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)
Meta LLaMA, 4 foundation models ranging from 7B to 65B parameters. LLaMA-13B outperforms OPT and GPT-3 175B on most benchmarks. LLaMA-65B is competitive with Chinchilla 70B and PaLM 540B. The weights for all models are open and available. Unlike Chinchilla, PaLM, or GPT-3, we only use datasets publicly available, making our work compatible with open-sourcing […]
The increasing complexity and scale of machine learning (ML) has led to the need for more efficient collaboration among multiple teams. For example, when a research team invents a new architecture like “ResNet,” it is desirable for multiple engineering teams to adopt it. However, the effort required for each team to study and understand the […]
Visual robotic manipulation research and applications often use multiple cameras, or views, to better perceive the world. How else can we utilize the richness of multi-view data? In this paper, we investigate how to learn good representations with multi-view data and utilize them for visual robotic manipulation. Specifically, we train a multi-view masked autoencoder which […]
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