Software

This is a legacy page, to be updated.

Highlighted software

Released packages (stable)

Bayesian Multi-View Tensor Factorization (R)
BMTMKL - Bayesian Multitask Multiple Kernel Learning (Matlab and R)
CCAGFA - Bayesian canonical correlation analysis and group factor analysis (R)
dmt - Dependency modeling toolkit. A unified framework for probabilistic dependency models, including probabilistic versions of PCA, factor analysis and CCA and their regularized variants. (R/CRAN; Leo Lahti and Olli-Pekka Huovilainen)
dredviz - dimensionality reduction for visualization. Implements the state of the art Neighbor Retrieval Visualizer (NeRV) method and local MDS.
GFA: Group factor analysis (R)
GPstuff - Gaussian process models for Bayesian analysis (Matlab/Octave)
KBMF - Kernelized Bayesian Matrix Factorization (Matlab and R)
MCMC Diagnostics toolbox (Matlab)
NetResponse - Functional network analysis for modeling context-specific responses in interaction networks (R/BioConductor, Matlab; Leo Lahti, Olli-Pekka Huovilainen, António Gusmão and Juuso Parkkinen)
pint - Genomic data integration for multi-source observations (R/BioConductor; Olli-Pekka Huovilainen and Leo Lahti)
RPA - Probe reliability and differential gene expression analysis (R/BioConductor; Leo Lahti)

Development versions (useful and functioning alpha/beta)

cwKBMF-Kernelized Bayesian Matrix Factorization with Component-Wise Multiple Kernel Learning (Matlab)
daSAr - Dependency analysis of survival associated regions (R)
DCA - discriminative component analysis (Python/C, beta-version)
drCCA data fusion package (R, BMC Bioinformatics)
ELFI - Engine for Likelihood-Free Inference
GFAtoxgen - Cross-organism toxicogenomics with group factor analysis (R)
GroupBN - Finding Bayesian network structures for variables groups (Matlab)
LinearTimeNeRV - fast dimensionality reduction for visualization (C++, MLSP2012)
ICMg - Interaction component models for gene modules (R; Juuso Parkkinen, included in NetResponse as well)
Multiple Output Regression with Latent Noise (R)
multiWayCCA - Multivariate multi-way analysis of multi-source data (R, ISMB'10)
Multi-tensor factorization (R)
NE - Neighbor Embedding (Matlab, ICML'13)
PeakANOVA - Stronger findings from mass spectral data through multi-peak modeling (R)
ProbCMap - Probabilistic drug connectivity mapping software (R)
Probabilistic retrieval and visualization of biologically relevant microarray experiments (ISMB'09, supplementary material)
SAT-NeRV - SAT-based Neighborhood Embedding Retrieval for Visualization (supplementary material)
Targeted Retrieval of Gene Expression Measurements Using Regulatory Models (R, MLSB'12)
Treebic - Hierarchical biclustering (C++, RECOMB'10)
vbmcca - Variational Bayesian mixture of robust CCAs (MATLAB, ECML'10)

Other software from the former Bayes group of the Department of Biomedical Engineering and Computational Science