# CoPeP: Benchmarking Continual Pretraining for Protein Language Models

arXiv: https://arxiv.org/abs/2603.00253 · HTML: https://mlsanity.com/paper/2603.00253/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 27 of its 56 references that are in the map.
- First posted on arXiv 27 Feb 2026.

## Builds on (most cited first, 27 of 27)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Overcoming catastrophic forgetting in neural networks](https://mlsanity.com/paper/1612.00796/) (2016)
- [Locating and Editing Factual Associations in GPT](https://mlsanity.com/paper/2202.05262/) (2022)
- [iCaRL: Incremental Classifier and Representation Learning](https://mlsanity.com/paper/1611.07725/) (2016)
- [Gradient Episodic Memory for Continual Learning](https://mlsanity.com/paper/1706.08840/) (2017)
- [Don't Stop Pretraining: Adapt Language Models to Domains and Tasks](https://mlsanity.com/paper/2004.10964/) (2020)
- [WILDS: A Benchmark of in-the-Wild Distribution Shifts](https://mlsanity.com/paper/2012.07421/) (2020)
- [Experience Replay for Continual Learning](https://mlsanity.com/paper/1811.11682/) (2018)
- [Machine Unlearning](https://mlsanity.com/paper/1912.03817/) (2019)
- [A Comprehensive Survey of Continual Learning: Theory, Method and Application](https://mlsanity.com/paper/2302.00487/) (2023)
- [MiniCPM: Unveiling the Potential of Small Language Models with Scalable Training Strategies](https://mlsanity.com/paper/2404.06395/) (2024)
- [An Empirical Investigation of Catastrophic Forgetting in Gradient-Based Neural Networks](https://mlsanity.com/paper/1312.6211/) (2013)
- [Eternal Sunshine of the Spotless Net: Selective Forgetting in Deep Networks](https://mlsanity.com/paper/1911.04933/) (2019)
- [Memory-Based Model Editing at Scale](https://mlsanity.com/paper/2206.06520/) (2022)
- [Knowledge Unlearning for Mitigating Privacy Risks in Language Models](https://mlsanity.com/paper/2210.01504/) (2022)
- [Editing Large Language Models: Problems, Methods, and Opportunities](https://mlsanity.com/paper/2305.13172/) (2023)
- [Evaluating Protein Transfer Learning with TAPE](https://mlsanity.com/paper/1906.08230/) (2019)
- [Continual Pre-training of Language Models](https://mlsanity.com/paper/2302.03241/) (2023)
- [ProGen2: Exploring the Boundaries of Protein Language Models](https://mlsanity.com/paper/2206.13517/) (2022)
- [Continual Pre-Training of Large Language Models: How to (re)warm your model?](https://mlsanity.com/paper/2308.04014/) (2023)
- [The CLEAR Benchmark: Continual LEArning on Real-World Imagery](https://mlsanity.com/paper/2201.06289/) (2022)
- [PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding](https://mlsanity.com/paper/2206.02096/) (2022)
- [Online Continual Learning with Natural Distribution Shifts: An Empirical Study with Visual Data](https://mlsanity.com/paper/2108.09020/) (2021)
- [Slow and Steady Wins the Race: Maintaining Plasticity with Hare and Tortoise Networks](https://mlsanity.com/paper/2406.02596/) (2024)
- [Model Merging in Pre-training of Large Language Models](https://mlsanity.com/paper/2505.12082/) (2025)
- [Learn Continually, Generalize Rapidly: Lifelong Knowledge Accumulation for Few-shot Learning](https://mlsanity.com/paper/2104.08808/) (2021)
- [NEVIS'22: A Stream of 100 Tasks Sampled from 30 Years of Computer Vision Research](https://mlsanity.com/paper/2211.11747/) (2022)

## Abstract (arXiv)

Protein language models (pLMs) have recently gained significant attention for their ability to uncover relationships between sequence, structure, and function from evolutionary statistics, thereby accelerating therapeutic drug discovery. These models learn from large protein databases that are continuously updated by the biology community and whose dynamic nature motivates the application of continual learning, not only to keep up with the ever-growing data, but also as an opportunity to take advantage of the temporal meta-information that is created during this process. As a result, we introduce the Continual Pretraining of Protein Language Models (CoPeP) benchmark, a novel benchmark for evaluating continual learning approaches on pLMs. Specifically, we curate a sequence of protein datasets derived from the UniProt Knowledgebase spanning a decade and define metrics to assess pLM performance across 31 protein understanding tasks. We evaluate several methods from the continual learning literature, including replay, unlearning, and plasticity-based methods, some of which have never been applied to models and data of this scale. Our findings reveal that incorporating temporal meta-information improves perplexity by up to 7% even when compared to training on data from all tasks jointly. Moreover, even at scale, several continual learning methods outperform naive continual pretraining. The CoPeP benchmark offers an exciting opportunity to study these methods at scale in an impactful real-world application.