oeg-upm / covid19

Contributions to analyze the COVID-19 Open Research Dataset (CORD-19)

covid19

En este repositorio estamos intentando enlazar todas las contribuciones que pueda ir haciendo la comunidad académica española para aplicar técnicas de Inteligencia Artificial sobre el conjunto de datos COVID-19 Open Research Dataset (CORD-19), así como animar a todos a sumarse de manera voluntaria a esta iniciativa.

In this repository we are providing links on the contributions that the Spanish academic community can provide in order to apply Artificial Intelligence techniques over the COVID-19 Open Research Dataset (CORD-19), as well as encouraging all to contribute to this voluntary initiative.

covid19's Issues

Automatic generation of medical image dataset

Maybe we can generate a medical image dataset by parsing the covid-papers that are related to diagnosis techniques using CT scans, x-rays images, etc. Usually, the papers results section is charged with lots of images, showing examples, graphs, etc.

A first proposal for the system pipeline could be:

1. Parsing all the pdfs and extracting all the figures.
2. Maybe a second parsing process to extract subfigures.
3. Classification of the figures (not all of them are medical images), in this point we could use a subset of the dataset to train a classifier or maybe use embeddings to differentiate medical images from the rest. We could also leverage information from captions.

I don't know if we could be able to extract a decent amount of images, it depends on how much papers addressed this type of diagnosis, but we give it a try.

Using these images we could then train classification models, using transfer learning, we could also apply visualization techniques to explain the most important regions of the image, etc.

Important Links:
http://ai2-website.s3.amazonaws.com/publications/Siegel16eccv.pdf
https://github.com/ieee8023/covid-chestxray-dataset

biomed sanity

Andrej Karpathy has extended his arxiv sanity prototype to biomed papers. The link is here http://biomed-sanity.com/ and it is open source. Given a collection of papers it may be relatively straightforward to do some initial setup of a search engine that health professionals can evaluate (or a baseline for comparison with other systems and proposals).

Cheers,

Add some of our APIs to the site that is compiling this

https://covid-19-apis.postman.com

Add reference to work on the evolution of cases estimation

This will be continuously updated at: https://gitlab.etsisi.upm.es/fserra/coronavirus-evolution
It is a Jupyter notebook that performs an estimation of the evolution of cases, from https://gitlab.etsisi.upm.es/fserra