Single-subject health data are becoming increasingly available thanks to advances in self-tracking technology (e.g., wearable devices, mobile apps, sensors, implants). Many users and health caregivers seek to use such observational time series data to recommend changing health practices in order to achieve desired health outcomes. However, there are few available causal inference approaches that are flexible enough to analyze such idiographic data. We develop a recently introduced causal-analysis framework based on n-of-1 randomized trials, and implement a flexible random-forests g-formula approach to estimating a recurring individualized effect called the "average period treatment effect". In the process, we argue that our approach essentially resembles that of a longitudinal study by partitioning a single time series into periods taking on binary treatment levels. We analyze six years of the author's own self-tracked physical activity and weight data to demonstrate our approach, and compare the results of our analysis to one that does not properly account for confounding.
Analyses of biomedical studies often necessitate modeling longitudinal causal effects. The current focus on personalized medicine and effect heterogeneity makes this task even more challenging. Towards this end, structural nested mean models (SNMMs) are fundamental tools for studying heterogeneous treatment effects in longitudinal studies. However, when outcomes are binary, current methods for estimating multiplicative and additive SNMM parameters suffer from variation dependence between the causal parameters and the non-causal nuisance parameters. This leads to a series of difficulties in int…
Personalized longitudinal disease assessment is central to quickly diagnosing, appropriately managing, and optimally adapting the therapeutic strategy of multiple sclerosis (MS). It is also important for identifying the idiosyncratic subject-specific disease profiles. Here, we design a novel longitudinal model to map individual disease trajectories in an automated way using sensor data that may contain missing values. First, we collect digital measurements related to gait and balance, and upper extremity functions using sensor-based assessments administered on a smartphone. Next, we treat miss…
The menstrual cycle is a key indicator of overall health for women of reproductive age. Previously, menstruation was primarily studied through survey results; however, as menstrual tracking mobile apps become more widely adopted, they provide an increasingly large, content-rich source of menstrual health experiences and behaviors over time. By exploring a database of user-tracked observations from the Clue app by BioWink of over 378,000 users and 4.9 million natural cycles, we show that self-reported menstrual tracker data can reveal statistically significant relationships between per-person c…
Sequence analysis is an increasingly popular approach for analysing life courses represented by ordered collections of activities experienced by subjects over time. Here, we analyse a survey data set containing information on the career trajectories of a cohort of Northern Irish youths tracked between the ages of 16 and 22. We propose a novel, model-based clustering approach suited to the analysis of such data from a holistic perspective, with the aims of estimating the number of typical career trajectories, identifying the relevant features of these patterns, and assessing the extent to which…
Longitudinal (panel) data provide the opportunity to examine temporal patterns of individuals, because measurements are collected on the same person at different, and often irregular, time points. The data is typically visualised using a "spaghetti plot", where a line plot is drawn for each individual. When overlaid in one plot, it can have the appearance of a bowl of spaghetti. With even a small number of subjects, these plots are too overloaded to be read easily. The interesting aspects of individual differences are lost in the noise. Longitudinal data is often modelled with a hierarchical l…
As we gain access to a greater depth and range of health-related information about individuals, three questions arise: (1) Can we build better models to predict individual-level risk of ill health? (2) How much data do we need to effectively predict ill health? (3) Are new methods required to process the added complexity that new forms of data bring? The aim of the study is to apply a machine learning approach to identify the relative contribution of personal, social, health-related, biomarker and genetic data as predictors of future health in individuals. Using longitudinal data from 6830 ind…
The focus of this paper is an approach to the modeling of longitudinal social network or relational data. Such data arise from measurements on pairs of objects or actors made at regular temporal intervals, resulting in a social network for each point in time. In this article we represent the network and temporal dependencies with a random effects model, resulting in a stochastic process defined by a set of stationary covariance matrices. Our approach builds upon the social relations models of Warner, Kenny and Stoto [Journal of Personality and Social Psychology 37 (1979) 1742--1757] and Gill a…
In this work we provide a couple of contributions to the analysis of longitudinal data collected by smartphones in mobile health applications. First, we propose a novel statistical approach to disentangle personalized treatment and "time-of-the-day" effects in observational studies. Under the assumption of no unmeasured confounders, we show how to use conditional independence relations in the data in order to determine if a difference in performance between activity tasks performed before and after the participant has taken medication, are potentially due to an effect of the medication or to a…
Prediction of the future trajectory of a disease is an important challenge for personalized medicine and population health management. However, many complex chronic diseases exhibit large degrees of heterogeneity, and furthermore there is not always a single readily available biomarker to quantify disease severity. Even when such a clinical variable exists, there are often additional related biomarkers routinely measured for patients that may better inform the predictions of their future disease state. To this end, we propose a novel probabilistic generative model for multivariate longitudinal…
Personality traits are latent variables, and as such, are impossible to measure without the use of an assessment. Responses on the assessments can be influenced by both transient (state-related) error and measurement error, obscuring the true trait levels. Typically, these assessments utilize Likert scales, which yield only discrete data. The loss of information due to the discrete nature of the data represents an additional challenge in assessing the ability of these instruments to measure the latent trait of interest. This paper is concerned with parameter estimation in a model relating a la…
Quantifying the relation between gut microbiome and body weight can provide insights into personalized strategies for improving digestive health. In this paper, we present an algorithm that predicts weight fluctuations using gut microbiome in a healthy cohort of newborns from a previously published dataset. Microbial data has been known to present unique statistical challenges that defy most conventional models. We propose a mixed effect Dirichlet-tree multinomial (DTM) model to untangle these difficulties as well as incorporate covariate information and account for species relatedness. The DT…
University of Zurich（苏黎世大学）；University Hospital of Zurich（苏黎世大学医院）；University of Applied Sciences and Arts Northwestern Switzerland（西北瑞士应用科学与艺术大学）；Yale University School of Medicine（耶鲁大学医学院）
Healthcare professionals have long envisioned using the enormous processing powers of computers to discover new facts and medical knowledge locked inside electronic health records. These vast medical archives contain time-resolved information about medical visits, tests and procedures, as well as outcomes, which together form individual patient journeys. By assessing the similarities among these journeys, it is possible to uncover clusters of common disease trajectories with shared health outcomes. The assignment of patient journeys to specific clusters may in turn serve as the basis for perso…
We present a novel longitudinal multimodal corpus of physiological and behavioral data collected from direct clinical providers in a hospital workplace. We designed the study to investigate the use of off-the-shelf wearable and environmental sensors to understand individual-specific constructs such as job performance, interpersonal interaction, and well-being of hospital workers over time in their natural day-to-day job settings. We collected behavioral and physiological data from $n = 212$ participants through Internet-of-Things Bluetooth data hubs, wearable sensors (including a wristband, a …
