402 research outputs found
Bayesian predictive modeling for genomic based personalized treatment selection
Efforts to personalize medicine in oncology have been limited by reductive characterizations of the intrinsically complex underlying biological phenomena. Future advances in personalized medicine will rely on molecular signatures that derive from synthesis of multifarious interdependent molecular quantities requiring robust quantitative methods. However, highly-parameterized statistical models when applied in these settings often require a prohibitively large database and are sensitive to proper characterizations of the treatment-by-covariate interactions, which in practice are difficult to specify and may be limited by generalized linear models. In this paper, we present a Bayesian predictive framework that enables the integration of a high-dimensional set of genomic features with clinical responses and treatment histories of historical patients, providing a probabilistic basis for using the clinical and molecular information to personalize therapy for future patients. Our work represents one of the first attempts to define personalized treatment assignment rules based on large-scale genomic data. We use actual gene expression data acquired from The Cancer Genome Atlas in the settings of leukemia and glioma to explore the statistical properties of our proposed Bayesian approach for personalizing treatment selection. The method is shown to yield considerable improvements in predictive accuracy when compared to penalized regression approaches
A Bayesian Nonparametric model for textural pattern heterogeneity
Cancer radiomics is an emerging discipline promising to elucidate lesion
phenotypes and tumor heterogeneity through patterns of enhancement, texture,
morphology, and shape. The prevailing technique for image texture analysis
relies on the construction and synthesis of Gray-Level Co-occurrence Matrices
(GLCM). Practice currently reduces the structured count data of a GLCM to
reductive and redundant summary statistics for which analysis requires variable
selection and multiple comparisons for each application, thus limiting
reproducibility. In this article, we develop a Bayesian multivariate
probabilistic framework for the analysis and unsupervised clustering of a
sample of GLCM objects. By appropriately accounting for skewness and
zero-inflation of the observed counts and simultaneously adjusting for existing
spatial autocorrelation at nearby cells, the methodology facilitates estimation
of texture pattern distributions within the GLCM lattice itself. The techniques
are applied to cluster images of adrenal lesions obtained from CT scans with
and without administration of contrast. We further assess whether the resultant
subtypes are clinically oriented by investigating their correspondence with
pathological diagnoses. Additionally, we compare performance to a class of
machine-learning approaches currently used in cancer radiomics with simulation
studies.Comment: 45 pages, 7 figures, 1 Tabl
Studies of Diffuse Interstellar Bands. V. Pairwise Correlations of Eight Strong DIBs and Neutral Hydrogen, Molecular Hydrogen, and Color Excess
We establish correlations between equivalent widths of eight diffuse
interstellar bands (DIBs), and examine their correlations with atomic hydrogen,
molecular hydrogen, and EB-V . The DIBs are centered at \lambda\lambda 5780.5,
6204.5, 6283.8, 6196.0, 6613.6, 5705.1, 5797.1, and 5487.7, in decreasing order
of Pearson\^as correlation coefficient with N(H) (here defined as the column
density of neutral hydrogen), ranging from 0.96 to 0.82. We find the equivalent
width of \lambda 5780.5 is better correlated with column densities of H than
with E(B-V) or H2, confirming earlier results based on smaller datasets. We
show the same is true for six of the seven other DIBs presented here. Despite
this similarity, the eight strong DIBs chosen are not well enough correlated
with each other to suggest they come from the same carrier. We further conclude
that these eight DIBs are more likely to be associated with H than with H2, and
hence are not preferentially located in the densest, most UV shielded parts of
interstellar clouds. We suggest they arise from different molecules found in
diffuse H regions with very little H (molecular fraction f<0.01). Of the 133
stars with available data in our study, there are three with significantly
weaker \lambda 5780.5 than our mean H-5780.5 relationship, all of which are in
regions of high radiation fields, as previously noted by Herbig. The
correlations will be useful in deriving interstellar parameters when direct
methods are not available. For instance, with care, the value of N(H) can be
derived from W{\lambda}(5780.5).Comment: Accepted for publication in The Astrophysical Journal; 37 pages, 11
figures, 6 table
Landmark mediation survival analysis using longitudinal surrogate
Clinical cancer trials are designed to collect radiographic measurements of each patient’s baseline and residual tumor burden at regular intervals over the course of study. For solid tumors, the extent of reduction in tumor size following treatment is used as a measure of a drug’s antitumor activity. Statistical estimation of treatment efficacy routinely reduce the longitudinal assessment of tumor burden to a binary outcome describing the presence versus absence of an objective tumor response as defined by RECIST criteria. The objective response rate (ORR) is the predominate method for evaluating an experimental therapy in a single-arm trial. Additionally, ORR is routinely compared against a control therapy in phase III randomized controlled trials. The longitudinal assessments of tumor burden are seldom integrated into a formal statistical model, nor integrated into mediation analysis to characterize the relationships among treatment, residual tumor burden, and survival. This article presents a frameworkfor landmark mediation survival analyses devised to incorporate longitudinal assessment of tumor burden. R2 effect-size measures are developed to quantify the survival treatment mediation effects using longitudinal predictors. Analyses are demonstrated with applications to two colorectal cancer trials. Survival prediction is compared in the presence versus absence of longitudinal analysis. Simulation studies elucidate settings wherein patterns of tumor burden dynamics require longitudinal analysis
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