Predicting COVID-19 and pneumonia complications from admission texts

In this paper we present a novel approach to risk assessment for patients hospitalized with pneumonia or COVID-19 based on their admission reports. We applied a Longformer neural network to admission reports and other textual data available shortly after admission to compute risk scores for the patients. We used patient data of multiple European hospitals to demonstrate that our approach outperforms the Transformer baselines. Our experiments show that the proposed model generalises across institutions and diagnoses. Also, our method has several other advantages described in the paper.

RuBioRoBERTa: a pre-trained biomedical language model for Russian language biomedical text mining

This paper presents several BERT-based models for Russian language biomedical text mining (RuBioBERT, RuBioRoBERTa). The models are pre-trained on a corpus of freely available texts in the Russian biomedical domain. With this pre-training, our models demonstrate state-of-the-art results on RuMedBench - Russian medical language understanding benchmark that covers a diverse set of tasks, including text classification, question answering, natural language inference, and named entity recognition.

Distantly supervised end-to-end medical entity extraction from electronic health records with human-level quality

Medical entity extraction (EE) is a standard procedure used as a first stage in medical texts processing. Usually Medical EE is a two-step process: named entity recognition (NER) and named entity normalization (NEN). We propose a novel method of doing medical EE from electronic health records (EHR) as a single-step multi-label classification task by fine-tuning a transformer model pretrained on a large EHR dataset. Our model is trained end-to-end in an distantly supervised manner using targets automatically extracted from medical knowledge base. We show that our model learns to generalize for entities that are present frequently enough, achieving human-level classification quality for most frequent entities. Our work demonstrates that medical entity extraction can be done end-to-end without human supervision and with human quality given the availability of a large enough amount of unlabeled EHR and a medical knowledge base.