Related papers: BetterBodies: Reinforcement Learning guided Diffus…

De novo molecular design has facilitated the exploration of large chemical space to accelerate drug discovery. Structure-based de novo method can overcome the data scarcity of active ligands by incorporating drug-target interaction into…

Unsupervised learning of generative models has seen tremendous progress over recent years, in particular due to generative adversarial networks (GANs), variational autoencoders, and flow-based models. GANs have dramatically improved sample…

Antibodies are versatile proteins that bind to pathogens like viruses and stimulate the adaptive immune system. The specificity of antibody binding is determined by complementarity-determining regions (CDRs) at the tips of these Y-shaped…

Generative models such as Variational Autoencoders (VAEs) and Generative Adversarial Networks (GANs) have shown promise in sequential recommendation tasks. However, they face challenges, including posterior collapse and limited…

Over the past decade, antibodies have steadily grown in therapeutic importance thanks to their high specificity and low risk of adverse effects compared to other drug modalities. While traditional antibody discovery is primarily wet lab…

Reinforcement learning (RL) has been effective for post-training autoregressive (AR) language models, but extending these methods to diffusion language models (DLMs) is challenging due to intractable sequence-level likelihoods. Existing…

Strong generative models can accurately learn channel distributions. This could save recurring costs for physical measurements of the channel. Moreover, the resulting differentiable channel model supports training neural encoders by…

Diffusion models have been applied to improve adversarial robustness of image classifiers by purifying the adversarial noises or generating realistic data for adversarial training. However, diffusion-based purification can be evaded by…

Breakthroughs in high-accuracy protein structure prediction, such as AlphaFold, have established receptor-based molecule design as a critical driver for rapid early-phase drug discovery. However, most approaches still struggle to balance…

Adeno-associated viral (AAV) vectors are widely used delivery platforms in gene therapy, and the design of improved capsids is key to expanding their therapeutic potential. A central challenge in AAV bioengineering, as in protein design…

Variational auto-encoders (VAEs) provide an attractive solution to image generation problem. However, they tend to produce blurred and over-smoothed images due to their dependence on pixel-wise reconstruction loss. This paper introduces 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…

Denoising diffusion probabilistic models (DDPMs) are a recent family of generative models that achieve state-of-the-art results. In order to obtain class-conditional generation, it was suggested to guide the diffusion process by gradients…

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…

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency.…

Autoregressive models recently achieved comparable results versus state-of-the-art Generative Adversarial Networks (GANs) with the help of Vector Quantized Variational AutoEncoders (VQ-VAE). However, autoregressive models have several…

Turbulence is still one of the main challenges for accurately predicting reactive flows. Therefore, the development of new turbulence closures which can be applied to combustion problems is essential. Data-driven modeling has become very…

Antibody design, a crucial task with significant implications across various disciplines such as therapeutics and biology, presents considerable challenges due to its intricate nature. In this paper, we tackle antigen-specific antibody…

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…

In recent years, reinforcement learning (RL) has acquired a prominent position in health-related sequential decision-making problems, gaining traction as a valuable tool for delivering adaptive interventions (AIs). However, in part due to a…