LM Design from Bytedance – A generic approach to reprogramming sequence-based protein language models
This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)
In this work, we define a diffusion-based generative model capable of both music synthesis and source separation by learning the score of the joint probability density of sources sharing a context. Alongside the classic total inference tasks (i.e. generating a mixture, separating the sources), we also introduce and experiment on the partial inference task of […]
Retrieval-Augmented Language Modeling (RALM) methods, that condition a language model (LM) on relevant documents from a grounding corpus during generation, have been shown to significantly improve language modeling while also providing a natural source attribution mechanism. Existing RALM approaches focus on modifying the LM architecture in order to facilitate the incorporation of external information, significantly […]
Recent work has shown that, in generative modeling, cross-entropy loss improves smoothly with model size and training compute, following a power law plus constant scaling law. One challenge in extending these results to reinforcement learning is that the main performance objective of interest, mean episode return, need not vary smoothly. To overcome this, we introduce […]
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