Hi, my name is Yifeng Li. This PGM toolbox accommodates my current implementations of popular probabilistic graphical models, particularly for bioinformatics research, for example the reconstruction of genetic regulatory networks (GRN). My current implementations include BDeu score, BIC score, a high-order dynamic Bayesian Network (HO-DBN) learning algorithm. Additionally, I also implemented some concepts in qualitative probabilistic networks, including the generalized influences, additive synergies, and influence score.
You can find a tutorial and the source codes at Tutorial and Source Code.
Some of my future works are listed below.
1. Implement Bayesian network and dynamic Bayesian network learning algorithms for continuous variables.
2. Implement Bayesian network and dynamic Bayesian network based prediction.
3. Implement a predictive model based on hidden Markov model (HMM).
Citation:
Yifeng Li, "Probabilistic graphical models and Its application in reconstructing gene regulatory networks", in "Sparse Machine Learning Models in Bioinformatics", PhD Thesis, School of Computer Science, University of Windsor, 2013. Thesis Available at http://scholar.uwindsor.ca/etd/5023/
Yifeng Li and Alioune Ngom, "The max-min high-order dynamic Bayesian network learning for identifying gene regulatory networks from time-series microarray data," IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB/SSCI), Singapore, Apr. 2013, pp.83-90.
You may be also interested in my
Non-Negative Matrix Factorization toolbox at https://sites.google.com/site/nmftool,
Sparse Representation toolbox at https://sites.google.com/site/sparsereptool,
Regularized Linear Models and Kernels toolbox: https://sites.google.com/site/rlmktool,
Probabilistic Graphical Models toolbox at https://sites.google.com/site/pgmtool,
Spectral Clustering toolbox at https://sites.google.com/site/speclust.
My contact information:
Yifeng Li
https://sites.google.com/site/yifengliresearch
Centre for Molecular Medicine and Therapeutics
Department of Medical Genetics
University of British Columbia
Vancouver, BC, Canada
Email: yifeng.li.cn{at}gmail.com and li11112c{at}uwindsor.ca
You can also contact my previous supervisor: Dr. Alioune Ngom.