dorsal/arxiv
View SchemaAttribute Exploration of Discrete Temporal Transitions
| Authors | Johannes Wollbold |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0701009 |
| URL | https://arxiv.org/abs/q-bio/0701009 |
| Journal | In: Gely, A. et al.. Contributions to ICFCA 2007 - 5th International Conference on Formal Concept Analysis. Clermont-Ferrand 2007, 121-130 |
Abstract
Discrete temporal transitions occur in a variety of domains, but this work is mainly motivated by applications in molecular biology: explaining and analyzing observed transcriptome and proteome time series by literature and database knowledge. The starting point of a formal concept analysis model is presented. The objects of a formal context are states of the interesting entities, and the attributes are the variable properties defining the current state (e.g. observed presence or absence of proteins). Temporal transitions assign a relation to the objects, defined by deterministic or non-deterministic transition rules between sets of pre- and postconditions. This relation can be generalized to its transitive closure, i.e. states are related if one results from the other by a transition sequence of arbitrary length. The focus of the work is the adaptation of the attribute exploration algorithm to such a relational context, so that questions concerning temporal dependencies can be asked during the exploration process and be answered from the computed stem base. Results are given for the abstract example of a game and a small gene regulatory network relevant to a biomedical question.
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"abstract": "Discrete temporal transitions occur in a variety of domains, but this work is\nmainly motivated by applications in molecular biology: explaining and analyzing\nobserved transcriptome and proteome time series by literature and database\nknowledge. The starting point of a formal concept analysis model is presented.\nThe objects of a formal context are states of the interesting entities, and the\nattributes are the variable properties defining the current state (e.g.\nobserved presence or absence of proteins). Temporal transitions assign a\nrelation to the objects, defined by deterministic or non-deterministic\ntransition rules between sets of pre- and postconditions. This relation can be\ngeneralized to its transitive closure, i.e. states are related if one results\nfrom the other by a transition sequence of arbitrary length. The focus of the\nwork is the adaptation of the attribute exploration algorithm to such a\nrelational context, so that questions concerning temporal dependencies can be\nasked during the exploration process and be answered from the computed stem\nbase. Results are given for the abstract example of a game and a small gene\nregulatory network relevant to a biomedical question.",
"arxiv_id": "q-bio/0701009",
"authors": [
"Johannes Wollbold"
],
"categories": [
"q-bio.QM",
"cs.AI",
"q-bio.MN"
],
"journal_ref": "In: Gely, A. et al.. Contributions to ICFCA 2007 - 5th\n International Conference on Formal Concept Analysis. Clermont-Ferrand 2007,\n 121-130",
"title": "Attribute Exploration of Discrete Temporal Transitions",
"url": "https://arxiv.org/abs/q-bio/0701009"
},
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