Oversampling effect in pretraining for bidirectional encoder representations from transformers (BERT) to localize medical BERT and enhance biomedical BERT.

BACKGROUND: Pretraining large-scale neural language models on raw texts has made a significant contribution to improving transfer learning in natural language processing. With the introduction of transformer-based language models, such as bidirectional encoder representations from transformers (BERT), the performance of information extraction from free text has improved significantly in both the general and medical domains. However, it is difficult to train specific BERT models to perform well in domains for which few databases of a high quality and large size are publicly available. OBJECTIVE: We hypothesized that this problem could be addressed by oversampling a domain-specific corpus and using it for pretraining with a larger corpus in a balanced manner. In the present study, we verified our hypothesis by developing pretraining models using our method and evaluating their performance. METHODS: Our proposed method was based on the simultaneous pretraining of models with knowledge from distinct domains after oversampling. We conducted three experiments in which we generated (1) English biomedical BERT from a small biomedical corpus, (2) Japanese medical BERT from a small medical corpus, and (3) enhanced biomedical BERT pretrained with complete PubMed abstracts in a balanced manner. We then compared their performance with those of conventional models. RESULTS: Our English BERT pretrained using both general and small medical domain corpora performed sufficiently well for practical use on the biomedical language understanding evaluation (BLUE) benchmark. Moreover, our proposed method was more effective than the conventional methods for each biomedical corpus of the same corpus size in the general domain. Our Japanese medical BERT outperformed the other BERT models built using a conventional method for almost all the medical tasks. The model demonstrated the same trend as that of the first experiment in English. Further, our enhanced biomedical BERT model, which was not pretrained on clinical notes, achieved superior clinical and biomedical scores on the BLUE benchmark with an increase of 0.3 points in the clinical score and 0.5 points in the biomedical score. These scores were above those of the models trained without our proposed method. CONCLUSIONS: Well-balanced pretraining using oversampling instances derived from a corpus appropriate for the target task allowed us to construct a high-performance BERT model.

Development of the Clinical Specimen Information Management System for Multicenter Clinical Studies.

Some multicenter clinical studies require the acquisition of clinical specimens from patients, and the centralized management and analysis of clinical specimens at a research institution. In such cases, it is necessary to manage clinical specimens with anonymized patient information. In addition, clinical specimens need to be managed in connection with clinical information in clinical studies. In this study, we have developed a clinical specimen information management system that works with electronic data capture system for efficient specimen information management and the system workflow has verified at Osaka University Hospital. In addition, by combining this system with medical image collection system that we have developed previously, the integrated management of clinical information, medical image, and clinical specimen information will become possible. This specimen information management system may be expected to provide the platform for integrated analysis utilizing clinical information, medical image, and data from clinical specimens in multicenter clinical studies.

Classification of Diagnostic Certainty in Radiology Reports with Deep Learning.

A radiology report is prepared for communicating clinical information about observed abnormal structures and clinically important findings with referring clinicians. However, such observations and findings are often accompanied by ambiguous expressions, which can prevent clinicians from accurately interpreting the content of reports. To systematically assess the degree of diagnostic certainty for each observation and finding in a report, we defined an ordinal scale comprising five classes: definite, likely, may represent, unlikely, and denial. Furthermore, we applied a deep learning classification model to determine its applicability to in-house radiology reports. We trained and evaluated the model using 540 in-house chest computed tomography reports. The deep learning model achieved a micro F1-score of 97.61%, which indicated that our ordinal scale was suitable for measuring the diagnostic certainty of observations and findings in a report.

Implementation of a Multilingual Electronic Medical Questionnaire: For Use Inside or Outside the Hospital.

We implemented a multilingual medical questionnaire system, which allows patients to answer questionnaires both in and out of the hospital. The response data are sent to and stored as structured data on the server in hospital information system, and could be converted to Japanese and quoted as part of progress notes in the electronic medical record.

Extracting Clinical Information From Japanese Radiology Reports Using a 2-Stage Deep Learning Approach: Algorithm Development and Validation.

Background: Radiology reports are usually written in a free-text format, which makes it challenging to reuse the reports. Objective: For secondary use, we developed a 2-stage deep learning system for extracting clinical information and converting it into a structured format. Methods: Our system mainly consists of 2 deep learning modules: entity extraction and relation extraction. For each module, state-of-the-art deep learning models were applied. We trained and evaluated the models using 1040 in-house Japanese computed tomography (CT) reports annotated by medical experts. We also evaluated the performance of the entire pipeline of our system. In addition, the ratio of annotated entities in the reports was measured to validate the coverage of the clinical information with our information model. Results: The microaveraged F1-scores of our best-performing model for entity extraction and relation extraction were 96.1% and 97.4%, respectively. The microaveraged F1-score of the 2-stage system, which is a measure of the performance of the entire pipeline of our system, was 91.9%. Our system showed encouraging results for the conversion of free-text radiology reports into a structured format. The coverage of clinical information in the reports was 96.2% (6595/6853). Conclusions: Our 2-stage deep system can extract clinical information from chest and abdomen CT reports accurately and comprehensively.

