Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add biomedical entity normalization #3180

Closed
wants to merge 30 commits into from
Closed

Add biomedical entity normalization #3180

wants to merge 30 commits into from

Commits on Mar 14, 2023

  1. Initial version (already adapted to recent Flair API changes)

    Mario Sänger committed Mar 14, 2023
    Configuration menu
    Copy the full SHA
    641a3c0 View commit details
    Browse the repository at this point in the history

  2. Revise mention text pre-processing: define general interface and adap… 

    …t basic text and Ab3P pre-processing to the new structure; fix bug in Ab3P abbreviation detection
    Mario Sänger committed Mar 14, 2023
    Configuration menu
    Copy the full SHA
    9779abf View commit details
    Browse the repository at this point in the history

Commits on Mar 15, 2023

  1. Refactor entity linking model structure

    Mario Sänger committed Mar 15, 2023
    Configuration menu
    Copy the full SHA
    8da7d75 View commit details
    Browse the repository at this point in the history

Commits on Mar 22, 2023

  1. Update documentation

    Mario Sänger committed Mar 22, 2023
    Configuration menu
    Copy the full SHA
    e34c831 View commit details
    Browse the repository at this point in the history

Commits on Mar 23, 2023

  1. Introduce separate methods for pre-processing (1) entity mentions fro… 

    …m text and (2) entity / concept names from an knowledge base or ontology
    Mario Sänger committed Mar 23, 2023
    Configuration menu
    Copy the full SHA
    f54925c View commit details
    Browse the repository at this point in the history

Commits on Apr 21, 2023

  1. Merge branch 'master' into bio-entity-normalization

    @alanakbik
    alanakbik authored Apr 21, 2023
    Configuration menu
    Copy the full SHA
    90a0acb View commit details
    Browse the repository at this point in the history

  2. Fix formatting

    @alanakbik
    alanakbik committed Apr 21, 2023
    Configuration menu
    Copy the full SHA
    f1f51fd View commit details
    Browse the repository at this point in the history

Commits on Apr 26, 2023

  1. feat(test): biomedical entity linking

    Samule Garda committed Apr 26, 2023
    Configuration menu
    Copy the full SHA
    f2f21d3 View commit details
    Browse the repository at this point in the history

  2. fix(requirements): add faiss

    Samule Garda committed Apr 26, 2023
    Configuration menu
    Copy the full SHA
    82c1b8b View commit details
    Browse the repository at this point in the history

  3. fix(test): hold on w/ automatic tests for now

    Samule Garda committed Apr 26, 2023
    Configuration menu
    Copy the full SHA
    2e3cda3 View commit details
    Browse the repository at this point in the history

  4. fix(bionel): start major refactoring 

    - improve name consistency

- make code more pythonic

- dictionaries always do lazy loading

- consistency in dictionary parsing: always yield (cui,name)

- clean up loading w/ CONSTANTS (easily swap models)

- allow access to sparse and dense search
    Samule Garda committed Apr 26, 2023
    Configuration menu
    Copy the full SHA
    adb231e View commit details
    Browse the repository at this point in the history

Commits on Apr 27, 2023

  1. fix(bionel): major refactor 

    - yet better naming

- add batched search

- fix dicionary loading
    Samule Garda committed Apr 27, 2023
    Configuration menu
    Copy the full SHA
    c80f1be View commit details
    Browse the repository at this point in the history

Commits on May 2, 2023

  1. fix(bionel): assign entity type 

    - predict only on mentions of give entity type
    Samule Garda committed May 2, 2023
    Configuration menu
    Copy the full SHA
    d10d297 View commit details
    Browse the repository at this point in the history

  2. fix(biencoder): set sparse encoder and weight

    Samule Garda committed May 2, 2023
    Configuration menu
    Copy the full SHA
    25ba2dd View commit details
    Browse the repository at this point in the history

Commits on May 11, 2023

  1. fix(bionel): address comments 

    - fix mypy typing

- fix typos

- update docstrings

- rm faiss from requirements

- better naming

- allow user to specify annotation layer in predict

- allow no mentions
    Samule Garda committed May 11, 2023
    Configuration menu
    Copy the full SHA
    4525d3b View commit details
    Browse the repository at this point in the history

Commits on May 12, 2023

  1. fix(candidate_generator): container for search result

    Samule Garda committed May 12, 2023
    Configuration menu
    Copy the full SHA
    3a5913d View commit details
    Browse the repository at this point in the history

Commits on May 19, 2023

  1. fix(predict): default annotation layer iff not provided by use 

    - fix typo
    Samule Garda committed May 19, 2023
    Configuration menu
    Copy the full SHA
    734d895 View commit details
    Browse the repository at this point in the history

  2. fix(label): scores can be >= or <=

    Samule Garda committed May 19, 2023
    Configuration menu
    Copy the full SHA
    d79f871 View commit details
    Browse the repository at this point in the history

  3. fix(candidate): parametrize database name

    Samule Garda committed May 19, 2023
    Configuration menu
    Copy the full SHA
    118fb95 View commit details
    Browse the repository at this point in the history

Commits on May 22, 2023

  1. feat(candidate_generator): cache sparse encoder 

    - better naming

- unique cache name
    Samule Garda committed May 22, 2023
    Configuration menu
    Copy the full SHA
    1fcfddf View commit details
    Browse the repository at this point in the history

Commits on May 23, 2023

  1. fix(candidate_generator): minor improvements 

    - add option to time search

- change error to warning if pre-trained model is not hybrid

- check if there are mentions to predict
    Samule Garda committed May 23, 2023
    Configuration menu
    Copy the full SHA
    9322c1b View commit details
    Browse the repository at this point in the history

Commits on May 24, 2023

  1. feat(linking_candidate): pretty print

    Samule Garda committed May 24, 2023
    Configuration menu
    Copy the full SHA
    071f51e View commit details
    Browse the repository at this point in the history

  2. fix(candidate_generator): check sparse encoder for sparse search

    Samule Garda committed May 24, 2023
    Configuration menu
    Copy the full SHA
    a23f360 View commit details
    Browse the repository at this point in the history

Commits on Jun 1, 2023

  1. chore: crystal clear dictionary name

    Samule Garda committed Jun 1, 2023
    Configuration menu
    Copy the full SHA
    ce29290 View commit details
    Browse the repository at this point in the history

  2. feat(candidate_generator): add sparse index

    Samule Garda committed Jun 1, 2023
    Configuration menu
    Copy the full SHA
    0d65336 View commit details
    Browse the repository at this point in the history

Commits on Jun 2, 2023

  1. fix(candidate_generator): KISS: sparse search w/ scipy sparse matrices

    Samule Garda committed Jun 2, 2023
    Configuration menu
    Copy the full SHA
    02812f0 View commit details
    Browse the repository at this point in the history

Commits on Jul 12, 2023

  1. Minor update to comments and documentation

    Mario Sänger committed Jul 12, 2023
    Configuration menu
    Copy the full SHA
    ca6eee8 View commit details
    Browse the repository at this point in the history

  2. Fix tests and type annotations

    Mario Sänger committed Jul 12, 2023
    Configuration menu
    Copy the full SHA
    6c8f219 View commit details
    Browse the repository at this point in the history

  3. Merge branch 'master' into bio-entity-normalization

    Mario Sänger committed Jul 12, 2023
    Configuration menu
    Copy the full SHA
    2fa43cc View commit details
    Browse the repository at this point in the history

  4. Merge

    Mario Sänger committed Jul 12, 2023
    Configuration menu
    Copy the full SHA
    d90d92d View commit details
    Browse the repository at this point in the history