Advertisement

Abductive Inference of Genetic Networks

  • Blaž Zupan
  • Ivan Bratko
  • Janez Demšar
  • J. Robert Beck
  • Adam Kuspa
  • Gad Shaulsky
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2101)

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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. [1]
    I. Bratko. Prolog Programming for Artificial Intelligence. Pearson Education / Addison-Wesley, Reading, MA, third edition, 2001.Google Scholar
  2. [2]
    d. L. Riddle, M. M. Swanson, and P. S. Albert. Interacting genes in nematode dauer larva formation. Nature, (290):668–671, 1981.Google Scholar
  3. [3]
    P. Flach. Simply Logical: Intelligent Reasoning by Example. John Wiley & Sons, 1994.Google Scholar
  4. [4]
    M. M. Metzstein, G. M. Stanfield, and H. R. Horvitz. Genetics of programmed cell death in C. elegans: past, present and future. Trends in Genetics, 14(10):410–416, 1998.CrossRefGoogle Scholar
  5. [5]
    G. M. Souza, A. M. da Silva, and A. Kuspa. Starvation promotes dictyostelium development by relieving PufA inhibition of PKA translation through the YakA kinase pathway. Development, 126(14):3263–3274, 1999.Google Scholar
  6. [6]
    G. M. Souza, S. Lu, and A. Kuspa. Yaka, a protein kinase, required for the transition from growth to development in Dictyostelium. Development, 125(12):2291–2302, 1998.Google Scholar
  7. [7]
    D. S. Weld and J. de Kleer. Readings in Qualitative Reasoning about Physical Systems. Morgan Kaufmann, Los Altos, CA, 1990.Google Scholar
  8. [8]
    C. Zimmer. The slime alternative. Discover, pages 86–93, May 1998.Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2001

Authors and Affiliations

  • Blaž Zupan
    • 1
    • 3
  • Ivan Bratko
    • 1
    • 2
  • Janez Demšar
    • 1
  • J. Robert Beck
    • 3
  • Adam Kuspa
    • 4
    • 5
  • Gad Shaulsky
    • 5
  1. 1.Faculty of Computer and Information ScienceUniversity of Ljubljana SloveniaSlovenia
  2. 2.Jožef Stefan InstituteLjubljanaSlovenia
  3. 3.Office of Information Technology and Dep. of Family and Community MedicineBaylor College of MedicineHoustonUSA
  4. 4.Department of Biochemistry and Molecular BiologyBaylor College of MedicineHoustonUSA
  5. 5.Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUSA

Personalised recommendations