Skip to content

Software created within Accumulate project (www.accumulate.be) at CLiPS, University of Antwerp

Notifications You must be signed in to change notification settings

clips/accumulate

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

8 Commits
 
 
 
 

Repository files navigation

⛳ Software for Clinical Natural Language Processing

This is a summary of openly available implementations (software deliverables) created in the Accumulate project at CLiPS.

List of repositories

Text Normalization (deliverable 2.2)

  • clinspell: Clinical spelling correction with word and character n-gram embeddings Alt text

Concept Extraction and Disambiguation (deliverable 2.3)

  • yarn: Disambiguating biomedical and clinical concepts with word embeddings Alt text

  • conch: Extracting medical concepts and terminology from patient records, and linking them to UMLS CUI Alt text

Evaluation of extracted terminology (task 2.5)

  • RDOC challenge: Psychiatric symptom severity identification. (Joint work with UZA)

Event Semantics (deliverables 3.1-3.3)

  • clicr: Machine reading and question answering on clinical case reports

Alt text

MemN2N picture

  • relex: Relation extraction between problem, treatment and test mentions in clinical notes with background knowledge integration. Alt text

Patient Representation Learning (precursor to task 5.2)

Representation Learning: Unsupervised representation learning. which is capable of learning patient representations for end tasks like mortality prediction, and diagnosis and procedural identification (Joint work with UZA). Alt text

Explaining clinical neural models for engendering trust during valorization

Interpret RNNs: Rule-based explanations of LSTM and GRU classifiers for sepsis classification. Alt text

Contributors

Walter Daelemans, Pieter Fivez, Simon Šuster, Stéphan Tulkens, Madhumita Sushil

Licensing

See individual repositories.