There are many cases where LLMs are used for specific tasks in a single domain. These usually require less general, but more domain-specific knowledge. Highly capable, general-purpose state-of-the-art language models like GPT-4 or Claude-3-opus can often be used for such tasks, but they are very large and cannot be run locally, even if they were not proprietary. This can be a problem when working with sensitive data. This paper focuses on domain-specific and mixed-domain pretraining as potentially more efficient methods than general pretraining for specialized language models. We will take a look at work related to domain-specific pretraining, specifically in the medical area, and compare benchmark results of specialized language models to general-purpose language models.

In the expanding field of language model applications, medical knowledge representation remains a significant challenge due to the specialized nature of the domain. Large language models, such as GPT-4, obtain reasonable scores on medical question answering tasks, but smaller models are far behind. In this work, we introduce a method to improve the proficiency of a small language model in the medical domain by employing a two-fold approach. We first fine-tune the model on a corpus of medical textbooks. Then, we use GPT-4 to generate questions similar to the downstream task, prompted with textbook knowledge, and use them to fine-tune the model. Additionally, we introduce ECN-QA, a novel medical question answering dataset containing ``progressive questions'' composed of related sequential questions. We show the benefits of our training strategy on this dataset. The study's findings highlight the potential of small language models in the medical domain when appropriately fine-tuned. The code and weights are available at https://github.com/raidium-med/MQG.

Large language models, such as GPT-4 and Med-PaLM, have shown impressive performance on clinical tasks; however, they require access to compute, are closed-source, and cannot be deployed on device. Mid-size models such as BioGPT-large, BioMedLM, LLaMA 2, and Mistral 7B avoid these drawbacks, but their capacity for clinical tasks has been understudied. To help assess their potential for clinical use and help researchers decide which model they should use, we compare their performance on two clinical question-answering (QA) tasks: MedQA and consumer query answering. We find that Mistral 7B is the best performing model, winning on all benchmarks and outperforming models trained specifically for the biomedical domain. While Mistral 7B's MedQA score of 63.0% approaches the original Med-PaLM, and it often can produce plausible responses to consumer health queries, room for improvement still exists. This study provides the first head-to-head assessment of open source mid-sized models on clinical tasks.

Large language models such as OpenAI's GPT-4 have become the dominant technology in modern natural language processing (Liu et al., 2023; Zhao et al., 2023). Trained on large corpora to predict the next token and refined with human feedback (Brown et al., 2020; Ouyang et al., 2022; Ziegler et al., 2020), these models develop impressive capabilities in areas such as summarization and questionanswering (Zhang et al., 2023; Goyal et al., 2023; Karpukhin et al., 2020). While the focus has been on these models' performance when responding to general English prompts, it is clear there is potential for specialist models to impact biomedical research and healthcare (Arora and Arora, 2023; Shah et al., 2023; Thirunavukarasu et al., 2023). Such applications include information retrieval and summarization from the ever-expanding biomedical literature (Wang et al., 2021; Yang, 2020), clinical information such as physician notes in electronic health records, and radiology reports (Murray et al., 2021; Feblowitz et al., 2011; Zhang et al., 2018). Improving domain-specific language models will help accelerate biomedical discovery, drive down healthcare costs, and improve patient care. Large, general models like GPT-4 and Med-PaLM 2 have set new standards for performance on question-answering and information extraction (Kung et al., 2022; Singhal et al., 2023a,b), but there are several drawbacks to these models. They are costly to train and utilize. Compute for training and inference of large language models have increased 10-to 100-fold since 2015 (Sevilla et al., 2022), translating to extremely high financial and

End-to-end relation extraction (E2ERE) is an important and realistic application of natural language processing (NLP) in biomedicine. In this paper, we aim to compare three prevailing paradigms for E2ERE using a complex dataset focused on rare diseases involving discontinuous and nested entities. We use the RareDis information extraction dataset to evaluate three competing approaches (for E2ERE): NER $\rightarrow$ RE pipelines, joint sequence to sequence models, and generative pre-trained transformer (GPT) models. We use comparable state-of-the-art models and best practices for each of these approaches and conduct error analyses to assess their failure modes. Our findings reveal that pipeline models are still the best, while sequence-to-sequence models are not far behind; GPT models with eight times as many parameters are worse than even sequence-to-sequence models and lose to pipeline models by over 10 F1 points. Partial matches and discontinuous entities caused many NER errors contributing to lower overall E2E performances. We also verify these findings on a second E2ERE dataset for chemical-protein interactions. Although generative LM-based methods are more suitable for zero-shot settings, when training data is available, our results show that it is better to work with more conventional models trained and tailored for E2ERE. More innovative methods are needed to marry the best of the both worlds from smaller encoder-decoder pipeline models and the larger GPT models to improve E2ERE. As of now, we see that well designed pipeline models offer substantial performance gains at a lower cost and carbon footprint for E2ERE. Our contribution is also the first to conduct E2ERE for the RareDis dataset.