CLEF 2020

CodiEsp is included in the 2020 Conference and Labs of the Evaluation Forum, eHealth track, this year, an online-only event.

Registration closes On September, 19th

CodiEsp videos available on YouTube:

CLEF eHealth Schedule

Day 1: Wednesday 23rd September – Presentation

Local Time (Amsterdam)TitlePresenterAffiliationMore info
09:00-09:10Welcome and IntroductionLiadh KellyTBC
09:10-09:25Task 1 Overview: CodiEspAntonio Miranda-EscaladaBarcelona Supercomputing CenterTBC
09:25-09:40Task 2 OverviewLorraine Goeuriot, Zhengyang Liu, Chenchen XuTBC
09:40-10:25Task 1 participant presentations
FLE at CLEF eHealth 2020: Text Mining and Semantic Knowledge for Automated Clinical EncodingNuria García-SantaFujitsu Laboratories of Europe (FLE), SpainTBC
IAM at CLEF eHealth 2020: concept annotation in Spanish electronic health recordsSebastien CossinUniv. Bordeaux, FranceTBC
ICD-10 coding based on semantic distance: LSI_UNED at CLEF eHealth 2020 Task 1Mario AlmagroNational University of Distance Education (UNED), SpainTBC

Day 2: Thursday 24th September – CodiEsp session

Local Time (Amsterdam) TitlePresenterAffiliationMore info
9:00-09:15Introduction and recap from CodiEsp OverviewAntonio Miranda-EscaladaBarcelona Supercomputing CenterTBC
09:15-10:20Task 1 participant presentations
ICB-UMA at CLEF e-Health 2020 Task 1: Automatic ICD-10 coding in Spanish with BERTGuillermo López-GarcíaUniversidad de Málaga, Spainvideo
A study of Machine Learning models for Clinical Coding of Medical Reports at CodiEsp 2020Marco PolignanoUniversity of Bari Aldo Moro, Italy.TBC
Using the R Tidyverse for Multilingual Information Extraction. IMS UniPD ad CLEF eHealth 2020 Task 1Giorgio Maria Di NunzioUniversity of Padua, Italyvideo
IXA-AAA at CLEF eHealth 2020 CodiEsp Automatic classification of medical records with Multi-label Classifiers and Similarity Match CodersAlberto BlancoUniversity of the Basque Country UPV/EHU, SpainTBC
Text Augmentation Techniques for Clinical Case ClassificationAnais OllagnierUniversity of Exeter, UKvideo
Convolutional Attention Models with Post-Processing Heuristics at CLEF eHealth 2020Elias MoonsKU Leuven, BelgiumTBC
Fraunhofer AICOS at CLEF eHealth 2020 Task 1: Clinical Code Extraction From Textual Data Using Fine-Tuned BERT ModelsJoão CostaFraunhofer Portugal AICOS, Portugalvideo
Multilingual ICD-10 Code Assignment with Transformer Architectures using MIMIC-III Discharge SummariesHenning SchäferUniversity of Applied Sciences and Arts
Dortmund, Germany
10:20-10:30Closing remarks and wrapupAntonio Miranda-EscaladaBarcelona Supercomputing CenterTBC

Day 3: Friday 25th September – Consumer Health Search

Local Time (Amsterdam)TitlePresenterAffiliationMore info
09:00-09:40TBCMarco VivianiTBC
09:40-10:10Task 2 participant presentations
SandiDoc at CLEF 2020 - Consumer Health Search : AdHoc IR TaskSandaru SeneviratneTBC
A Study on Reciprocal Ranking Fusion in Consumer Health SearchGiorgio Di NunzioTBC
10:10-10:30Discussion and wrapupLorraine GoeuriotTBC


Participants’ working notes will be published in the CEUR-WS proceedings ( Task overview paper will also be published in the CEUR-WS proceedings.

author={Antonio Miranda-Escalada and Aitor Gonzalez-Agirre and Jordi Armengol-Estapé and Martin Krallinger},
title="Overview of automatic clinical coding: annotations, guidelines, and solutions for non-English clinical cases at CodiEsp track of {CLEF eHealth} 2020",
booktitle = {{Working Notes of Conference and Labs of the Evaluation (CLEF) Forum}},
series    = {{CEUR} Workshop Proceedings},
year      = {2020},

