How to evaluate uncertainty estimates in machine learning for regression?

As neural networks become more popular, the need for accompanying uncertainty estimates increases. There are currently two main approaches to test the quality of these estimates. Most methods output a density. They can be compared by evaluating their loglikelihood on a test set. Other methods output a prediction interval directly. These methods are often tested by examining the fraction of test points that fall inside the corresponding prediction intervals. Intuitively, both approaches seem logical. However, we demonstrate through both theoretical arguments and simulations that both ways of evaluating the quality of uncertainty estimates have serious flaws. Firstly, both approaches cannot disentangle the separate components that jointly create the predictive uncertainty, making it difficult to evaluate the quality of the estimates of these components. Specifically, the quality of a confidence interval cannot reliably be tested by estimating the performance of a prediction interval. Secondly, the loglikelihood does not allow a comparison between methods that output a prediction interval directly and methods that output a density. A better loglikelihood also does not necessarily guarantee better prediction intervals, which is what the methods are often used for in practice. Moreover, the current approach to test prediction intervals directly has additional flaws. We show why testing a prediction or confidence interval on a single test set is fundamentally flawed. At best, marginal coverage is measured, implicitly averaging out overconfident and underconfident predictions. A much more desirable property is pointwise coverage, requiring the correct coverage for each prediction. We demonstrate through practical examples that these effects can result in favouring a method, based on the predictive uncertainty, that has undesirable behaviour of the confidence or prediction intervals. Finally, we propose a simulation-based testing approach that addresses these problems while still allowing easy comparison between different methods. This approach can be used for the development of new uncertainty quantification methods.

The effect of cardiovascular risk on disease progression in de novo Parkinson's disease patients: An observational analysis.

Background: Currently available treatment options for Parkinson's disease are symptomatic and do not alter the course of the disease. Recent studies have raised the possibility that cardiovascular risk management may slow the progression of the disease. Objectives: We estimated the effect of baseline cardiovascular risk factors on the progression of Parkinson's disease, using measures for PD-specific motor signs and cognitive functions. Methods: We used data from 424 de novo Parkinson's disease patients and 199 age-matched controls from the observational, multicenter Parkinson's Progression Markers Initiative (PPMI) study, which included follow-up of up to 9 years. The primary outcome was the severity of PD-specific motor signs, assessed with the MDS-UPDRS part III in the "OFF"-state. The secondary outcome was cognitive function, measured with the Montreal Cognitive Assessment, Symbol Digit Modalities Test, and Letter-Number Sequencing task. Exposures of interest were diabetes mellitus, hypertension, body mass index, cardiovascular event history and hypercholesterolemia, and a modified Framingham risk score, measured at baseline. The effect of each of these exposures on disease progression was modeled using linear mixed models, including adjustment for identified confounders. A secondary analysis on the Tracking Parkinson's cohort including 1,841 patients was performed to validate our findings in an independent patient cohort. Results: Mean age was 61.4 years, and the average follow-up was 5.5 years. We found no statistically significant effect of any individual cardiovascular risk factor on the MDS-UPDRS part III progression (all 95% confidence intervals (CIs) included zero), with one exception: in the PD group, the estimated effect of a one-point increase in body mass index was 0.059 points on the MDS-UPDRS part III per year (95% CI: 0.017 to 0.102). We found no evidence for an effect of any of the exposures on the rate of change in cognitive functioning in the PD group. Similar results were observed for the Tracking Parkinson's cohort (all 95% CIs overlapped with PPMI), but the 95% CI of the effect of body mass index on the MDS-UPDRS part III progression included zero. Conclusions: Based on this analysis of two large cohorts of de novo PD patients, we found no evidence to support clinically relevant effects of cardiovascular risk factors on the clinical progression of Parkinson's disease.

Personalized monitoring of ambulatory function with a smartphone 2-minute walk test in multiple sclerosis.

