Transforming Digital Phenotyping Raw Data Into Actionable Biomarkers, Quality Metrics, and Data Visualizations Using Cortex Software Package: Tutorial.

As digital phenotyping, the capture of active and passive data from consumer devices such as smartphones, becomes more common, the need to properly process the data and derive replicable features from it has become paramount. Cortex is an open-source data processing pipeline for digital phenotyping data, optimized for use with the mindLAMP apps, which is used by nearly 100 research teams across the world. Cortex is designed to help teams (1) assess digital phenotyping data quality in real time, (2) derive replicable clinical features from the data, and (3) enable easy-to-share data visualizations. Cortex offers many options to work with digital phenotyping data, although some common approaches are likely of value to all teams using it. This paper highlights the reasoning, code, and example steps necessary to fully work with digital phenotyping data in a streamlined manner. Covering how to work with the data, assess its quality, derive features, and visualize findings, this paper is designed to offer the reader the knowledge and skills to apply toward analyzing any digital phenotyping data set. More specifically, the paper will teach the reader the ins and outs of the Cortex Python package. This includes background information on its interaction with the mindLAMP platform, some basic commands to learn what data can be pulled and how, and more advanced use of the package mixed with basic Python with the goal of creating a correlation matrix. After the tutorial, different use cases of Cortex are discussed, along with limitations. Toward highlighting clinical applications, this paper also provides 3 easy ways to implement examples of Cortex use in real-world settings. By understanding how to work with digital phenotyping data and providing ready-to-deploy code with Cortex, the paper aims to show how the new field of digital phenotyping can be both accessible to all and rigorous in methodology.

Digital phenotyping correlates of mobile cognitive measures in schizophrenia: A multisite global mental health feasibility trial.

Traditional cognitive assessments in schizophrenia are time-consuming and necessitate specialized training, making routine evaluation challenging. To overcome these limitations, this study investigates the feasibility and advantages of utilizing smartphone-based assessments to capture both cognitive functioning and digital phenotyping data and compare these results to gold standard measures. We conducted a secondary analysis of data from 76 individuals with schizophrenia, who were recruited across three sites (one in Boston, two in India) was conducted. The open-source mindLAMP smartphone app captured digital phenotyping data and Trails A/B assessments of attention / memory for up to 12 months. The smartphone-cognitive tasks exhibited potential for normal distribution and these scores showed small but significant correlations with the results from the Brief Assessment of Cognition in Schizophrenia, especially the digital span and symbol coding tasks (r2 = 0.21). A small but significant correlation (r2 = 0.29) between smartphone-derived cognitive scores and health-related behaviors such as sleep duration patterns was observed. Smartphone-based cognitive assessments show promise as cross-cultural tools that can capture relevant data on momentary states among individuals with schizophrenia. Cognitive results related to sleep suggest functional applications to digital phenotyping data, and the potential of this multimodal data approach in research.

Classifying and clustering mood disorder patients using smartphone data from a feasibility study.

Differentiating between bipolar disorder and major depressive disorder can be challenging for clinicians. The diagnostic process might benefit from new ways of monitoring the phenotypes of these disorders. Smartphone data might offer insight in this regard. Today, smartphones collect dense, multimodal data from which behavioral metrics can be derived. Distinct patterns in these metrics have the potential to differentiate the two conditions. To examine the feasibility of smartphone-based phenotyping, two study sites (Mayo Clinic, Johns Hopkins University) recruited patients with bipolar I disorder (BPI), bipolar II disorder (BPII), major depressive disorder (MDD), and undiagnosed controls for a 12-week observational study. On their smartphones, study participants used a digital phenotyping app (mindLAMP) for data collection. While in use, mindLAMP gathered real-time geolocation, accelerometer, and screen-state (on/off) data. mindLAMP was also used for EMA delivery. MindLAMP data was then used as input variables in binary classification, three-group k-nearest neighbors (KNN) classification, and k-means clustering. The best-performing binary classification model was able to classify patients as control or non-control with an AUC of 0.91 (random forest). The model that performed best at classifying patients as having MDD or bipolar I/II had an AUC of 0.62 (logistic regression). The k-means clustering model had a silhouette score of 0.46 and an ARI of 0.27. Results support the potential for digital phenotyping methods to cluster depression, bipolar disorder, and healthy controls. However, due to inconsistencies in accuracy, more data streams are required before these methods can be applied to clinical practice.

Digital Phenotyping for Mood Disorders: Methodology-Oriented Pilot Feasibility Study.

