Related papers: Differential Expression Analysis of Dynamical Sequ…

In clinical biomarker studies, the Dynamic Network Biomarker (DNB) is sometimes used. DNB is a composite variable derived from the variance and the Pearson correlation coefficient of biological signals. When applying DNB to clinical data,…

Biomedical research increasingly relies on integrating diverse data modalities, including gene expression profiles, medical images, and clinical metadata. While medical images and clinical metadata are routinely collected in clinical…

Graph Neural Networks (GNNs) have received increasing attention due to their ability to learn from graph-structured data. However, their predictions are often not interpretable. Post-hoc instance-level explanation methods have been proposed…

Motivation: Recent advances in high-throughput sequencing (HTS) have made it possible to monitor genomes in great detail. New experiments not only use HTS to measure genomic features at one time point but to monitor them changing over time…

Generative moment matching networks (GMMNs) are introduced as dependence models for the joint innovation distribution of multivariate time series (MTS). Following the popular copula-GARCH approach for modeling dependent MTS data, a…

Gibbs sampling is one of the most commonly used Markov Chain Monte Carlo (MCMC) algorithms due to its simplicity and efficiency. It cycles through the latent variables, sampling each one from its distribution conditional on the current…

We introduce graph gamma process (GGP) linear dynamical systems to model real-valued multivariate time series. For temporal pattern discovery, the latent representation under the model is used to decompose the time series into a…

High-throughput sequencing is now regularly used for studies of the transcriptome (RNA-seq), particularly for comparisons among experimental conditions. For the time being, a limited number of biological replicates are typically considered…

While deep generative models (DGMs) have gained popularity, their susceptibility to biases and other inefficiencies that lead to undesirable outcomes remains an issue. With their growing complexity, there is a critical need for early…

Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. This novel approach is a newbie and has critical advantages over the traditional Capillary…

In recent years, there has been an increasing interest in the use of graph neural networks (GNNs) for analyzing dynamic graphs, which are graphs that evolve over time. However, there is still a lack of understanding of how different…

The modelling of temporal patterns in dynamic graphs is an important current research issue in the development of time-aware GNNs. Whether or not a specific sequence of events in a temporal graph constitutes a temporal pattern not only…

In today's data-intensive landscape, where high-dimensional datasets are increasingly common, reducing the number of input features is essential to prevent overfitting and improve model accuracy. Despite numerous efforts to tackle…

Many biological data analysis processes like Cytometry or Next Generation Sequencing (NGS) produce massive amounts of data which needs to be processed in batches for down-stream analysis. Such datasets are prone to technical variations due…

Graph Neural Networks (GNNs) have demonstrated remarkable success in modeling complex relationships in graph-structured data. A recent innovation in this field is the family of Differential Equation-Inspired Graph Neural Networks (DE-GNNs),…

Cellular response to environmental and internal signals can be modeled by dynamical gene regulatory networks (GRN). In the literature, three main classes of gene network models can be distinguished: (i) non-quantitative (or data-based)…

The regression of multiple inter-connected sequence data is a problem in various disciplines. Formally, we name the regression problem of multiple inter-connected data entities as the "dynamic network regression" in this paper. Within the…

We describe the time evolution of gene expression levels by using a time translational matrix to predict future expression levels of genes based on their expression levels at some initial time. We deduce the time translational matrix for…

In recent years, numerous graph generative models (GGMs) have been proposed. However, evaluating these models remains a considerable challenge, primarily due to the difficulty in extracting meaningful graph features that accurately…

In this paper, we propose a closed form approximation to the mean and variance of a new generalization of negative binomial (NGNB) distribution arising from the Extended COM-Poisson (ECOMP) distribution developed by Chakraborty and Imoto…