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Register a new userRare Disease Identification from Clinical Notes with Ontologies and Weak Supervision
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Added by
Hang Dong
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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The identification of rare diseases from clinical notes with Natural Language Processing (NLP) is challenging due to the few cases available for machine learning and the need of data annotation from clinical experts. We propose a method using ontologies and weak supervision. The approach includes two steps: (i) Text-to-UMLS, linking text mentions to concepts in Unified Medical Language System (UMLS), with a named entity linking tool (e.g. SemEHR) and weak supervision based on customised rules and Bidirectional Encoder Representations from Transformers (BERT) based contextual representations, and (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). Using MIMIC-III US intensive care discharge summaries as a case study, we show that the Text-to-UMLS process can be greatly improved with weak supervision, without any annotated data from domain experts. Our analysis shows that the overall pipeline processing discharge summaries can surface rare disease cases, which are mostly uncaptured in manual ICD codes of the hospital admissions.
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Current deep learning based disease diagnosis systems usually fall short in catastrophic forgetting, i.e., directly fine-tuning the disease diagnosis model on new tasks usually leads to abrupt decay of performance on previous tasks. What is worse, the trained diagnosis system would be fixed once deployed but collecting training data that covers enough diseases is infeasible, which inspires us to develop a lifelong learning diagnosis system. In this work, we propose to adopt attention to combine medical entities and context, embedding episodic memory and consolidation to retain knowledge, such that the learned model is capable of adapting to sequential disease-diagnosis tasks. Moreover, we establish a new benchmark, named Jarvis-40, which contains clinical notes collected from various hospitals. Our experiments show that the proposed method can achieve state-of-the-art performance on the proposed benchmark.
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In a large-scale knowledge graph (KG), an entity is often described by a large number of triple-structured facts. Many applications require abridge
Recently, there is an effort to extend fine-grained entity typing by using a richer and ultra-fine set of types, and labeling noun phrases including pronouns and nominal nouns instead of just named entity mentions. A key challenge for this ultra-fine entity typing task is that human annotated data are extremely scarce, and the annotation ability of existing distant or weak supervision approaches is very limited. To remedy this problem, in this paper, we propose to obtain training data for ultra-fine entity typing by using a BERT Masked Language Model (MLM). Given a mention in a sentence, our approach constructs an input for the BERT MLM so that it predicts context dependent hypernyms of the mention, which can be used as type labels. Experimental results demonstrate that, with the help of these automatically generated labels, the performance of an ultra-fine entity typing model can be improved substantially. We also show that our approach can be applied to improve traditional fine-grained entity typing after performing simple type mapping.
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