Impact of an Electronic Medical Record-Connected Questionnaire on Efficient Nursing Documentation: Usability and Efficacy Study.

BACKGROUND: Documentation tasks comprise a large percentage of nurses' workloads. Nursing records were partially based on a report from the patient. However, it is not a verbatim transcription of the patient's complaints but a type of medical record. Therefore, to reduce the time spent on nursing documentation, it is necessary to assist in the appropriate conversion or citation of patient reports to professional records. However, few studies have been conducted on systems for capturing patient reports in electronic medical records. In addition, there have been no reports on whether such a system reduces the time spent on nursing documentation. OBJECTIVE: This study aims to develop a patient self-reporting system that appropriately converts data to nursing records and evaluate its effect on reducing the documenting burden for nurses. METHODS: An electronic medical record-connected questionnaire and a preadmission nursing questionnaire were administered. The questionnaire responses entered by the patients were quoted in the patient profile for inpatient assessment in the nursing system. To clarify its efficacy, this study examined whether the use of the electronic questionnaire system saved the nurses' time entering the patient profile admitted between August and December 2022. It also surveyed the usability of the electronic questionnaire between April and December 2022. RESULTS: A total of 3111 (78%) patients reported that they answered the electronic medical questionnaire by themselves. Of them, 2715 (88%) felt it was easy to use and 2604 (85%) were willing to use it again. The electronic questionnaire was used in 1326 of 2425 admission cases (use group). The input time for the patient profile was significantly shorter in the use group than in the no-use group (P<.001). Stratified analyses showed that in the internal medicine wards and in patients with dependent activities of daily living, nurses took 13%-18% (1.3 to 2 minutes) less time to enter patient profiles within the use group (both P<.001), even though there was no difference in the amount of information. By contrast, in the surgical wards and in the patients with independent activities of daily living, there was no difference in the time to entry (P=.50 and P=.20, respectively), but there was a greater amount of information in the use group. CONCLUSIONS: The study developed and implemented a system in which self-reported patient data were captured in the hospital information network and quoted in the nursing system. This system contributes to improving the efficiency of nurses' task recordings.

Automatic creation of annotations for chest radiographs based on the positional information extracted from radiographic image reports.

BACKGROUND AND OBJECTIVE: In this study, we tried to create a machine-learning method that detects disease lesions from chest X-ray (CXR) images using a data set annotated with extracted CXR reports information. We set the nodule as the target disease lesion. Manually annotating nodules is costly in terms of time. Therefore, we used the report information to automatically produce training data for the object detection task. METHODS: First, we use semantic segmentation model PSP-Net to recognize lung fields described in the CXR reports. Next, a classification model ResNeSt-50 is used to discriminate the nodule in segmented right and left field. It also can provide attention map by Grad-Cam. If the attention region corresponds to the location of the nodule in the CXR reports, an attention bounding box is generated. Finally, object detection model Faster-RCNN was performed using generated attention bounding box. The bounding boxes predicted by Faster-RCNN were filtered to satisfy the location extracted from CXR reports. RESULTS: For lung field segmentation, a mean intersection of union of 0.889 was achieved in our best model. 15,156 chest radiographs are used for classification. The area under the receiver operating characteristics curve was 0.843 and 0.852 for the left and right lung, respectively. The detection precision of the generated attention bounding box was 0.341 to 0.531 depending on the binary setting for attention map. Through object detection process, the detection precisions of the bounding boxes were improved to 0.567 to 0.800. CONCLUSION: We successfully generated bounding boxes with nodule on CXR images based on the positional information of the diseases extracted from the CXR reports. Our method has the potential to provide bounding boxes for various lung lesions which can reduce the annotation burden for specialists. SHORT ABSTRACT: Machine learning for computer aided image diagnosis requires annotation of images, but manual annotation is time-consuming for medical doctor. In this study, we tried to create a machine-learning method that creates bounding boxes with disease lesions on chest X-ray (CXR) images using the positional information extracted from CXR reports. We set the nodule as the target lesion. First, we use PSP-Net to segment the lung field according to the CXR reports. Next, a classification model ResNeSt-50 was used to discriminate the nodule in segmented lung field. We also created an attention map using the Grad-Cam algorithm. If the area of attention matched the area annotated by the CXR report, the coordinate of the bounding box was considered as a possible nodule area. Finally, we used the attention information obtained from the nodule classification model and let the object detection model trained by all of the generated bounding boxes. Through object detection model, the precision of the bounding boxes to detect nodule is improved.

