Multivariate functional response regression, with application to fluorescence spectroscopy in a cervical pre-cancer study.

Many scientific studies measure different types of high-dimensional signals or images from the same subject, producing multivariate functional data. These functional measurements carry different types of information about the scientific process, and a joint analysis that integrates information across them may provide new insights into the underlying mechanism for the phenomenon under study. Motivated by fluorescence spectroscopy data in a cervical pre-cancer study, a multivariate functional response regression model is proposed, which treats multivariate functional observations as responses and a common set of covariates as predictors.

Efficient Bayesian hierarchical functional data analysis with basis function approximations using Gaussian-Wishart processes.

Functional data are defined as realizations of random functions (mostly smooth functions) varying over a continuum, which are usually collected on discretized grids with measurement errors. In order to accurately smooth noisy functional observations and deal with the issue of high-dimensional observation grids, we propose a novel Bayesian method based on the Bayesian hierarchical model with a Gaussian-Wishart process prior and basis function representations. We first derive an induced model for the basis-function coefficients of the functional data, and then use this model to conduct posterior inference through Markov chain Monte Carlo methods.

Smoothing and Mean-Covariance Estimation of Functional Data with a Bayesian Hierarchical Model.

Functional data, with basic observational units being functions (e.g., curves, surfaces) varying over a continuum, are frequently encountered in various applications.

An alternative approach for estimating the accuracy of colposcopy in detecting cervical precancer.

Introduction: Since colposcopy helps to detect cervical cancer in its precancerous stages, as new strategies and technologies are developed for the clinical management of cervical neoplasia, precisely determining the accuracy of colposcopy is important for characterizing its continued role. Our objective was to employ a more precise methodology to estimate of the accuracy of colposcopy to better reflect clinical practice.

Study Design: For each patient, we compared the worst histology result among colposcopically positive sites to the worst histology result among all sites biopsied, thereby more accurately determining the number of patients that would have been underdiagnosed by colposcopy than previously estimated.

A statistical model for removing inter-device differences in spectroscopy.

We are investigating spectroscopic devices designed to make in vivo cervical tissue measurements to detect pre-cancerous and cancerous lesions. All devices have the same design and ideally should record identical measurements. However, we observed consistent differences among them.

Accuracy of optical spectroscopy for the detection of cervical intraepithelial neoplasia without colposcopic tissue information; a step toward automation for low resource settings.

Optical spectroscopy has been proposed as an accurate and low-cost alternative for detection of cervical intraepithelial neoplasia. We previously published an algorithm using optical spectroscopy as an adjunct to colposcopy and found good accuracy (sensitivity=1.00 [95% confidence interval (CI)=0.

Optical technologies and molecular imaging for cervical neoplasia: a program project update.

There is an urgent global need for effective and affordable approaches to cervical cancer screening and diagnosis. In developing nations, cervical malignancies remain the leading cause of cancer-related deaths in women. This reality may be difficult to accept given that these deaths are largely preventable; where cervical screening programs have been implemented, cervical cancer-related deaths have decreased dramatically.

Classifying tissue samples from measurements on cells with within-class tissue sample heterogeneity.

We consider here the problem of classifying a macro-level object based on measurements of embedded (micro-level) observations within each object, for example, classifying a patient based on measurements on a collection of a random number of their cells. Classification problems with this hierarchical, nested structure have not received the same statistical understanding as the general classification problem. Some heuristic approaches have been developed and a few authors have proposed formal statistical models.

Repeatability of tissue fluorescence measurements for the detection of cervical intraepithelial neoplasia.

We examined intensity and shape differences in 378 repeated spectroscopic measures of the cervix. We examined causes of variability such as presence of precancer or cancer, pathologic tissue type, menopausal status, hormone or oral contraceptive use, and age; as well as technology related variables like generation of device and provider making exam. Age, device generation, and provider were statistically significantly related to intensity differences.

Likelihood of achieving air quality targets under model uncertainties.

Regulatory attainment demonstrations in the United States typically apply a bright-line test to predict whether a control strategy is sufficient to attain an air quality standard. Photochemical models are the best tools available to project future pollutant levels and are a critical part of regulatory attainment demonstrations. However, because photochemical models are uncertain and future meteorology is unknowable, future pollutant levels cannot be predicted perfectly and attainment cannot be guaranteed.

Accuracy of optical spectroscopy for the detection of cervical intraepithelial neoplasia: Testing a device as an adjunct to colposcopy.

Testing emerging technologies involves the evaluation of biologic plausibility, technical efficacy, clinical effectiveness, patient satisfaction, and cost-effectiveness. The objective of this study was to select an effective classification algorithm for optical spectroscopy as an adjunct to colposcopy and obtain preliminary estimates of its accuracy for the detection of CIN 2 or worse. We recruited 1,000 patients from screening and prevention clinics and 850 patients from colposcopy clinics at two comprehensive cancer centers and a community hospital.

