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Recent Publications
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Manindra Agrawal, S. Akshay, Blaise Genest and P.S. Thiagarajan:
Approximate Verification of the Symbolic Dynamics of Markov Chains.
In Proc. of the 27th ACM/IEEE Symposium on Logic in Computer
Science (LICS 2012), Dubrovnik, Croatia (2012).
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Bing Liu, Andrei Hagiescu, Sucheendra K. Palaniappan, Bipasa Chattopadhyay, Zheng Cui, Weng Fai Wong and P.S. Thiagarajan:
Approximate Probabilistic Analysis of Biopathway Dynamics.
Bioinformatics, doi: 10.1093/bioinformatics/bts166, (2012).
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Sucheendra K. Palaniappan, S. Akshay, Bing Liu, Blaise Genest
and P.S. Thiagarajan:
A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Networks with a Biopathway Application.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (Expanded and invited version of the CMSB 2011 conference paper) (2012).
Pre-print: http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.60
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Bing Liu and P.S. Thiagarajan:
Modeling and Analysis of Biopathways Dynamics.
Journal of Bioinformatics and Computational Biology, Vol. 10(4), pp. 1231001 (2012).
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P.S. Thiagarajan and Shaofa Yang:
Modular Discrete Time Approximations of Distributed Hybrid Automata.
Theoretical Computer Science, Vol. 429, pp. 292-304 (2012) .
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Sucheendra K. Palaniappan, S. Akshay, Blaise Genest
and P.S. Thiagarajan:
A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Network models of Biopathways.
In Proc. of the 9th Conference on Computational Methods in Systems Biology (CMSB 2011), Paris, France (2011).
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Bing Liu, Jing Zhang, Pei Yi Tan, David Hsu, Anna M. Blom, Benjamin Leong, Sunil Sethi, Bow Ho, Jeak Ling Ding, and P. S. Thiagarajan:
A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System.
PLoS Computational Biology, Vol. 7(1), pp. e1001059 (2011).
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Geoffrey Koh, David Hsu, and P. S. Thiagarajan:
Component-based construction of bio-pathway models: The parameter estimation problem.
Theoretical Computer Science (Special Issue on Foundations of Formal Reconstruction of Biochemical Networks), Vol. 412(26), pp. 2840-2853 (2011).
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Bing Liu, David Hsu, and P. S. Thiagarajan:
Probabilistic Approximations of ODEs based Bio-Pathway Dynamics.
Theoretical Computer Science (Selected Papers from the 7th International Conference on Computational Methods in Systems Biology), Vol. 412(21), pp. 2188-2206 (2011).
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P. S. Thiagarajan and Shaofa Yang:
Succinct Discrete Time Approximations of Distributed Hybrid Automata.
In Proc. of the 13th International Conference on Hybrid Systems: Computation and Control (HSCC 2010), Stockholm, Sweden (2010).
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Geoffrey Koh, David Hsu and P.S. Thiagarajan:
Incremental Signaling Pathway Modeling by Data Integration.
In Proc. of the 14th International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisbon, Portugal (2010).
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Philippe Darondeau, Blaise Genest, P.S. Thiagarajan and Shaofa Yang:
Quasi-Static Scheduling of Communicating Tasks.
Journal of Information and Computation, Vol. 208(10) pp. 1154-1168 (2010).
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Thomas Gazagnaire, Blaise Genest, Loic Helouet, P.S. Thiagarajan and Shaofa Yang:
Causal Message Sequence Charts.
Theoretical Computer Science, Vol. 410(41), pp. 4094-4110 (2009).
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Bing Liu, P.S. Thiagarajan and David Hsu:
Probabilistic Approximations of Signaling
Pathway Dynamics.
In Proc. of the 7th Conference on Computational Methods in Systems Biology (CMSB 2009), Bologna, Italy (2009).
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Ankit Goel, Abhik Roychoudhury and P.S. Thiagarajan:
Interacting Process Classes.
ACM Transactions on Software Engineering and Methodology, Vol. 18(4), pp. 1-47 (2009).
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Linh Thi Xuan Phan, Samarjit Chakraborty and P.S. Thiagarajan:
A Multi-mode Real Time Calculus.
In Proc. of the 29th IEEE Real Time Systems Symposium (RTSS 2008),
Tucson, Arizona, USA (2008).
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Linh Thi Xuan Phan, Lothar Thiele, Samarjit Chakraborty and P.S. Thiagarajan:
Composing Functional and State-based Performance Modes for Analyzing Heterogeneous
Real-Time Systems.
In Proc. of the 28th IEEE Real Time Systems Symposium (RTSS 2007),
Tucson, Arizona, USA (2007).
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Kathy Dang Nguyes, P S Thiagarajan and Weng-Fai Wong:
A UML-based Design Framework for Time-triggered Applications.
In Proc. of the 28th IEEE Real Time Systems Symposium (RTSS 2007),
Tucson, Arizona, USA (2007).
