Adaptive Multi-Channel Event Segmentation and Feature Extraction for Monitoring Health Outcomes

A Systematic Review of Time Series Classification Techniques Used in Biomedical Applications

Background: Digital clinical measures collected via various digital sensing technologies such as smartphones, smartwatches, wearables, and ingestible and implantable sensors are increasingly used by individuals and clinicians to capture the health outcomes or behavioral and physiological characteristics of individuals. Time series classification (TSC) is very commonly used for modeling digital clinical measures. While deep learning models for TSC are very common and powerful, there exist some fundamental challenges. This review presents the non-deep learning models that are commonly used for time series classification in biomedical applications that can achieve high performance. Objective: We performed a systematic review to characterize the techniques that are used in time series classification of digital clinical measures throughout all the stages of data processing and model building. Methods: We conducted a literature search on PubMed, as well as the Institute of Electrical and Electronics Engineers (IEEE), Web of Science, and SCOPUS databases using a range of search terms to retrieve peer-reviewed articles that report on the academic research about digital clinical measures from a five-year period between June 2016 and June 2021. We identified and categorized the research studies based on the types of classification algorithms and sensor input types. Results: We found 452 papers in total from four different databases: PubMed, IEEE, Web of Science Database, and SCOPUS. After removing duplicates and irrelevant papers, 135 articles remained for detailed review and data extraction. Among these, engineered features using time series methods that were subsequently fed into widely used machine learning classifiers were the most commonly used technique, and also most frequently achieved the best performance metrics (77 out of 135 articles). Statistical modeling (24 out of 135 articles) algorithms were the second most common and also the second-best classification technique. Conclusions: In this review paper, summaries of the time series classification models and interpretation methods for biomedical applications are summarized and categorized. While high time series classification performance has been achieved in digital clinical, physiological, or biomedical measures, no standard benchmark datasets, modeling methods, or reporting methodology exist. There is no single widely used method for time series model development or feature interpretation, however many different methods have proven successful.

A Pattern Dictionary Method for Anomaly Detection

In this paper, we propose a compression-based anomaly detection method for time series and sequence data using a pattern dictionary. The proposed method is capable of learning complex patterns in a training data sequence, using these learned patterns to detect potentially anomalous patterns in a test data sequence. The proposed pattern dictionary method uses a measure of complexity of the test sequence as an anomaly score that can be used to perform stand-alone anomaly detection. We also show that when combined with a universal source coder, the proposed pattern dictionary yields a powerful atypicality detector that is equally applicable to anomaly detection. The pattern dictionary-based atypicality detector uses an anomaly score defined as the difference between the complexity of the test sequence data encoded by the trained pattern dictionary (typical) encoder and the universal (atypical) encoder, respectively. We consider two complexity measures: the number of parsed phrases in the sequence, and the length of the encoded sequence (codelength). Specializing to a particular type of universal encoder, the Tree-Structured Lempel-Ziv (LZ78), we obtain a novel non-asymptotic upper bound, in terms of the Lambert W function, on the number of distinct phrases resulting from the LZ78 parser. This non-asymptotic bound determines the range of anomaly score. As a concrete application, we illustrate the pattern dictionary framework for constructing a baseline of health against which anomalous deviations can be detected.

Assessment of the Feasibility of Using Noninvasive Wearable Biometric Monitoring Sensors to Detect Influenza and the Common Cold Before Symptom Onset

IMPORTANCE

Currently, there are no presymptomatic screening methods to identify individuals infected with a respiratory virus to prevent disease spread and to predict their trajectory for resource allocation.

OBJECTIVE

To evaluate the feasibility of using noninvasive, wrist-worn wearable biometric monitoring sensors to detect presymptomatic viral infection after exposure and predict infection severity in patients exposed to H1N1 influenza or human rhinovirus.

DESIGN, SETTING, AND PARTICIPANTS

The cohort H1N1 viral challenge study was conducted during 2018; data were collected from September 11, 2017, to May 4, 2018. The cohort rhinovirus challenge study was conducted during 2015; data were collected from September 14 to 21, 2015. A total of 39 adult participants were recruited for the H1N1 challenge study, and 24 adult participants were recruited for the rhinovirus challenge study. Exclusion criteria for both challenges included chronic respiratory illness and high levels of serum antibodies. Participants in the H1N1 challenge study were isolated in a clinic for a minimum of 8 days after inoculation. The rhinovirus challenge took place on a college campus, and participants were not isolated.

EXPOSURES

Participants in the H1N1 challenge study were inoculated via intranasal drops of diluted influenza A/California/03/09 (H1N1) virus with a mean count of 106 using the median tissue culture infectious dose (TCID50) assay. Participants in the rhinovirus challenge study were inoculated via intranasal drops of diluted human rhinovirus strain type 16 with a count of 100 using the TCID50 assay.

MAIN OUTCOMES AND MEASURES

The primary outcome measures included cross-validated performance metrics of random forest models to screen for presymptomatic infection and predict infection severity, including accuracy, precision, sensitivity, specificity, F1 score, and area under the receiver operating characteristic curve (AUC).

RESULTS

A total of 31 participants with H1N1 (24 men [77.4%]; mean [SD] age, 34.7 [12.3] years) and 18 participants with rhinovirus (11 men [61.1%]; mean [SD] age, 21.7 [3.1] years) were included in the analysis after data preprocessing. Separate H1N1 and rhinovirus detection models, using only data on wearble devices as input, were able to distinguish between infection and noninfection with accuracies of up to 92% for H1N1 (90% precision, 90% sensitivity, 93% specificity, and 90% F1 score, 0.85 [95% CI, 0.70-1.00] AUC) and 88% for rhinovirus (100% precision, 78% sensitivity, 100% specificity, 88% F1 score, and 0.96 [95% CI, 0.85-1.00] AUC). The infection severity prediction model was able to distinguish between mild and moderate infection 24 hours prior to symptom onset with an accuracy of 90% for H1N1 (88% precision, 88% sensitivity, 92% specificity, 88% F1 score, and 0.88 [95% CI, 0.72-1.00] AUC) and 89% for rhinovirus (100% precision, 75% sensitivity, 100% specificity, 86% F1 score, and 0.95 [95% CI, 0.79-1.00] AUC).

CONCLUSIONS AND RELEVANCE

This cohort study suggests that the use of a noninvasive, wrist-worn wearable device to predict an individual's response to viral exposure prior to symptoms is feasible. Harnessing this technology would support early interventions to limit presymptomatic spread of viral respiratory infections, which is timely in the era of COVID-19.