BACKGROUND: Remote smartphone-based 2-minute walking tests (s2MWTs) allow frequent and potentially sensitive measurements of ambulatory function. OBJECTIVE: To investigate the s2MWT on assessment of, and responsiveness to change in ambulatory function in MS. METHODS: One hundred two multiple sclerosis (MS) patients and 24 healthy controls (HCs) performed weekly s2MWTs on self-owned smartphones for 12 and 3 months, respectively. The timed 25-foot walk test (T25FW) and Expanded Disability Status Scale (EDSS) were assessed at 3-month intervals. Anchor-based (using T25FW and EDSS) and distribution-based (curve fitting) methods were used to assess responsiveness of the s2MWT. A local linear trend model was used to fit weekly s2MWT scores of individual patients. RESULTS: A total of 4811 and 355 s2MWT scores were obtained in patients (n = 94) and HC (n = 22), respectively. s2MWT demonstrated large variability (65.6 m) compared to the average score (129.5 m), and was inadequately responsive to anchor-based change in clinical outcomes. Curve fitting separated the trend from noise in high temporal resolution individual-level data, and statistically reliable changes were detected in 45% of patients. CONCLUSIONS: In group-level analyses, clinically relevant change was insufficiently detected due to large variability with sporadic measurements. Individual-level curve fitting reduced the variability in s2MWT, enabling the detection of statistically reliable change in ambulatory function.

Development and validation of the patient-reported "Facial Function Scale" for facioscapulohumeral muscular dystrophy.

PURPOSE: Facial weakness and its functional consequences are an often underappreciated clinical feature of facioscapulohumeral muscular dystrophy (FSHD) by healthcare professionals and researchers. This is at least in part due to the fact that there are few adequate clinical outcome measures available. METHODS: We developed the Facial Function Scale, a Rasch-built questionnaire on the functional disabilities relating to facial weakness in FSHD. A preliminary 33-item questionnaire was created based on semi-structured interviews with 16 FSHD patients and completed by 119 patients. For reliability studies, 73 patients completed it again after a two-week interval. Data were subjected to semi-automated Rasch analysis to select the most appropriate item set to fit model expectations. RESULTS: This resulted in a 25-item unidimensional, linear-weighted questionnaire with high internal consistency (person separation index = 0.92) and test-retest reliability (patients' locations ICC = 0.98 and items' locations ICC = 0.99). Good external construct validity scores were obtained through correlation with the Communicative Participation Item Bank questionnaire, examiner-reported Facial Weakness Score and facial weakness subscale of the FSHD evaluation score (respectively r = 0.733, r = -0.566, and r = 0.441, all p < 0.001). CONCLUSIONS: This study provides a linear-weighted, clinimetrically sound, patient-reported outcome measure on the functional disabilities relating to facial weakness in FSHD, to enable further research on this relevant topic.Implications for rehabilitationFacial weakness and its functional consequences are an often underappreciated clinical feature of facioscapulohumeral muscular dystrophy (FSHD), both in symptomatic treatment and in research.To enable the development and testing of therapeutic symptomatic interventions for facial weakness, clinical outcome measures are required.This study provides a linear-weighted, clinimetrically sound, patient-reported outcome measure on the functional disabilities relating to facial weakness in FSHD patients.

Semi-automated Rasch analysis with differential item functioning.

Rasch analysis is a procedure to develop and validate instruments that aim to measure a person's traits. However, manual Rasch analysis is a complex and time-consuming task, even more so when the possibility of differential item functioning (DIF) is taken into consideration. Furthermore, manual Rasch analysis by construction relies on a modeler's subjective choices. As an alternative approach, we introduce a semi-automated procedure that is based on the optimization of a new criterion, called in-plus-out-of-questionnaire log likelihood with differential item functioning (IPOQ-LL-DIF), which extends our previous criterion. We illustrate our procedure on artificially generated data as well as on several real-world datasets containing potential DIF items. On these real-world datasets, our procedure found instruments with similar clinimetric properties as those suggested by experts through manual analyses.

Specialized Versus Generic Allied Health Therapy and the Risk of Parkinson's Disease Complications.

