Lightweight transformers for clinical natural language processing

Specialised pre-trained language models are becoming more frequent in Natural language Processing (NLP) since they can potentially outperform models trained on generic texts. BioBERT (Sanh et al., Distilbert, a distilled version of bert: smaller, faster, cheaper and lighter. arXiv preprint arXiv: 1910.01108, 2019) and BioClinicalBERT (Alsentzer et al., Publicly available clinical bert embeddings. In Proceedings of the 2nd Clinical Natural Language Processing Workshop, pp. 72–78, 2019) are two examples of such models that have shown promise in medical NLP tasks. Many of these models are overparametrised and resource-intensive, but thanks to techniques like knowledge distillation, it is possible to create smaller versions that perform almost as well as their larger counterparts. In this work, we specifically focus on development of compact language models for processing clinical texts (i.e. progress notes, discharge summaries, etc). We developed a number of efficient lightweight clinical transformers using knowledge distillation and continual learning, with the number of parameters ranging from million to million. These models performed comparably to larger models such as BioBERT and ClinicalBioBERT and significantly outperformed other compact models trained on general or biomedical data. Our extensive evaluation was done across several standard datasets and covered a wide range of clinical text-mining tasks, including natural language inference, relation extraction, named entity recognition and sequence classification. To our knowledge, this is the first comprehensive study specifically focused on creating efficient and compact transformers for clinical NLP tasks. The models and code used in this study can be found on our Huggingface profile at https://huggingface.co/nlpie and Github page at https://github.com/nlpie-research/Lightweight-Clinical-Transformers, respectively, promoting reproducibility of our results

Clustering Italian medical texts: a case study on referrals

In the medical domain, there is a large amount of valuable information that is stored in textual format. These unstructured data have long been ignored, due to the difficulties of introducing them in statistical models, but in the last years, the field of Natural Language Processing (NLP) has seen relevant improvements, with models capable of achieving relevant results in various tasks, including information extraction, classification and clustering. NLP models are typically language-specific and often domain-specific, but most of the work to date has been focused on the English language, especially in the medical domain. In this work, we propose a pipeline for clustering Italian medical texts, with a case study on clinical questions reported in referral

Assessing mortality prediction through different representation models based on concepts extracted from clinical notes

Recent years have seen particular interest in using electronic medical records (EMRs) for secondary purposes to enhance the quality and safety of healthcare delivery. EMRs tend to contain large amounts of valuable clinical notes. Learning of embedding is a method for converting notes into a format that makes them comparable. Transformer-based representation models have recently made a great leap forward. These models are pre-trained on large online datasets to understand natural language texts effectively. The quality of a learning embedding is influenced by how clinical notes are used as input to representation models. A clinical note has several sections with different levels of information value. It is also common for healthcare providers to use different expressions for the same concept. Existing methods use clinical notes directly or with an initial preprocessing as input to representation models. However, to learn a good embedding, we identified the most essential clinical notes section. We then mapped the extracted concepts from selected sections to the standard names in the Unified Medical Language System (UMLS). We used the standard phrases corresponding to the unique concepts as input for clinical models. We performed experiments to measure the usefulness of the learned embedding vectors in the task of hospital mortality prediction on a subset of the publicly available Medical Information Mart for Intensive Care (MIMIC-III) dataset. According to the experiments, clinical transformer-based representation models produced better results with getting input generated by standard names of extracted unique concepts compared to other input formats. The best-performing models were BioBERT, PubMedBERT, and UmlsBERT, respectively