hu-ner/hunflair2-experiments

Code for reproducing the evaluation results from our HunFlair2 paper

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 Central
• 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