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Thomas Gazagnaire, Blaise Genest, Loic Helouet, P S Thiagarajan and Shaofa Yang:
Causal Message Sequence Charts.
In Proc. of the 18th International Conference on Concurrency Theory (CONCUR 2007),
Springer Lecture Notes in Computer Science, Vol, 4703, (2007).
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Geoffrey Koh, Lisa Tucker-Kellog, David Hsu and P S Thiagarajan:
Composing Globally Consistent Pathway Parameter Estimates through Belief Propagation.
In Proc. of the 7th Workshop on Algorithms in Bioinformatics (WABI 2007), Springer Lecture Notes in
Bioinformatics, Vol, 4645, (2007).
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Geoffrey Koh, Huey Fern Carol Teong, Marie-Veronique Clement, David Hsu and P S Thiagarajan:
A Decompositional Approach to Parameter Estimation in Pathway Modeling:
A Case Study of the Akt and MAPK Pathways and their Crosstalk.
In Proc. of the 14th International Conference on Intelligent Systems
for Molecular Biology (ISMB 2006), Forteliza, Brazil (2006).
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Ankit Goel, Sun Meng, Abhik Roychoudhury and P S Thiagarajan:
Interacting Process Classes. In Proc. of the 28th International
Conference on Software Engineering (ICSE 2006), Shangai, China, IEEE Press.
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Manindra Agrawal, Frank Stephan, P. S. Thiagarajan and Shaofa Yang:
Behavioural Approximations for Restricted Linear Differential Hybrid Automata.
In Proc. of the 9th International Workshop on Hybrid Systems:
Computation and Control, LNCS 3927, pages 4-18, Springer, 2006.
Edited by J. P. Hespanha and A. Tiwari.
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P. Madhusudan, P. S. Thiagarajan and Shaofa Yang:
The MSO Theory of Connectedly Communicating Processes.
In Proc. of the 25th Conference on Foundations of Software Technology
and Theoretical Computer Science, LNCS 3821, pages 201-212, Springer, 2005.
Edited by R. Ramanujam, S. Sen.
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Manindra Agrawal and P S Thiagarajan:
The Discrete Time Behaviour of Lazy Linear Hybrid Automata.
In Proc. of 8th International HSCC Conference,
Edited by M. Morari and L. Thiele, pp. 55-69. Lecture Notes in
Computer Science, 3414. Springer, 2005. (Paper presented at Hybrid
systems: Computation and Control, 9-11 March 2005, ETH, Zurich, Switzerland.
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Chakraborty, S, P S Thiagarajan and T X L Phan:
Event Count Automata: A State-based Model for Stream Processing Systems.
In Proc. of the 26th IEEE Real-Time Systems Symposium (RTSS), Florida, Miami, Dec 2005.
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Nguyen, K D, Z Sun, P S Thiagarajan and W F Wong: Model-Driven SoC
Design: The UML-SystemC Bridge. In UML for SOC Design, edited by G.
Martin and W. Mueller. Springer, October 2005.
J. G. Henriksen, M. Mukund, K. Narayan Kumar, M. Sohoni and P.S. Thiagarajan:
A Theory of Regular MSC Languages. Information and Computation,
Vol. 202(1), pp. 1-38 (2005)
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Roychoudhury, A, P S Thiagarajan, T.A. Tran and V Zvereva:
Automatic Generation of Protocol Converters from Scenario-based Specifications.
Proc. 25th IEEE International Real-time Systems Symposium (RTSS 2004).
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Nguyen, K.D, Z Sun, P S Thiagarajan and W F Wong:
Model-driven SOC Design via Executable UML to SystemC.
Proc. 25th IEEE International Real-time Systems Symposium (RTSS 2004).
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Krcal, P, L Mokrushin, P S Thiagarajan and W Yi:
Timed vs. Time-Triggered Automata. Proc. of CONCUR'04, LNCS 3170, pp. 340-354, Springer, 2004.
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M. Agrawal and P.S. Thiagarajan:
Lazy Rectangular Hybrid Automata. Proc. of 7th International Workshop on Hybrid Systems:
Computation and Control, Springer lecture Notes in Computer Science 2003.
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M. Mukund, K Narayan Kumar and P.S. Thiagarajan:
Netcharts: Bridging the gap between HMSCs and executable specifications.
Proc. of the 14th International Conference on Concurrency Theory (CONCUR'03),
Springer Lecture Notes in Computer Science 2761, Springer-Verlag, 2003.
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A. Roychoudhury and P.S. Thiagarajan: Communicating Transaction Processes.
Proc. of the 3rd IEEE International Conference on Application of Concurrency in System Design (ACSD'03),
IEEE Press, 2003.
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D. Harel and P.S. Thiagarajan: Message Sequence Charts,
In: UML for Real: Design of Embedded Real-time Systems, Eds.: Luciano Lavagno, Grant Martin
and Bran Selic, Kluwer Academic Publishers, 2003.
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