# Efficient and Scalable Fine-Tune of Language Models for Genome Understanding

arXiv: https://arxiv.org/abs/2402.08075 · HTML: https://mlsanity.com/paper/2402.08075/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 17 of its 37 references that are in the map.
- First posted on arXiv 12 Feb 2024.

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

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Prefix-Tuning: Optimizing Continuous Prompts for Generation](https://mlsanity.com/paper/2101.00190/) (2021)
- [The Power of Scale for Parameter-Efficient Prompt Tuning](https://mlsanity.com/paper/2104.08691/) (2021)
- [P-Tuning v2: Prompt Tuning Can Be Comparable to Fine-tuning Universally Across Scales and Tasks](https://mlsanity.com/paper/2110.07602/) (2021)
- [LLM-Pruner: On the Structural Pruning of Large Language Models](https://mlsanity.com/paper/2305.11627/) (2023)
- [InternImage: Exploring Large-Scale Vision Foundation Models with Deformable Convolutions](https://mlsanity.com/paper/2211.05778/) (2022)
- [DyLoRA: Parameter Efficient Tuning of Pre-trained Models using Dynamic Search-Free Low-Rank Adaptation](https://mlsanity.com/paper/2210.07558/) (2022)
- [Language Modeling Is Compression](https://mlsanity.com/paper/2309.10668/) (2023)
- [LIFT: Language-Interfaced Fine-Tuning for Non-Language Machine Learning Tasks](https://mlsanity.com/paper/2206.06565/) (2022)
- [DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome](https://mlsanity.com/paper/2306.15006/) (2023)
- [FedPara: Low-Rank Hadamard Product for Communication-Efficient Federated Learning](https://mlsanity.com/paper/2108.06098/) (2021)
- [On the Effectiveness of Parameter-Efficient Fine-Tuning](https://mlsanity.com/paper/2211.15583/) (2022)
- [KronA: Parameter Efficient Tuning with Kronecker Adapter](https://mlsanity.com/paper/2212.10650/) (2022)
- [State-of-the-art generalisation research in NLP: A taxonomy and review](https://mlsanity.com/paper/2210.03050/) (2022)
- [PLATON: Pruning Large Transformer Models with Upper Confidence Bound of Weight Importance](https://mlsanity.com/paper/2206.12562/) (2022)

## Abstract (arXiv)

Although DNA foundation models have advanced the understanding of genomes, they still face significant challenges in the limited scale and diversity of genomic data. This limitation starkly contrasts with the success of natural language foundation models, which thrive on substantially larger scales. Furthermore, genome understanding involves numerous downstream genome annotation tasks with inherent data heterogeneity, thereby necessitating more efficient and robust fine-tuning methods tailored for genomics. Here, we present textscLingo: textscLanguage prefix ftextscIne-tuning for textscGentextscOmes. Unlike DNA foundation models, textscLingo strategically leverages natural language foundation models' contextual cues, recalibrating their linguistic knowledge to genomic sequences. textscLingo further accommodates numerous, heterogeneous downstream fine-tune tasks by an adaptive rank sampling method that prunes and stochastically reintroduces pruned singular vectors within small computational budgets. Adaptive rank sampling outperformed existing fine-tuning methods on all benchmarked 14 genome understanding tasks, while requiring fewer than 2% of trainable parameters as genomic-specific adapters. Impressively, applying these adapters on natural language foundation models matched or even exceeded the performance of DNA foundation models. textscLingo presents a new paradigm of efficient and scalable genome understanding via genomic-specific adapters on language models.