There is a pressing need to exploit health-related content from social media, a global source of data where key health information is posted directly by citizens, patients and other healthcare stakeholders. Use cases of disease related social media mining include disease outbreak/surveillance, mental health and pharmacovigilance. Current efforts address the exploitation of social media beyond English. The SocialDisNER task, organized as part of the SMM4H 2022 initiative, has applied the LINKAGE methodology to select and annotate a Gold Standard corpus of 9,500 tweets in Spanish enriched with disease mentions generated by patients and medical professionals. As a complementary resource for teams participating in the SocialDisNER track, we have also created a large-scale corpus of 85,000 tweets, where in addition to disease mentions, other medical entities of relevance (e.g., medications, symptoms and procedures, among others) have been automatically labelled. Using these large-scale datasets, co-mention networks or knowledge graphs were released for each entity pair type. Out of the 47 teams registered for the task, 17 teams uploaded a total of 32 runs. The top-performing team achieved a very competitive 0.891 f-score, with a system trained following a continue pre-training strategy. We anticipate that the corpus and systems resulting from the SocialDisNER track might further foster health related text mining of social media content in Spanish and inspire disease detection strategies in other languages.

For the past seven years, the Social Media Mining for Health Applications (#SMM4H) shared tasks have promoted the community-driven development and evaluation of advanced natural language processing systems to detect, extract, and normalize health-related information in public, user-generated content. This seventh iteration consists of ten tasks that include English and Spanish posts on Twitter, Reddit, and WebMD. Interest in the #SMM4H shared tasks continues to grow, with 117 teams that registered and 54 teams that participated in at least one task—a 17.5% and 35% increase in registration and participation, respectively, over the last iteration. This paper provides an overview of the tasks and participants’ systems. The data sets remain available upon request, and new systems can be evaluated through the post-evaluation phase on CodaLab.

In the seventh edition of the WMT Biomedical Task, we addressed a total of seven languagepairs, namely English/German, English/French, English/Spanish, English/Portuguese, English/Chinese, English/Russian, English/Italian. This year’s test sets covered three types of biomedical text genre. In addition to scientific abstracts and terminology items used in previous editions, we released test sets of clinical cases. The evaluation of clinical cases translations were given special attention by involving clinicians in the preparation of reference translations and manual evaluation. For the main MEDLINE test sets, we received a total of 609 submissions from 37 teams. For the ClinSpEn sub-task, we had the participation of five teams.

Detection of occupations in texts is relevant for a range of important application scenarios, like competitive intelligence, sociodemographic analysis, legal NLP or health-related occupational data mining. Despite the importance and heterogeneous data types that mention occupations, text mining efforts to recognize them have been limited. This is due to the lack of clear annotation guidelines and high-quality Gold Standard corpora. Social media data can be regarded as a relevant source of information for real-time monitoring of at-risk occupational groups in the context of pandemics like the COVID-19 one, facilitating intervention strategies for occupations in direct contact with infectious agents or affected by mental health issues. To evaluate current NLP methods and to generate resources, we have organized the ProfNER track at SMM4H 2021, providing ProfNER participants with a Gold Standard corpus of manually annotated tweets (human IAA of 0.919) following annotation guidelines available in Spanish and English, an occupation gazetteer, a machine-translated version of tweets, and FastText embeddings. Out of 35 registered teams, 11 submitted a total of 27 runs. Best-performing participants built systems based on recent NLP technologies (e.g. transformers) and achieved 0.93 F-score in Text Classification and 0.839 in Named Entity Recognition. Corpus: https://doi.org/10.5281/zenodo.4309356

The global growth of social media usage over the past decade has opened research avenues for mining health related information that can ultimately be used to improve public health. The Social Media Mining for Health Applications (#SMM4H) shared tasks in its sixth iteration sought to advance the use of social media texts such as Twitter for pharmacovigilance, disease tracking and patient centered outcomes. #SMM4H 2021 hosted a total of eight tasks that included reruns of adverse drug effect extraction in English and Russian and newer tasks such as detecting medication non-adherence from Twitter and WebMD forum, detecting self-reported adverse pregnancy outcomes, detecting cases and symptoms of COVID-19, identifying occupations mentioned in Spanish by Twitter users, and detecting self-reported breast cancer diagnosis. The eight tasks included a total of 12 individual subtasks spanning three languages requiring methods for binary classification, multi-class classification, named entity recognition and entity normalization. With a total of 97 registering teams and 40 teams submitting predictions, the interest in the shared tasks grew by 70% and participation grew by 38% compared to the previous iteration.

