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Register a new userExtracting Symptoms and their Status from Clinical Conversations
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Izhak Shafran
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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This paper describes novel models tailored for a new application, that of extracting the symptoms mentioned in clinical conversations along with their status. Lack of any publicly available corpus in this privacy-sensitive domain led us to develop our own corpus, consisting of about 3K conversations annotated by professional medical scribes. We propose two novel deep learning approaches to infer the symptom names and their status: (1) a new hierarchical span-attribute tagging (SAT) model, trained using curriculum learning, and (2) a variant of sequence-to-sequence model which decodes the symptoms and their status from a few speaker turns within a sliding window over the conversation. This task stems from a realistic application of assisting medical providers in capturing symptoms mentioned by patients from their clinical conversations. To reflect this application, we define multiple metrics. From inter-rater agreement, we find that the task is inherently difficult. We conduct comprehensive evaluations on several contrasting conditions and observe that the performance of the models range from an F-score of 0.5 to 0.8 depending on the condition. Our analysis not only reveals the inherent challenges of the task, but also provides useful directions to improve the models.
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Recently we proposed the Span Attribute Tagging (SAT) Model (Du et al., 2019) to infer clinical entities (e.g., symptoms) and their properties (e.g., duration). It tackles the challenge of large label space and limited training data using a hierarchical two-stage approach that identifies the span of interest in a tagging step and assigns labels to the span in a classification step. We extend the SAT model to jointly infer not only entities and their properties but also relations between them. Most relation extraction models restrict inferring relations between tokens within a few neighboring sentences, mainly to avoid high computational complexity. In contrast, our proposed Relation-SAT (R-SAT) model is computationally efficient and can infer relations over the entire conversation, spanning an average duration of 10 minutes. We evaluate our model on a corpus of clinical conversations. When the entities are given, the R-SAT outperforms baselines in identifying relations between symptoms and their properties by about 32% (0.82 vs 0.62 F-score) and by about 50% (0.60 vs 0.41 F-score) on medications and their properties. On the more difficult task of jointly inferring entities and relations, the R-SAT model achieves a performance of 0.34 and 0.45 for symptoms and medications respectively, which is significantly better than 0.18 and 0.35 for the baseline model. The contributions of different components of the model are quantified using ablation analysis.
The best evidence concerning comparative treatment effectiveness comes from clinical trials, the results of which are reported in unstructured articles. Medical experts must manually extract information from articles to inform decision-making, which is time-consuming and expensive. Here we consider the end-to-end task of both (a) extracting treatments and outcomes from full-text articles describing clinical trials (entity identification) and, (b) inferring the reported results for the former with respect to the latter (relation extraction). We introduce new data for this task, and evaluate models that have recently achieved state-of-the-art results on similar tasks in Natural Language Processing. We then propose a new method motivated by how trial results are typically presented that outperforms these purely data-driven baselines. Finally, we run a fielded evaluation of the model with a non-profit seeking to identify existing drugs that might be re-purposed for cancer, showing the potential utility of end-to-end evidence extraction systems.
Extracting structured clinical information from free-text radiology reports can enable the use of radiology report information for a variety of critical healthcare applications. In our work, we present RadGraph, a dataset of entities and relations in full-text chest X-ray radiology reports based on a novel information extraction schema we designed to structure radiology reports. We release a development dataset, which contains board-certified radiologist annotations for 500 radiology reports from the MIMIC-CXR dataset (14,579 entities and 10,889 relations), and a test dataset, which contains two independent sets of board-certified radiologist annotations for 100 radiology reports split equally across the MIMIC-CXR and CheXpert datasets. Using these datasets, we train and test a deep learning model, RadGraph Benchmark, that achieves a micro F1 of 0.82 and 0.73 on relation extraction on the MIMIC-CXR and CheXpert test sets respectively. Additionally, we release an inference dataset, which contains annotations automatically generated by RadGraph Benchmark across 220,763 MIMIC-CXR reports (around 6 million entities and 4 million relations) and 500 CheXpert reports (13,783 entities and 9,908 relations) with mappings to associated chest radiographs. Our freely available dataset can facilitate a wide range of research in medical natural language processing, as well as computer vision and multi-modal learning when linked to chest radiographs.
With the rise of social media, millions of people are routinely expressing their moods, feelings, and daily struggles with mental health issues on social media platforms like Twitter. Unlike traditional observational cohort studies conducted through questionnaires and self-reported surveys, we explore the reliable detection of clinical depression from tweets obtained unobtrusively. Based on the analysis of tweets crawled from users with self-reported depressive symptoms in their Twitter profiles, we demonstrate the potential for detecting clinical depression symptoms which emulate the PHQ-9 questionnaire clinicians use today. Our study uses a semi-supervised statistical model to evaluate how the duration of these symptoms and their expression on Twitter (in terms of word usage patterns and topical preferences) align with the medical findings reported via the PHQ-9. Our proactive and automatic screening tool is able to identify clinical depressive symptoms with an accuracy of 68% and precision of 72%.
We focus on exploring various approaches of Zero-Shot Learning (ZSL) and their explainability for a challenging yet important supervised learning task notorious for training data scarcity, i.e. Depression Symptoms Detection (DSD) from text. We start with a comprehensive synthesis of different components of our ZSL modeling and analysis of our ground truth samples and Depression symptom clues curation process with the help of a practicing clinician. We next analyze the accuracy of various state-of-the-art ZSL models and their potential enhancements for our task. Further, we sketch a framework for the use of ZSL for hierarchical text-based explanation mechanism, which we call, Syntax Tree-Guided Semantic Explanation (STEP). Finally, we summarize experiments from which we conclude that we can use ZSL models and achieve reasonable accuracy and explainability, measured by a proposed Explainability Index (EI). This work is, to our knowledge, the first work to exhaustively explore the efficacy of ZSL models for DSD task, both in terms of accuracy and explainability.
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