coveffect

Coveffect is a project that aim to automatically extract informations from covid-related articles. In particular what we want to extract from each paper a table containing the list of variants/mutation and their corresponding effects

• An instance of the system is available at this link: http://geco.deib.polimi.it/coveffect/#/

Requirements

• Install the last version of Docker
• Install docker-compose

Installation

• clone the coveffect repository
• download the model checkpoint using gdown:

gdown 1VOF7NCqgM5pFaJcexhXjvp-OsLkza5lz

• or download it at the following link drive
• unzip the folder model_0 in the coveffect/backend/api/checkpoints/ folder

System Usage

To start the application run in the main folder:

docker-compose up

open the browser at the following link

• http://localhost:8080/#/

How to use the model to extract information from a list of abstract

• create a python enviroment and install the backend/requirements.txt
• run the batch_prediction.ipynb notebook