Extracting clinical terms from radiology reports with deep learning.

Extracting clinical terms from free-text format radiology reports is a first important step toward their secondary use. However, there is no general consensus on the kind of terms to be extracted. In this paper, we propose an information model comprising three types of clinical entities: observations, clinical findings, and modifiers. Furthermore, to determine its applicability for in-house radiology reports, we extracted clinical terms with state-of-the-art deep learning models and compared the results. We trained and evaluated models using 540 in-house chest computed tomography (CT) reports annotated by multiple medical experts. Two deep learning models were compared, and the effect of pre-training was explored. To investigate the generalizability of the model, we evaluated the use of other institutional chest CT reports. The micro F1-score of our best performance model using in-house and external datasets were 95.36% and 94.62%, respectively. Our results indicated that entities defined in our information model were suitable for extracting clinical terms from radiology reports, and the model was sufficiently generalizable to be used with dataset from other institutions.

End-to-End Approach for Structuring Radiology Reports.

Radiology reports include various types of clinical information that are used for patient care. Reports are also expected to have secondary uses (e.g., clinical research and the development of decision support systems). For secondary use, it is necessary to extract information from the report and organize it in a structured format. Our goal is to build an application to transform radiology reports written in a free-text form into a structured format. To this end, we propose an end-to-end method that consists of three elements. First, we built a neural network model to extract clinical information from the reports. We experimented on a dataset of chest X-ray reports. Second, we transformed the extracted information into a structured format. Finally, we built a tool that enabled the transformation of terms in reports to standard forms. Through our end-to-end method, we could obtain a structured radiology dataset that was easy to access for secondary use.

Extracting Symptom Names and Disease-Symptom Relationships from Web Texts Using a Multi-Column Convolutional Neural Network.

We propose a method to create large-scale Japanese medical dictionaries that include symptom names and information about the relationship between a disease and its symptoms using a large web archive that includes large amounts of text written by non-medical experts. Our goal is to develop a diagnosis support system that makes a diagnosis according to the natural language (NL) inputs provided by patients. To achieve this, two medical dictionaries need to be constructed: one that includes a wide variety of symptom names expressed in NL and another that includes information about the relationship between a disease and its symptoms. Dictionaries will then be used to predict the patient's disease via two developed methods that extract symptom names and disease-symptom relationships. Both methods retrieve sentences using WISDOM X and then apply neural classifiers to them. Our experimental results show that our methods achieved 93.8% and 88.3% in the F1-score, respectively.

The Acquisition of Structured Clinical Data from a Document-Based Electronic Medical Record System.

Our hospital stores all clinical records as Portable Document Formats (PDFs). These PDFs are delivered by each system with a document profile XML file. Using this interface, the items thought to be important for clinical studies are described in the document profile XML and delivered to the data warehouse (DWH). In case clinical data not stored in the DWH are needed, we extract the data from PDF documents. Even from scanned PDFs, the data can be extracted with high accuracy.

Rhinocerebral Mucormycosis With Temporal Artery Thrombosis in an Adolescent Following HLA-haploidentical Stem Cell Transplantation.

Rhinocerebral mucormycosis (RCM) can lead to internal carotid artery thrombosis. Here, we report the first case of RCM with temporal artery thrombosis following HLA-haploidentical stem cell transplantation in an adolescent presenting with low-grade fever, right mandibular pain, and right jaw claudication. This case suggests that RCM can cause temporal artery thrombosis and should be considered as a differential diagnosis in severely immunocompromised patients with maxillary sinusitis presenting with jaw claudication.

Mesalazine allergy in a boy with ulcerative colitis: clinical usefulness of mucosal biopsy criteria.

5-Aminosalicylic acid preparations have been used as first-line drugs for treatment of ulcerative colitis (UC). However, some patients with UC present with exacerbation of symptoms because of allergy to mesalazine. Diagnosis of mesalazine allergy in active UC may be challenging because its symptoms mimic those of UC. Here we describe a 13-year-old boy with mesalazine allergy who achieved remission when his medication was changed from mesalazine to salazosulfapyridine. During his clinical course mesalazine was prescribed twice, and on each occasion exacerbation of the symptoms occurred. We considered a diagnosis of mesalazine allergy, and this was confirmed by a drug lymphocyte stimulation test; the result for salazosulfapyridine was negative. On the basis of criteria involving simple mucosal biopsy combined with endoscopy for predicting patients with UC who would ultimately require surgery, we considered that the UC in this case might be susceptible to steroid treatment, and we therefore treated the patient with salazosulfapyridine and prednisolone. Shortly afterwards, remission was achieved and the patient has remained in good condition on salazosulfapyridine alone. When treating patients with mesalazine, the possibility of allergy should always be borne in mind, especially when the clinical course is inconsistent with the results of biopsy.