M. Bhattacharyya and S. Bandyopadhyay, Mining the Largest Quasi-clique in Human Protein
Interactome, In Proceedings of the International Conference on Adaptive and Intelligent Systems
(ICAIS), Klagenfurt, Austria, September 24-26, pp. 194-199, 2009 (ISBN: 978-0-7695-3827-3).
[Acceptance: 44%]
6. M. Bhattacharyya and S. Bandyopadhyay, Integration of Co-expression Networks for Gene
Clustering, In Proceedings of the 7 th International Conference on Advances in Pattern Recognition
(ICAPR), Kolkata, India, February 04-06, pp. 355-358, 2009 (ISBN: 978-0-7695-3520-3).
[Acceptance: 42%]
7. S. Bandyopadhyay and M. Bhattacharyya, A Chaotic Neuro-GA Synergism for Solving Maximum
Fuzzy Clique Problem, In Proceedings of the 15 th International Conference on Neural
Information Processing (ICONIP), Auckland, New Zealand, November 25-28, pp. 209-210,
2008. [Acceptance: 65%]
8. M. Bhattacharyya, On Heuristics in Population Initialization to Control the Time Factor of a
Class of EvolutionaryAlgorithms for Real-life Problems, A Handbook of Information Technology,
Vitasta Publishing Pvt Ltd, India, C. T. Bhunia (Ed.), Proceedings of the 1 st International
Conference on Information Technology (INTL-INFOTECH), Haldia, India, March 19-21, pp.
502-505, 2007 (ISBN: 81-89766-74-0).
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Posters in
Peer-reviewed
Conference
Proceedings
Technical
Reports
Programming
Skills
References
9. M. Bhattacharyya, A Hybrid Algorithm using Genetic Adaptive Systems and Heuristics for
Partition Problem, In Proceedings of the 1 st International Conference on Intelligent Systems
and Networks (IISN), Haryana, India, February 23-25, pp. 184-189, 2007.
1. M. Bhattacharyya M. Das and S. Bandyopadhyay, Assimilating Knowledge from Multiple Coexpression
Networks based on Disease Association of MicroRNAs, In Proceedings of the 8 th
ISCB Student Council Symposium 2012 (SCS8), Long Beach, California, USA, July 13, 2012.
2. M. Bhattacharyyaand Srinath. M, Co-expressionTogglingofMicroRNAs in Alzheimer’s Brain,
InProceedingsoftheSiNAPSANeuroscienceConference(SNC),Ljubljana,Slovenia, September
22-25, 2011.
3. D. Sengupta, R. Mitra and M. Bhattacharyya, Mining the Gene-TF-miRNA Inter-regulatory
Network, In TechVista 2011, Pune, India, January 21, 2011.
4. M. Bhattacharyya, S. Bandyopadhyay and U. Maulik, HIV-1 Regulatory Pathway in Human:
Studying the Involvement of microRNAs, In Proceedings of the 1 st Cellular NetworksConference
(CNC), Heidelberg, Germany, September 23-26, no. D2, 2010.
1. M. Bhattacharyyaand S. Bandyopadhyay, Identification of MicroRNAs Differentially Expressed
in Gray Matter and White Matter in Alzheimer’s Subjects, Technical Report No. MIU/TR-
01/2011, Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India, 2011.
2. M. Bhattacharyya and S. Bandyopadhyay, Some Investigations on Quasi-cliques, Technical
Report No. MIU/TR-01/2010, Machine Intelligence Unit, Indian Statistical Institute, Kolkata,
India, 2010.
3. S. Bandyopadhyay and M. Bhattacharyya, Mining the Largest Dense N-vertexlet in a Fuzzy
Scale-free Graph, Technical Report No. MIU/TR-03/2008, Machine Intelligence Unit, Indian
Statistical Institute, Kolkata, India, 2008.
R, C, C++, Java and MATLAB.
Dr. Sanghamitra Bandyopadhyay Dr. C. A. Murthy
Professor, Machine Intelligence Unit Professor, Machine Intelligence Unit
Indian Statistical Institute Indian Statistical Institute
203 B. T. Road, Kolkata - 700 108, India 203 B. T. Road, Kolkata - 700 108, India
E-mail: sanghami@isical.ac.in E-mail: murthy@isical.ac.in
Web: http://www.isical.ac.in/∼sanghami Web: http://www.isical.ac.in/∼murthy
Dr. Blaˇz Zupan Dr. Dr. Thomas Lengauer
Professor, Faculty of Computer and Information Sci- Professor, Computational Biology and Applied
ence
Algorithmics
University of Ljubljana Max Planck Institute for Informatics
Ljubljana, Slovenia 66123 Saarbrücken, Germany
E-mail: blaz.zupan@fri.uni-lj.si E-mail: lengauer@mpi-sb.mpg.de
Web: http://www.biolab.si/en/blaz Web: http://bioinf.mpi-inf.mpg.de/∼lengauer
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