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

Delays in protein synthesis cause a confounding effect when constructing Gene Regulatory Networks (GRNs) from RNA-sequencing time-series data. Accurate GRNs can be very insightful when modelling development, disease pathways, and drug…

The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction…

Deep learning-based AI models have been extensively applied in genomics, achieving remarkable success across diverse applications. As these models gain prominence, there exists an urgent need for interpretability methods to establish…

Variational Autoencoders (VAEs) are expressive latent variable models that can be used to learn complex probability distributions from training data. However, the quality of the resulting model crucially relies on the expressiveness of the…

As an important problem in causal inference, we discuss the estimation of treatment effects (TEs). Representing the confounder as a latent variable, we propose Intact-VAE, a new variant of variational autoencoder (VAE), motivated by the…

We introduce the variational graph auto-encoder (VGAE), a framework for unsupervised learning on graph-structured data based on the variational auto-encoder (VAE). This model makes use of latent variables and is capable of learning…

Deep generative models are commonly used for generating images and text. Interpretability of these models is one important pursuit, other than the generation quality. Variational auto-encoder (VAE) with Gaussian distribution as prior has…

Distributed learning and Edge AI necessitate efficient data processing, low-latency communication, decentralized model training, and stringent data privacy to facilitate real-time intelligence on edge devices while reducing dependency on…

Our ability to generalize beyond training data to novel, out-of-distribution, image degradations is a hallmark of primate vision. The predictive brain, exemplified by predictive coding networks (PCNs), has become a prominent neuroscience…

This tutorial focuses on the fundamental architectures of Variational Autoencoders (VAE) and Generative Adversarial Networks (GAN), disregarding their numerous variations, to highlight their core principles. Both VAE and GAN utilize simple…

The performance of $\beta$-Variational-Autoencoders ($\beta$-VAEs) and their variants on learning semantically meaningful, disentangled representations is unparalleled. On the other hand, there are theoretical arguments suggesting the…

We present new intuitions and theoretical assessments of the emergence of disentangled representation in variational autoencoders. Taking a rate-distortion theory perspective, we show the circumstances under which representations aligned…

Recently, Graph Neural Networks (GNNs) have significantly advanced the performance of machine learning tasks on graphs. However, this technological breakthrough makes people wonder: how does a GNN make such decisions, and can we trust its…

A major goal in genomics is to properly capture the complex dynamical behaviors of gene regulatory networks (GRNs). This includes inferring the complex interactions between genes, which can be used for a wide range of genomics analyses,…

Deep generative models have recently yielded encouraging results in producing subjectively realistic samples of complex data. Far less attention has been paid to making these generative models interpretable. In many scenarios, ranging from…

Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…

Generative AI models for music and the arts in general are increasingly complex and hard to understand. The field of eXplainable AI (XAI) seeks to make complex and opaque AI models such as neural networks more understandable to people. One…

Modern generative models are usually designed to match target distributions directly in the data space, where the intrinsic dimension of data can be much lower than the ambient dimension. We argue that this discrepancy may contribute to the…

VAEs (Variational AutoEncoders) have proved to be powerful in the context of density modeling and have been used in a variety of contexts for creative purposes. In many settings, the data we model possesses continuous attributes that we…

Variational auto-encoders (VAEs) are a powerful approach to unsupervised learning. They enable scalable approximate posterior inference in latent-variable models using variational inference (VI). A VAE posits a variational family…