DrugSemantics: A corpus for Named Entity Recognition in Spanish Summaries of Product Characteristics

The Hmong Medical Corpus: a biomedical corpus for a minority language

Biomedical communication is an area that increasingly benefits from natural language processing (NLP) work. Biomedical named entity recognition (NER) in particular provides a foundation for advanced NLP applications, such as automated medical question-answering and translation services. However, while a large body of biomedical documents are available in an array of languages, most work in biomedical NER remains in English, with the remainder in official national or regional languages. Minority languages so far remain an underexplored area. The Hmong language, a minority language with sizable populations in several countries and without official status anywhere, represents an exceptional challenge for effective communication in medical contexts. Taking advantage of the large number of government-produced medical information documents in Hmong, we have developed the first named entity-annotated biomedical corpus for a resource-poor minority language. The Hmong Medical Corpus contains 100,535 tokens with 4554 named entities (NEs) of three UMLS semantic types: diseases/syndromes, signs/symptoms, and body parts/organs/organ components. Furthermore, a subset of the corpus is annotated for word position and parts of speech, representing the first such gold-standard dataset publicly available for Hmong. The methodology presented provides a readily reproducible approach for the creation of biomedical NE-annotated corpora for other resource-poor languages.

A clinical trials corpus annotated with UMLS entities to enhance the access to evidence-based medicine

BACKGROUND

The large volume of medical literature makes it difficult for healthcare professionals to keep abreast of the latest studies that support Evidence-Based Medicine. Natural language processing enhances the access to relevant information, and gold standard corpora are required to improve systems. To contribute with a new dataset for this domain, we collected the Clinical Trials for Evidence-Based Medicine in Spanish (CT-EBM-SP) corpus.

METHODS

We annotated 1200 texts about clinical trials with entities from the Unified Medical Language System semantic groups: anatomy (ANAT), pharmacological and chemical substances (CHEM), pathologies (DISO), and lab tests, diagnostic or therapeutic procedures (PROC). We doubly annotated 10% of the corpus and measured inter-annotator agreement (IAA) using F-measure. As use case, we run medical entity recognition experiments with neural network models.

RESULTS

This resource contains 500 abstracts of journal articles about clinical trials and 700 announcements of trial protocols (292 173 tokens). We annotated 46 699 entities (13.98% are nested entities). Regarding IAA agreement, we obtained an average F-measure of 85.65% (±4.79, strict match) and 93.94% (±3.31, relaxed match). In the use case experiments, we achieved recognition results ranging from 80.28% (±00.99) to 86.74% (±00.19) of average F-measure.

CONCLUSIONS

Our results show that this resource is adequate for experiments with state-of-the-art approaches to biomedical named entity recognition. It is freely distributed at: http://www.lllf.uam.es/ESP/nlpmedterm_en.html . The methods are generalizable to other languages with similar available sources.

Fine-Grained Mechanical Chinese Named Entity Recognition Based on ALBERT-AttBiLSTM-CRF and Transfer Learning

Manufacturing text often exists as unlabeled data; the entity is fine-grained and the extraction is difficult. The above problems mean that the manufacturing industry knowledge utilization rate is low. This paper proposes a novel Chinese fine-grained NER (named entity recognition) method based on symmetry lightweight deep multinetwork collaboration (ALBERT-AttBiLSTM-CRF) and model transfer considering active learning (MTAL) to research fine-grained named entity recognition of a few labeled Chinese textual data types. The method is divided into two stages. In the first stage, the ALBERT-AttBiLSTM-CRF was applied for verification in the CLUENER2020 dataset (Public dataset) to get a pretrained model; the experiments show that the model obtains an F1 score of 0.8962, which is better than the best baseline algorithm, an improvement of 9.2%. In the second stage, the pretrained model was transferred into the Manufacturing-NER dataset (our dataset), and we used the active learning strategy to optimize the model effect. The final F1 result of Manufacturing-NER was 0.8931 after the model transfer (it was higher than 0.8576 before the model transfer); so, this method represents an improvement of 3.55%. Our method effectively transfers the existing knowledge from public source data to scientific target data, solving the problem of named entity recognition with scarce labeled domain data, and proves its effectiveness.

A computational ecosystem to support eHealth Knowledge Discovery technologies in Spanish

The massive amount of biomedical information published online requires the development of automatic knowledge discovery technologies to effectively make use of this available content. To foster and support this, the research community creates linguistic resources, such as annotated corpora, and designs shared evaluation campaigns and academic competitive challenges. This work describes an ecosystem that facilitates research and development in knowledge discovery in the biomedical domain, specifically in Spanish language. To this end, several resources are developed and shared with the research community, including a novel semantic annotation model, an annotated corpus of 1045 sentences, and computational resources to build and evaluate automatic knowledge discovery techniques. Furthermore, a research task is defined with objective evaluation criteria, and an online evaluation environment is setup and maintained, enabling researchers interested in this task to obtain immediate feedback and compare their results with the state-of-the-art. As a case study, we analyze the results of a competitive challenge based on these resources and provide guidelines for future research. The constructed ecosystem provides an effective learning and evaluation environment to encourage research in knowledge discovery in Spanish biomedical documents.

Towards the Construction of a Gold Standard Biomedical Corpus for the Romanian Language

Gold standard corpora (GSCs) are essential for the supervised training and evaluation of systems that perform natural language processing (NLP) tasks. Currently, most of the resources used in biomedical NLP tasks are mainly in English. Little effort has been reported for other languages including Romanian and, thus, access to such language resources is poor. In this paper, we present the construction of the first morphologically and terminologically annotated biomedical corpus of the Romanian language (MoNERo), meant to serve as a gold standard for biomedical part-of-speech (POS) tagging and biomedical named entity recognition (bioNER). It contains 14,012 tokens distributed in three medical subdomains: cardiology, diabetes and endocrinology, extracted from books, journals and blogposts. In order to automatically annotate the corpus with POS tags, we used a Romanian tag set which has 715 labels, while diseases, anatomy, procedures and chemicals and drugs labels were manually annotated for bioNER with a Cohen Kappa coefficient of 92.8% and revealed the occurrence of 1877 medical named entities. The automatic annotation of the corpus has been manually checked. The corpus is publicly available and can be used to facilitate the development of NLP algorithms for the Romanian language.