Linguistically inspired roadmap for building biologically reliable protein language models

Author:

Vu Mai HaORCID,Akbar RahmadORCID,Robert Philippe A.ORCID,Swiatczak BartlomiejORCID,Sandve Geir KjetilORCID,Greiff VictorORCID,Haug Dag Trygve TruslewORCID

Funder

University of Oslo | Livsvitenskap, Universitetet i Oslo

Norges Forskningsråd

Stiftelsen Kristian Gerhard Jebsen

Leona M. and Harry B. Helmsley Charitable Trust

EC | Horizon 2020 Framework Programme

Kreftforeningen

Publisher

Springer Science and Business Media LLC

Subject

Artificial Intelligence,Computer Networks and Communications,Computer Vision and Pattern Recognition,Human-Computer Interaction,Software

Reference122 articles.

1. Devlin, J., Chang, M.-W., Lee, K. & Toutanova, K. BERT: Pre-training of deep bidirectional transformers for language understanding. In Proc. 2019 Conf. of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies Vol. 1, 4171–4186 (Association for Computational Linguistics, 2019).

2. Liu, Y. et al. RoBERTa: A Robustly Optimized BERT Pretraining Approach. Preprint at https://doi.org/10.48550/arXiv.1907.11692 (2019).

3. Brown, T. B. et al. Language models are few-shot learners. Adv. Neural Inf. Process. Syst. 33, 1877–1901 (2020).

4. Bepler, T. & Berger, B. Learning the protein language: evolution, structure, and function. Cell Syst. 12, 654–669 (2021).

5. Ofer, D., Brandes, N. & Linial, M. The language of proteins: NLP, machine learning & protein sequences. Comput. Struct. Biotechnol. J. 19, 1750–1758 (2021).

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