# MediSwift: Efficient Sparse Pre-trained Biomedical Language Models

arXiv: https://arxiv.org/abs/2403.00952 · HTML: https://mlsanity.com/paper/2403.00952/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 51 of its 75 references that are in the map.
- First posted on arXiv 1 Mar 2024.

## Builds on (most cited first, 30 of 51)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [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)
- [Evaluating Large Language Models Trained on Code](https://mlsanity.com/paper/2107.03374/) (2021)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [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)
- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [OPT: Open Pre-trained Transformer Language Models](https://mlsanity.com/paper/2205.01068/) (2022)
- [QLoRA: Efficient Finetuning of Quantized LLMs](https://mlsanity.com/paper/2305.14314/) (2023)
- [The Pile: An 800GB Dataset of Diverse Text for Language Modeling](https://mlsanity.com/paper/2101.00027/) (2020)
- [The Lottery Ticket Hypothesis: Finding Sparse, Trainable Neural Networks](https://mlsanity.com/paper/1803.03635/) (2018)
- [Fine-Tuning Language Models from Human Preferences](https://mlsanity.com/paper/1909.08593/) (2019)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Megatron-LM: Training Multi-Billion Parameter Language Models Using Model Parallelism](https://mlsanity.com/paper/1909.08053/) (2019)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [Capabilities of GPT-4 on Medical Challenge Problems](https://mlsanity.com/paper/2303.13375/) (2023)
- [Prompt Programming for Large Language Models: Beyond the Few-Shot Paradigm](https://mlsanity.com/paper/2102.07350/) (2021)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Rigging the Lottery: Making All Tickets Winners](https://mlsanity.com/paper/1911.11134/) (2019)
- [The State of Sparsity in Deep Neural Networks](https://mlsanity.com/paper/1902.09574/) (2019)
- [Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine](https://mlsanity.com/paper/2311.16452/) (2023)
- [Scalable Training of Artificial Neural Networks with Adaptive Sparse Connectivity inspired by Network Science](https://mlsanity.com/paper/1707.04780/) (2017)
- [The Lottery Ticket Hypothesis for Pre-trained BERT Networks](https://mlsanity.com/paper/2007.12223/) (2020)

## Abstract (arXiv)

Large language models (LLMs) are typically trained on general source data for various domains, but a recent surge in domain-specific LLMs has shown their potential to outperform general-purpose models in domain-specific tasks (e.g., biomedicine). Although domain-specific pre-training enhances efficiency and leads to smaller models, the computational costs of training these LLMs remain high, posing budgeting challenges. We introduce MediSwift, a suite of biomedical LMs that leverage sparse pre-training on domain-specific biomedical text data. By inducing up to 75% weight sparsity during the pre-training phase, MediSwift achieves a 2-2.5x reduction in training FLOPs. Notably, all sparse pre-training was performed on the Cerebras CS-2 system, which is specifically designed to realize the acceleration benefits from unstructured weight sparsity, thereby significantly enhancing the efficiency of the MediSwift models. Through subsequent dense fine-tuning and strategic soft prompting, MediSwift models outperform existing LLMs up to 7B parameters on biomedical tasks, setting new benchmarks w.r.t efficiency-accuracy on tasks such as PubMedQA. Our results show that sparse pre-training, along with dense fine-tuning and soft prompting, offers an effective method for creating high-performing, computationally efficient models in specialized domains.