Connectionists: 1st CFP MultiCardioNER (CLEF/BioASQ 2024): Clinical Named Entity Recognition adaptation shared task (multilingual & cardiology)

[Martin Krallinger]

(Apologies for cross-posting)





*CFP MultiCardioNER (CLEF/BioASQ 2024): Clinical Named Entity Recognition
adaptation shared task (multilingual & cardiology)*



*https://temu.bsc.es/multicardioner/ <https://temu.bsc.es/multicardioner/>*



The MultiCardioNER track focuses on the adaptation of clinical NER systems
to specific high impact clinical application domains (cardiovascular
diseases, the leading cause of death globally) as well as to multiple
languages (English, Spanish and Italian), focusing on two clinical entity
types: diseases and medications.



*Key information:*

·       *Web*: https://temu.bsc.es/multicardioner

·       *Data*: https://zenodo.org/records/10948355

·       *BioASQ** web*: http://bioasq.org/

·       *Registration**:* https://temu.bsc.es/multicardioner/registration/



*Motivation *The extraction of clinical variables from medical content is
key to enable efficient healthcare data analytics. Due to the highly
specialized medical language, with considerable variation depending on the
medical discipline, more specialized automatic semantic annotation
resources are needed, not only for English but also other languages.

This is particularly true for clinical content related to cardiovascular
diseases (CVDs), which represent the leading cause of death globally,
responsible for approximately 17.9 million deaths/year.

The MultiCardioNER task will focus on the automatic recognition of two key
clinical variables or concept types, namely diseases and medications in
cardiology clinical case documents with the following two aims:

·       Adaptation of general clinical concept recognition systems to
cardiology case reports to assess and determine how well such systems can
be adapted to high impact clinical application domains / specialties
(cardiology disease NER - CardioDis subtrack: Spanish).

·       Promote the comparative assessment and development of clinical
entity recognition systems for multiple languages (i.e., medication mention
detection) as well as adaptation to specific medical specialties (MultiDrug
subtrack: English, Spanish and Italian)

To enable the adaptation of general medical NER systems for diseases and
medications the MultiCardioNER task will rely on a training collection of
1000 general clinical case reports in Spanish annotated with diseases
(Spanish) and medications (English, Spanish and Italian).

Moreover, to be able to adapt such general medical NER approaches to
cardiology case reports a development set of 250 cardiology cases will be
released. The test set will consist of an additional test collection of 250
cardiology case reports.

The evaluation of systems for this task will use flat evaluation, mainly
micro-averaged Precision, Recall and F-measure (MiF).



Sub-tracks:

*Subtask 1 (CardioDis): *Spanish adaptation of disease recognition systems
to the cardiology domain



*Subtask 2 (MultiDrug): *Multilingual (Spanish, English and Italian)
adaptation of medication recognition systems to the cardiology domain


*Tentative schedule*

·       MultiCardioNER Train+Dev Set Release           April 9th, 2024

·       MultiCardioNER Annotation Guidelines Release            April 17th,
2024

·       MultiCardioNER Gazetteer Release  April 17th, 2024

·       MultiCardioNER Test Set Texts Release            May 2nd, 2024

·       Participant Test Predictions Deadline

·       May 15th, 2024

·       Participant Evaluation Result Release               May 19th, 2024

·       Submission of Participant Papers Deadline     May 31st, 2024

·       Notification of Acceptance of Participant Papers           June
24th, 2024

·       Submission of Camera-ready Participant Papers Deadline
July 8th, 2024

·      BioASQ @ CLEF2024             September 9th-12th, 2024


*Publications & conference*

Following previous BioASQ/CLEF efforts, participating teams will be invited
to contribute a short systems description paper for the CLEF 2024
proceedings, and to give a short presentation of their approach at the
BioASQ workshop at the CLEF 2024 conference (September 09-12, 2024, in
Grenoble, France)






*The **MultiCardioNER Organizers & collaborators:*



   - Salvador Lima-López, Barcelona Supercomputing Center (BSC), Spain
   - Eulàlia Farré-Maduell, Barcelona Supercomputing Center (BSC), Spain
   - Jan Rodríguez-Miret, Barcelona Supercomputing Center (BSC), Spain
   - Martin Krallinger, Barcelona Supercomputing Center (BSC), Spain


   - Anastasios Nentidis, National Center for Scientific Research
   Demokritos, Greece
   - Anastasia Krithara, National Center for Scientific Research
   Demokritos, Greece
   - Georgios Katsimpras, National Center for Scientific Research
   Demokritos, Greece


   - Livia Lilli, Fondazione Policlinico Universitario Agostino Gemelli
   IRCCS, Italy
   - Jacopo Lenkowicz, Fondazione Policlinico Universitario Agostino
   Gemelli IRCCS, Italy
   - Jonathan Kossoff, University College London Hospitals NHS Foundation
   Trust, UK
   - Giovanna Ceroni, University College London, UK
   - Anoop Shah, University College London Hospitals NHS Foundation Trust,
   UK




=======================================
Martin Krallinger, Dr.
Head of NLP for Biomedical Information Analysis Unit
Barcelona Supercomputing Center (BSC-CNS)
https://www.linkedin.com/in/martin-krallinger-85495920/
 =======================================
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.srv.cs.cmu.edu/pipermail/connectionists/attachments/20240415/e9fa5c11/attachment.html>