BACKGROUND: Specialized versus generic physiotherapy (PT) reduces Parkinson's disease (PD)-related complications. It is unclear (1) whether other specialized allied heath disciplines, including occupational therapy (OT) and speech and language therapy (S<), also reduce complications; (2) whether there is a synergistic effect among multiple specialized disciplines; and (3) whether each allied health discipline prevents specific complications. OBJECTIVES: To longitudinally assessed whether the level of expertise (specialized vs. generic training) of PT, OT, and S< was associated with the incidence rate of PD-related complications. METHODS: We used claims data of all insured persons with PD in the Netherlands between January 1, 2010, and December 31, 2018. ParkinsonNet-trained therapists were classified as specialized, and other therapists as generic. We used mixed-effects Poisson regression models to estimate rate ratios adjusting for sociodemographic and clinical characteristics. RESULTS: The population of 51,464 persons with PD (mean age, 72.4 years; standard deviation 9.8) sustained 10,525 PD-related complications during follow-up (median 3.3 years). Specialized PT was associated with fewer complications (incidence rate ratio [IRR] of specialized versus generic = 0.79; 95% confidence interval, [0.74-0.83]; P < 0.0001), as was specialized OT (IRR = 0.88 [0.77-0.99]; P = 0.03). We found a trend of an association between specialized S< and a lower rate of PD-related complications (IRR = 0.88 [0.74-1.04]; P = 0.18). The inverse association of specialized OT persisted in the stratum, which also received specialized PT (IRR = 0.62 [0.42-0.90]; P = 0.001). The strongest inverse association of PT was seen with orthopedic injuries (IRR = 0.78 [0.73-0.82]; P < 0.0001) and of S< with pneumonia (IRR = 0.70 [0.53-0.93]; P = 0.03). CONCLUSIONS: These findings support a wider introduction of specialized allied health therapy expertise in PD care and conceivably for other medical conditions. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

autoRasch: An R Package to Do Semi-Automated Rasch Analysis.

The R package autoRasch has been developed to perform a Rasch analysis in a (semi-)automated way. The automated part of the analysis is achieved by optimizing the so-called in-plus-out-of-questionnaire log-likelihood (IPOQ-LL) or IPOQ-LL-DIF when differential item functioning (DIF) is included. These criteria measure the quality of fit on a pre-collected survey, depending on which items are included in the final instrument. To compute these criteria, autoRasch fits the generalized partial credit model (GPCM) or the generalized partial credit model with differential item functioning (GPCM-DIF) using penalized joint maximum likelihood estimation (PJMLE). The package further allows the user to reevaluate the output of the automated method and use it as a basis for performing a manual Rasch analysis and provides standard statistics of Rasch analyses (e.g., outfit, infit, person separation reliability, and residual correlation) to support the model reevaluation.

Towards individualized monitoring of cognition in multiple sclerosis in the digital era: A one-year cohort study.

BACKGROUND: Cognitive impairment is frequent in multiple sclerosis (MS), but reliable, sensitive and individualized monitoring in clinical practice is still limited. Smartphone-adapted tests may enhance the assessment of function as tests can be performed more frequently and within the daily living environment. The objectives were to prove reproducibility of a smartphone-based Symbol Digit Modalities Test (sSDMT), its responsiveness to relevant change in clinical cognitive outcomes, and develop an individual-based monitoring method for cognition. METHODS: In a one-year cohort study with 102 patients with MS, weekly sSDMTs were performed and analyzed on reproducibility parameters: the standard error of measurement (SEM) and smallest detectable change (SDC). Responsiveness of the sSDMT to relevant change in the 3-monthly clinically assessed SDMT (i.e. 4-point change) was quantified with the area under the receiver operating characteristic curve (AUC). Curve fitting of the weekly sSDMT scores of individual patients was performed with a local linear trend model to estimate and visualize the de-noised cognitive state and 95% confidence interval (CI). The optimal assessment frequency was determined by analyzing the CI bandwidth as a function of sSDMT assessment frequency. RESULTS: Weekly sSDMT showed improved reproducibility estimates (SEM=2.94, SDC=8.15) compared to the clinical SDMT. AUC-values did not exceed 0.70 in classifying relevant change in cSDMT. However, utilizing weekly sSDMT measurements, estimated state curves and the 95% CI were plotted showing detailed changes within individuals over time. With a test frequency of once per 12 days, 4-point changes in sSDMT can be detected. CONCLUSION: A local linear trend model applied on sSDMT scores of individual patients increases the signal-to-noise ratio substantially, which improves the detection of statistically reliable changes. Therefore, this fine-grained individual-based monitoring approach can be used to complement current clinical assessment to enhance clinical care in MS. TRIAL REGISTRATION: Netherlands Trial Register NL7070; https://www.trialregister.nl/trial/7070.

