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Many real-world problems require reasoning across multiple scales, demanding models which operate not on single data points, but on entire distributions. We introduce generative distribution embeddings (GDE), a framework that lifts…

Materials design aims to discover novel compounds with desired properties. However, prevailing strategies face critical trade-offs. Conventional element-substitution approaches readily and adaptively incorporate various domain knowledge but…

We develop a framework for incorporating structured graphical models in the \emph{encoders} of variational autoencoders (VAEs) that allows us to induce interpretable representations through approximate variational inference. This allows us…

Extracting insight from the enormous quantity of data generated from molecular simulations requires the identification of a small number of collective variables whose corresponding low-dimensional free-energy landscape retains the essential…

We construct a physically-parameterized probabilistic autoencoder (PAE) to learn the intrinsic diversity of type Ia supernovae (SNe Ia) from a sparse set of spectral time series. The PAE is a two-stage generative model, composed of an…

With the introduction of the variational autoencoder (VAE), probabilistic latent variable models have received renewed attention as powerful generative models. However, their performance in terms of test likelihood and quality of generated…

Optimizing molecular design and discovering novel chemical structures to meet certain objectives, such as quantitative estimates of the drug-likeness score (QEDs), is NP-hard due to the vast combinatorial design space of discrete molecular…

Analyzing the structure of proteins is a key part of understanding their functions and thus their role in biology at the molecular level. In addition, design new proteins in a methodical way is a major engineering challenge. In this work,…

Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…

Embedding is a useful technique to project a high-dimensional feature into a low-dimensional space, and it has many successful applications including link prediction, node classification and natural language processing. Current approaches…

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…

Recent work in synthetic data generation in the time-series domain has focused on the use of Generative Adversarial Networks. We propose a novel architecture for synthetically generating time-series data with the use of Variational…

Advances in latent diffusion models (LDMs) have revolutionized high-resolution image generation, but the design space of the autoencoder that is central to these systems remains underexplored. In this paper, we introduce LiteVAE, a new…

While the beta-VAE family is aiming to find disentangled representations and acquire human-interpretable generative factors, like what an ICA (from the linear domain) does, we propose Full Encoder, a novel unified autoencoder framework as a…

Sparse autoencoders (SAEs) operationalise the linear representation hypothesis: they reconstruct model activations as sparse linear combinations of interpretable dictionary atoms, on the implicit assumption that activation space is well…

In this paper we propose Structuring AutoEncoders (SAE). SAEs are neural networks which learn a low dimensional representation of data which are additionally enriched with a desired structure in this low dimensional space. While traditional…

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…

Learning interpretable representations of data remains a central challenge in deep learning. When training a deep generative model, the observed data are often associated with certain categorical labels, and, in parallel with learning to…

Visual generative models (e.g., diffusion models) typically operate in compressed latent spaces to balance training efficiency and sample quality. In parallel, there has been growing interest in leveraging high-quality pre-trained visual…

Pan-cancer classification using transcriptomic (RNA-Seq) data can inform tumor subtyping and therapy selection, but is challenging due to extremely high dimensionality and limited sample sizes. In this study, we propose a novel deep…