Related papers: Variational inference for rare variant detection i…
Ensembles of deep neural networks have achieved great success recently, but they do not offer a proper Bayesian justification. Moreover, while they allow for averaging of predictions over several hypotheses, they do not provide any…
The Stochastic Extragradient (SEG) method is one of the most popular algorithms for solving min-max optimization and variational inequalities problems (VIP) appearing in various machine learning tasks. However, several important questions…
In this study, an efficient stochastic gradient-free method, the ensemble neural networks (ENN), is developed. In the ENN, the optimization process relies on covariance matrices rather than derivatives. The covariance matrices are…
Targeted amplicon panels are widely used in oncology diagnostics, but providing per-gene performance guarantees for copy number variant (CNV) detection remains challenging due to amplification artifacts, process-mismatch heterogeneity, and…
In a mixture of linear regression model, the regression coefficients are treated as random vectors that may follow either a continuous or discrete distribution. We propose two Expectation-Maximization (EM) algorithms to estimate this prior…
Random feature latent variable models (RFLVMs) represent the state-of-the-art in latent variable models, capable of handling non-Gaussian likelihoods and effectively uncovering patterns in high-dimensional data. However, their heavy…
Simultaneous analysis of gene expression data and genetic variants is highly of interest, especially when the number of gene expressions and genetic variants are both greater than the sample size. Association of both causal genes and…
Nonlinear equations systems (NESs) are widely used in real-world problems while they are also difficult to solve due to their characteristics of nonlinearity and multiple roots. Evolutionary algorithm (EA) is one of the methods for solving…
Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid (DNA/RNA) sequencing technology that estimates sequence as an emergent property of the binding and localization of a repertoire of short oligonucleotide probes. SEQE…
Clustering algorithms have wide applications and play an important role in data analysis fields including time series data analysis. However, in time series analysis, most of the algorithms used signal shape features or the initial value of…
Advancement in sequencing technology enables the study of association between complex disorders and rare variants with low minor allele frequencies. One of the major challenges in rare variant testing is lack of statistical power of…
The Stochastic Approximation EM (SAEM) algorithm, a variant stochastic approximation of EM, is a versatile tool for inference in incomplete data models. In this paper, we review the fundamental EM algorithm and then focus especially on the…
Clustering analysis is one of the most widely used statistical tools in many emerging areas such as microarray data analysis. For microarray and other high-dimensional data, the presence of many noise variables may mask underlying…
Graphical Gaussian models have proven to be useful tools for exploring network structures based on multivariate data. Applications to studies of gene expression have generated substantial interest in these models, and resulting recent…
Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…
This article focuses on parameter estimation of multi-levels nonlinear mixed effects models (MNLMEMs). These models are used to analyze data presenting multiple hierarchical levels of grouping (cluster data, clinical trials with several…
In this work, we present an extension to the context of Stochastic Reaction Networks (SRNs) of the forward-reverse representation introduced in "Simulation of forward-reverse stochastic representations for conditional diffusions", a 2014…
Bayesian Neural Networks with Latent Variables (BNN+LVs) capture predictive uncertainty by explicitly modeling model uncertainty (via priors on network weights) and environmental stochasticity (via a latent input noise variable). In this…
We propose a novel deep clustering method that integrates Variational Autoencoders (VAEs) into the Expectation-Maximization (EM) framework. Our approach models the probability distribution of each cluster with a VAE and alternates between…
In a variety of application areas, there is interest in assessing evidence of differences in the intensity of event realizations between groups. For example, in cancer genomic studies collecting data on rare variants, the focus is on…