Automatic Placenta Localization From Ultrasound Imaging in a Resource-Limited Setting Using a Predefined Ultrasound Acquisition Protocol and Deep Learning.

Placenta localization from obstetric 2-D ultrasound (US) imaging is unattainable for many pregnant women in low-income countries because of a severe shortage of trained sonographers. To address this problem, we present a method to automatically detect low-lying placenta or placenta previa from 2-D US imaging. Two-dimensional US data from 280 pregnant women were collected in Ethiopia using a standardized acquisition protocol and low-cost equipment. The detection method consists of two parts. First, 2-D US segmentation of the placenta is performed using a deep learning model with a U-Net architecture. Second, the segmentation is used to classify each placenta as either normal or a class including both low-lying placenta and placenta previa. The segmentation model was trained and tested on 6574 2-D US images, achieving a median test Dice coefficient of 0.84 (interquartile range = 0.23). The classifier achieved a sensitivity of 81% and a specificity of 82% on a holdout test set of 148 cases. Additionally, the model was found to segment in real time (19 ± 2 ms per 2-D US image) using a smartphone paired with a low-cost 2-D US device. This work illustrates the feasibility of using automated placenta localization in a resource-limited setting.

Non-parametric synergy modeling of chemical compounds with Gaussian processes.

BACKGROUND: Understanding the synergetic and antagonistic effects of combinations of drugs and toxins is vital for many applications, including treatment of multifactorial diseases and ecotoxicological monitoring. Synergy is usually assessed by comparing the response of drug combinations to a predicted non-interactive response from reference (null) models. Possible choices of null models are Loewe additivity, Bliss independence and the recently rediscovered Hand model. A different approach is taken by the MuSyC model, which directly fits a generalization of the Hill model to the data. All of these models, however, fit the dose-response relationship with a parametric model. RESULTS: We propose the Hand-GP model, a non-parametric model based on the combination of the Hand model with Gaussian processes. We introduce a new logarithmic squared exponential kernel for the Gaussian process which captures the logarithmic dependence of response on dose. From the monotherapeutic response and the Hand principle, we construct a null reference response and synergy is assessed from the difference between this null reference and the Gaussian process fitted response. Statistical significance of the difference is assessed from the confidence intervals of the Gaussian process fits. We evaluate performance of our model on a simulated data set from Greco, two simulated data sets of our own design and two benchmark data sets from Chou and Talalay. We compare the Hand-GP model to standard synergy models and show that our model performs better on these data sets. We also compare our model to the MuSyC model as an example of a recent method on these five data sets and on two-drug combination screens: Mott et al. anti-malarial screen and O'Neil et al. anti-cancer screen. We identify cases in which the HandGP model is preferred and cases in which the MuSyC model is preferred. CONCLUSION: The Hand-GP model is a flexible model to capture synergy. Its non-parametric and probabilistic nature allows it to model a wide variety of response patterns.

Understanding the assumptions underlying Mendelian randomization.

With the rapidly increasing availability of large genetic data sets in recent years, Mendelian Randomization (MR) has quickly gained popularity as a novel secondary analysis method. Leveraging genetic variants as instrumental variables, MR can be used to estimate the causal effects of one phenotype on another even when experimental research is not feasible, and therefore has the potential to be highly informative. It is dependent on strong assumptions however, often producing biased results if these are not met. It is therefore imperative that these assumptions are well-understood by researchers aiming to use MR, in order to evaluate their validity in the context of their analyses and data. The aim of this perspective is therefore to further elucidate these assumptions and the role they play in MR, as well as how different kinds of data can be used to further support them.

Methodology of the DCCSS later fatigue study: a model to investigate chronic fatigue in long-term survivors of childhood cancer.

