The DOI matches its Crossref record; 66 of the 66 references it cites were found in a registry or an index.
Transformer protein language models are unsupervised structure learners
Open accessAbstract
A bstract: Unsupervised contact prediction is central to uncovering physical, structural, and functional constraints for protein structure determination and design. For decades, the predominant approach has been to infer evolutionary constraints from a set of related sequences. In the past year, protein language models have emerged as a potential alternative, but performance has fallen short of state-of-the-art approaches in bioinformatics. In this paper we demonstrate that Transformer attention maps learn contacts from the unsupervised language modeling objective. We find the highest capacity models that have been trained to date already outperform a state-of-the-art unsupervised contact prediction pipeline, suggesting these pipelines can be replaced with a single forward pass of an end-to-end model. 1
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“Among many successful neural network architectures, attention-based networks are extremely powerful for modeling complicated interactions between entities, making them suitable for modeling proteins whose functions are largely determined by interactions between amino acids (34–37).”
From Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization (2022) · cites this paper as [37]
In the citing paper
“Since then, various language model-based protein embedding methods have been applied to these and other protein prediction problems through transfer learning, including protein phenotype prediction 28,32-34, residue-residue contact prediction 32,70, fold recognition 33, protein-protein 71,72 and protein-drug interaction prediction 35,73.”
From Learning the protein language: Evolution, structure, and function (2021) · cites this paper as [70]
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“Recent works have shown that increasing language model scale leads to continued improvements in downstream applications, such as residue-residue contact prediction 70.”
From Learning the protein language: Evolution, structure, and function (2021) · cites this paper as [70]
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BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding
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Language Models are Few-Shot Learners
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RoBERTa: A Robustly Optimized BERT Pretraining Approach
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Scaling Laws for Neural Language Models
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“A similar scaling law has been observed previously for supervised secondary structure prediction (Rives et al., 2019), and parallels observations in the NLP community (Kaplan et al., 2020; Brown et al., 2020).”
BackgroundmixOmics: An R package for ‘omics feature selection and multiple data integration
Rohart, F., Gautier, B., Singh, A., & Lê Cao, K.-A. (2017) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1005752 · Cited by 4,056
Improved protein structure prediction using potentials from deep learning
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Self-citationRives, A., Meier, J., Sercu, T., Goyal, S., Lin, Z., Liu, J., Guo, D., Ott, M., Zitnick, C. L., Ma, J., et al. (2019) · doi:10.1101/622803 · Cited by 3,280
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Research works printed but not linked: 4
- 10.1002/(SICI)1097-0134(19990301)34:4(508::AID-PROT10)3.0.CO;2-4 · DOI
- Robert D. Finn , Alex Bateman , Jody Clements , Penelope Coggill , Ruth Y. Eberhardt , Sean R. Eddy , Andreas Heger , Kirstie Hetherington , Liisa Holm , Jaina Mistry , Erik L.L. Sonnhammer , John Tate , and Marco Punta . Pfam: The protein families database, 1 2014. ISSN 03051048. URL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965110/.
- 10.1101/622803 · DOI · Paper page
- 10.1101/2020.10.12.336859 · DOI
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Metadata
- Authors
- Rao, R., Meier, J., Sercu, T., Ovchinnikov, S., & Rives, A.
- Affiliations
- University of California, Berkeley (US)
- Meta (United States) (US)
- Harvard University (US)
- Corresponding author
- Rao, Roshan
- Meier, Joshua
- Sercu, Tom
- Ovchinnikov, Sergey
- Rives, Alexander
- Venue
- bioRxiv (Cold Spring Harbor Laboratory)
- Publisher
- openRxiv
- Published
- 2020-12-15
- OpenAlex
- W3111174583
- Cited by
- 341
- References
- 63
- Citations by year
- 2026: 51 · 2025: 67 · 2024: 79 · 2023: 56 · 2022: 49 · 2021: 37 · 2020: 2
- Type
- posted content
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Funders
- National Institutes of Health (DP5OD026389)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- protein language models, protein structure prediction, protein structure design, evolutionary constraints
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