An Introduction to Variational Methods for Graphical Models
Machine Learning
DNA segmentation as a model selection process
RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
Learning Dynamic Bayesian Networks
Adaptive Processing of Sequences and Data Structures, International Summer School on Neural Networks, "E.R. Caianiello"-Tutorial Lectures
Pattern Classification (2nd Edition)
Pattern Classification (2nd Edition)
Joint discovery of haplotype blocks and complex trait associations from SNP sequences
UAI '04 Proceedings of the 20th conference on Uncertainty in artificial intelligence
CVPR '06 Proceedings of the 2006 IEEE Computer Society Conference on Computer Vision and Pattern Recognition - Volume 1
A hidden markov technique for haplotype reconstruction
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
Paper: Modeling by shortest data description
Automatica (Journal of IFAC)
Guest editorial: Computational intelligence and machine learning in bioinformatics
Artificial Intelligence in Medicine
International Journal of Data Mining and Bioinformatics
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Objective: In the last decade, haplotype reconstruction in unrelated individuals and haplotype block discovery have riveted the attention of computer scientists due to the involved strong computational aspects. Such tasks are usually addressed separately, but recently, statistical techniques have permitted them to be solved jointly. Following this trend we propose a generative model that permits researchers to solve the two problems jointly. Method: The model inference is based on variational learning, which permits one to estimate quickly the model parameters while remaining robust even to local minima. The model parameters are then used to segment genotypes into blocks by thresholding a quantitative measure of boundary presence. Results: Experiments on real data are presented, and state-of-the-art systems for haplotype reconstruction and strategies for block estimation are considered as comparison. Conclusions: The proposed method can be used for a fast and reliable estimation of haplotype frequencies and the relative block structure. Moreover, the method can be easily used as part of a more complex system. The threshold used for block discovery can be related to the quality-of-fit reached in the model learning, resulting in an unsupervised strategy for block estimation.