Health data science最新文献

Background: Machine learning models are not in routine use for predicting HIV status. Our objective is to describe the development of a machine learning model to predict HIV viral load (VL) hotspots as an early warning system in Kenya, based on routinely collected data by affiliate entities of the Ministry of Health. Based on World Health Organization's recommendations, hotspots are health facilities with ≥20% people living with HIV whose VL is not suppressed. Prediction of VL hotspots provides an early warning system to health administrators to optimize treatment and resources distribution.

Methods: A random forest model was built to predict the hotspot status of a health facility in the upcoming month, starting from 2016. Prior to model building, the datasets were cleaned and checked for outliers and multicollinearity at the patient level. The patient-level data were aggregated up to the facility level before model building. We analyzed data from 4 million tests and 4,265 facilities. The dataset at the health facility level was divided into train (75%) and test (25%) datasets.

Results: The model discriminates hotspots from non-hotspots with an accuracy of 78%. The F1 score of the model is 69% and the Brier score is 0.139. In December 2019, our model correctly predicted 434 VL hotspots in addition to the observed 446 VL hotspots.

Conclusion: The hotspot mapping model can be essential to antiretroviral therapy programs. This model can provide support to decision-makers to identify VL hotspots ahead in time using cost-efficient routinely collected data.

Background: Logistic regression models are widely used in clinical prediction, but their application in resource-poor settings or areas without internet access can be challenging. Nomograms can serve as a useful visualization tool to speed up the calculation procedure, but existing nomogram generators often require the input of raw data, inhibiting the transformation of established logistic regression models that only provide coefficients. Developing a tool that can generate nomograms directly from logistic regression coefficients would greatly increase usability and facilitate the translation of research findings into patient care.

Methods: We designed and developed simpleNomo, an open-source Python toolbox that enables the construction of nomograms for logistic regression models. Uniquely, simpleNomo allows for the creation of nomograms using only the coefficients of the model. Further, we also devoloped an online website for nomogram generation.

Results: simpleNomo properly maintains the predictive ability of the original logistic regression model and easy to follow. simpleNomo is compatible with Python 3 and can be installed through Python Package Index (PyPI) or https://github.com/Hhy096/nomogram.

Conclusion: This paper presents simpleNomo, an open-source Python toolbox for generating nomograms for logistic regression models. It facilitates the process of transferring established logistic regression models to nomograms and can further convert more existing works into practical use.

Background: Chinese medical entities have not been organized comprehensively due to the lack of well-developed terminology systems, which poses a challenge to processing Chinese medical texts for fine-grained medical knowledge representation. To unify Chinese medical terminologies, mapping Chinese medical entities to their English counterparts in the Unified Medical Language System (UMLS) is an efficient solution. However, their mappings have not been investigated sufficiently in former research. In this study, we explore strategies for mapping Chinese medical entities to the UMLS and systematically evaluate the mapping performance.

Methods: First, Chinese medical entities are translated to English using multiple web-based translation engines. Then, 3 mapping strategies are investigated: (a) string-based, (b) semantic-based, and (c) string and semantic similarity combined. In addition, cross-lingual pretrained language models are applied to map Chinese medical entities to UMLS concepts without translation. All of these strategies are evaluated on the ICD10-CN, Chinese Human Phenotype Ontology (CHPO), and RealWorld datasets.

Results: The linear combination method based on the SapBERT and term frequency-inverse document frequency bag-of-words models perform the best on all evaluation datasets, with 91.85%, 82.44%, and 78.43% of the top 5 accuracies on the ICD10-CN, CHPO, and RealWorld datasets, respectively.

Conclusions: In our study, we explore strategies for mapping Chinese medical entities to the UMLS and identify a satisfactory linear combination method. Our investigation will facilitate Chinese medical entity normalization and inspire research that focuses on Chinese medical ontology development.

Background: Ovarian hyperstimulation syndrome (OHSS) occurs in women receiving fertility treatments. Moderate and severe OHSS cases are required to be admitted to hospital for treatment. The incidence of moderate and severe OHSS and the characteristics of these cases are unknown in China. We aimed to assess the incidence of moderate and severe OHSS in national databases from China between 2013 and 2017.

Methods: We extracted moderate and severe OHSS cases from the Hospital Quality Monitoring System, the nationwide inpatient data collection system. We used ovum pick-up (OPUbaidu) cycle data from the annual report of China's National Health Commission, developed on the basis of OPU data collected by National ART Management Information System. Overall incidence of moderate and severe OHSS (women aged 20 to 50 years) and year-specific incidence by each calendar year in China were calculated. We also investigated the age distribution in OHSS and OHSS with different comorbidities.

Results: We extracted 18,022 eligible patients with moderate or severe OHSS and 1,581,703 OPU cycles. The overall incidence of moderate and severe OHSS between 2013 and 2017 was 1.14%. The year-specific moderate and severe OHSS incidence was 1.1% in 2013, 1.4% in 2014, 1.4% in 2015, 1.1% in 2016, 0.9% in 2017, respectively. Women aged 26 to 30 years accounted for 48.4% of OHSS cases, followed by women aged 31 to 35 years (30%) and 20 to 25 years (14.2%). The age distribution pattern was consistent across OHSS with different comorbidities.

Conclusions: This study reported the incidence of moderate and severe OHSS in China using nationwide data for the first time. Our findings support that women aged under 35 years receiving assisted reproductive technology need more attention than other age groups in terms of OHSS risk control.