Related papers: Poisson process factorization for mutational signa…
We present a general framework, the coupled compound Poisson factorization (CCPF), to capture the missing-data mechanism in extremely sparse data sets by coupling a hierarchical Poisson factorization with an arbitrary data-generating model.…
Non-negative matrix factorization (NMF) is widely used as a feature extraction technique for matrices with non-negative entries, such as image data, purchase histories, and other types of count data. In NMF, a non-negative matrix is…
Beta process is the standard nonparametric Bayesian prior for latent factor model. In this paper, we derive a structured mean-field variational inference algorithm for a beta process non-negative matrix factorization (NMF) model with…
Bayesian Non-negative Matrix Factorization (NMF) is a promising approach for understanding uncertainty and structure in matrix data. However, a large volume of applied work optimizes traditional non-Bayesian NMF objectives that fail to…
Recent studies of cancer somatic mutation profiles seek to identify mutations for targeted therapy in personalized medicine. Analysis of profiles, however, is not trivial, as each profile is heterogeneous and there are multiple confounding…
Factors models are routinely used to analyze high-dimensional data in both single-study and multi-study settings. Bayesian inference for such models relies on Markov Chain Monte Carlo (MCMC) methods which scale poorly as the number of…
Probabilistic matrix factorization (PMF) is a powerful method for modeling data associated with pairwise relationships, finding use in collaborative filtering, computational biology, and document analysis, among other areas. In many…
Discrete biomarkers derived as cell densities or counts from tissue microarrays and immunostaining are widely used to study immune signatures in relation to survival outcomes in cancer. Although routinely collected, these signatures are not…
Identifying altered pathways that are associated with specific cancer types can potentially bring a significant impact on cancer patient treatment. Accurate identification of such key altered pathways information can be used to develop…
We propose a flexible change-point model for inhomogeneous Poisson Processes, which arise naturally from next-generation DNA sequencing, and derive score and generalized likelihood statistics for shifts in intensity functions. We construct…
We present a unified algorithmic framework for quantum simulation of non-unitary dynamics and matrix functions, governed by the principle of spectral aliasing derived from the Poisson Summation Formula (PSF). By reinterpreting…
We introduce negative binomial matrix factorization (NBMF), a matrix factorization technique specially designed for analyzing over-dispersed count data. It can be viewed as an extension of Poisson matrix factorization (PF) perturbed by a…
Spatial Poisson point processes on finite-dimensional Euclidean space provide fundamental mathematical tools for modeling random spatial point patterns. In this paper, we introduce and analyze several Poisson-type spatial point processes.…
The aim of this study is to provide a foundation to understand the relationship between non-negative matrix factorization (NMF) and non-negative autoencoders enabling proper interpretation and understanding of autoencoder-based alternatives…
One of the central goals in precision health is the understanding and interpretation of high-dimensional biological data to identify genes and markers associated with disease initiation, development, and outcomes. Though significant effort…
Dimensionality reduction methods for count data are critical to a wide range of applications in medical informatics and other fields where model interpretability is paramount. For such data, hierarchical Poisson matrix factorization (HPF)…
Understanding the association between dietary patterns and health outcomes, such as the cancer risk, is crucial to inform public health guidelines and shaping future dietary interventions. However, dietary intake data present several…
Diffusion and Poisson flow models have shown impressive performance in a wide range of generative tasks, including low-dose CT image denoising. However, one limitation in general, and for clinical applications in particular, is slow…
Various Non-negative Matrix factorization (NMF) based methods add new terms to the cost function to adapt the model to specific tasks, such as clustering, or to preserve some structural properties in the reduced space (e.g., local…
Nonnegative matrix factorization (NMF) has become a workhorse for signal and data analytics, triggered by its model parsimony and interpretability. Perhaps a bit surprisingly, the understanding to its model identifiability---the major…