/openbiolink-2021-symbolic-baseline

Primary LanguageJava

Installation

Build AnyBURL (License: https://web.informatik.uni-mannheim.de/AnyBURL/)

  1. Create folder build in folder AnyBURL-RE
  2. Compile with javac de/unima/ki/anyburl/*.java -d build
  3. Package with jar cfv AnyBURL-RE.jar -C build .

Build SAFRAN

  1. Create directory build in folder SAFRAN
  2. Download and extract boost 1.76.0 to folder SAFRAN
    1. Windows: https://boostorg.jfrog.io/artifactory/main/release/1.76.0/source/boost_1_76_0.zip
    2. Unix: https://boostorg.jfrog.io/artifactory/main/release/1.76.0/source/boost_1_76_0.tar.gz
  3. Have cmake installed (> 9.6.0)
  4. Run cmake ../ from newely created folder build
  5. Run make

Install openbiolink

pip install torch openbiolink

Training

Run from project root:

python3 train.py

Evaluation

For maximum (default AnyBURL) aggregation approach run:

python3 save_test_submission.py ./dataset/prediction_max

For Non-redundant Noisy-OR (SAFRAN) aggregation approach run:

python3 save_test_submission.py ./dataset/prediction_nrno