Active Mutual Conjoint Estimation of Multiple Contrast Sensitivity Functions.

Recent advances in nonparametric Contrast Sensitivity Function (CSF) estimation have yielded a new tradeoff between accuracy and efficiency not available to classical parametric estimators. An additional advantage of this new framework is the ability to independently tune multiple aspects of the estimator to seek further improvements. Machine Learning CSF (MLCSF) estimation with Gaussian processes allows for design optimization in the kernel, acquisition function and underlying task representation, to name a few. This paper describes a novel kernel for CSF estimation that is more flexible than a kernel based on strictly functional forms. Despite being more flexible, it can result in a more efficient estimator. Further, trial selection for data acquisition that is generalized beyond pure information gain can also improve estimator quality. Finally, introducing latent variable representations underlying general CSF shapes can enable simultaneous estimation of multiple CSFs, such as from different eyes, eccentricities or luminances. The conditions under which the new procedures perform better than previous nonparametric estimation procedures are presented and quantified.

Contrast response function estimation with nonparametric Bayesian active learning.

Multidimensional psychometric functions can typically be estimated nonparametrically for greater accuracy or parametrically for greater efficiency. By recasting the estimation problem from regression to classification, however, powerful machine learning tools can be leveraged to provide an adjustable balance between accuracy and efficiency. Contrast sensitivity functions (CSFs) are behaviorally estimated curves that provide insight into both peripheral and central visual function. Because estimation can be impractically long, current clinical workflows must make compromises such as limited sampling across spatial frequency or strong assumptions on CSF shape. This article describes the development of the machine learning contrast response function (MLCRF) estimator, which quantifies the expected probability of success in performing a contrast detection or discrimination task. A machine learning CSF can then be derived from the MLCRF. Using simulated eyes created from canonical CSF curves and actual human contrast response data, the accuracy and efficiency of the machine learning contrast sensitivity function (MLCSF) was evaluated to determine its potential utility for research and clinical applications. With stimuli selected randomly, the MLCSF estimator converged slowly toward ground truth. With optimal stimulus selection via Bayesian active learning, convergence was nearly an order of magnitude faster, requiring only tens of stimuli to achieve reasonable estimates. Inclusion of an informative prior provided no consistent advantage to the estimator as configured. MLCSF achieved efficiencies on par with quickCSF, a conventional parametric estimator, but with systematically higher accuracy. Because MLCSF design allows accuracy to be traded off against efficiency, it should be explored further to uncover its full potential.

Filling in the white space: Spatial interpolation with Gaussian processes and social media data.

Full national coverage below the state level is difficult to attain through survey-based data collection. Even the largest survey-based data collections, such as the CDC's Behavioral Risk Factor Surveillance System or the Gallup-Healthways Well-being Index (both with more than 300,000 responses p.a.) only allow for the estimation of annual averages for about 260 out of roughly U.S. 3,000 counties when a threshold of 300 responses per county is used. Using a relatively high threshold of 300 responses gives substantially higher convergent validity-higher correlations with health variables-than lower thresholds but covers a reduced and biased sample of the population. We present principled methods to interpolate spatial estimates and show that including large-scale geotagged social media data can increase interpolation accuracy. In this work, we focus on Gallup-reported life satisfaction, a widely-used measure of subjective well-being. We use Gaussian Processes (GP), a formal Bayesian model, to interpolate life satisfaction, which we optimally combine with estimates from low-count data. We interpolate over several spaces (geographic and socioeconomic) and extend these evaluations to the space created by variables encoding language frequencies of approximately 6 million geotagged Twitter users. We find that Twitter language use can serve as a rough aggregate measure of socioeconomic and cultural similarity, and improves upon estimates derived from a wide variety of socioeconomic, demographic, and geographic similarity measures. We show that applying Gaussian Processes to the limited Gallup data allows us to generate estimates for a much larger number of counties while maintaining the same level of convergent validity with external criteria (i.e., N = 1,133 vs. 2,954 counties). This work suggests that spatial coverage of psychological variables can be reliably extended through Bayesian techniques while maintaining out-of-sample prediction accuracy and that Twitter language adds important information about cultural similarity over and above traditional socio-demographic and geographic similarity measures. Finally, to facilitate the adoption of these methods, we have also open-sourced an online tool that researchers can freely use to interpolate their data across geographies.

Contrast Response Function Estimation with Nonparametric Bayesian Active Learning.

