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In genetic studies of complex diseases, the underlying mode of inheritance is often not known. Thus, the most powerful test or other optimal procedure for one model, e.g. recessive, may be quite inefficient if another model, e.g. dominant,…

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…

Copy number variants (CNVs) account for more polymorphic base pairs in the human genome than do single nucleotide polymorphisms (SNPs). CNVs encompass genes as well as noncoding DNA, making these polymorphisms good candidates for functional…

Motivation :Reconstructing the topology of a gene regulatory network is one of the key tasks in systems biology. Despite of the wide variety of proposed methods, very little work has been dedicated to the assessment of their stability…

Genome-wide association studies, in which as many as a million single nucleotide polymorphisms (SNP) are measured on several thousand samples, are quickly becoming a common type of study for identifying genetic factors associated with many…

Modern bio-technologies have produced a vast amount of high-throughput data with the number of predictors far greater than the sample size. In order to identify more novel biomarkers and understand biological mechanisms, it is vital to…

A daunting challenge faced by modern biological sciences is finding an efficient and computationally feasible approach to deal with the curse of high dimensionality. The problem becomes even more severe when the research focus is on…

In recent years, Convolutional Neural Network (CNN) based trackers have achieved state-of-the-art performance on multiple benchmark datasets. Most of these trackers train a binary classifier to distinguish the target from its background.…

Kernel Principal Component Analysis (KPCA) is a popular dimensionality reduction technique with a wide range of applications. However, it suffers from the problem of poor scalability. Various approximation methods have been proposed in the…

In this work, we present a quantum circuit model for inferring gene regulatory networks (GRNs). The model is based on the idea of using qubit-qubit entanglement to simulate interactions between genes. We provide preliminary results that…

Principal Component Analysis (PCA) and its nonlinear extension Kernel PCA (KPCA) are widely used across science and industry for data analysis and dimensionality reduction. Modern deep learning tools have achieved great empirical success,…

Reconstruction of gene regulatory networks is the process of identifying gene dependency from gene expression profile through some computation techniques. In our human body, though all cells pose similar genetic material but the activation…

Transcriptional regulatory network inference methods have been studied for years. Most of them relie on complex mathematical and algorithmic concepts, making them hard to adapt, re-implement or integrate with other methods. To address this…

Modelling and understanding directional gene networks is a major challenge in biology as they play an important role in the architecture and function of genetic systems. Copula Directional Dependence (CDD) can measure the directed…

Last-generation GAN models allow to generate synthetic images which are visually indistinguishable from natural ones, raising the need to develop tools to distinguish fake and natural images thus contributing to preserve the trustworthiness…

Canonical correlation analysis (CCA) is a statistical learning method that seeks to build view-independent latent representations from multi-view data. This method has been successfully applied to several pattern analysis tasks such as…

While measurement advances now allow extensive surveys of gene activity (large numbers of genes across many samples), interpretation of these data is often confounded by noise -- expression counts can differ strongly across samples due to…

With the development of Earth observation technology, very-high-resolution (VHR) image has become an important data source of change detection. Nowadays, deep learning methods have achieved conspicuous performance in the change detection of…

Despite the availability of various sequence analysis models, comparative genomic analysis remains a challenge in genomics, genetics, and phylogenetics. Commutative algebra, a fundamental tool in algebraic geometry and number theory, has…

Canonical correlation analysis (CCA) is a technique for finding correlations between different data modalities and learning low-dimensional representations. As fairness becomes crucial in machine learning, fair CCA has gained attention.…