Breast Cancer PLN Experiment

This repo contains the code for inference experiments using Probabilistic Logic Networks, PLN, on breast cancer dataset. It is based on the work in singnet/cancer

Prerequisites

• AtomSpace - we use the AtomSpace to store the patient, gene expression, biological process etc in hypergraph form.

• PLN - used for inference, deducing patient, GO biological process relationships and the intentional similarity between pathways and biological processes

• Unified Rule Engine - This is an indirect dependency used by PLN.

• Knowledge Import scripts - used to convert Patient gene expression table to Atomese

Building & Installation

1. Clone the repo
2. Run autoreconf -vif inside the project directory
3. Run the following in the project directory:

   $ mdkir build && cd build
   $ ../configure
   $ make && makie install

Datasets

Note: All the datasets are assumed to be in kbs directory under the root directory of the project. Also create results directory to save the results

• GO Files: GO, GO_annotation

• Pathway files: Reactome , Reactome_annotation

• Patient gene expressions

Running the code

1. Similarity Experiment

• Start Guile and run the following

    scheme@(guile-user)> (use-modules (opencog) (opencog exec)
    (opencog bioscience) (opencog ure) (opencog pln) 
    (opencog logger))

    scheme@(guile-user)> (use-modules 
    (pln-bio preprocess) (pln-bio bio-utils) 
    (pln-bio intensional-similarity))

    scheme@(guile-user)> (go-pathway-intentional-similarity (list "kbs/GO_2020-10-20.scm" "kbs/GO_annotation_2020-10-20.scm"
 "kbs/reactome_2020-10-20.scm" "kbs/NCBI2Reactome_PE_Pathway.txt_2020-10-20.scms"))

2. Patient Biological process deduction

• Start Guile and run the following

    scheme@(guile-user)> (use-modules (opencog) (opencog exec)
    (opencog bioscience) (opencog ure) (opencog pln) 
    (opencog logger))

    scheme@(guile-user)> (use-modules (pln-bio bio-utils) (pln-bio expr) (pln-bio bp-deduction))

    ;;set #t for overexpression #f for underexpression
    scheme@(guile-user)> (run-deduction-expr #t)