bioasq11b-public

Public code for Macquarie University's participation at bioASQ 11b

What is this repository for?

This code implements Macquarie University's experiments and participation in BioASQ 11b.

• BioASQ

How do I get set up?

Apart from the code in this repository, you will need the following files:

• BioASQ-training11b/training11b.json - available from BioASQ

Reading

If you use this code, please cite the following paper:

TBA

Examples of runs

The following runs can be made with the files available in this repository:

  python GPTZero.py -t BioASQ-task11bPhaseB-testset1.json

  python GPTWithContext.py -t BioASQ-task11bPhaseB-testset1.json

The following run will also require the file BioASQ-training11b/training11b.json:

  python GPTNoContext.py -t BioASQ-task11bPhaseB-testset1.json

The following runs will require the output of an existing summariser. We used the summariser available in https://github.com/dmollaaliod/bioasq10b-public and we have included its output for your convenience (TODO). The output will need to be saved in the file MQ5-DistilBERT.json:

python GPTBioASQ10bContext.py -t BioASQ-task11bPhaseB-testset4.json -c MQ5-DistilBERT.json

python GPTBioASQ10bFewShotContext.py -t BioASQ-task11bPhaseB-testset4.json -c MQ5-DistilBERT.json

(GPTBioASQ10bFewShotContext.py also requires Task10BGoldenEnriched/10B2_golden.json and the output of a summariser on that file; edit lines 14 and 15 accordingly. Again, we used https://github.com/dmollaaliod/bioasq10b-public and we have included its output for your convenience - TODO)

Who do I talk to?

Diego Molla: diego.molla-aliod@mq.edu.au