Physiological sleep measures predict time to 15-year mortality in community adults: Application of a novel machine learning framework.

Clarifying whether physiological sleep measures predict mortality could inform risk screening; however, such investigations should account for complex and potentially non-linear relationships among health risk factors. We aimed to establish the predictive utility of polysomnography (PSG)-assessed sleep measures for mortality using a novel permutation random forest (PRF) machine learning framework. Data collected from the years 1995 to present are from the Sleep Heart Health Study (SHHS; n = 5,734) and the Wisconsin Sleep Cohort Study (WSCS; n = 1,015), and include initial assessments of sleep and health, and up to 15 years of follow-up for all-cause mortality. We applied PRF models to quantify the predictive abilities of 24 measures grouped into five domains: PSG-assessed sleep (four measures), self-reported sleep (three), health (eight), health behaviours (four), and sociodemographic factors (five). A 10-fold repeated internal validation (WSCS and SHHS combined) and external validation (training in SHHS; testing in WSCS) were used to compute unbiased variable importance metrics and associated p values. We observed that health, sociodemographic factors, and PSG-assessed sleep domains predicted mortality using both external validation and repeated internal validation. The PSG-assessed sleep efficiency and the percentage of sleep time with oxygen saturation <90% were among the most predictive individual measures. Multivariable Cox regression also revealed the PSG-assessed sleep domain to be predictive, with very low sleep efficiency and high hypoxaemia conferring the highest risk. These findings, coupled with the emergence of new low-burden technologies for objectively assessing sleep and overnight oxygen saturation, suggest that consideration of physiological sleep measures may improve risk screening.

The Importance of Calibration in Clinical Psychology.

Accuracy has several elements, not all of which have received equal attention in the field of clinical psychology. Calibration, the degree to which a probabilistic estimate of an event reflects the true underlying probability of the event, has largely been neglected in the field of clinical psychology in favor of other components of accuracy such as discrimination (e.g., sensitivity, specificity, area under the receiver operating characteristic curve). Although it is frequently overlooked, calibration is a critical component of accuracy with particular relevance for prognostic models and risk-assessment tools. With advances in personalized medicine and the increasing use of probabilistic (0% to 100%) estimates and predictions in mental health research, the need for careful attention to calibration has become increasingly important.

Integrative modelling of tumour DNA methylation quantifies the contribution of metabolism.

Altered DNA methylation is common in cancer and often considered an early event in tumorigenesis. However, the sources of heterogeneity of DNA methylation among tumours remain poorly defined. Here we capitalize on the availability of multi-platform data on thousands of human tumours to build integrative models of DNA methylation. We quantify the contribution of clinical and molecular factors in explaining intertumoral variability in DNA methylation. We show that the levels of a set of metabolic genes involved in the methionine cycle is predictive of several features of DNA methylation in tumours, including the methylation of cancer genes. Finally, we demonstrate that patients whose DNA methylation can be predicted from the methionine cycle exhibited improved survival over cases where this regulation is disrupted. This study represents a comprehensive analysis of the determinants of methylation and demonstrates the surprisingly large interaction between metabolism and DNA methylation variation. Together, our results quantify links between tumour metabolism and epigenetics and outline clinical implications.