kasimebrahim/bioatomspace_reasoning

Experiments about reasoning over various datasets such as GO and SMPDB, etc, and how they relate.

Reasoning Bio-AtomSpace Experiment

Prerequisites

1. Install the following projects

cogutil atomspace ure miner pln agi-bio

from the SingularityNET github project

https://github.com/singnet

To do that, for projects cogutil, atomspace, ure, miner, pln and agi-bio use the master branches of the opencog repositories. That is type the following:

git clone https://github.com/singnet/<PROJECT>.git
cd <PROJECT>
mkdir build
cd build
cmake ..
make -j4
sudo make install
sudo ldconfig /usr/local/lib/opencog

Usage

Prepare datasets

Download and unpack the datasets. From the root folder of that project, type the following

cd kbs
wget https://mozi.ai/datasets/gene-level-dataset_2020-04-21.tar.gz
tar xvzf gene-level-dataset_2020-04-21.tar.gz
cd ..

Run experiments

Pattern miner xp

guile -l mine-bio-as.scm

should output a scheme file

results/miner-bio-as-results-<PARAMETERS>.scm

containing mined patterns.

Turn patterns into relationships

guile -l pattern-to-relationship.scm

loads a file containing mined pattern (see previous step), and produces a file

results/subset-links.scm

containing inheritance relationships gotten by applying PLN to surprising patterns.

Preprocess KBs

guile -l preprocess-kbs.scm

which should create

results/preprocess-kbs-<PARAMETERS>.scm

Simple intensional reasoning example

guile -l intensional-reasoning-test.scm

which should create

results/intentional-reasoning-test-<PARAMETERS>.scm

Simple PLN reasoning example

A simple reasoning example to infer that some genes likely relate to aging due being intensionally similar to other genes that are known to relate to aging.

guile -l simple-pln-inference.scm

which should create

results/simple-pln-inference-<PARAMETERS>.scm

Complex (or rather less simple) PLN reasoning example

Like above but replace "relate to aging" by gene increase or decrease with aging.

guile -l complex-pln-inference.scm

which should create

results/complex-pln-inference-<PARAMETERS>.scm

More information on the broader project

https://docs.google.com/document/d/16zfY7OZtHO66mfujLdZ0-3VALXUTvxeeo4dW2ASBiNs/edit

Related work

https://gitlab.com/opencog-bio/pln_mozi