Related papers: Reconstructing DNA copy number by penalized estima…

In recent years, a variety of methods based on Transformer and state space model (SSM) architectures have been proposed, advancing foundational DNA language models. However, there is a lack of comparison between these recent approaches and…

Despite the outstanding performance of convolutional neural networks (CNNs) for many vision tasks, the required computational cost during inference is problematic when resources are limited. In this context, we propose Convolutional Neural…

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…

Conducting genome-wide association studies (GWAS) in copy number variation (CNV) level is a field where few people involves and little statistical progresses have been achieved, traditional methods suffer from many problems such as batch…

The recently established Convolution Nuclear Norm Minimization (CNNM) addresses the problem of \textit{tensor completion with arbitrary sampling} (TCAS), which involves restoring a tensor from a subset of its entries sampled in an arbitrary…

Compressed Sensing MRI (CS-MRI) has shown promise in reconstructing under-sampled MR images, offering the potential to reduce scan times. Classical techniques minimize a regularized least-squares cost function using an expensive iterative…

The $\ell_1$-penalized method, or the Lasso, has emerged as an important tool for the analysis of large data sets. Many important results have been obtained for the Lasso in linear regression which have led to a deeper understanding of…

We introduce a new algorithm for approximate inference that combines reparametrization, Markov chain Monte Carlo and variational methods. We construct a very flexible implicit variational distribution synthesized by an arbitrary Markov…

The Lasso is biased. Concave penalized least squares estimation (PLSE) takes advantage of signal strength to reduce this bias, leading to sharper error bounds in prediction, coefficient estimation and variable selection. For prediction and…

The paper proposes a new covariance estimator for large covariance matrices when the variables have a natural ordering. Using the Cholesky decomposition of the inverse, we impose a banded structure on the Cholesky factor, and select the…

The tuning parameter selection strategy for penalized estimation is crucial to identify a model that is both interpretable and predictive. However, popular strategies (e.g., minimizing average squared prediction error via cross-validation)…

Data analysis usually suffers from the Missing Not At Random (MNAR) problem, where the cause of the value missing is not fully observed. Compared to the naive Missing Completely At Random (MCAR) problem, it is more in line with the…

Biological networks often change under different environmental and genetic conditions. Understanding how these networks change becomes an important problem in biological studies. In this paper, we model the network change as the difference…

Evolutionary computation methods have been successfully applied to neural networks since two decades ago, while those methods cannot scale well to the modern deep neural networks due to the complicated architectures and large quantities of…

Components of biological systems interact with each other in order to carry out vital cell functions. Such information can be used to improve estimation and inference, and to obtain better insights into the underlying cellular mechanisms.…

Recurrent neural networks (RNNs) have recently achieved remarkable successes in a number of applications. However, the huge sizes and computational burden of these models make it difficult for their deployment on edge devices. A practically…

Accelerated MRI reconstructs images of clinical anatomies from sparsely sampled signal data to reduce patient scan times. While recent works have leveraged deep learning to accomplish this task, such approaches have often only been explored…

Graphical lasso is one of the most used estimators for inferring genetic networks. Despite its diffusion, there are several fields in applied research where the limits of detection of modern measurement technologies make the use of this…

The adaptive lasso refers to a class of methods that use weighted versions of the $L_1$-norm penalty, with weights derived from an initial estimate of the parameter vector to be estimated. Irrespective of the method chosen to compute this…

Regularized regression approaches such as the Lasso have been widely adopted for constructing sparse linear models in high-dimensional datasets. A complexity in fitting these models is the tuning of the parameters which control the level of…