A pre-trained BERT for Korean medical natural language processing | Scientific Reports – Nature. com

Through NLP experiments, we evaluated the language understanding capability of KM-BERT and compared its performance with that of other language models. The M-BERT and KR-BERT models were considered as baseline models in the tests.


We performed pre-training, two types of intrinsic evaluation, and two types of extrinsic assessment. The Korean medical corpus was used for pre-training; the corpus was randomly split into a training set of 90% and a validation arranged of 10%. The model was trained on the training established and its performance was measured using a validation set.

Additionally, we collected an external dataset to intrinsically evaluate the models. The dataset comprised three sets associated with 294 sentence pairs, with the next sentence relationship. Sentence pair examples in each set were extracted from medical textbooks, health information news, and medical research articles after manual inspection for errors, such as encoding failures. We selected informative sentences by manual investigation to exclude meaningless sentences, such as sentences that had been extremely short and only human names. However, there was no overlap between the Korean medical corpus and the particular external dataset. The healthcare textbooks utilized in the external dataset were not from the 2 mentioned publishers. In addition , we only considered information about health news uploaded within January plus February 2021 and medical research articles published in 2009.

Finally, we acquired the Korean medical semantic textual similarity (MedSTS) dataset, wherein each sentence was translated from your original MedSTS, which consisted of 3121 English sentence pairs and the corresponding likeness score of 0–5 18 . First, all of us translated every English phrase in the MedSTS dataset in to Korean using the Python library associated with Google Machine Translation. All of us manually reviewed each translation result and refined the particular mistranslation plus low-quality interpretation results. During this process, the similarity scores for each sentence set did not change. We used 2393 sentence pairs for the training set and 728 for the test fixed 19 , 20 . We also acquired the particular Korean healthcare named entity recognition (NER) dataset consisting of 2189 Korean medical phrases with tagged clinical terminology 21 . We all used 5-fold cross validation to evaluate the medical tagging overall performance of each model. Table 1 shows an overview of the evaluation plus datasets utilized.

Table 1 Description for datasets used within evaluations.

All the experiments were performed on an Ubuntu 18. 04. 2 LTS server along with two Intel (R) Xeon (R) Silver 4210R CPU 2 . 40  GHz, 256  GB RAM, and dual GPUs of RTX 3090.


The collected Korean medical corpus was used for the pre-training associated with BERT for that MLM and NSP tasks. The MLM task aims to predict an appropriate token label for each masked token, plus the NSP task performs classification making use of two labels ( IsNext or NotNext ). Each task follows a supervised mechanism during the learning process. However, the required data can be constructed from an unlabeled corpus by randomly joining two phrases and masking the token. Half of the particular sentence pairs were replaced with two irrelevant sentences. In other words, the ratio of IsNext in order to NotNext labels was one-to-one for your NSP task. Next, the sentences were tokenized into tokens, and each token was arbitrarily masked with regard to the MULTILEVEL MARKETING task. Therefore , we built a six-million sentence pair dataset regarding pre-training based on the Korean healthcare corpus.

Considering the computational specifications, we utilized a batch size associated with 32 and a maximum word length of 128 bridal party. Additionally , we all used a learning rate of 1e−6.

The change in efficiency throughout the pre-training process over the epochs is depicted (Fig.   2 ). For comparison with the particular baseline vocabulary models, we measured the performance associated with pre-trained KR-BERT and M-BERT over the affirmation set. M-BERT achieved a good MLM accuracy of 0. 547, an NSP precision of 0. 786, a good MLM loss of second . 295, and an NSP loss of 0. 479. KR-BERT achieved an MLM accuracy associated with 0. 619, an NSP accuracy of 0. 821, an MULTILEVEL MARKETING loss of one. 869, plus an NSP lack of 0. 916. KR-BERT showed slightly better functionality than M-BERT, except for the particular NSP reduction. Both KM-BERT and KM-BERT-vocab showed improved performance in comparison to the baseline language models. The performance gap appears even after one training epoch. This implies that coaching with domain-specific medical corpora enhances vocabulary understanding of medical texts.

Figure two
figure 2

Pre-training results of KM-BERT and KM-BERT-vocab for MLM and NSP tasks more than epoch. Dashed line representing KR-BERT and dot-dashed line representing M-BERT denotes the particular performance associated with the final pre-trained versions. ( A ) MULTILEVEL MARKETING accuracy. ( B ) NSP accuracy. ( C ) MLM loss. ( D ) NSP loss.

Intrinsic evaluation

Intrinsic evaluation was carried out for MULTILEVEL MARKETING and NSP on external Korean healthcare text that will consists of medical textbooks, health information, and medical research content articles to compare the language understanding capability associated with the design.

The MLM task was performed on three sets of 294 sentence sets. In this assessment, identical rules were used to mask the tokens. The rules contained random aspects. Thus, performance has been measured using 100 repetitions from the MULTILEVEL MARKETING task.

The particular MLM precision of every language model intended for the external Korean healthcare corpus had been evaluated through repeated trials (Fig.   3 ). KM-BERT outperformed the pre-trained language models on MLM and KM-BERT-vocab, regardless of the corpus type. M-BERT exhibited the lowest performance. The performance of the four identical models can vary depending upon the type of corpus utilized. Except to get M-BERT, the particular overall performance of the models has been higher pertaining to information about health news than meant for other medical textbooks plus medical study articles. Considering that medical textbooks and research articles are specialized and difficult to decipher, it can be inferred that these versions performed better for general and popular health information. This suggests that the development of domain-specific NLP models is necessary, highlighting the particular effectiveness plus urgent requirements of pre-trained models (KM-BERT and KM-BERT-vocab). Furthermore, the difference in the performance on information about health news between KM-BERT and KR-BERT was 0. 067, whereas it was 0. 119 designed for medical analysis articles.

