MOTIVATION: There is a growing interest in longitudinal omics data paired with some longitudinal clinical outcome. Given a large set of continuous omics variables and some continuous clinical outcome, each measured for a few subjects at only a few time points, we seek to identify those variables that co-vary over time with the outcome. To motivate this problem we study a dataset with hundreds of urinary metabolites along with Tuberculosis mycobacterial load as our clinical outcome, with the objective of identifying potential biomarkers for disease progression. For such data clinicians usually apply simple linear mixed effects models which often lack power given the low number of replicates and time points. We propose a penalized regression approach on the first differences of the data that extends the lasso + Laplacian method [Li and Li (Network-constrained regularization and variable selection for analysis of genomic data. Bioinformatics 2008;24:1175-82.)] to a longitudinal group lasso + Laplacian approach. Our method, PROLONG, leverages the first differences of the data to increase power by pairing the consecutive time points. The Laplacian penalty incorporates the dependence structure of the variables, and the group lasso penalty induces sparsity while grouping together all contemporaneous and lag terms for each omic variable in the model. RESULTS: With an automated selection of model hyper-parameters, PROLONG correctly selects target metabolites with high specificity and sensitivity across a wide range of scenarios. PROLONG selects a set of metabolites from the real data that includes interesting targets identified during EDA. AVAILABILITY AND IMPLEMENTATION: An R package implementing described methods called "prolong" is available at https://github.com/stevebroll/prolong. Code snapshot available at 10.5281/zenodo.14804245.

Deep neural networks achieve state-of-the-art performance in a variety of tasks by extracting a rich set of features from unstructured data, however this performance is closely tied to model size. Modern techniques for inducing sparsity and reducing model size are (1) network pruning, (2) training with a sparsity inducing penalty, and (3) training a binary mask jointly with the weights of the network. We study different sparsity inducing penalties from the perspective of Bayesian hierarchical models and present a novel penalty called Hierarchical Adaptive Lasso (HALO) which learns to adaptively sparsify weights of a given network via trainable parameters. When used to train over-parametrized networks, our penalty yields small subnetworks with high accuracy without fine-tuning. Empirically, on image recognition tasks, we find that HALO is able to learn highly sparse network (only 5% of the parameters) with significant gains in performance over state-of-the-art magnitude pruning methods at the same level of sparsity. Code is available at https://github.com/skyler120/sparsity-halo.

BACKGROUND: Identifying quantitative trait loci (QTL) for both additive and epistatic effects raises the statistical issue of selecting variables from a large number of candidates using a small number of observations. Missing trait and/or marker values prevent one from directly applying the classical model selection criteria such as Akaike's information criterion (AIC) and Bayesian information criterion (BIC). RESULTS: We propose a two-step Bayesian variable selection method which deals with the sparse parameter space and the small sample size issues. The regression coefficient priors are flexible enough to incorporate the characteristic of "large p small n" data. Specifically, sparseness and possible asymmetry of the significant coefficients are dealt with by developing a Gibbs sampling algorithm to stochastically search through low-dimensional subspaces for significant variables. The superior performance of the approach is demonstrated via simulation study. We also applied it to real QTL mapping datasets. CONCLUSION: The two-step procedure coupled with Bayesian classification offers flexibility in modeling "large p small n" data, especially for the sparse and asymmetric parameter space. This approach can be extended to other settings characterized by high dimension and low sample size.

A simple and practical probabilistic comparison-based model, employing multiple incomplete test concepts, for handling fault location in distributed systems using a Bayesian analysis procedure is proposed. This approach is more practical and complete than previous ones since it does not assume any conditions such as permanently faulty units, complete tests, perfect environments, or non-malicious environments. Fault-free systems are handled without overhead; hence, the test procedure may be used to monitor a functioning system. Given a system S with a specific test graph, the corresponding conditional distribution between the comparison test results (syndrome) and the fault patterns of S can be generated. To avoid the complex global Bayesian estimation process, a simple bitwise Bayesian algorithm is developed for fault location in S, which locates system failures with linear complexity, suitable for hard real-time systems.>