Temporal reasoning with medical data--a review with emphasis on medical natural language processing

Abstract

Temporal information is crucial in electronic medical records and biomedical information systems. Processing temporal information in medical narrative data is a very challenging area. It lies at the intersection of temporal representation and reasoning (TRR) in artificial intelligence and medical natural language processing (MLP). Some fundamental concepts and important issues in relation to TRR have previously been discussed, mainly in the context of processing structured data in biomedical informatics; however, it is important that these concepts be re-examined in the context of processing narrative data using MLP. Theoretical and methodological TRR studies in biomedical informatics can be classified into three main categories: category 1 applies theories and models from temporal reasoning in AI; category 2 defines frameworks that meet needs from clinical applications; category 3 resolves issues such as temporal granularity and uncertainty. Currently, most MLP systems are not designed with a formal representation of time, and their ability to reason about temporal relations among medical events is limited. Previous work in processing time with clinical narrative data includes processing time in clinical reports, modeling textual temporal expressions in clinical databases, processing time in clinical guidelines, and building time standards for data exchange and integration. In addition to common problems in MLP, there are challenges specific to TRR in medical text, which occur at each level of linguistic structure and analysis. Despite advances in temporal reasoning in biomedical informatics, processing time in medical text deserves more attention. Besides the need for more research in temporal granularity, fuzzy time, temporal contradiction, intermittent events and uncertainty, broad areas for future research include enhancing functions of current MLP systems on processing temporal information, incorporating medical knowledge into temporal reasoning systems, resolving coreference, integrating narrative data with structured data and evaluating these systems.

Figures

Figure 1.

Types of Processes (adapted from [53])

Figure 2.

Levels of linguistic structure and analysis (see details in section 4.1), and related challenges in processing time in medical text (see details in section 4.3)

Figure 3.

A simple timeline and selected work of processing temporal information in natural language

Figure 4.

Time representation for medical text in “the time program” (adapted from [204])

Figure 5.

Time representation for medical text in GROK system (adapted from [206])

Figure 6:

A simplified XML output of MedLEE. In this case temporal information is tagged using semantic types “date”, “reltime” and “status.” The output also contains other contextual information.

Figure 7.

(Adapted from [8]) Example temporal expression “his cough started at least two weeks before admission” modeled on a time line, depicting the event “cough” anchored by “admission.” The bars represent the vagueness of the temporal information, which widen the limits of the constraints.

Figure 8.

A statement encoded using TSMI standard (adapted from [233])

Figure 9.

Input to temporal abstraction tasks from structured data and narrative data