HunFlair2

This repository contains the source code to reproduce the experiments conducted in

Setup

Setup environment and install necessary packages / models:

Reproduce paper results

To reproduce the main result from the paper simply run:

python evaluate.py

This will load the pre-computed predictions of several tools along with the gold labels.

Corpora and tools

Results are computed on the following corpora:

• MedMentions
• BioID
• tmVar (v3)

We obtiained the prediction and stored them in the pubtator format in the annotations folder for the following tools:

• PubTator
• BERN2
• SciSpacy
• bent

See the paper for more details.

Run HunFlair2

You can obtain the predictions from our HunFlair2 tool with the following command:

python predict_hunflair2.py \
    --input ./annotations/raw/bioid_text.txt \
    --output ./annotations/hunflair2/bioid_text.txt \
    --entity_types species

This will load a file in the PubTator formatand store the predictions into the --output file