biomed-mlps

Requirements

(Optional: Install graphviz lib (binary) on your machine for plots)

Two options:

1. use make deps if you want to use pipenv

2. • pip install scitkit-learn pandas numpy keras \ 
     tensorflow stanza nltk mathplot seaborn
     

   • python3 setup.py
     

Run tool

Two options:

1. make main

   cd biomed
   python3 main.py

Use different PubMed dataset

Two options:

1. change train.tsv file in training_data directory
2. change file path in biomed/main.py

Change configuration

Preprocessor

Possible flags:

• l: lower-case
• s: stemmer (porter)
• w: stop words
• n: nouns
• a: adjectives
• v: verbs
• u: numerals
• y: symbols

Don't s or w in combination with n, a, v, u or y

NN Model

important parameters:

• classifier: is_cancer (for binary classification) or doid (multi-class/cancer types)
• model:
  • s: simple (binary)
  • sb: simple binominal (binary)
  • ms: multi simple (multi-class)