Related papers: Poisson process factorization for mutational signa…

Nonnegative Matrix Factorization(NMF) is a common used technique in machine learning to extract features out of data such as text documents and images thanks to its natural clustering properties. In particular, it is popular in image…

We derive a Poisson random field model for population site polymorphisms differences within and between two species that share a relatively recent common ancestor. The model can be either equilibrium or time inhomogeneous. We first consider…

A central goal in cancer genomics is to identify the somatic alterations that underpin tumor initiation and progression. This task is challenging as the mutational profiles of cancer genomes exhibit vast heterogeneity, with many alterations…

Motivation: Human cancer is caused by the accumulation of somatic mutations in tumor suppressors and oncogenes within the genome. In the case of oncogenes, recent theory suggests that there are only a few key "driver" mutations responsible…

In this paper, we consider a fractional Poisson random field (FPRF) on positive plane. It is defined as a process whose one dimensional distribution is the solution of a system of fractional partial differential equations. A time-changed…

We introduce a biologically detailed, stochastic model of gene expression describing the multiple rate-limiting steps of transcription, nuclear pre-mRNA processing, nuclear mRNA export, cytoplasmic mRNA degradation and translation of mRNA…

In cancer genomics, it is of great importance to distinguish driver mutations, which contribute to cancer progression, from causally neutral passenger mutations. We propose a random-effect regression approach to estimate the effects of…

Over the past few years, there has been a considerable spread of microarray technology in many biological patterns, particularly in those pertaining to cancer diseases like leukemia, prostate, colon cancer, etc. The primary bottleneck that…

We present an applied study in cancer genomics for integrating data and inferences from laboratory experiments on cancer cell lines with observational data obtained from human breast cancer studies. The biological focus is on improving…

Pathology foundation models (PFMs) have emerged as powerful pretrained encoders for computational pathology, but their robustness under clinically relevant distribution shifts remains insufficiently understood. We benchmark the robustness…

Nonnegative matrix factorization (NMF) is a known unsupervised data-reduction method. The principle of the common cause (PCC) is a basic methodological approach in probabilistic causality, which seeks an independent mixture model for the…

Non-negative Matrix Factorization (NMF) is an intensively used technique for obtaining parts-based, lower dimensional and non-negative representation. Researchers in biology, medicine, pharmacy and other fields often prefer NMF over other…

Matrix factorization (MF) has become a common approach to collaborative filtering, due to ease of implementation and scalability to large data sets. Two existing drawbacks of the basic model is that it does not incorporate side information…

Pathology Foundation Models (FMs) hold great promise for healthcare. Before they can be used in clinical practice, it is essential to ensure they are robust to variations between medical centers. We measure whether pathology FMs focus on…

Inference on modern Bayesian Neural Networks (BNNs) often relies on a variational inference treatment, imposing violated assumptions of independence and the form of the posterior. Traditional MCMC approaches avoid these assumptions at the…

We introduce a novel Bayesian hybrid matrix factorisation model (HMF) for data integration, based on combining multiple matrix factorisation methods, that can be used for in- and out-of-matrix prediction of missing values. The model is very…

Most of previous works and applications of Bayesian factor model have assumed the normal likelihood regardless of its validity. We propose a Bayesian factor model for heavy-tailed high-dimensional data based on multivariate Student-$t$…

We introduce the Poisson Log-Normal Graphical Model for count data, and present a normality transformation for data arising from this distribution. The model and transformation are feasible for high-throughput microRNA (miRNA) sequencing…

Cancer, with its inherent heterogeneity, is commonly categorized into distinct subtypes based on unique traits, cellular origins, and molecular markers specific to each type. However, current studies primarily rely on complete multi-omics…

This paper introduces a new stochastic process with values in the set Z of integers with sign. The increments of process are Poisson differences and the dynamics has an autoregressive structure. We study the properties of the process and…