BACKGROUND: A debilitating late effect for childhood cancer survivors (CCS) is cancer-related fatigue (CRF). Little is known about the prevalence and risk factors of fatigue in this population. Here we describe the methodology of the Dutch Childhood Cancer Survivor Late Effect Study on fatigue (DCCSS LATER fatigue study). The aim of the DCCSS LATER fatigue study is to examine the prevalence of and factors associated with CRF, proposing a model which discerns predisposing, triggering, maintaining and moderating factors. Triggering factors are related to the cancer diagnosis and treatment during childhood and are thought to trigger fatigue symptoms. Maintaining factors are daily life- and psychosocial factors which may perpetuate fatigue once triggered. Moderating factors might influence the way fatigue symptoms express in individuals. Predisposing factors already existed before the diagnosis, such as genetic factors, and are thought to increase the vulnerability to develop fatigue. Methodology of the participant inclusion, data collection and planned analyses of the DCCSS LATER fatigue study are presented. RESULTS: Data of 1955 CCS and 455 siblings was collected. Analysis of the data is planned and we aim to start reporting the first results in 2022. CONCLUSION: The DCCSS LATER fatigue study will provide information on the epidemiology of CRF and investigate the role of a broad range of associated factors in CCS. Insight in associated factors for fatigue in survivors experiencing severe and persistent fatigue may help identify individuals at risk for developing CRF and may aid in the development of interventions.

Spectral Ranking of Causal Influence in Complex Systems.

Similar to natural complex systems, such as the Earth's climate or a living cell, semiconductor lithography systems are characterized by nonlinear dynamics across more than a dozen orders of magnitude in space and time. Thousands of sensors measure relevant process variables at appropriate sampling rates, to provide time series as primary sources for system diagnostics. However, high-dimensionality, non-linearity and non-stationarity of the data are major challenges to efficiently, yet accurately, diagnose rare or new system issues by merely using model-based approaches. To reliably narrow down the causal search space, we validate a ranking algorithm that applies transfer entropy for bivariate interaction analysis of a system's multivariate time series to obtain a weighted directed graph, and graph eigenvector centrality to identify the system's most important sources of original information or causal influence. The results suggest that this approach robustly identifies the true drivers or causes of a complex system's deviant behavior, even when its reconstructed information transfer network includes redundant edges.

Potential mechanisms of the fatigue-reducing effect of cognitive-behavioral therapy in cancer survivors: Three randomized controlled trials.

OBJECTIVE: Fatigue is a common symptom among cancer survivors that can be successfully treated with cognitive-behavioral therapy (CBT). Insights into the working mechanisms of CBT are currently limited. The aim of this study was to investigate whether improvements in targeted cognitive-behavioral variables and reduced depressive symptoms mediate the fatigue-reducing effect of CBT. METHODS: We pooled data from three randomized controlled trials that tested the efficacy of CBT to reduce severe fatigue. In all three trials, fatigue severity (checklist individual strength) decreased significantly following CBT. Assessments were conducted pre-treatment and 6 months later. Classical mediation analysis testing a pre-specified model was conducted and its results compared to those of causal discovery, an explorative data-driven approach testing all possible causal associations and retaining the most likely model. RESULTS: Data from 250 cancer survivors (n = 129 CBT, n = 121 waitlist) were analyzed. Classical mediation analysis suggests that increased self-efficacy and decreased fatigue catastrophizing, focusing on symptoms, perceived problems with activity and depressive symptoms mediate the reduction of fatigue brought by CBT. Conversely, causal discovery and post-hoc analyses indicate that fatigue acts as mediator, not outcome, of changes in cognitions, sleep disturbance and depressive symptoms. CONCLUSIONS: Cognitions, sleep disturbance and depressive symptoms improve during CBT. When assessed pre- and post-treatment, fatigue acts as a mediator, not outcome, of these improvements. It seems likely that the working mechanism of CBT is not a one-way causal effect but a dynamic reciprocal process. Trials integrating intermittent assessments are needed to shed light on these mechanisms and inform optimization of CBT.

Semi-automated Rasch analysis using in-plus-out-of-questionnaire log likelihood.

Rasch analysis is a popular statistical tool for developing and validating instruments that aim to measure human performance, attitudes and perceptions. Despite the availability of various software packages, constructing a good instrument based on Rasch analysis is still considered to be a complex, labour-intensive task, requiring human expertise and rather subjective judgements along the way. In this paper we propose a semi-automated method for Rasch analysis based on first principles that reduces the need for human input. To this end, we introduce a novel criterion, called in-plus-out-of-questionnaire log likelihood (IPOQ-LL). On artificial data sets, we confirm that optimization of IPOQ-LL leads to the desired behaviour in the case of multi-dimensional and inhomogeneous surveys. On three publicly available real-world data sets, our method leads to instruments that are, for all practical purposes, indistinguishable from those obtained by Rasch analysis experts through a manual procedure.

