Approach for Named Entity Recognition and Case Identification Implemented by ZuKyo-JA Sub-team at the NTCIR-16 Real-MedNLP Task

In this NTCIR-16 Real-MedNLP shared task paper, we present the methods of the ZuKyo-JA subteam for solving the Japanese part of Subtask1 and Subtask3 (Subtask1-CR-JA, Subtask1-RR- JA, Subtask3-RR-JA). Our solution is based on a sliding- window approach using a Japanese BERT pre-trained masked- language model., which was used as a common architecture for addressing the specific subtasks. We additionally present a method that makes extensive use of medical knowledge for the same case identification subtask3-RR-JA

Leveraging Token-Based Concept Information and Data Augmentation in Few-Resource NER: ZuKyo-EN at the NTCIR-16 Real-MedNLP task

In this paper, we discuss our contribution to the NII Testbeds and Community for Information Access Research (NTCIR) - 16 Real- MedNLP shared task. Our team (ZuKyo) participated in the English subtask: Few-resource Named Entity Recognition. The main challenge in this low-resource task was a low number of training documents annotated with a high number of tags and attributes. For our submissions, we used different general and domain-specific transfer learning approaches in combination with multiple data augmentation methods. In addition, we experimented with models enriched with biomedical concepts encoded as token-based input feature

Test collections for medical information retrieval evaluation

The web has rapidly become one of the main resources for medical information for many people: patients, clinicians, medical doctors, etc. Measuring the effectiveness with which information can be retrieved from web resources for these users is crucial: it brings better information to professionals for better diagnosis, treatment, patient care; and helps patients and relatives get informed on their condition. Several existing information retrieval (IR) evaluation campaigns have been developed to assess and improve medical IR methods, for example the TREC Medical Record Track [11] and TREC Genomics Track [10]. These campaigns only target certain type of users, mainly clinicians and some medical professionals: queries are mainly centered on cohorts of records describing a specific patient cases or on biomedical reports. Evaluating search effectiveness over the many heterogeneous online medical information sources now available, which are increasingly used by a diverse range of medical professionals and, very importantly, the general public, is vital to the understanding and development of medical IR. We describe the development of two benchmarks for medical IR evaluation from the Khresmoi project. The first of these has been developed using existing medical query logs for internal research within the Khresmoi project and targets both medical professionals and general public; the second has been created in the framework of a new CLEFeHealth evaluation campaign and is designed to evaluate patient search in context

The USMLE® Step 2 clinical skills patient note corpus

© 2022 The Authors. Published by ACL. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://aclanthology.org/2022.naacl-main.208This paper presents a corpus of 43,985 clinical patient notes (PNs) written by 35,156 examinees during the high-stakes USMLE® Step 2 Clinical Skills examination. In this exam, examinees interact with standardized patients - people trained to portray simulated scenarios called clinical cases. For each encounter, an examinee writes a PN, which is then scored by physician raters using a rubric of clinical concepts, expressions of which should be present in the PN. The corpus features PNs from 10 clinical cases, as well as the clinical concepts from the case rubrics. A subset of 2,840 PNs were annotated by 10 physician experts such that all 143 concepts from the case rubrics (e.g., shortness of breath) were mapped to 34,660 PN phrases (e.g., dyspnea, difficulty breathing). The corpus is available via a data sharing agreement with NBME and can be requested at https://www.nbme.org/services/data-sharing.Published versio

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

Wada S., Takeda T., Okada K., et al. Oversampling effect in pretraining for bidirectional encoder representations from transformers (BERT) to localize medical BERT and enhance biomedical BERT. Artificial Intelligence in Medicine 153, 102889 (2024); https://doi.org/10.1016/j.artmed.2024.102889.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

Task 1 of the CLEF eHealth Evaluation Lab 2016: Handover Information Extraction

Cascaded speech recognition (SR) and information extraction(IE) could support the best practice for clinical handover and release clinicians’ time from writing documents to patient interaction and education. However, high requirements for processing correctness evoke methodological challenges and hence, processing correctness needs to be carefully evaluated as meeting the requirements. This overview paper reports on how these issues were addressed in a shared task of the eHealth evaluation lab of the Conference and Labs of the Evaluation Forum (CLEF) in 2016. This IE task built on the 2015 CLEF eHealth Task on SR by using its 201 synthetic handover documents for training and validation (appr. 8, 500 + 7, 700 words) and releasing another 100 documents with over 6, 500 expert-annotated words for testing. It attracted 25 team registrations and 3 team submissions with 2 methods each. When using the macro-averaged F1 over the 35 form headings present in the training documents for evaluation on the test documents, all participant methods outperformed all 4 baselines, including the organizers’ method (F1 = 0.25), published in 2015 in a top-tier medical informatics journal and provided to the participants as an option to build on, a random classifier (F1 = 0.02), and majority classifiers for the two most common classes (i.e., NA to filter out text irrelevant to the form and the most common form heading, both with F1 < 0.00). The top-2 methods (F1 = 0.38 and 0.37) had statistically significantly (p < 0.05, Wilcoxon signed-rank test) better performance than the third-best method (F1 = 0.35). In comparison, the top-3 methods and the organizers’ method (7th) had F1 of 0.81, 0.80, 0.81, and 0.75 in the NA class, respectivel

Exploring Optimal Granularity for Extractive Summarization of Unstructured Health Records: Analysis of the Largest Multi-Institutional Archive of Health Records in Japan

Automated summarization of clinical texts can reduce the burden of medical professionals. "Discharge summaries" are one promising application of the summarization, because they can be generated from daily inpatient records. Our preliminary experiment suggests that 20-31% of the descriptions in discharge summaries overlap with the content of the inpatient records. However, it remains unclear how the summaries should be generated from the unstructured source. To decompose the physician's summarization process, this study aimed to identify the optimal granularity in summarization. We first defined three types of summarization units with different granularities to compare the performance of the discharge summary generation: whole sentences, clinical segments, and clauses. We defined clinical segments in this study, aiming to express the smallest medically meaningful concepts. To obtain the clinical segments, it was necessary to automatically split the texts in the first stage of the pipeline. Accordingly, we compared rule-based methods and a machine learning method, and the latter outperformed the formers with an F1 score of 0.846 in the splitting task. Next, we experimentally measured the accuracy of extractive summarization using the three types of units, based on the ROUGE-1 metric, on a multi-institutional national archive of health records in Japan. The measured accuracies of extractive summarization using whole sentences, clinical segments, and clauses were 31.91, 36.15, and 25.18, respectively. We found that the clinical segments yielded higher accuracy than sentences and clauses. This result indicates that summarization of inpatient records demands finer granularity than sentence-oriented processing. Although we used only Japanese health records, it can be interpreted as follows: physicians extract "concepts of medical significance" from patient records and recombine them ..