Biclustering Gene Expressions Using Factor Graphs and the Max-Sum Algorithm

Denitto, Matteo; Farinelli, Alessandro; Bicego, Manuele

Biclustering Gene Expressions Using Factor Graphs and the Max-Sum Algorithm

Matteo Denitto, Alessandro Farinelli, Manuele Bicego

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Proceedings of the Twenty-Fourth International Joint Conference on Artificial Intelligence. Main Track. Pages 925-930.

Abstract

Biclustering is an intrinsically challenging and highly complex problem, particularly studied in the biology field, where the goal is to simultaneously cluster genes and samples of an expression data matrix. In this paper we present a novel approach to gene expression biclustering by providing a binary Factor Graph formulation to such problem. In more detail, we reformulate biclustering as a sequential search for single biclusters and use an efficient optimization procedure based on the Max Sum algorithm. Such approach, drastically alleviates the scaling issues of previous approaches for biclustering based on Factor Graphs obtaining significantly more accurate results on synthetic datasets. A further analysis on two real-world datasets confirms the potentials of the proposed methodology when compared to alternative state of the art methods.

Matteo Denitto, Alessandro Farinelli, and Manuele Bicego. 2015. Biclustering Gene Expressions Using Factor Graphs and the Max-Sum Algorithm. In Proceedings of the Twenty-Fourth International Joint Conference on Artificial Intelligence, IJCAI-15. IJCAI, 925–930. https://ijcai.org/proceedings/2015/135

@inproceedings{ijcai2015p135,
  title     = {Biclustering Gene Expressions Using Factor Graphs and the Max-Sum Algorithm},
  author    = {Denitto, Matteo and Farinelli, Alessandro and Bicego, Manuele},
  booktitle = {Proceedings of the Twenty-Fourth International Joint Conference on
               Artificial Intelligence, {IJCAI-15}},
  publisher = {International Joint Conferences on Artificial Intelligence},
  editor    = {Qiang Yang and Michael Wooldridge},
  pages     = {925--930},
  year      = {2015},
  month     = {7},
  note      = {Main Track},
  url       = {https://ijcai.org/proceedings/2015/135},
}

TY  - CPAPER
TI  - Biclustering Gene Expressions Using Factor Graphs and the Max-Sum Algorithm
AU  - Denitto, Matteo
AU  - Farinelli, Alessandro
AU  - Bicego, Manuele
T2  - Proceedings of the Twenty-Fourth International Joint Conference on Artificial Intelligence, IJCAI-15
PB  - International Joint Conferences on Artificial Intelligence
PY  - 2015
SP  - 925
EP  - 930
UR  - https://ijcai.org/proceedings/2015/135
ER  -