Code and data to study deep active learning for biomedical relation extraction (bioRE), article can be found here.
Data sets can be found in the data folder.
Scripts to reproduce the results of the article can be found in the launchers folder.
The experiments were conducted on a server with Ubuntu Desktop 20.04.5 LTS (GNU/Linux 5.15.0-56-generic x86_64) operating system, Nvidia driver 470.161.03, CUDA version 11.4, with 32GB RAM on 2 Asus GTX 1080 TI GPUs. You may want to modify the config_accelerate.yaml file to fit your hardware.
An environment to run the experiments can be built with the environment_pytorch.yaml file using conda :
conda env create -f environment_pytorch.yaml
and then activated with :
conda activate pytorch
This project was realised at the Interuniversity Institute of Bioinformatics in Brussels (IB2), a collaborative bioinformatics research initiative between Université Libre de Bruxelles (ULB) and Vrije Universiteit Brussel (VUB). This work was supported by the Service Public de Wallonie Recherche by DIGITALWALLONIA4.AI [2010235—ARIAC]; the European Regional Development Fund (ERDF) and the Brussels-Capital Region-Innoviris within the framework of the Operational Programme 2014-2020 through the ERDF-2020 project ICITY-RDI.BRU [27.002.53.01.4524]; an F.N.R.S-F.R.S PDR project [35276964]; Innoviris Joint R&D project Genome4Brussels [2020 RDIR 55b]; and the Research Foundation-Flanders (F.W.O.) Infrastructure project associated with ELIXIR Belgium [I002819N].
This work is under a MIT license.
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