# Investigating Data Pruning for Pretraining Biological Foundation Models at Scale

arXiv: https://arxiv.org/abs/2512.12932 · HTML: https://mlsanity.com/paper/2512.12932/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 17 of its 48 references that are in the map.
- First posted on arXiv 15 Dec 2025.

## Builds on (most cited first, 17 of 17)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [Understanding Black-box Predictions via Influence Functions](https://mlsanity.com/paper/1703.04730/) (2017)
- [Optimizing Neural Networks with Kronecker-factored Approximate Curvature](https://mlsanity.com/paper/1503.05671/) (2015)
- [Dataset Cartography: Mapping and Diagnosing Datasets with Training Dynamics](https://mlsanity.com/paper/2009.10795/) (2020)
- [Selection via Proxy: Efficient Data Selection for Deep Learning](https://mlsanity.com/paper/1906.11829/) (2019)
- [Identifying Mislabeled Data using the Area Under the Margin Ranking](https://mlsanity.com/paper/2001.10528/) (2020)
- [Revisiting Natural Gradient for Deep Networks](https://mlsanity.com/paper/1301.3584/) (2013)
- [Coverage-centric Coreset Selection for High Pruning Rates](https://mlsanity.com/paper/2210.15809/) (2022)
- [PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding](https://mlsanity.com/paper/2206.02096/) (2022)
- [Coresets and Sketches](https://mlsanity.com/paper/1601.00617/) (2016)
- [Large-scale Dataset Pruning with Dynamic Uncertainty](https://mlsanity.com/paper/2306.05175/) (2023)
- [SmallToLarge (S2L): Scalable Data Selection for Fine-tuning Large Language Models by Summarizing Training Trajectories of Small Models](https://mlsanity.com/paper/2403.07384/) (2024)
- [ProteinNet: a standardized data set for machine learning of protein structure](https://mlsanity.com/paper/1902.00249/) (2019)
- [TAGCOS: Task-agnostic Gradient Clustered Coreset Selection for Instruction Tuning Data](https://mlsanity.com/paper/2407.15235/) (2024)
- [Lightweight Dataset Pruning without Full Training via Example Difficulty and Prediction Uncertainty](https://mlsanity.com/paper/2502.06905/) (2025)

## Built on by (most cited first, 1 of 1)

- [Distill on a Diet: Efficient Knowledge Distillation via Learnable Data Pruning](https://mlsanity.com/paper/2606.25488/) (2026)

## Abstract (arXiv)

Biological foundation models (BioFMs), pretrained on large-scale biological sequences, have recently shown strong potential in providing meaningful representations for diverse downstream bioinformatics tasks. However, such models often rely on millions to billions of training sequences and billions of parameters, resulting in prohibitive computational costs and significant barriers to reproducibility and accessibility, particularly for academic labs. To address these challenges, we investigate the feasibility of data pruning for BioFM pretraining and propose a post-hoc influence-guided data pruning framework tailored to biological domains. Our approach introduces a subset-based self-influence formulation that enables efficient estimation of sample importance at low computational cost, and builds upon it two simple yet effective selection strategies, namely Top-k Influence (Top I) and Coverage-Centric Influence (CCI). We empirically validate our method on two representative BioFMs, RNA-FM and ESM-C. For RNA, our framework consistently outperforms random selection baselines under an extreme pruning rate of over 99 percent, demonstrating its effectiveness. Furthermore, we show the generalizability of our framework on protein-related tasks using ESM-C. In particular, our coreset even outperforms random subsets that are ten times larger in both RNA and protein settings, revealing substantial redundancy in biological sequence datasets. These findings underscore the potential of influence-guided data pruning to substantially reduce the computational cost of BioFM pretraining, paving the way for more efficient, accessible, and sustainable biological AI research.