Multidimensional psychometric functions can typically be estimated nonparametrically for greater accuracy or parametrically for greater efficiency. By recasting the estimation problem from regression to classification, however, powerful machine learning tools can be leveraged to provide an adjustable balance between accuracy and efficiency. Contrast Sensitivity Functions (CSFs) are behaviorally estimated curves that provide insight into both peripheral and central visual function. Because estimation can be impractically long, current clinical workflows must make compromises such as limited sampling across spatial frequency or strong assumptions on CSF shape. This paper describes the development of the Machine Learning Contrast Response Function (MLCRF) estimator, which quantifies the expected probability of success in performing a contrast detection or discrimination task. A machine learning CSF can then be derived from the MLCRF. Using simulated eyes created from canonical CSF curves and actual human contrast response data, the accuracy and efficiency of the MLCSF was evaluated in order to determine its potential utility for research and clinical applications. With stimuli selected randomly, the MLCSF estimator converged slowly toward ground truth. With optimal stimulus selection via Bayesian active learning, convergence was nearly an order of magnitude faster, requiring only tens of stimuli to achieve reasonable estimates. Inclusion of an informative prior provided no consistent advantage to the estimator as configured. MLCSF achieved efficiencies on par with quickCSF, a conventional parametric estimator, but with systematically higher accuracy. Because MLCSF design allows accuracy to be traded off against efficiency, it should be explored further to uncover its full potential. Precis: Machine learning classifiers enable accurate and efficient contrast sensitivity function estimation with item-level prediction for individual eyes.

wenda_gpu: fast domain adaptation for genomic data.

MOTIVATION: Domain adaptation allows for the development of predictive models even in cases with limited sample data. Weighted elastic net domain adaptation specifically leverages features of genomic data to maximize transferability but the method is too computationally demanding to apply to many genome-sized datasets. RESULTS: We developed wenda_gpu, which uses GPyTorch to train models on genomic data within hours on a single GPU-enabled machine. We show that wenda_gpu returns comparable results to the original wenda implementation, and that it can be used for improved prediction of cancer mutation status on small sample sizes than regular elastic net. AVAILABILITY AND IMPLEMENTATION: wenda_gpu is available on GitHub at https://github.com/greenelab/wenda_gpu/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM.

Epigenetic changes, such as aberrant DNA methylation, contribute to cancer clonal expansion and disease progression. However, identifying subpopulation-level changes in a heterogeneous sample remains challenging. Thus, we have developed a computational approach, DXM, to deconvolve the methylation profiles of major allelic subpopulations from the bisulfite sequencing data of a heterogeneous sample. DXM does not require prior knowledge of the number of subpopulations or types of cells to expect. We benchmark DXM's performance and demonstrate improvement over existing methods. We further experimentally validate DXM predicted allelic subpopulation-methylation profiles in four Diffuse Large B-Cell Lymphomas (DLBCLs). Lastly, as proof-of-concept, we apply DXM to a cohort of 31 DLBCLs and relate allelic subpopulation methylation profiles to relapse. We thus demonstrate that DXM can robustly find allelic subpopulation methylation profiles that may contribute to disease progression using bisulfite sequencing data of any heterogeneous sample.

Fast, Continuous Audiogram Estimation Using Machine Learning.

OBJECTIVES: Pure-tone audiometry has been a staple of hearing assessments for decades. Many different procedures have been proposed for measuring thresholds with pure tones by systematically manipulating intensity one frequency at a time until a discrete threshold function is determined. The authors have developed a novel nonparametric approach for estimating a continuous threshold audiogram using Bayesian estimation and machine learning classification. The objective of this study was to assess the accuracy and reliability of this new method relative to a commonly used threshold measurement technique. DESIGN: The authors performed air conduction pure-tone audiometry on 21 participants between the ages of 18 and 90 years with varying degrees of hearing ability. Two repetitions of automated machine learning audiogram estimation and one repetition of conventional modified Hughson-Westlake ascending-descending audiogram estimation were acquired by an audiologist. The estimated hearing thresholds of these two techniques were compared at standard audiogram frequencies (i.e., 0.25, 0.5, 1, 2, 4, 8 kHz). RESULTS: The two threshold estimate methods delivered very similar estimates at standard audiogram frequencies. Specifically, the mean absolute difference between estimates was 4.16 ± 3.76 dB HL. The mean absolute difference between repeated measurements of the new machine learning procedure was 4.51 ± 4.45 dB HL. These values compare favorably with those of other threshold audiogram estimation procedures. Furthermore, the machine learning method generated threshold estimates from significantly fewer samples than the modified Hughson-Westlake procedure while returning a continuous threshold estimate as a function of frequency. CONCLUSIONS: The new machine learning audiogram estimation technique produces continuous threshold audiogram estimates accurately, reliably, and efficiently, making it a strong candidate for widespread application in clinical and research audiometry.