Takashi Okumura

Kenichiro Ando, Takashi Okumura, Mamoru Komachi et al.

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 ...

Kenichiro Ando, Mamoru Komachi, Takashi Okumura et al.

During the patient's hospitalization, the physician must record daily observations of the patient and summarize them into a brief document called "discharge summary" when the patient is discharged. Automated generation of discharge summary can greatly relieve the physicians' burden, and has been addressed recently in the research community. Most previous studies of discharge summary generation using the sequence-to-sequence architecture focus on only inpatient notes for input. However, electric health records (EHR) also have rich structured metadata (e.g., hospital, physician, disease, length of stay, etc.) that might be useful. This paper investigates the effectiveness of medical meta-information for summarization tasks. We obtain four types of meta-information from the EHR systems and encode each meta-information into a sequence-to-sequence model. Using Japanese EHRs, meta-information encoded models increased ROUGE-1 by up to 4.45 points and BERTScore by 3.77 points over the vanilla Longformer. Also, we found that the encoded meta-information improves the precisions of its related terms in the outputs. Our results showed the benefit of the use of medical meta-information.

Shusaku Egami, Yasunori Yamamoto, Ikki Ohmukai et al.

Public health authorities perform contact tracing for highly contagious agents to identify close contacts with the infected cases. However, during the pandemic caused by coronavirus disease 2019 (COVID-19), this operation was not employed in countries with high patient volumes. Meanwhile, the Japanese government conducted this operation, thereby contributing to the control of infections, at the cost of arduous manual labor by public health officials. To ease the burden of the officials, this study attempted to automate the assessment of each person's infection risk through an ontology, called COVID-19 Infection Risk Ontology (CIRO). This ontology expresses infection risks of COVID-19 formulated by the Japanese government, toward automated assessment of infection risks of individuals, using Resource Description Framework (RDF) and SPARQL (SPARQL Protocol and RDF Query Language) queries. For evaluation, we demonstrated that the knowledge graph built could infer the risks, formulated by the government. Moreover, we conducted reasoning experiments to analyze the computational efficiency. The experiments demonstrated usefulness of the knowledge processing, and identified issues left for deployment.

Ikki Ohmukai, Yasunori Yamamoto, Maori Ito et al.

In the cases when public health authorities confirm a patient with highly contagious disease, they release the summaries about patient locations and travel information. However, due to privacy concerns, these releases do not include the detailed data and typically comprise the information only about commercial facilities and public transportation used by the patients. We addressed this problem and proposed to release the patient location data as open data represented in a structured form of the information described in press releases. Therefore, residents would be able to use these data for automated estimation of the potential risks of contacts combined with the location information stored in their mobile phones. This paper proposes the design of the open data based on Resource Description Framework (RDF), and performs a preliminary evaluation of the first draft of the specification followed by a discussion on possible future directions.