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Variational autoencoder (VAE) estimates the posterior parameters (mean and variance) of latent variables corresponding to each input data. While it is used for many tasks, the transparency of the model is still an underlying issue. This…

Variational autoencoder (VAE) is a deep generative model for unsupervised learning, allowing to encode observations into the meaningful latent space. VAE is prone to catastrophic forgetting when tasks arrive sequentially, and only the data…

Integrating physics models within machine learning models holds considerable promise toward learning robust models with improved interpretability and abilities to extrapolate. In this work, we focus on the integration of incomplete physics…

Variational Autoencoders (VAEs) are a popular framework for unsupervised learning and data generation. A plethora of methods have been proposed focusing on improving VAEs, with the incorporation of adversarial objectives and the integration…

Adapting foundation models for specific purposes has become a standard approach to build machine learning systems for downstream applications. Yet, it is an open question which mechanisms take place during adaptation. Here we develop a new…

Without knowledge of specific pockets, generating ligands based on the global structure of a protein target plays a crucial role in drug discovery as it helps reduce the search space for potential drug-like candidates in the pipeline.…

Granger causality has been widely used in various application domains to capture lead-lag relationships amongst the components of complex dynamical systems, and the focus in extant literature has been on a single dynamical system. In…

"Masked Autoencoders (MAE) Are Scalable Vision Learners" revolutionizes the self-supervised learning method in that it not only achieves the state-of-the-art for image pre-training, but is also a milestone that bridges the gap between…

Defining and separating cancer subtypes is essential for facilitating personalized therapy modality and prognosis of patients. The definition of subtypes has been constantly recalibrated as a result of our deepened understanding. During…

Understanding how generative models represent and transform data is a foundational problem in deep learning interpretability. While mechanistic interpretability of discriminative architectures has yielded substantial insights, relatively…

Disentangled representation learning aims to learn low-dimensional representations where each dimension corresponds to an underlying generative factor. While the Variational Auto-Encoder (VAE) is widely used for this purpose, most existing…

We propose to learn model invariances as a means of interpreting a model. This is motivated by a reverse engineering principle. If we understand a problem, we may introduce inductive biases in our model in the form of invariances.…

Density estimation, compression and data generation are crucial tasks in artificial intelligence. Variational Auto-Encoders (VAEs) constitute a single framework to achieve these goals. Here, we present a novel class of generative models,…

Multiple modalities often co-occur when describing natural phenomena. Learning a joint representation of these modalities should yield deeper and more useful representations. Previous generative approaches to multi-modal input either do not…

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…

Variational autoencoders (VAE) are directed generative models that learn factorial latent variables. As noted by Burda et al. (2015), these models exhibit the problem of factor over-pruning where a significant number of stochastic factors…

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…

Neural Networks play a growing role in many science disciplines, including physics. Variational Autoencoders (VAEs) are neural networks that are able to represent the essential information of a high dimensional data set in a low dimensional…

We introduce ProtoPathway, an interpretable-by-design multimodal framework for cancer survival prediction that unifies whole slide imaging and transcriptomics through encoders producing biologically grounded representations on both sides of…

Deep learning became the method of choice in recent year for solving a wide variety of predictive analytics tasks. For sequence prediction, recurrent neural networks (RNN) are often the go-to architecture for exploiting sequential…