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Abductive Inference of Genetic Networks

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Artificial Intelligence in Medicine (AIME 2001)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 2101))

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Abstract

GenePath is an automated system for reasoning on genetic networks, wherein a set of genes have various influences on one another and on a biological outcome. It acts on a set of experiments in which genes are knocked out or overexpressed, and the outcome of interest is evaluated. Implemented in Prolog, GenePath uses abductive inference to elucidate network constraints based on prior knowledge and experimental results. Two uses of the system are demonstrated: synthesis of a consistent network from abduced constraints, and qualitative reasoning-based approach that generates a set of networks consistent with the data. In practice, illustrated by an example using Dictyostelium aggregation, a combination of constraint satisfaction and qualitative reasoning produces a small set of plausible networks.

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Author information

Authors and Affiliations

  1. Faculty of Computer and Information Science, University of Ljubljana Slovenia, Slovenia

    Blaž Zupan, Ivan Bratko & Janez Demšar

  2. Jožef Stefan Institute, Ljubljana, Slovenia

    Ivan Bratko

  3. Office of Information Technology and Dep. of Family and Community Medicine, Baylor College of Medicine, Houston, TX, USA

    Blaž Zupan & J. Robert Beck

  4. Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA

    Adam Kuspa

  5. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA

    Adam Kuspa & Gad Shaulsky

Authors
  1. Blaž Zupan
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  2. Ivan Bratko
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  3. Janez Demšar
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  4. J. Robert Beck
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  5. Adam Kuspa
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  6. Gad Shaulsky
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Editor information

Editors and Affiliations

  1. Department of Computer Science, University of Pavia, Via Ferrata, 1, 27100, Pavia, Italy

    Silvana Quaglini

  2. Departamento de Informática Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2825-114, Caparica, Portugal

    Pedro Barahona

  3. Department of Medical Informatics and Image Analysis, Aalborg University, Fredrik Bajersv ej 7D, 9220, AlborgØst, Denmark

    Steen Andreassen

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© 2001 Springer-Verlag Berlin Heidelberg

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Zupan, B., Bratko, I., Demšar, J., Beck, J.R., Kuspa, A., Shaulsky, G. (2001). Abductive Inference of Genetic Networks. In: Quaglini, S., Barahona, P., Andreassen, S. (eds) Artificial Intelligence in Medicine. AIME 2001. Lecture Notes in Computer Science(), vol 2101. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-48229-6_42

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  • DOI: https://doi.org/10.1007/3-540-48229-6_42

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-42294-5

  • Online ISBN: 978-3-540-48229-1

  • eBook Packages: Springer Book Archive

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