Aug 2026· Journal of Chemical Information and Modeling· Vol 66, pp. 10896 - 10918· 0 citations· 49 references
Medicine
TL;DR
Results demonstrate that domain-specific BERT models only need to be finetuned from vanilla BERT models (i.e. no domain-adaptive pretraining is needed), pending the availability of sufficiently large, high-quality, domain-specific QA data sets that this work shows how to autogenerate.
Abstract
Domain-specific language models are attractive because they can be tailored to suit their users. However, the high-end computational resources needed to pretrain large language models (LLMs) by conventional methods tend to prohibit their development. Furthermore, there is a dearth of large, domain-specific, question-answering (QA) data sets to finetune LLMs for prompt engineering, even when computational resources can be found to pretrain LLMs. Our paper presents a method for autogenerating a data set of 168,080 domain-specific QA pairs relating to magnetic materials. We show how this can be employed to finetune LLMs for the downstream task of Question-Answering (QA) for the magnetic materials domain. We use the bidirectional encoder representations from transformers (BERT) architecture as our benchmark LLM to compare the relative performance of 6 LLMs. These include 3 vanilla (BERT-base-cased) LLMs that have been finetuned on various QA data sets (i) our domain-specific QA data set (MagQA); (ii) the Stanford Question-Answering Data set (SQuAD v2); (iii) our QA data set mixed with SQuAD v2. The other 3 (BERT-base-cased) LLMs have been subjected to domain-adaptive pretraining on a corpus of 97,308 magnetic papers prior to their finetuning on the same combination of QA data sets (i)-(iii). As well as our QA data set autogeneration pipeline, we show how our work can be extrapolated to the larger architectures of RoBERTa-base and DeBERTa-base. We also undertake an ablation study of the finetuning process using four sizes of QA data sets to gain insights into the quantity of data that are needed for sufficient domain-specification. The highest performing LLM was MagBERT_MagQA_Mixed, a vanilla BERT-base-cased LLM that had been finetuned on the combination of our autogenerated MagQA data set and SQuAD v2, achieving an F1 score of 78.43% and an exact-match score of 72.84% when tested on a manually annotated data set on magnetic materials. These results demonstrate that domain-specific BERT models only need to be finetuned from vanilla BERT models (i.e. no domain-adaptive pretraining is needed), pending the availability of sufficiently large, high-quality, domain-specific QA data sets that this work shows how to autogenerate.
The results provide a case study in which a medically fine-tuned checkpoint does not improve jargon comprehension over its general-purpose counterpart, highlighting that domain adaptation should not be assumed to yield better performance on specialized terminology.
Large Language Models have demonstrated remarkable progress in general-purpose capabilities and can achieve strong performance in specific domains through fine-tuning on domain-specific data. However, acquiring high-quality data for target domains remains a significant challenge. Existing data synthesis approaches foll...
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