Figure 3
figure 3

Distribution of MULTILEVEL MARKETING accuracy simply by 100 reps for every vocabulary model over each corpus type. ( A ) Medical textbook. ( B ) Health information. ( C ) Medical research article.

Additionally, all of us performed the particular NSP task on the same exterior dataset used in the MLM task. For the NSP, we all generated three additional sets associated with 294 arbitrary sentence pairs with simply no next partnership. Quite simply, just for each type, there were 294 sentence in your essay pairs that needed to be classified as following sentence relationships and 294 random term pairs that will should not be.

We measured the predicted probability for the NSP sorted in increasing order for each model (Fig.   4 ). Every model classified three groups of next sentence pairs for the purpose of medical books, health information news, and medical research articles. All samples in the 3 groups had been constructed to have the next phrase relationship. The remaining three groups consisted of random sentence pairs for medical textbooks, health information news, and healthcare research posts. Overall, NSP performance was high in the particular next phrase groups (Fig.   4 A–C). These four models showed error rates associated with less than 10% with regard to binary classification on the next relationship. By contrast, NSP performance has been lower within data organizations with no following sentence associations (Fig.   4 D–F). KR-BERT showed a considerably large mistake for that NotNext label compared with an extremely low error for the IsNext brand. Despite this degradation, KM-BERT plus KM-BERT-vocab demonstrated relatively low errors regarding the NotNext label compared to the other models. The results clearly show that domain-specific pre-training can influence language knowledge of the particular corresponding domain corpus.

Figure four
figure 4

Submission from the expected next word probability intended for the NSP task. ( The C ) Medical book, health info news, and medical study article with the next sentence connection. ( D F ) Random sentence sets for corpus types that correspond to ( A C ) along with no following sentence romantic relationship.

This overall tendency coincides with the outcomes of previous studies upon the effects of pre-training using an unsupervised NSP task. It has been reported that will BERT representations become increasingly sensitive in order to discourse expectations, such as conjunction plus negation, in biomedical texts when BERT architecture is further pre-trained on biomedical corpora making use of the NSP training objective 22 . Specifically, BioBERT qualified on PubMed articles and abstracts showed some improvements in understanding the underlying discourse relations suggested by the particular Biomedical Discourse Relation Bank 23 .

The particular details of NSP accuracy shown within Fig.   4 are presented (Table 2 ). The NSP accuracy had been evaluated by determining the next sentence human relationships with the predicted probability of 0. 5, because the threshold. KM-BERT-vocab demonstrated the highest NSP precision among the groupings with the next sentence interactions. In the same group, M-BERT exhibited the lowest NSP accuracy. The gap inside NSP accuracy by design was greater in data groups that had no next relationship than in data groups using the following relationship. The particular language model with the particular best NSP accuracy was KM-BERT. KM-BERT achieved somewhat higher NSP accuracy compared to KM-BERT-vocab. KR-BERT showed the lowest precision in the particular same information group, with performance differences compared with KM-BERT. This can be interpreted as a limitation within the word relation inference of KR-BERT for medical domain text messages.

Desk 2 NSP accuracy associated with the intrinsic evaluation dataset.

Extrinsic evaluation

Extrinsic evaluations were performed for your MedSTS dataset and the Korean healthcare NER dataset to demonstrate the particular performance of fine-tuning to get downstream jobs. We investigated the Pearson correlation plus Spearman correlation between the similarity measured simply by each vocabulary model and the likeness measured by human verification of MedSTS. We assessed the F1-score for the tagging job of the Korean Medical NER dataset. Each model has been fine-tuned using the teaching set, plus their overall performance was examined using the particular test set. We used a set size associated with 32 and considered learning rates of 2e−5, 3e−5, and 5e−5, and education epochs associated with 2, a few, and four.

Korean MedSTS task

For the MedSTS task, the best performance of each language design trained making use of hyperparameter candidates is offered (Table three or more ). The best-performing language model for the sentence similarity measurement task was KM-BERT. By contrast, KR-BERT showed the particular lowest scored correlation with all the predicted sentence in your essay similarity. This indicates that the sentence partnership in the MedSTS dataset had been properly skilled through pre-training on Korean medical corpora.

Table 3 Extrinsic evaluation outcomes on MedSTS.

We explored 2 cases of similarity measurements using KM-BERT and KR-BERT with examples through the MedSTS dataset. Two cases associated with sentence pairs that showed performance variations in phrase similarity tested in each model are presented (Table 4 ). Within the above example, the likeness score forecasted by KM-BERT was comparable to the similarity measured simply by human experts. This is probably because the embeddings for the particular drugs plus formulations are usually different among KM-BERT and KR-BERT. The bottom is a case in which KR-BERT measures the likeness closer to the human score. This example is related to the general instruction of patient care in the particular management associated with medical systems or hospitals, and therefore, it may not really require expert knowledge to understand the instructions.

Table 4 Examples of the MedSTS dataset containing the true MedSTS similarity plus similarities sized by KM-BERT and KR-BERT.

Korean Medical NER task

In addition in order to the MedSTS task, we evaluated the particular pre-trained design using the Korean Healthcare NER dataset. The dataset was composed of three medical tags: body parts, diseases, and symptoms. The performance associated with the Korean medical NER was deliberated using the particular averaged F1-score for the 3 medical labels (Table 5 ). KM-BERT demonstrated the highest F1-score with a performance gap of 0. 019. A overall performance increase was observed in assessment with KR-BERT and M-BERT. This implies that will pre-training in the Korean medical corpus is effective for Korean medical NER tasks.

Table five Extrinsic evaluation results on Korean clinical NER.

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