Causal Explorer 1.5
MATLAB library for computational causal discovery and variable selection.
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Software
Software tools, research code, and featured resources from mens X machina.
Software & Research Code
Tools and code releases listed on the group’s September 2024 software page. Links point to their original destinations; version numbers reflect that listing.
SCENERY
A web application for network reconstruction, statistical analysis, and visualization of cytometry (single-cell) data.
View software →Gene–gene interaction reconstruction
Code for “A comparative evaluation of data-merging and meta-analysis methods for reconstructing gene-gene interactions”.
View software →omicsNPC
Code for applying the Non-Parametric Combination methodology to integrative analysis of heterogeneous omics data.
View software →Bayesian Networks with Informative, Causal and Associative Priors
MATLAB implementation for “Scoring and Searching over Bayesian Networks with Informative, Causal and Associative Priors”.
Download ZIP →MXM package 1.4.2
R package for feature selection, statistically equivalent predictive subsets, Bayesian networks, and conditional independence testing.
View software →Causally Interpreting Directed Edges in Maximal Ancestral Graphs
MATLAB experimental code for “Tools and Algorithms for Causally Interpreting Directed Edges in Maximal Ancestral Graphs”.
Download ZIP →Causal Prior Knowledge as Path-Constraints
MATLAB experimental code for “Incorporating Causal Prior Knowledge as Path-Constraints in Bayesian Networks and Maximal Ancestral Graphs”.
Download ZIP →Integrative Causal Analysis of Heterogeneous Datasets and Studies
MATLAB experimental code for “Towards Integrative Causal Analysis of Heterogeneous Datasets and Studies”.
Download ZIP →Learning Causal Structure From Overlapping Variable Sets
MATLAB experimental code accompanying the AISTATS 2010 publication.
Download ZIP →GEMS — Gene Expression Model Selector
Automated cancer diagnosis and biomarker discovery from microarray gene expression data, developed at Vanderbilt University in collaboration with Ioannis Tsamardinos.
View software →Structure-based Variable Selection for Survival Data
MATLAB and R experimental code accompanying the survival-data variable selection paper.
Download ZIP →Mens X Machina Commons Toolbox
Common MATLAB functions used by other toolboxes from the Mens X Machina group.
View software →Mens X Machina Probabilistic Graphical Model Toolbox
MATLAB tools for Bayesian networks and probabilistic graphical models, including local and skeleton learning using MMPC.
View software →Featured Resources
BioDataome
Creation of a large database of uniformly preprocessed and disease-annotated genomic and epigenomic data. Currently includes 7,345 datasets spanning 847 diseases, enabling large-scale meta-analysis.
View resource →HUNT — Cancer-Biomarkers in HUNT
An international discovery study seeking the earliest molecular signals of lung cancer and mesothelioma in blood serum. The consortium brings together five universities in five countries, aiming to develop a blood test for screening smokers and people exposed to asbestos.
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