Task description

This task aims to evaluate systems on the translation of documents from the biomedical domain. The test data will consist of biomedical abstracts and terminologies. This year, the biomedical translation task will address the following language pairs:

• English-Basque (en/eu) NEW
• English-Chinese and Chinese-English (en/zh, zh/en)
• English-French and French-English (en/fr, fr/en)
• English-German and German-English (en/de, de/en)
• English-Italian and Italian-English (en/it, it/en) NEW
• English-Portuguese and Portuguese-English (en/pt, pt/en)
• English-Russian and Russian-English (en/ru, ru/en) NEW
• English-Spanish and Spanish-English (en/es, es/en)

Data

Participants can rely on training (and development) data from various sources, for instance:

• The Biomedical Translation repository includes links to parallel corpora of scientific publications (en/pt, en/es, en/fr, en/de, en/zh, en/it, en/ru), among others. NEW
• The UFAL Medical Corpus (formerly HimLCorpus) includes medical text from various sources for many language pairs (en/es, en/de, en/fr, en/ro). HimL test sets can be used as the development sets for some language pairs (en/es, en/de, en/fr, en/ro).
• The Khresmoi development data can be used for some language pairs (en/es, en/de, en/fr).
• The UNCorpus contains training data for some languages (en/es, en/fr, en/zh).
• The MeSpEn corpus contains many parallel documents of en/es.
• The Scielo full text corpus for en, es and pt.
• The Brazilian Thesis and Dissertations for en/pt.
• The ICD-10 codes translation train/dev datasets for en/eu. NEW
• The medical domain monolingual corpora includes hospital notes, medical domain wikipedia articles and medical dictionaries (eu). NEW
• Out-of-domain monolingual corpora for eu. NEW
• Out-of-domain parallel corpora (en/eu). NEW

Participants are also free to use out-of-domain data.

Other resources:

• BERTeus, pre-trained model for Basque

Evaluation

• Scientific abstracts:
• English to Basque
• Chinese/English (both directions)
• French/English (both directions)
• German/English (both directions)
• Italian/English (both directions)
• Portuguese/English (both directions)
• Spanish/English (both directions)
• Translation of terms from biomedical terminologies:
• English to Basque

Test Sets and Submission formats

Terms from biomedical terminologies:

  
Traumatic rupture of left ulnar collateral ligament, subsequent encounter
posterior dislocation of left hip, sequela
Anterior subluxation of right humerus
other subluxation of left foot, subsequent encounter
Hypothermia of newborn
Absence and agenesis of lacrimal apparatus
poisoning by unspecified primarily systemic and hematological agent, assault, initial encounter
Disorders of glycoprotein metabolism

 
ezkerreko kubitu aldeko lotailu albokideko etendura traumatikoa, segidako harremana
ezkerreko aldakako atzeko lokadura, sekuela
eskuineko besahezurraren aurreko subluxazio
ezkerreko oineko beste subluxazio batzuk, segidako harremana
jaioberriaren hipotermia
malko-aparatuaren absentzia eta agenesia
nagusiki sistemikoa eta hematologikoa den agente zehaztugabeak eragindako pozoidura, erasoa, hasierako harremana
glukoproteinen metabolismoaren nahasmenduak

Scientific abstracts:

For the test set of Medline abstracts, the format will be plain text files. The format will be the following:

DOC_ID	SENT_ID	SENTENCE_TEXT

• DOC_ID: sequential one, e.g. doc1, doc8, not the original PMID in Medline
• SENT_ID: a sequential number from 1 to n
• SENTENCE_TEXT: the sentence text to be translated by the participants

doc1	1	sentence_1
doc2	2	sentence_2
doc2	3	sentence_3
doc2	4	sentence_4
doc2	5	sentence_5
...
doc2	n	sentence_n
doc4	1	sentence_1
doc4	2	sentence_2
...

doc1	1	translated_sentence_1
doc2	2	translated_sentence_2
doc2	3	translated_sentence_3
doc2	4	translated_sentence_4
doc2	5	translated_sentence_5
...
doc2	n	translated_sentence_n
doc4	1	translated_sentence_1
doc4	2	translated_sentence_2
...

Submission Requirements

Please notice that, following general WMT policy explicitly enforced in other tasks, we will release all participants' submissions after this year's edition of the task to promote further studies.

Please register your team using this form. You will receive a mail with the confirmation of your registration. The link for submission site will be informed in this mail Please register your team as soon as possible.

The test files will be available in the WMT'20 biomedical task Google Drive folder ("test_sets" folder).

The format for the submission files should include the original test file name preceded by the team identifier (as registered in the form above) and the run number, following this example for the abstracts:

• The submission file for run 1 of the "ABC" team for the Medline abstracts from English to Spanish should be called "ABC_run1_abstract_en2es_es.txt".
• The submission file for run 3 of the "ABC" team for the Medline abstracts from Spanish to English should be called "ABC_run3_abstract_es2en_en.txt".
• The submission file for run 1 of the "ABC" team for the abstracts from English to Basque should be called "ABC_run1_abstract_en2eu_eu.txt".

• The submission file for run 1 of the "ABC" team for the terminology dataset should be called "ABC_run1_terms.txt".

Each team will be allowed to submit up to 3 runs per test set.

Results

The keys for the test sets are available in the WMT'20 biomedical task Google Drive folder ("gold_sets" folder).

• "gold_test_files" folder: 14 "medline_*.txt" files, one file for the Basque abstract translation and one gold file for the terminology task, i.e., the reference sentences for all test sets.
• "docid_mapping_files" folder: Eight "*_mapping.txt" files for each Medline language pair for mapping document sequentials to PubMed PMIDs.
• "alignment_files" folder: Eight MEDLINE "*_align_validation.tsv" files for each language pair with the manual validation of the automatic alignment. The order of the languages in the alignment (column 2 in the TAB-separated file) is foreign language vs. (<=>) English.
• wmt20bio_align.py: Python script to produce the submission and gold files before carrying out an evaluation.

Important dates

Organisers