Probabilistic Modelling of Gait for Robust Passive Monitoring in Daily Life.

Passive monitoring in daily life may provide valuable insights into a person's health throughout the day. Wearable sensor devices play a key role in enabling such monitoring in a non-obtrusive fashion. However, sensor data collected in daily life reflect multiple health and behavior-related factors together. This creates the need for a structured principled analysis to produce reliable and interpretable predictions that can be used to support clinical diagnosis and treatment. In this work we develop a principled modelling approach for free-living gait (walking) analysis. Gait is a promising target for non-obtrusive monitoring because it is common and indicative of many different movement disorders such as Parkinson's disease (PD), yet its analysis has largely been limited to experimentally controlled lab settings. To locate and characterize stationary gait segments in free-living using accelerometers, we present an unsupervised probabilistic framework designed to segment signals into differing gait and non-gait patterns. We evaluate the approach using a new video-referenced dataset including 25 PD patients with motor fluctuations and 25 age-matched controls, performing unscripted daily living activities in and around their own houses. Using this dataset, we demonstrate the framework's ability to detect gait and predict medication induced fluctuations in PD patients based on free-living gait. We show that our approach is robust to varying sensor locations, including the wrist, ankle, trouser pocket and lower back.

Estimating the Effect of Early Treatment Initiation in Parkinson's Disease Using Observational Data.

BACKGROUND: Both patients and physicians may choose to delay initiation of dopamine replacement therapy in Parkinson's disease (PD) for various reasons. We used observational data to estimate the effect of earlier treatment in PD. Observational data offer a valuable source of evidence, complementary to controlled trials. METHOD: We studied the Parkinson's Progression Markers Initiative cohort of patients with de novo PD to estimate the effects of duration of PD treatment during the first 2 years of follow-up, exploiting natural interindividual variation in the time to start first treatment. We estimated the Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) Part III (primary outcome) and several functionally relevant outcomes at 2, 3, and 4 years after baseline. To adjust for time-varying confounding, we used marginal structural models with inverse probability of treatment weighting and the parametric g-formula. RESULTS: We included 302 patients from the Parkinson's Progression Markers Initiative cohort. There was a small improvement in MDS-UPDRS Part III scores after 2 years of follow-up for patients who started treatment earlier, and similar, but nonstatistically significant, differences in subsequent years. We found no statistically significant differences in most secondary outcomes, including the presence of motor fluctuations, nonmotor symptoms, MDS-UPDRS Part II scores, and the Schwab and England Activities of Daily Living Scale. CONCLUSION: Earlier treatment initiation does not lead to worse MDS-UPDRS motor scores and may offer small improvements. These findings, based on observational data, are in line with earlier findings from clinical trials. Observational data, when combined with appropriate causal methods, are a valuable source of additional evidence to support real-world clinical decisions. © 2020 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Real-Life Gait Performance as a Digital Biomarker for Motor Fluctuations: The Parkinson@Home Validation Study.