Word embeddings are representations of words in a dense vector space. Although they are not recent phenomena in Natural Language Processing (NLP), they have gained momentum after the recent developments of neural methods and Word2Vec. Regarding their applications in medical and clinical NLP, they are invaluable resources when training in-domain named entity recognition systems, classifiers or taggers, for instance. Thus, the development of tailored word embeddings for medical NLP is of great interest. However, we identified a gap in the literature which we aim to fill in this paper: the availability of embeddings for medical NLP in Spanish, as well as a standardized form of intrinsic evaluation. Since most work has been done for English, some established datasets for intrinsic evaluation are already available. In this paper, we show the steps we employed to adapt such datasets for the first time to Spanish, of particular relevance due to the considerable volume of EHRs in this language, as well as the creation of in-domain medical word embeddings for the Spanish using the state-of-the-art FastText model. We performed intrinsic evaluation with our adapted datasets, as well as extrinsic evaluation with a named entity recognition systems using a baseline embedding of general-domain. Both experiments proved that our embeddings are suitable for use in medical NLP in the Spanish language, and are more accurate than general-domain ones.

In the fourth edition of the WMT Biomedical Translation task, we considered a total of six languages, namely Chinese (zh), English (en), French (fr), German (de), Portuguese (pt), and Spanish (es). We performed an evaluation of automatic translations for a total of 10 language directions, namely, zh/en, en/zh, fr/en, en/fr, de/en, en/de, pt/en, en/pt, es/en, and en/es. We provided training data based on MEDLINE abstracts for eight of the 10 language pairs and test sets for all of them. In addition to that, we offered a new sub-task for the translation of terms in biomedical terminologies for the en/es language direction. Higher BLEU scores (close to 0.5) were obtained for the es/en, en/es and en/pt test sets, as well as for the terminology sub-task. After manual validation of the primary runs, some submissions were judged to be better than the reference translations, for instance, for de/en, en/es and es/en.

This paper describes the machine translation systems developed by the Barcelona Supercomputing (BSC) team for the biomedical translation shared task of WMT19. Our system is based on Neural Machine Translation unsing the OpenNMT-py toolkit and Transformer architecture. We participated in four translation directions for the English/Spanish and English/Portuguese language pairs. To create our training data, we concatenated several parallel corpora, both from in-domain and out-of-domain sources, as well as terminological resources from UMLS.

One of the biomedical entity types of relevance for medicine or biosciences are chemical compounds and drugs. The correct detection these entities is critical for other text mining applications building on them, such as adverse drug-reaction detection, medication-related fake news or drug-target extraction. Although a significant effort was made to detect mentions of drugs/chemicals in English texts, so far only very limited attempts were made to recognize them in medical documents in other languages. Taking into account the growing amount of medical publications and clinical records written in Spanish, we have organized the first shared task on detecting drug and chemical entities in Spanish medical documents. Additionally, we included a clinical concept-indexing sub-track asking teams to return SNOMED-CT identifiers related to drugs/chemicals for a collection of documents. For this task, named PharmaCoNER, we generated annotation guidelines together with a corpus of 1,000 manually annotated clinical case studies. A total of 22 teams participated in the sub-track 1, (77 system runs), and 7 teams in the sub-track 2 (19 system runs). Top scoring teams used sophisticated deep learning approaches yielding very competitive results with F-measures above 0.91. These results indicate that there is a real interest in promoting biomedical text mining efforts beyond English. We foresee that the PharmaCoNER annotation guidelines, corpus and participant systems will foster the development of new resources for clinical and biomedical text mining systems of Spanish medical data.