# Energy Efficient Protein Language Models: Leveraging Small Language Models with LoRA for Controllable Protein Generation

arXiv: https://arxiv.org/abs/2411.05966 · HTML: https://mlsanity.com/paper/2411.05966/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 29 references that are in the map.
- First posted on arXiv 8 Nov 2024.

## Builds on (most cited first, 9 of 9)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [A Survey of Large Language Models](https://mlsanity.com/paper/2303.18223/) (2023)
- [Phi-3 Technical Report: A Highly Capable Language Model Locally on Your Phone](https://mlsanity.com/paper/2404.14219/) (2024)
- [A Comprehensive Overview of Large Language Models](https://mlsanity.com/paper/2307.06435/) (2023)
- [ProGen2: Exploring the Boundaries of Protein Language Models](https://mlsanity.com/paper/2206.13517/) (2022)
- [Instruct-FinGPT: Financial Sentiment Analysis by Instruction Tuning of General-Purpose Large Language Models](https://mlsanity.com/paper/2306.12659/) (2023)
- [ProLLaMA: A Protein Large Language Model for Multi-Task Protein Language Processing](https://mlsanity.com/paper/2402.16445/) (2024)
- [Peptide-GPT: Generative Design of Peptides using Generative Pre-trained Transformers and Bio-informatic Supervision](https://mlsanity.com/paper/2410.19222/) (2024)

## Abstract (arXiv)

Large language models (LLMs) have demonstrated significant success in natural language processing (NLP) tasks and have shown promising results in other domains such as protein sequence generation. However, there remain salient differences between LLMs used for NLP, which effectively handle multiple tasks and are available in small sizes, and protein language models that are often specialized for specific tasks and only exist in larger sizes. In this work, we introduce two small protein language models, based on Llama-3-8B and Phi-3-mini, that are capable of both uncontrollable and controllable protein generation. For the uncontrollable generation task, our best model achieves an average pLDDT score of 69.75, demonstrating robust performance in generating viable protein structures. For the controllable generation task, in which the model generates proteins according to properties specified in the prompt, we achieve a remarkable average TM-Score of 0.84, indicating high structural similarity to target proteins. We chose 10 properties, including six classes of enzymes, to extend the capabilities of prior protein language models. Our approach utilizes the Low-Rank Adaptor (LoRA) technique, reducing trainable parameters to just 4% of the original model size, lowering computational requirements. By using a subset of the UniRef50 dataset and small models, we reduced the overall training time by 70% without compromising performance. Notably, Phi-3-mini reduced trainable parameters by 60%, decreasing training cost by 30% compared to Llama 3. Consequently, Phi-3 achieved a comparable TM-Score of 0.81, demonstrating that smaller models can match the performance of larger ones, like Llama 3. We also demonstrate the deployment of our models on the energy efficient ET-SoC-1 chip, significantly improving the TPS/W by a factor of 3.