Related papers: Conditional $\beta$-VAE for De Novo Molecular Gene…
Deep generative models have recently emerged as a promising de novo drug design method. In this respect, deep generative conditional variational autoencoder (CVAE) models are a powerful approach for generating novel molecules with desired…
Molecule generation is to design new molecules with specific chemical properties and further to optimize the desired chemical properties. Following previous work, we encode molecules into continuous vectors in the latent space and then…
Deep generative models have been praised for their ability to learn smooth latent representation of images, text, and audio, which can then be used to generate new, plausible data. However, current generative models are unable to work with…
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,…
Disentangled and interpretable latent representations in generative models typically come at the cost of generation quality. The $\beta$-VAE framework introduces a hyperparameter $\beta$ to balance disentanglement and reconstruction…
In data-driven drug discovery, designing molecular descriptors is a very important task. Deep generative models such as variational autoencoders (VAEs) offer a potential solution by designing descriptors as probabilistic latent vectors…
Variational Autoencoders and Generative Adversarial Networks remained the state-of-the-art (SOTA) generative models until 2022. Now they are superseded by diffusion-based models. Efforts to improve traditional models have stagnated as a…
Recent state-of-the-art autoencoder based generative models have an encoder-decoder structure and learn a latent representation with a pre-defined distribution that can be sampled from. Implementing the encoder networks of these models in a…
We present two deep generative models based on Variational Autoencoders to improve the accuracy of drug response prediction. Our models, Perturbation Variational Autoencoder and its semi-supervised extension, Drug Response Variational…
Variational autoencdoers (VAE) are a popular approach to generative modelling. However, exploiting the capabilities of VAEs in practice can be difficult. Recent work on regularised and entropic autoencoders have begun to explore 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…
Variational autoencoders (VAEs) are essential tools in end-to-end representation learning. However, the sequential text generation common pitfall with VAEs is that the model tends to ignore latent variables with a strong auto-regressive…
We introduce the Kernel-Elastic Autoencoder (KAE), a self-supervised generative model based on the transformer architecture with enhanced performance for molecular design. KAE is formulated based on two novel loss functions: modified…
The application of deep learning to generative molecule design has shown early promise for accelerating lead series development. However, questions remain concerning how factors like training, dataset, and seed bias impact the technology's…
Variational Autoencoders (VAEs) provide a theoretically-backed and popular framework for deep generative models. However, learning a VAE from data poses still unanswered theoretical questions and considerable practical challenges. In this…
In many data analysis tasks, it is beneficial to learn representations where each dimension is statistically independent and thus disentangled from the others. If data generating factors are also statistically independent, disentangled…
Deep generative models are increasingly becoming integral parts of the in silico molecule design pipeline and have dual goals of learning the chemical and structural features that render candidate molecules viable while also being flexible…
The chemical space of drug-like molecules is vast, motivating the development of generative models that must learn broad chemical distributions, enable conditional generation by capturing structure-property representations, and provide fast…
Bayesian optimisation in the latent space of a Variational AutoEncoder (VAE) is a powerful framework for optimisation tasks over complex structured domains, such as the space of scientifically interesting molecules. However, existing…
The surrogate loss of variational autoencoders (VAEs) poses various challenges to their training, inducing the imbalance between task fitting and representation inference. To avert this, the existing strategies for VAEs focus on adjusting…