Related papers: GSAE: an autoencoder with embedded gene-set nodes …

Modern deep learning systems rely on (a) a hand-tuned neural network topology, (b) massive amounts of labeled training data, and (c) extensive training over large-scale compute resources to build a system that can perform efficient image…

Sparse Autoencoders (SAEs) are a promising approach for extracting neural network representations by learning a sparse and overcomplete decomposition of the network's internal activations. However, SAEs are traditionally trained considering…

Motivation: Gene set testing is typically performed in a supervised context to quantify the association between groups of genes and a clinical phenotype. In many cases, however, a gene set-based interpretation of genomic data is desired in…

The characterization of Tumor MicroEnvironment (TME) is challenging due to its complexity and heterogeneity. Relatively consistent TME characteristics embedded within highly specific tissue features, render them difficult to predict. The…

This study introduces a compositional autoencoder (CAE) framework designed to disentangle the complex interplay between genotypic and environmental factors in high-dimensional phenotype data to improve trait prediction in plant breeding and…

Inferring Gene Regulatory Networks (GRNs) from gene expression data is crucial for understanding biological processes. While supervised models are reported to achieve high performance for this task, they rely on costly ground truth (GT)…

Breast cancer has long been a prominent cause of mortality among women. Diagnosis, therapy, and prognosis are now possible, thanks to the availability of RNA sequencing tools capable of recording gene expression data. Molecular subtyping…

Variational autoencoders (VAEs) are widely used deep generative models capable of learning unsupervised latent representations of data. Such representations are often difficult to interpret or control. We consider the problem of…

By composing graphical models with deep learning architectures, we learn generative models with the strengths of both frameworks. The structured variational autoencoder (SVAE) inherits structure and interpretability from graphical models,…

The application of machine learning to transcriptomics data has led to significant advances in cancer research. However, the high dimensionality and complexity of RNA sequencing (RNA-seq) data pose significant challenges in pan-cancer…

Molecular data from tumor profiles is high dimensional. Tumor profiles can be characterized by tens of thousands of gene expression features. Due to the size of the gene expression feature set machine learning methods are exposed to noisy…

Masked Autoencoders (MAEs) have emerged as a dominant strategy for self-supervised representation learning in natural images, where models are pre-trained to reconstruct masked patches with a pixel-wise mean squared error (MSE) between…

This work contributes to breast cancer sub-type classification using histopathological images. We utilize masked autoencoders (MAEs) to learn a self-supervised embedding tailored for computer vision tasks in this domain. This embedding…

Deep learning is a kind of feature learning method with strong nonliear feature transformation and becomes more and more important in many fields of artificial intelligence. Deep autoencoder is one representative method of the deep learning…

Autoencoders and their variants are among the most widely used models in representation learning and generative modeling. However, autoencoder-based models usually assume that the learned representations are i.i.d. and fail to capture the…

Segmentation of Prostate Cancer (PCa) tissues from Gleason graded histopathology images is vital for accurate diagnosis. Although deep learning (DL) based segmentation methods achieve state-of-the-art accuracy, they rely on large datasets…

Cancer is a complex disease with significant social and economic impact. Advancements in high-throughput molecular assays and the reduced cost for performing high-quality multi-omics measurements have fuelled insights through machine…

The Genebass dataset, released by Karczewski et al. (2022), provides a comprehensive resource elucidating associations between genes and 4,529 phenotypes based on nearly 400,000 exomes from the UK Biobank. This extensive dataset enables the…

Stack autoencoder (SAE), as a representative deep network, has unique and excellent performance in feature learning, and has received extensive attention from researchers. However, existing deep SAEs focus on original samples without…

Predicting phenotypes from gene expression data is a crucial task in biomedical research, enabling insights into disease mechanisms, drug responses, and personalized medicine. Traditional machine learning and deep learning rely on…