Formal Analysis of Uncertain Continuous Markov Chains in Systems Biology

Krishnendu Ghosh; Caroline Goodman

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Paper

Formal Analysis of Uncertain Continuous Markov Chains in Systems Biology

Topics: Formal Verification and Validation of Biological Systems; Model Design and Evaluation; Simulation and Modeling; Systems Biology and Computational Network Biology

In Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS, 519-526, 2024 , Rome, Italy

Authors: Krishnendu Ghosh and Caroline Goodman

Affiliation: Department of Computer Science, College of Charleston, SC, U.S.A.

Keyword(s): Probabilistic Model Checking, Uncertain Continuous-Time Markov Chain, Computational Feasibility, Tractable, Phylogenetic Tree.

Abstract: Data dependent abstraction for continuous-time Markov chain is often challenging given the incompleteness and imprecision of data. Uncertainty in the environment is modeled in the form of uncertain continuous-time Markov chain. In this work, a tractable model checking methodology, stochastic partial model set checking is formalized by approximation of the uncertain continuous-time Markov chain. The methodology was applied in querying to infer on a phylogenetic tree, constructed under uncertainty. Queries were posed on the formalism using continuous stochastic logic formula. Experimental results demonstrate the computational feasibility of the model.

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Paper citation in several formats:

Ghosh, K. and Goodman, C. (2024). Formal Analysis of Uncertain Continuous Markov Chains in Systems Biology. In Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOINFORMATICS; ISBN 978-989-758-688-0; ISSN 2184-4305, SciTePress, pages 519-526. DOI: 10.5220/0012466000003657

@conference{bioinformatics24,
author={Krishnendu Ghosh and Caroline Goodman},
title={Formal Analysis of Uncertain Continuous Markov Chains in Systems Biology},
booktitle={Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOINFORMATICS},
year={2024},
pages={519-526},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0012466000003657},
isbn={978-989-758-688-0},
issn={2184-4305},
}

TY - CONF

JO - Proceedings of the 17th International Joint Conference on Biomedical Engineering Systems and Technologies - BIOINFORMATICS
TI - Formal Analysis of Uncertain Continuous Markov Chains in Systems Biology
SN - 978-989-758-688-0
IS - 2184-4305
AU - Ghosh, K.
AU - Goodman, C.
PY - 2024
SP - 519
EP - 526
DO - 10.5220/0012466000003657
PB - SciTePress