Visualization in Bayesian Workflow

Gabry, Jonah; Simpson, Daniel; Vehtari, Aki; Betancourt, Michael; Gelman, Andrew

doi:10.1111/rssa.12378

Cited by 749 publications

(728 citation statements)

References 20 publications

(29 reference statements)

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“…The remaining models were submodels of the first model. Binding potentials were log-transformed because posterior predictive checking 33,34 indicated that log-transformation significantly improves model fit (see Supplementary Figure 2). The log-transformation essentially switches the model from additive to multiplicative; it also helps in model fitting because the assumption of linear additivity works poorly when the dependent variable is restricted to positive values 35 .…”

Section: Model Comparisonmentioning

confidence: 99%

Interindividual variability and lateralization of µ-opioid receptors in the human brain

Kantonen

Karjalainen

Isojärvi

et al. 2019

Preprint

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AbstractThe brain’s µ-opioid receptors (MORs) are involved in analgesia, reward and mood regulation. Several neuropsychiatric diseases have been associated with dysfunctional MOR system, and there is also considerable variation in receptor density among healthy individuals. Sex, age, body mass and smoking have been proposed to influence the MOR system, but due to small sample sizes the magnitude of their influence remains inconclusive. Here we quantified in vivo MOR availability in the brains of 204 individuals with no neurologic or psychiatric disorders using positron emission tomography (PET) with tracer [11C]carfentanil. We then used Bayesian hierarchical modeling to estimate the effects of sex, age, body mass index (BMI) and smoking on [11C]carfentanil binding potential. We also examined hemispheric lateralization of MOR availability. Age had regionally specific effects on MOR availability, with age-dependent increase in frontotemporal areas but decrease in amygdala, thalamus, and nucleus accumbens. The age-dependent increase was stronger in males. MOR availability was globally lowered in smokers but independent of BMI. Finally, MOR availability was higher in the right versus the left hemisphere. The presently observed variation in MOR availability may explain why some individuals are prone to develop MOR-linked pathological states, such as chronic pain or psychiatric disorders.

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Section: Model Comparisonmentioning

confidence: 99%

Interindividual variability and lateralization of µ-opioid receptors in the human brain

Kantonen

Karjalainen

Isojärvi

et al. 2019

Preprint

Self Cite

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“…We tested each random effects standard deviation using the Bayes Factor 10 to further quantify evidence in favor of geographic heterogeneity. SEER-wide and within-state goodness-of-fit was assessed using standard posterior distribution predictive checks 13 (Supporting Information Figs. S1-S8).…”

Section: Methodsmentioning

confidence: 99%

Heterogeneity of colon and rectum cancer incidence across 612 SEER counties, 2000–2014

Chernyavskiy

Kennerley

Jemal

et al. 2019

Intl Journal of Cancer

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Recent analyses have suggested decreases over time in colorectal cancer incidence at older ages (≥55 years) but increases at younger ages (20-54 years). Understanding the geographic heterogeneity of incidence facilitates resource allocation for potential interventions and advances our knowledge of differential etiologies for these cancers. We performed age-period-cohort analysis using 2000-2014 county-level incidence from the Surveillance, Epidemiology, and End Results (SEER) database, estimating relative risk (RR) and age-adjusted annual percent change (Net Drifts) simultaneously for 612 counties via a hierarchical model, separately for colon and rectum cancer, stratified by age group (20-54 vs. 55-84). We also studied correlates of RR and Net Drift with various county-level characteristics. In all SEER counties, colon and rectum cancer incidence rates increased at ages 20-54, whereas rates decreased at ages 55-84. There was marked heterogeneity in both RR and Net Drift among states and counties for both cancer types. Maps of county RR and Net Drift revealed localized clusters in several states. For both cancer types, counties with high RR and unfavorable Net Drift tended to have higher prevalence of obesity and diabetes and to be of a lower socioeconomic status. Counties with higher overall screening rates tended to have lower Net Drifts for both cancer types. Increasing colorectal cancer incidence in the younger age group is geographically widespread, although there is significant heterogeneity in temporal trends and risk both within and between states. These geographic patterns correlate with different county-level characteristics depending on cancer type and age group. This article is protected by copyright. All rights reserved.

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“…This is illustrated with prior-predictive check and assessment of CPM assumptions in Supplemental Material 3, which also shows detailed workflow and visualizations for each observed bacteria. Our prior choice resulted from model comparison with approximate leave-one-out cross-validation 35,36 . Figure 3E shows the corresponding posterior predictive check, suggesting the data is well captured by the modelimplied data generation process for all bacteria.…”

Section: Hierarchical Cpm Predicts Absolute Bacterial Abundancesmentioning

confidence: 99%

Equivolumetric protocol generates library sizes proportional to total microbial load in next-generation sequencing

Gnf¹,

Ap²,

Lfv³

2020

Preprint

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Next-generation sequencing (NGS) has been extensively employed to perform microbiome characterization worldwide. As a culture-independent methodology, it has allowed high-level profiling of sample microbial composition. However, most studies are limited to information regarding relative bacterial abundances, ignoring scenarios in which sample microbe biomass can vary widely. Here, we develop an equivolumetric protocol for amplicon library preparation capable of generating NGS data responsive to input DNA, recovering proportionality between observed read counts and absolute bacterial abundances. Under specified conditions, we argue that the estimation of colony-forming units (CFU), the most common unit of bacterial abundance in classical microbiology, is challenged mostly by resolution and taxon-to-taxon variation. We propose Bayesian cumulative probability models to address such issues. Our results indicate that predictive errors vary consistently below one order of magnitude for observed bacteria. We also demonstrate our approach has the potential to generalize to previously unseen bacteria, but predictive performance is hampered by specific taxa of uncommon profile. Finally, it remains clear that NGS data are not inherently restricted to relative information only, and microbiome science can indeed meet the working scales of traditional microbiology.

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Visualization in Bayesian Workflow

Cited by 749 publications

References 20 publications

Interindividual variability and lateralization of µ-opioid receptors in the human brain

Interindividual variability and lateralization of µ-opioid receptors in the human brain

Heterogeneity of colon and rectum cancer incidence across 612 SEER counties, 2000–2014

Equivolumetric protocol generates library sizes proportional to total microbial load in next-generation sequencing

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