Search for: All records

Abstract MotivationIn a genome-wide association study, analyzing multiple correlated traits simultaneously is potentially superior to analyzing the traits one by one. Standard methods for multivariate genome-wide association study operate marker-by-marker and are computationally intensive. ResultsWe present a sparsity constrained regression algorithm for multivariate genome-wide association study based on iterative hard thresholding and implement it in a convenient Julia package MendelIHT.jl. In simulation studies with up to 100 quantitative traits, iterative hard thresholding exhibits similar true positive rates, smaller false positive rates, and faster execution times than GEMMA’s linear mixed models and mv-PLINK’s canonical correlation analysis. On UK Biobank data with 470 228 variants, MendelIHT completed a three-trait joint analysis (n=185 656) in 20 h and an 18-trait joint analysis (n=104 264) in 53 h with an 80 GB memory footprint. In short, MendelIHT enables geneticists to fit a single regression model that simultaneously considers the effect of all SNPs and dozens of traits. Availability and implementationSoftware, documentation, and scripts to reproduce our results are available from https://github.com/OpenMendel/MendelIHT.jl. 

Differential sensitivity analysis is indispensable in fitting parameters, understanding uncertainty, and forecasting the results of both thought and lab experiments. Although there are many methods currently available for performing differential sensitivity analysis of biological models, it can be difficult to determine which method is best suited for a particular model. In this paper, we explain a variety of differential sensitivity methods and assess their value in some typical biological models. First, we explain the mathematical basis for three numerical methods: adjoint sensitivity analysis, complex perturbation sensitivity analysis, and forward mode sensitivity analysis. We then carry out four instructive case studies. (a) The CARRGO model for tumor-immune interaction highlights the additional information that differential sensitivity analysis provides beyond traditional naive sensitivity methods, (b) the deterministic SIR model demonstrates the value of using second-order sensitivity in refining model predictions, (c) the stochastic SIR model shows how differential sensitivity can be attacked in stochastic modeling, and (d) a discrete birth-death-migration model illustrates how the complex perturbation method of differential sensitivity can be generalized to a broader range of biological models. Finally, we compare the speed, accuracy, and ease of use of these methods. We find that forward mode automatic differentiation has the quickest computational time, while the complex perturbation method is the simplest to implement and the most generalizable. 

This paper discusses algorithms for phase retrieval where the measurements follow independent Poisson distributions. We developed an optimization problem based on maximum likelihood estimation (MLE) for the Poisson model and applied Wirtinger flow algorithm to solve it. Simulation results with a random Gaussian sensing matrix and Poisson measurement noise demonstrated that the Wirtinger flow algorithm based on the Poisson model produced higher quality reconstructions than when algorithms derived from Gaussian noise models (Wirtinger flow, Gerchberg Saxton) are applied to such data, with significantly improved computational efficiency.