Robust Smoothing: Smoothing Parameter Selection and Applications to Fluorescence Spectroscopy.

Fluorescence spectroscopy has emerged in recent years as an effective way to detect cervical cancer. Investigation of the data preprocessing stage uncovered a need for a robust smoothing to extract the signal from the noise. Various robust smoothing methods for estimating fluorescence emission spectra are compared and data driven methods for the selection of smoothing parameter are suggested.

A bayesian hierarchical model for classification with selection of functional predictors.

In functional data classification, functional observations are often contaminated by various systematic effects, such as random batch effects caused by device artifacts, or fixed effects caused by sample-related factors. These effects may lead to classification bias and thus should not be neglected. Another issue of concern is the selection of functions when predictors consist of multiple functions, some of which may be redundant.

Analyzing single-molecule manipulation experiments.

Single-molecule manipulation studies can provide quantitative information about the physical properties of complex biological molecules without ensemble artifacts obscuring the measurements. We demonstrate computational techniques which aim at more fully utilizing the wealth of information contained in noisy experimental time series. The "noise" comes from multiple sources e.

Model-based analysis of reflectance and fluorescence spectra for in vivo detection of cervical dysplasia and cancer.

Development, validation, and implementation of an analytical model to extract biologically and diagnostically relevant parameters from measured cervical tissue reflectance and fluorescence spectra are presented. Monte Carlo simulations of tissue reflectance are used to determine the relative contribution of the signal from the epithelium and stroma. The results indicate that the clinical probe used collects a majority of its reflectance signal from the stroma; therefore, a one-layer analytical model of reflectance is used.

Quantifying multiscale noise sources in single-molecule time series.

When analyzing single-molecule data, a low-dimensional set of system observables typically serves as the observational data. We calibrate stochastic dynamical models from time series that record such observables. Numerical techniques for quantifying noise from multiple time scales in a single trajectory, including experimental instrument and inherent thermal noise, are demonstrated.

Accuracy of colposcopy in the diagnostic setting compared with the screening setting.

Objective: To estimate the accuracy of colposcopy to identify cervical precancer in screening and diagnostic settings.

Methods: As part of a larger clinical trial to evaluate the diagnostic accuracy of optical spectroscopy, we recruited 1,850 patients into a diagnostic or a screening group depending on their history of abnormal findings on Papanicolaou tests. Colposcopic examinations were performed and biopsies specimens obtained from abnormal and normal colposcopic sites for all patients.

The clinical effectiveness of optical spectroscopy for the in vivo diagnosis of cervical intraepithelial neoplasia: where are we?

Objective: In this review, we evaluate the diagnostic efficacy of optical spectroscopy technologies (fluorescence and reflectance spectroscopy) for the in vivo diagnosis of cervical neoplasia using both point probe and multispectral imaging approaches.

Methods: We searched electronic databases using the following terms: cervical cancer, cervical intraepithelial neoplasia, squamous intraepithelial lesion, and spectroscopy, fluorescence spectroscopy, or reflectance spectroscopy. We included studies that evaluated fluorescence and reflectance spectroscopy devices for in vivo diagnosis, compared those results with biopsy results, and reported on the sensitivity and specificity of the devices tested.

Bayesian meta-analysis of Papanicolaou smear accuracy.

Objective: To perform a Bayesian analysis of data from a previous meta-analysis of Papanicolaou (Pap) smear accuracy (Fahey et al. Am J Epidemiol 1995; 141:680-689) and compare the results.

Methods: We considered two Bayesian models for the same data set used in the Fahey et al.

Inverse decision theory with applications to screening and diagnosis of cervical intraepithelial neoplasia.

Objective: Medical decision makers would like to use decision theory to determine optimal treatment strategies for patients, but this requires priors, likelihoods, and losses. It can be very difficult to specify a loss or utility function in a medical setting, especially when considering both patient health outcomes and economic costs. These issues led to the development of Inverse Decision Theory (IDT), which involves determining the set of losses under which a given decision rule is optimal.

Sources of variability in fluorescence spectroscopic measurements in a Phase II clinical trial of 850 patients.

Background: Devices using fluorescence spectroscopy to differentiate high grade squamous intraepithelial lesions from normal tissue in the cervix have shown some diagnostic efficacy. Measurements from these devices produce large amounts of complex, multi-factored data. The purpose of this study is to isolate the effects of the particular care providers and equipment operators who are involved in taking measurements.

Fluorescence and reflectance device variability throughout the progression of a phase II clinical trial to detect and screen for cervical neoplasia using a fiber optic probe.

Large phase II trials of fluorescence and reflectance spectroscopy using a fiber optic probe in the screening and diagnostic settings for detecting cervical neoplasia have been conducted. We present accrual and histopathology data, instrumentation, data processing, and the preliminary results of interdevice consistencies throughout the progression of a trial. Patients were recruited for either a screening trial (no history of abnormal Papanicolaou smears) or a diagnostic trial (a history of abnormal Papanicolaou smears).