Related papers: GPO-VAE: Modeling Explainable Gene Perturbation Re…

The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…

Understanding the complex and stochastic nature of Gene Regulatory Networks (GRNs) remains a central challenge in systems biology. Existing modeling paradigms often struggle to effectively capture the intricate, multi-factor regulatory…

Variational autoencoders (VAEs) and generative adversarial networks (GANs) enjoy an intuitive connection to manifold learning: in training the decoder/generator is optimized to approximate a homeomorphism between the data distribution and…

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in…

Variational Auto-Encoders (VAEs) are capable of learning latent representations for high dimensional data. However, due to the i.i.d. assumption, VAEs only optimize the singleton variational distributions and fail to account for the…

Unsupervised representation learning via generative modeling is a staple to many computer vision applications in the absence of labeled data. Variational Autoencoders (VAEs) are powerful generative models that learn representations useful…

We present a novel introspective variational autoencoder (IntroVAE) model for synthesizing high-resolution photographic images. IntroVAE is capable of self-evaluating the quality of its generated samples and improving itself accordingly.…

Graph Neural Networks (GNNs) are deep learning models that take graph data as inputs, and they are applied to various tasks such as traffic prediction and molecular property prediction. However, owing to the complexity of the GNNs, it has…

In this article, we present a data-driven method for parametric models with noisy observation data. Gaussian process regression based reduced order modeling (GPR-based ROM) can realize fast online predictions without using equations in the…

Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…

High-dimensional clinical data have become invaluable resources for genetic studies, due to their accessibility in biobank-scale datasets and the development of high performance modeling techniques especially using deep learning. Recent…

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…

Deep learning (DL) methods where interpretability is intrinsically considered as part of the model are required to better understand the relationship of clinical and imaging-based attributes with DL outcomes, thus facilitating their use in…

Biological structure and function depend on complex regulatory interactions between many genes. A wealth of gene expression data is available from high-throughput genome-wide measurement technologies, but effective gene regulatory network…

Recent work in unsupervised learning has focused on efficient inference and learning in latent variables models. Training these models by maximizing the evidence (marginal likelihood) is typically intractable. Thus, a common approximation…

Variational AutoEncoders (VAEs) are powerful generative models that merge elements from statistics and information theory with the flexibility offered by deep neural networks to efficiently solve the generation problem for high dimensional…

Deep convolutional neural networks (CNNs) have proven highly effective for visual recognition, where learning a universal representation from activations of convolutional layer plays a fundamental problem. In this paper, we present Fisher…

Although variational autoencoders (VAE) are successfully used to obtain meaningful low-dimensional representations for high-dimensional data, the characterization of critical points of the loss function for general observation models is not…

Semi-supervised learning is sought for leveraging the unlabelled data when labelled data is difficult or expensive to acquire. Deep generative models (e.g., Variational Autoencoder (VAE)) and semisupervised Generative Adversarial Networks…

Recent advancements have established Reinforcement Learning (RL) as a pivotal paradigm for aligning generative models with human intent. However, group-based optimization frameworks (e.g., GRPO) face a critical limitation: the rapid decay…