With the growing number of electronic health record data, clinical NLP tasks have become increasingly relevant to unlock valuable information from unstructured clinical text. Although the performance of downstream NLP tasks, such as named-entity recognition (NER), in English corpus has recently improved by contextualised language models, less research is available for clinical texts in low resource languages. Our goal is to assess a deep contextual embedding model for Portuguese, so called BioBERTpt, to support clinical and biomedical NER. We transfer learned information encoded in a multilingual-BERT model to a corpora of clinical narratives and biomedical-scientific papers in Brazilian Portuguese. To evaluate the performance of BioBERTpt, we ran NER experiments on two annotated corpora containing clinical narratives and compared the results with existing BERT models. Our in-domain model outperformed the baseline model in F1-score by 2.72%, achieving higher performance in 11 out of 13 assessed entities. We demonstrate that enriching contextual embedding models with domain literature can play an important role in improving performance for specific NLP tasks. The transfer learning process enhanced the Portuguese biomedical NER model by reducing the necessity of labeled data and the demand for retraining a whole new model.

We consider the hierarchical representation of documents as graphs and use geometric deep learning to classify them into different categories. While graph neural networks can efficiently handle the variable structure of hierarchical documents using the permutation invariant message passing operations, we show that we can gain extra performance improvements using our proposed selective graph pooling operation that arises from the fact that some parts of the hierarchy are invariable across different documents. We applied our model to classify clinical trial (CT) protocols into completed and terminated categories. We use bag-of-words based, as well as pre-trained transformer-based embeddings to featurize the graph nodes, achieving f1-scores 0.85 on a publicly available large scale CT registry of around 360K protocols. We further demonstrate how the selective pooling can add insights into the CT termination status prediction. We make the source code and dataset splits accessible.

Recent improvements in machine-reading technologies attracted much attention to automation problems and their possibilities. In this context, WNUT 2020 introduces a Name Entity Recognition (NER) task based on wet laboratory procedures. In this paper, we present a 3-step method based on deep neural language models that reported the best overall exact match F 1 -score (77.99%) of the competition. By fine-tuning 10 times, 10 different pretrained language models, this work shows the advantage of having more models in an ensemble based on a majority of votes strategy. On top of that, having 100 different models allowed us to analyse the combinations of ensemble that demonstrated the impact of having multiple pretrained models versus fine-tuning a pretrained model multiple times. Entity BERT (cased) BioClinical BERT BioBERT RoBERTa BioMed RoBERTa PubMed BERT XLNet Ensemble Baseline base large base large base large Action 88.

The health and life science domains are well known for their wealth of named entities found in large free text corpora, such as scientific literature and electronic health records. To unlock the value of such corpora, named entity recognition (NER) methods are proposed. Inspired by the success of transformer-based pretrained models for NER, we assess how individual and ensemble of deep masked language models perform across corpora of different health and life science domains—biology, chemistry, and medicine—available in different languages—English and French. Individual deep masked language models, pretrained on external corpora, are fined-tuned on task-specific domain and language corpora and ensembled using classical majority voting strategies. Experiments show statistically significant improvement of the ensemble models over an individual BERT-based baseline model, with an overall best performance of 77% macro F1-score. We further perform a detailed analysis of the ensemble results and show how their effectiveness changes according to entity properties, such as length, corpus frequency, and annotation consistency. The results suggest that the ensembles of deep masked language models are an effective strategy for tackling NER across corpora from the health and life science domains.