Temporal disambiguation of relative temporal expressions in clinical texts using temporally fine-tuned contextual word embeddings.

Temporal reasoning is the ability to extract and assimilate temporal information to reconstruct a series of events such that they can be reasoned over to answer questions involving time. Temporal reasoning in the clinical domain is challenging due to specialized medical terms and nomenclature, shorthand notation, fragmented text, a variety of writing styles used by different medical units, redundancy of information that has to be reconciled, and an increased number of temporal references as compared to general domain texts. Work in the area of clinical temporal reasoning has progressed, but the current state-of-the-art still has a ways to go before practical application in the clinical setting will be possible. Much of the current work in this field is focused on direct and explicit temporal expressions and identifying temporal relations. However, there is little work focused on relative temporal expressions, which can be difficult to normalize, but are vital to ordering events on a timeline. This work introduces a new temporal expression recognition and normalization tool, Chrono, that normalizes temporal expressions into both SCATE and TimeML schemes. Chrono advances clinical timeline extraction as it is capable of identifying more vague and relative temporal expressions than the current state-of-the-art and utilizes contextualized word embeddings from fine-tuned BERT models to disambiguate temporal types, which achieves state-of-the-art performance on relative temporal expressions. In addition, this work shows that fine-tuning BERT models on temporal tasks modifies the contextualized embeddings so that they achieve improved performance in classical SVM and CNN classifiers. Finally, this works provides a new tool for linking temporal expressions to events or other entities by introducing a novel method to identify which tokens an entire temporal expression is paying the most attention to by summarizing the attention weight matrices output by BERT models

Extracting Temporal and Causal Relations between Events

Structured information resulting from temporal information processing is crucial for a variety of natural language processing tasks, for instance to generate timeline summarization of events from news documents, or to answer temporal/causal-related questions about some events. In this thesis we present a framework for an integrated temporal and causal relation extraction system. We first develop a robust extraction component for each type of relations, i.e. temporal order and causality. We then combine the two extraction components into an integrated relation extraction system, CATENA---CAusal and Temporal relation Extraction from NAtural language texts---, by utilizing the presumption about event precedence in causality, that causing events must happened BEFORE resulting events. Several resources and techniques to improve our relation extraction systems are also discussed, including word embeddings and training data expansion. Finally, we report our adaptation efforts of temporal information processing for languages other than English, namely Italian and Indonesian.Comment: PhD Thesi

Natural Language Processing and Temporal Information Extraction in Emergency Department Triage Notes

Electronic patient records, including the Emergency Department (ED) Triage Note (TN), provide a rich source of textual information. Processing clinical texts to create important pieces of structured information will be useful to clinicians treating patients, clinicians in training, and researchers and practitioners in biosurveillance. This work applies natural language processing (NLP) and information extraction (IE) techniques to the TN genre of text. In particular, it presents the Triage Note Temporal Information Extraction System (TN-TIES), which combines a shallow parser, machine learned classifiers, and handwritten rules to identify, extract, and interpret temporal information in TNs in preparation for the automatic creation of a timeline of events leading up to a patient's visit to the ED. The success of TN-TIES suggests that NLP and IE techniques are appropriate for the genre and that the automatic production of a timeline of TN events is a realistic application

2022 SDSU Data Science Symposium Presentation Abstracts

This document contains abstracts for presentations and posters 2022 SDSU Data Science Symposium

2022 SDSU Data Science Symposium Presentation Abstracts

This document contains abstracts for presentations and posters 2022 SDSU Data Science Symposium