Ensembits is the first tokenizer of protein conformational ensembles that outperforms static tokenizers on RMSF prediction and matches them on function and mutation tasks while using less pretraining data.
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Neural Discrete Representation Learning
Canonical reference. 71% of citing Pith papers cite this work as background.
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abstract
Learning useful representations without supervision remains a key challenge in machine learning. In this paper, we propose a simple yet powerful generative model that learns such discrete representations. Our model, the Vector Quantised-Variational AutoEncoder (VQ-VAE), differs from VAEs in two key ways: the encoder network outputs discrete, rather than continuous, codes; and the prior is learnt rather than static. In order to learn a discrete latent representation, we incorporate ideas from vector quantisation (VQ). Using the VQ method allows the model to circumvent issues of "posterior collapse" -- where the latents are ignored when they are paired with a powerful autoregressive decoder -- typically observed in the VAE framework. Pairing these representations with an autoregressive prior, the model can generate high quality images, videos, and speech as well as doing high quality speaker conversion and unsupervised learning of phonemes, providing further evidence of the utility of the learnt representations.
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representative citing papers
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Hierarchical Text-Conditional Image Generation with CLIP Latents
A hierarchical prior-decoder model using CLIP latents generates more diverse text-conditional images than direct methods while preserving photorealism and caption fidelity.