David L. Buckeridge

Ziyang Song, Qincheng Lu, Hao Xu et al.

Large-scale pre-trained models (PTMs) such as BERT and GPT have recently achieved great success in Natural Language Processing and Computer Vision domains. However, the development of PTMs on healthcare time-series data is lagging behind.This underscores the limitations of the existing transformer-based architectures, particularly their scalability to handle large-scale time series and ability to capture long-term temporal dependencies. In this study, we present Timely Generative Pre-trained Transformer (TimelyGPT). TimelyGPT employs an extrapolatable position (xPos) embedding to encode trend and periodic patterns into time-series representations. It also integrates recurrent attention and temporal convolution modules to effectively capture global-local temporal dependencies. We evaluated TimelyGPT on two large-scale healthcare time series datasets corresponding to continuous biosignals and irregularly-sampled time series, respectively. Our experiments show that during pre-training, TimelyGPT excels in learning time-series representations from continuously monitored biosignals and irregularly-sampled time series data commonly observed in longitudinal electronic health records (EHRs). In forecasting continuous biosignals, TimelyGPT achieves accurate extrapolation up to 6,000 timesteps of body temperature during the sleep stage transition, given a short look-up window (i.e., prompt) containing only 2,000 timesteps. For irregularly-sampled time series, TimelyGPT with a proposed time-specific inference demonstrates high top recall scores in predicting future diagnoses using early diagnostic records, effectively handling irregular intervals between clinical records. Together, we envision TimelyGPT to be useful in a broad spectrum of health domains, including long-term patient health state forecasting and patient risk trajectory prediction.

Nii Antiaye Addy, Arash Shaban-Nejad, David L. Buckeridge et al.

The purpose of this paper is to describe and analyze the development of a knowledge-based infrastructure to support MSP decision-making processes. The paper emerged from a study to define specifications for a knowledge-based infrastructure to provide decision support for community-level MSPs in the Canadian province of Quebec. As part of the study, a process assessment was conducted to understand the needs of communities as they collect, organize, and analyze data to make decisions about their priorities. The result of this process is a portrait, which is an epidemiological profile of health and nutrition in their community. Portraits inform strategic planning and development of interventions and are used to assess the impact of interventions. Our key findings indicate ambiguities and disagreement among MSP decision-makers regarding causal relationships between actions and outcomes, and the relevant data needed for making decisions. MSP decision-makers expressed a desire for easy-to-use tools that facilitate the collection, organization, synthesis, and analysis of data, to enable decision-making in a timely manner. Findings inform conceptual modeling and ontological analysis to capture the domain knowledge and specify relationships between actions and outcomes. This modeling and analysis provide the foundation for an ontology, encoded using OWL 2 Web Ontology Language. The ontology is developed to provide semantic support for the MSP process, defining objectives, strategies, actions, indicators, and data sources. In the future, software interacting with the ontology can facilitate interactive browsing by decision-makers in the MSP in the form of concepts, instances, relationships, and axioms. Our ontology also facilitates the integration and interpretation of community data and can help in managing semantic interoperability between different knowledge sources.

Aman Verma, Guido Powell, Yu Luo et al.

Modeling disease progression in healthcare administrative databases is complicated by the fact that patients are observed only at irregular intervals when they seek healthcare services. In a longitudinal cohort of 76,888 patients with chronic obstructive pulmonary disease (COPD), we used a continuous-time hidden Markov model with a generalized linear model to model healthcare utilization events. We found that the fitted model provides interpretable results suitable for summarization and hypothesis generation.