Since CodiEsp is part of CLEF eHealth lab, lab overview paper will be published in the Springer LNCS proceedings.

author={Lorraine Goeuriot and Hanna Suominen and Liadh Kelly and Antonio Miranda-Escalada and Martin Krallinger and Zhengyang Liu and Gabriella Pasi and Gabriela {Saez Gonzales} and Marco Viviani and Chenchen Xu},
title="Overview of the {CLEF eHealth} Evaluation Lab 2020},
booktitle = {{Experimental IR Meets Multilinguality, Multimodality, and Interaction: Proceedings of the Eleventh International Conference of the CLEF Association (CLEF 2020)
series    = {LNCS Volume number: 12260},
year      = {2020},
editor = {Avi Arampatzis and Evangelos Kanoulas and Theodora Tsikrika and Stefanos Vrochidis and Hideo Joho and Christina Lioma and Carsten Eickhoff and Aurélie Névéol and Linda Cappellato andNicola Ferro},

First Multilingual clinical NLP workshop: MUCLIN (MIE2020/EFMI)

There is an increasing interest in exploiting clinical texts by means of language technologies and text mining approaches. Structured clinical information, in the form of codified clinical records relying on controlled vocabularies such as ICD10 is a key resource for statistical analysis techniques applied to patient data.

Clinical natural language processing (NLP) and AI-based document indexing can result in tools for automatic clinical coding by exploiting directly the unstructured content of EHRs. Such tools are playing an increasing role to generate results that do complement health informatics approaches focusing on translational medicine challenges, by providing relevant diagnostic information extracted from clinical narratives. This implies that text mining generated clinical coding results can provide a rich clinical context for patient health information necessary for other data analysis processes like bioinformatics and OMICS data exploration.

The workshop will include a panel discussion and short flash talks with experts on the role of shared tasks to promote clinical and biomedical NLP.

Some of the proposed topics for the discussion are: generation of shareable data collections for clinical NLP and automatic coding systems, use of AI and deep learning methods applied to clinical text mining, exploitation of unstructured content of EHRs for translational medicine, explainable IA strategies, evaluation metrics and scenarios for automatic clinical coding systems, multilingual clinical coding strategies and shared tasks.

CodiEsp setting and results were presented at the workshop First Multilingual clinical NLP workshop (MUCLIN) at MIE2020. The original MIE programme can be accessed here. This year, MIE was virtual thanks to the collaboration of EFMI and took place on July 4th, 2020.

This workshop had two parts:

First, there had been a general overview presentation on shared tasks and the results and setting of a particular shared task, i.e. CodiEsp.

Then, there had been a panel discussion including flash talks by experts on the role of the shared tasks to promote clinical NLP, resources, tools, evaluation methods.

The talks are available in the MUCLIN youtube playlist.

Local Time (GMT+2)TitlePresenterAffiliationMore info
1:00 pmOpening RemarksMartin KrallingerBarcelona Supercomputing CenterVideo
1:05 pmCodiEsp: clinical coding shared task in Spanish clinical case reportsAntonio MirandaBarcelona Supercomputing CenterVideo
1:20 pmPanel Session: flash talks
Flash talk 1FLE at CLEF eHealth 2020: Text Mining and Semantic Knowledge for Automated Clinical EncodingNuria García-SantaFujistsuVideo
Flash talk 2Contribution of CLEF eHealth and WMT biomedical translation task to multilingual clinical NLPAurélie NévéolCNRS, FranceVideo
Flash talk 3The importance of shared tasks for biomedical text miningFabio RinaldiUniversity of ZurichVideo
Flash talk 4Multilingual Text MiningFrancisco CoutoUniversity of LisbonVideo
Flash talk 5Lessons learnt on benchmarking at ELIXIRSalvador Capella-GutierrezINB/Elixir, Barcelona Supercomputing CenterTBA
1:55Closing remarksMartin KrallingerBarcelona Supercomputing Center

See EFMI program.

MUCLIN program