BACKGROUND: Wearable sensors have been used successfully to characterize bradykinetic gait in patients with Parkinson disease (PD), but most studies to date have been conducted in highly controlled laboratory environments. OBJECTIVE: This paper aims to assess whether sensor-based analysis of real-life gait can be used to objectively and remotely monitor motor fluctuations in PD. METHODS: The Parkinson@Home validation study provides a new reference data set for the development of digital biomarkers to monitor persons with PD in daily life. Specifically, a group of 25 patients with PD with motor fluctuations and 25 age-matched controls performed unscripted daily activities in and around their homes for at least one hour while being recorded on video. Patients with PD did this twice: once after overnight withdrawal of dopaminergic medication and again 1 hour after medication intake. Participants wore sensors on both wrists and ankles, on the lower back, and in the front pants pocket, capturing movement and contextual data. Gait segments of 25 seconds were extracted from accelerometer signals based on manual video annotations. The power spectral density of each segment and device was estimated using Welch's method, from which the total power in the 0.5- to 10-Hz band, width of the dominant frequency, and cadence were derived. The ability to discriminate between before and after medication intake and between patients with PD and controls was evaluated using leave-one-subject-out nested cross-validation. RESULTS: From 18 patients with PD (11 men; median age 65 years) and 24 controls (13 men; median age 68 years), ≥10 gait segments were available. Using logistic LASSO (least absolute shrinkage and selection operator) regression, we classified whether the unscripted gait segments occurred before or after medication intake, with mean area under the receiver operator curves (AUCs) varying between 0.70 (ankle of least affected side, 95% CI 0.60-0.81) and 0.82 (ankle of most affected side, 95% CI 0.72-0.92) across sensor locations. Combining all sensor locations did not significantly improve classification (AUC 0.84, 95% CI 0.75-0.93). Of all signal properties, the total power in the 0.5- to 10-Hz band was most responsive to dopaminergic medication. Discriminating between patients with PD and controls was generally more difficult (AUC of all sensor locations combined: 0.76, 95% CI 0.62-0.90). The video recordings revealed that the positioning of the hands during real-life gait had a substantial impact on the power spectral density of both the wrist and pants pocket sensor. CONCLUSIONS: We present a new video-referenced data set that includes unscripted activities in and around the participants' homes. Using this data set, we show the feasibility of using sensor-based analysis of real-life gait to monitor motor fluctuations with a single sensor location. Future work may assess the value of contextual sensors to control for real-world confounders.

Identification and validation of risk factors for antisocial behaviour involving police.

Adult antisocial behaviour has precursors in childhood and adolescence and is most successfully treated using childhood interventions. The aim of this study was to identify and validate robust risk factors for antisocial behaviour involving police contact in a data-driven, hypothesis-free framework. Antisocial behavior involving police contact (20/25% incidence) as well as 554 other behavioural and environmental measures were assessed in the longitudinal general population Estonian Children Personality Behaviour and Health Study sample (n=872). The strongest risk factors for antisocial behaviour included past substance use disorder, gender, aggressive mode of action upon provocation, and concentration difficulties and physical fighting in school at age 15 years. Prediction using the selected variables for both methods in the other, unseen cohort resulted in an area under the receiver operating characteristics curve of 0.78-0.84. Our work confirms known risk factors for antisocial behaviour as well as identifies novel specific risk factors. Together, these provide good predictive power in an unseen cohort. Our identification and validation of risk factors for antisocial behaviour can aid early intervention for at-risk individuals.

Investigating the effect of dependence between conditions with Bayesian Linear Mixed Models for motif activity analysis.

MOTIVATION: Cellular identity and behavior is controlled by complex gene regulatory networks. Transcription factors (TFs) bind to specific DNA sequences to regulate the transcription of their target genes. On the basis of these TF motifs in cis-regulatory elements we can model the influence of TFs on gene expression. In such models of TF motif activity the data is usually modeled assuming a linear relationship between the motif activity and the gene expression level. A commonly used method to model motif influence is based on Ridge Regression. One important assumption of linear regression is the independence between samples. However, if samples are generated from the same cell line, tissue, or other biological source, this assumption may be invalid. This same assumption of independence is also applied to different yet similar experimental conditions, which may also be inappropriate. In theory, the independence assumption between samples could lead to loss in signal detection. Here we investigate whether a Bayesian model that allows for correlations results in more accurate inference of motif activities. RESULTS: We extend the Ridge Regression to a Bayesian Linear Mixed Model, which allows us to model dependence between different samples. In a simulation study, we investigate the differences between the two model assumptions. We show that our Bayesian Linear Mixed Model implementation outperforms Ridge Regression in a simulation scenario where the noise, which is the signal that can not be explained by TF motifs, is uncorrelated. However, we demonstrate that there is no such gain in performance if the noise has a similar covariance structure over samples as the signal that can be explained by motifs. We give a mathematical explanation to why this is the case. Using four representative real datasets we show that at most ∼â€<40% of the signal is explained by motifs using the linear model. With these data there is no advantage to using the Bayesian Linear Mixed Model, due to the similarity of the covariance structure. AVAILABILITY & IMPLEMENTATION: The project implementation is available at https://github.com/Sim19/SimGEXPwMotifs.