BACKGROUND: In the burgeoning area of clinical digital phenotyping research, there is a dearth of literature that details methodology, including the key challenges and dilemmas in developing and implementing a successful architecture for technological infrastructure, patient engagement, longitudinal study participation, and successful reporting and analysis of diverse passive and active digital data streams. OBJECTIVE: This article provides a narrative rationale for our study design in the context of the current evidence base and best practices, with an emphasis on our initial lessons learned from the implementation challenges and successes of this digital phenotyping study. METHODS: We describe the design and implementation approach for a digital phenotyping pilot feasibility study with attention to synthesizing key literature and the reasoning for pragmatic adaptations in implementing a multisite study encompassing distinct geographic and population settings. This methodology was used to recruit patients as study participants with a clinician-validated diagnostic history of unipolar depression, bipolar I disorder, or bipolar II disorder, or healthy controls in 2 geographically distinct health care systems for a longitudinal digital phenotyping study of mood disorders. RESULTS: We describe the feasibility of a multisite digital phenotyping pilot study for patients with mood disorders in terms of passively and actively collected phenotyping data quality and enrollment of patients. Overall data quality (assessed as the amount of sensor data obtained vs expected) was high compared to that in related studies. Results were reported on the relevant demographic features of study participants, revealing recruitment properties of age (mean subgroup age ranged from 31 years in the healthy control subgroup to 38 years in the bipolar I disorder subgroup), sex (predominance of female participants, with 7/11, 64% females in the bipolar II disorder subgroup), and smartphone operating system (iOS vs Android; iOS ranged from 7/11, 64% in the bipolar II disorder subgroup to 29/32, 91% in the healthy control subgroup). We also described implementation considerations around digital phenotyping research for mood disorders and other psychiatric conditions. CONCLUSIONS: Digital phenotyping in affective disorders is feasible on both Android and iOS smartphones, and the resulting data quality using an open-source platform is higher than that in comparable studies. While the digital phenotyping data quality was independent of gender and race, the reported demographic features of study participants revealed important information on possible selection biases that may result from naturalistic research in this domain. We believe that the methodology described will be readily reproducible and generalizable to other study settings and patient populations given our data on deployment at 2 unique sites.

Exploring the Potential of Apple SensorKit and Digital Phenotyping Data as New Digital Biomarkers for Mental Health Research.

The use of digital phenotyping continues to expand across all fields of health. By collecting quantitative data in real-time using devices such as smartphones or smartwatches, researchers and clinicians can develop a profile of a wide range of conditions. Smartphones contain sensors that collect data, such as GPS or accelerometer data, which can inform secondary metrics such as time spent at home, location entropy, or even sleep duration. These metrics, when used as digital biomarkers, are not only used to investigate the relationship between behavior and health symptoms but can also be used to support personalized and preventative care. Successful phenotyping requires consistent long-term collection of relevant and high-quality data. In this paper, we present the potential of newly available, for approved research, opt-in SensorKit sensors on iOS devices in improving the accuracy of digital phenotyping. We collected opt-in sensor data over 1 week from a single person with depression using the open-source mindLAMP app developed by the Division of Digital Psychiatry at Beth Israel Deaconess Medical Center. Five sensors from SensorKit were included. The names of the sensors, as listed in official documentation, include the following: phone usage, messages usage, visits, device usage, and ambient light. We compared data from these five new sensors from SensorKit to our current digital phenotyping data collection sensors to assess similarity and differences in both raw and processed data. We present sample data from all five of these new sensors. We also present sample data from current digital phenotyping sources and compare these data to SensorKit sensors when applicable. SensorKit offers great potential for health research. Many SensorKit sensors improve upon previously accessible features and produce data that appears clinically relevant. SensorKit sensors will likely play a substantial role in digital phenotyping. However, using these data requires advanced health app infrastructure and the ability to securely store high-frequency data.

Monitoring sleep using smartphone data in a population of college students.

Sleep is fundamental to all health, especially mental health. Monitoring sleep is thus critical to delivering effective healthcare. However, measuring sleep in a scalable way remains a clinical challenge because wearable sleep-monitoring devices are not affordable or accessible to the majority of the population. However, as consumer devices like smartphones become increasingly powerful and accessible in the United States, monitoring sleep using smartphone patterns offers a feasible and scalable alternative to wearable devices. In this study, we analyze the sleep behavior of 67 college students with elevated levels of stress over 28 days. While using the open-source mindLAMP smartphone app to complete daily and weekly sleep and mental health surveys, these participants also passively collected phone sensor data. We used these passive sensor data streams to estimate sleep duration. These sensor-based sleep duration estimates, when averaged for each participant, were correlated with self-reported sleep duration (r = 0.83). We later constructed a simple predictive model using both sensor-based sleep duration estimates and surveys as predictor variables. This model demonstrated the ability to predict survey-reported Pittsburgh Sleep Quality Index (PSQI) scores within 1 point. Overall, our results suggest that smartphone-derived sleep duration estimates offer practical results for estimating sleep duration and can also serve useful functions in the process of digital phenotyping.