Ontology-driven and weakly supervised rare disease identification from clinical notes

BACKGROUND: Computational text phenotyping is the practice of identifying patients with certain disorders and traits from clinical notes. Rare diseases are challenging to be identified due to few cases available for machine learning and the need for data annotation from domain experts. METHODS: We propose a method using ontologies and weak supervision, with recent pre-trained contextual representations from Bi-directional Transformers (e.g. BERT). The ontology-driven framework includes two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking mentions to concepts in Unified Medical Language System (UMLS), with a Named Entity Recognition and Linking (NER+L) tool, SemEHR, and weak supervision with customised rules and contextual mention representation; (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). The weakly supervised approach is proposed to learn a phenotype confirmation model to improve Text-to-UMLS linking, without annotated data from domain experts. We evaluated the approach on three clinical datasets, MIMIC-III discharge summaries, MIMIC-III radiology reports, and NHS Tayside brain imaging reports from two institutions in the US and the UK, with annotations. RESULTS: The improvements in the precision were pronounced (by over 30% to 50% absolute score for Text-to-UMLS linking), with almost no loss of recall compared to the existing NER+L tool, SemEHR. Results on radiology reports from MIMIC-III and NHS Tayside were consistent with the discharge summaries. The overall pipeline processing clinical notes can extract rare disease cases, mostly uncaptured in structured data (manually assigned ICD codes). CONCLUSION: The study provides empirical evidence for the task by applying a weakly supervised NLP pipeline on clinical notes. The proposed weak supervised deep learning approach requires no human annotation except for validation and testing, by leveraging ontologies, NER+L tools, and contextual representations. The study also demonstrates that Natural Language Processing (NLP) can complement traditional ICD-based approaches to better estimate rare diseases in clinical notes. We discuss the usefulness and limitations of the weak supervision approach and propose directions for future studies

Rare Disease Identification from Clinical Notes with Ontologies and Weak Supervision

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.Comment: 5 pages, 3 figures, accepted for IEEE EMBC 202

Binary Classification with Positive Labeling Sources

To create a large amount of training labels for machine learning models effectively and efficiently, researchers have turned to Weak Supervision (WS), which uses programmatic labeling sources rather than manual annotation. Existing works of WS for binary classification typically assume the presence of labeling sources that are able to assign both positive and negative labels to data in roughly balanced proportions. However, for many tasks of interest where there is a minority positive class, negative examples could be too diverse for developers to generate indicative labeling sources. Thus, in this work, we study the application of WS on binary classification tasks with positive labeling sources only. We propose WEAPO, a simple yet competitive WS method for producing training labels without negative labeling sources. On 10 benchmark datasets, we show WEAPO achieves the highest averaged performance in terms of both the quality of synthesized labels and the performance of the final classifier supervised with these labels. We incorporated the implementation of \method into WRENCH, an existing benchmarking platform.Comment: CIKM 2022 (short

When Silver Is As Good As Gold: Using Weak Supervision to Train Machine Learning Models on Social Media Data

Over the last decade, advances in machine learning have led to an exponential growth in artificial intelligence i.e., machine learning models capable of learning from vast amounts of data to perform several tasks such as text classification, regression, machine translation, speech recognition, and many others. While massive volumes of data are available, due to the manual curation process involved in the generation of training datasets, only a percentage of the data is used to train machine learning models. The process of labeling data with a ground-truth value is extremely tedious, expensive, and is the major bottleneck of supervised learning. To curtail this, the theory of noisy learning can be employed where data labeled through heuristics, knowledge bases and weak classifiers can be utilized for training, instead of data obtained through manual annotation. The assumption here is that a large volume of training data, which contains noise and acquired through an automated process, can compensate for the lack of manual labels. In this study, we utilize heuristic based approaches to create noisy silver standard datasets. We extensively tested the theory of noisy learning on four different applications by training several machine learning models using the silver standard dataset with several sample sizes and class imbalances and tested the performance using a gold standard dataset. Our evaluations on the four applications indicate the success of silver standard datasets in identifying a gold standard dataset. We conclude the study with evidence that noisy social media data can be utilized for weak supervisio