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Bayesian Poisson Non-Negative Matrix Factorization (NMF) is widely used to model count data, including in cancer mutational signature analysis. However, standard Gibbs samplers rely on computationally expensive Poisson augmentation, and…

Variational AutoEncoder (VAE) has been extended as a representative nonlinear method for collaborative filtering. However, the bottleneck of VAE lies in the softmax computation over all items, such that it takes linear costs in the number…

We propose a framework for the statistical evaluation of variational auto-encoders (VAEs) and test two instances of this framework in the context of modelling images of handwritten digits and a corpus of English text. Our take on evaluation…

In this study, we present Flatsomatic - a Variational Auto Encoder (VAE) optimized to compress somatic mutations that allow for unbiased data compression whilst maintaining the signal. We compared two different neural network architectures…

Due to their unsupervised training and uncertainty estimation, deep Variational Autoencoders (VAEs) have become powerful tools for reconstruction-based Time Series Anomaly Detection (TSAD). Existing VAE-based TSAD methods, either…

Estimation of uncertainty in deep learning models is of vital importance, especially in medical imaging, where reliance on inference without taking into account uncertainty could lead to misdiagnosis. Recently, the probabilistic Variational…

Non-negative matrix factorization (NMF) is widely used in many applications for dimensionality reduction. Inferring an appropriate number of factors for NMF is a challenging problem, and several approaches based on information criteria or…

Ultrasound imaging is one of the most widely used diagnostic modalities, offering real-time, radiation-free assessment across diverse clinical domains. However, interpretation of ultrasound images remains challenging due to high noise…

We present a novel method for extracting cancer signatures by applying statistical risk models (http://ssrn.com/abstract=2732453) from quantitative finance to cancer genome data. Using 1389 whole genome sequenced samples from 14 cancers, we…

Interpretable machine learning is rapidly becoming a crucial tool for scientific discovery. Among existing approaches, variational autoencoders (VAEs) have shown promise in extracting the hidden physical features of some input data, with no…

We present a coupled Variational Auto-Encoder (VAE) method that improves the accuracy and robustness of the probabilistic inferences on represented data. The new method models the dependency between input feature vectors (images) and weighs…

Electrocardiogram (ECG) analysis is a fundamental tool for diagnosing cardiovascular conditions, yet anomaly detection in ECG signals remains challenging due to their inherent complexity and variability. We propose Multi-scale Masked…

Optimal computations under uncertainty require an adequate probabilistic representation about beliefs. Deep generative models, and specifically Variational Autoencoders (VAEs), have the potential to meet this demand by building latent…

Artificial Intelligence (AI) has the potential to revolutionize diagnosis and segmentation in medical imaging. However, development and clinical implementation face multiple challenges including limited data availability, lack of…

A novel framework for Bayesian structural model updating is presented in this study. The proposed method utilizes the surrogate unimodal encoders of a multimodal variational autoencoder (VAE). The method facilitates an approximation of the…

The surrogate loss of variational autoencoders (VAEs) poses various challenges to their training, inducing the imbalance between task fitting and representation inference. To avert this, the existing strategies for VAEs focus on adjusting…

The development of deep learning methods for magnetic resonance spectroscopy (MRS) is often hindered by limited availability of large, high-quality training datasets. While physics-based simulations are commonly used to mitigate this…

Vision Transformer (ViT) suffers from data scarcity in semi-supervised learning (SSL). To alleviate this issue, inspired by masked autoencoder (MAE), which is a data-efficient self-supervised learner, we propose Semi-MAE, a pure ViT-based…

Variational autoencoders (VAEs) have been used extensively to discover low-dimensional latent factors governing neural activity and animal behavior. However, without careful model selection, the uncovered latent factors may reflect noise in…

Human cancers present a significant public health challenge and require the discovery of novel drugs through translational research. Transcriptomics profiling data that describes molecular activities in tumors and cancer cell lines are…