I9 The size of the CAG-expansion mutation can be predicted in hd based on phenotypic data using a machine learning approach

Machine learning in Huntington's disease: exploring the Enroll-HD dataset for prognosis and driving capability prediction

BACKGROUND

In biomedicine, machine learning (ML) has proven beneficial for the prognosis and diagnosis of different diseases, including cancer and neurodegenerative disorders. For rare diseases, however, the requirement for large datasets often prevents this approach. Huntington's disease (HD) is a rare neurodegenerative disorder caused by a CAG repeat expansion in the coding region of the huntingtin gene. The world's largest observational study for HD, Enroll-HD, describes over 21,000 participants. As such, Enroll-HD is amenable to ML methods. In this study, we pre-processed and imputed Enroll-HD with ML methods to maximise the inclusion of participants and variables. With this dataset we developed models to improve the prediction of the age at onset (AAO) and compared it to the well-established Langbehn formula. In addition, we used recurrent neural networks (RNNs) to demonstrate the utility of ML methods for longitudinal datasets, assessing driving capabilities by learning from previous participant assessments.

RESULTS

Simple pre-processing imputed around 42% of missing values in Enroll-HD. Also, 167 variables were retained as a result of imputing with ML. We found that multiple ML models were able to outperform the Langbehn formula. The best ML model (light gradient boosting machine) improved the prognosis of AAO compared to the Langbehn formula by 9.2%, based on root mean squared error in the test set. In addition, our ML model provides more accurate prognosis for a wider CAG repeat range compared to the Langbehn formula. Driving capability was predicted with an accuracy of 85.2%. The resulting pre-processing workflow and code to train the ML models are available to be used for related HD predictions at: https://github.com/JasperO98/hdml/tree/main .

CONCLUSIONS

Our pre-processing workflow made it possible to resolve the missing values and include most participants and variables in Enroll-HD. We show the added value of a ML approach, which improved AAO predictions and allowed for the development of an advisory model that can assist clinicians and participants in estimating future driving capability.

Prediction of Hypertension Outcomes Based on Gain Sequence Forward Tabu Search Feature Selection and XGBoost

For patients with hypertension, serious complications, such as myocardial infarction, a common cause of heart failure, occurs in the late stage of hypertension. Hypertension outcomes can lead to complications, including death. Hypertension outcomes threaten patients’ lives and need to be predicted. In our research, we reviewed the hypertension medical data from a tertiary-grade A class hospital in Beijing, and established a hypertension outcome prediction model with the machine learning theory. We first proposed a gain sequence forward tabu search feature selection (GSFTS-FS) method, which can search the optimal combination of medical variables that affect hypertension outcomes. Based on this, the XGBoost algorithm established a prediction model because of its good stability. We verified the proposed method by comparing other commonly used models in similar works. The proposed GSFTS-FS improved the performance by about 10%. The proposed prediction method has the best performance and its AUC value, accuracy, F1 value, and recall of 10-fold cross-validation were 0.96. 0.95, 0.88, and 0.82, respectively. It also performed well on test datasets with 0.92, 0.94, 0.87, and 0.80 for AUC, accuracy, F1, and recall, respectively. Therefore, the XGBoost with GSFTS-FS can accurately and effectively predict the occurrence of outcomes for patients with hypertension, and can provide guidance for doctors in clinical diagnoses and medical decision-making.