Koeppl, Heinz ; Petrov, Tatjana (2024)
Stochastic Semantics of Signaling as a Composition of Agent-view Automata.
In: Electronic Notes in Theoretical Computer Science, 2011, 272
doi: 10.26083/tuprints-00026721
Artikel, Zweitveröffentlichung, Verlagsversion
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Kurzbeschreibung (Abstract)
In this paper we present a formalism based on stochastic automata to describe the stochastic dynamics of signal transduction networks that are specified by rule-sets. Our formalism gives a modular description of the underlying stochastic process, in the sense that it is a composition of smaller units, agent-views. The view of an agent is an automaton that identifies all local modification changes of that agent (internal state modifications, binding and unbinding), but also those of interacting agents, which are tested within the same rule. We show how to represent the generator matrix of the underlying Markov process of the whole rule-set as Kronecker sums of the rate matrices belonging to individual view-automata. In the absence of birth the automata are finite, since the number of different contexts in which one agent can appear in a rule-set is finite. We illustrate the framework by an example that is related to cellular signaling events.
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2024 |
| Autor(en): | Koeppl, Heinz ; Petrov, Tatjana |
| Art des Eintrags: | Zweitveröffentlichung |
| Titel: | Stochastic Semantics of Signaling as a Composition of Agent-view Automata |
| Sprache: | Englisch |
| Publikationsjahr: | 30 April 2024 |
| Ort: | Darmstadt |
| Publikationsdatum der Erstveröffentlichung: | 4 Mai 2011 |
| Ort der Erstveröffentlichung: | Amsterdam |
| Verlag: | Elsevier |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | Electronic Notes in Theoretical Computer Science |
| Jahrgang/Volume einer Zeitschrift: | 272 |
| DOI: | 10.26083/tuprints-00026721 |
| URL / URN: | https://tuprints.ulb.tu-darmstadt.de/26721 |
| Zugehörige Links: | |
| Herkunft: | Zweitveröffentlichungsservice |
| Kurzbeschreibung (Abstract): | In this paper we present a formalism based on stochastic automata to describe the stochastic dynamics of signal transduction networks that are specified by rule-sets. Our formalism gives a modular description of the underlying stochastic process, in the sense that it is a composition of smaller units, agent-views. The view of an agent is an automaton that identifies all local modification changes of that agent (internal state modifications, binding and unbinding), but also those of interacting agents, which are tested within the same rule. We show how to represent the generator matrix of the underlying Markov process of the whole rule-set as Kronecker sums of the rate matrices belonging to individual view-automata. In the absence of birth the automata are finite, since the number of different contexts in which one agent can appear in a rule-set is finite. We illustrate the framework by an example that is related to cellular signaling events. |
| Freie Schlagworte: | Cell signaling, Continuous-time Markov chain, Stochastic automata composition |
| Status: | Verlagsversion |
| URN: | urn:nbn:de:tuda-tuprints-267211 |
| Sachgruppe der Dewey Dezimalklassifikatin (DDC): | 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie 600 Technik, Medizin, angewandte Wissenschaften > 621.3 Elektrotechnik, Elektronik |
| Hinterlegungsdatum: | 30 Apr 2024 09:13 |
| Letzte Änderung: | 13 Mai 2024 09:50 |
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| Suche nach Titel in: | TUfind oder in Google |
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- Stochastic Semantics of Signaling as a Composition of Agent-view Automata. (deposited 30 Apr 2024 09:13) [Gegenwärtig angezeigt]
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