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 our approach outperforms the state-of-the-art methods by a large margin, leading to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65% and 56.63% on CATH 4.2 and 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).
Existing neural machine translation systems do not explicitly model what has been translated and what has not during the decoding phase. To address this problem, we propose a novel mechanism that separates the source information into two parts: translated PAST contents and untranslated FUTURE contents, which are modeled by two additional recurrent layers. The PAST and FUTURE contents are fed to both the attention model and the decoder states, which provides NMT systems with the knowledge of translated and untranslated contents. Experimental results show that the proposed approach significantly improves the performance in Chinese-English, German-English, and English-German translation tasks. Specifically, the proposed model outperforms the conventional coverage model in terms of both the translation quality and the alignment error rate. † * Equal contributions. † Our code can be downloaded from https://github. com/zhengzx-nlp/past-and-future-nmt.
In the encoder-decoder architecture for neural machine translation (NMT), the hidden states of the recurrent structures in the encoder and decoder carry the crucial information about the sentence.These vectors are generated by parameters which are updated by back-propagation of translation errors through time. We argue that propagating errors through the end-to-end recurrent structures are not a direct way of control the hidden vectors. In this paper, we propose to use word predictions as a mechanism for direct supervision. More specifically, we require these vectors to be able to predict the vocabulary in target sentence. Our simple mechanism ensures better representations in the encoder and decoder without using any extra data or annotation. It is also helpful in reducing the target side vocabulary and improving the decoding efficiency. Experiments on Chinese-English and German-English machine translation tasks show BLEU improvements by 4.53 and 1.3, respectively.
The choice of token vocabulary affects the performance of machine translation. This paper aims to figure out what is a good vocabulary and whether one can find the optimal vocabulary without trial training. To answer these questions, we first provide an alternative understanding of the role of vocabulary from the perspective of information theory. Motivated by this, we formulate the quest of vocabularization -finding the best token dictionary with a proper size -as an optimal transport (OT) problem. We propose VOLT, a simple and efficient solution without trial training. Empirical results show that VOLT outperforms widely-used vocabularies in diverse scenarios, including WMT-14 English-German and TED's 52 translation directions. For example, VOLT achieves 70% vocabulary size reduction and 0.5 BLEU gain on English-German translation. Also, compared to BPE-search, VOLT reduces the search time from 384 GPU hours to 30 GPU hours on English-German translation. Codes are available at https: //github.com/Jingjing-NLP/VOLT.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.