Dataset Information

T4SE-XGB: Interpretable Sequence-Based Prediction of Type IV Secreted Effectors Using eXtreme Gradient Boosting Algorithm.

ABSTRACT: Type IV secreted effectors (T4SEs) can be translocated into the cytosol of host cells via type IV secretion system (T4SS) and cause diseases. However, experimental approaches to identify T4SEs are time- and resource-consuming, and the existing computational tools based on machine learning techniques have some obvious limitations such as the lack of interpretability in the prediction models. In this study, we proposed a new model, T4SE-XGB, which uses the eXtreme gradient boosting (XGBoost) algorithm for accurate identification of type IV effectors based on optimal features based on protein sequences. After trying 20 different types of features, the best performance was achieved when all features were fed into XGBoost by the 5-fold cross validation in comparison with other machine learning methods. Then, the ReliefF algorithm was adopted to get the optimal feature set on our dataset, which further improved the model performance. T4SE-XGB exhibited highest predictive performance on the independent test set and outperformed other published prediction tools. Furthermore, the SHAP method was used to interpret the contribution of features to model predictions. The identification of key features can contribute to improved understanding of multifactorial contributors to host-pathogen interactions and bacterial pathogenesis. In addition to type IV effector prediction, we believe that the proposed framework can provide instructive guidance for similar studies to construct prediction methods on related biological problems. The data and source code of this study can be freely accessed at https://github.com/CT001002/T4SE-XGB.

SUBMITTER: Chen T

PROVIDER: S-EPMC7541839 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

T4SE-XGB: Interpretable Sequence-Based Prediction of Type IV Secreted Effectors Using eXtreme Gradient Boosting Algorithm.

Chen Tianhang T Wang Xiangeng X Chu Yanyi Y Wang Yanjing Y Jiang Mingming M Wei Dong-Qing DQ Xiong Yi Y

Frontiers in microbiology 20200924

Type IV secreted effectors (T4SEs) can be translocated into the cytosol of host cells via type IV secretion system (T4SS) and cause diseases. However, experimental approaches to identify T4SEs are time- and resource-consuming, and the existing computational tools based on machine learning techniques have some obvious limitations such as the lack of interpretability in the prediction models. In this study, we proposed a new model, T4SE-XGB, which uses the eXtreme gradient boosting (XGBoost) algor ...[more]

PMID: 33072049

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Project description:BackgroundThe non-invasive preoperative diagnosis of microvascular invasion (MVI) in hepatocellular carcinoma (HCC) is vital for precise surgical decision-making and patient prognosis. Herein, we aimed to develop an MVI prediction model with valid performance and clinical interpretability.MethodsA total of 2160 patients with HCC without macroscopic invasion who underwent hepatectomy for the first time in West China Hospital from January 2015 to June 2019 were retrospectively included, and randomly divided into training and a validation cohort at a ratio of 8:2. Preoperative demographic features, imaging characteristics, and laboratory indexes of the patients were collected. Five machine learning algorithms were used: logistic regression, random forest, support vector machine, extreme gradient boosting (XGBoost), and multilayer perception. Performance was evaluated using the area under the receiver operating characteristic curve (AUC). We also determined the Shapley Additive exPlanation value to explain the influence of each feature on the MVI prediction model.ResultsThe top six important preoperative factors associated with MVI were the maximum image diameter, protein induced by vitamin K absence or antagonist-II, α-fetoprotein level, satellite nodules, alanine aminotransferase (AST)/aspartate aminotransferase (ALT) ratio, and AST level, according to the XGBoost model. The XGBoost model for preoperative prediction of MVI exhibited a better AUC (0.8, 95% confidence interval: 0.74-0.83) than the other prediction models. Furthermore, to facilitate use of the model in clinical settings, we developed a user-friendly online calculator for MVI risk prediction based on the XGBoost model.ConclusionsThe XGBoost model achieved outstanding performance for non-invasive preoperative prediction of MVI based on big data. Moreover, the MVI risk calculator would assist clinicians in conveniently determining the optimal therapeutic remedy and ameliorating the prognosis of patients with HCC.

Project description:BackgroundAccurate classification of type 1 diabetes (T1DM) and type 2 diabetes (T2DM) in the early phase is crucial for individual precision treatment. This study aimed to develop a classification model having fewer and easier to access clinical variables to distinguish T1DM in newly diagnosed diabetes in adults.MethodsClinical and laboratory data were collected from 15,206 adults with newly diagnosed diabetes in this cross-sectional study. This cohort represented 20 provinces and 4 municipalities in China. Types of diabetes were determined based on postprandial C-peptide (PCP) level and glutamic acid decarboxylase autoantibody (GADA) titer. We developed multivariable clinical diagnostic models using the eXtreme Gradient Boosting (XGBoost) algorithm. Classification variables included in the final model were based on their scores of importance. Model performance was evaluated by area under the receiver operating characteristic curve (ROC AUC), sensitivity, and specificity. The performance of models with different variable combinations was compared. Calibration intercept and slope were evaluated for the final model.ResultsAmong the newly diagnosed diabetes cohort, 1,465 (9.63%) persons had T1DM and 13,741 (90.37%) had T2DM. Body mass index (BMI) contributed the most to the model, followed by age of onset and hemoglobin A1c (HbA1c). Compared with models with other clinical variable combinations, a final model that integrated age of onset, BMI and HbA1c had relatively higher performance. The ROC AUC, sensitivity, and specificity for this model were 0.83 (95% CI, 0.80 to 0.85), 0.77, and 0.76, respectively. The calibration intercept and slope were 0.02 (95% CI, -0.03 to 0.06) and 0.90 (95% CI, 0.79 to 1.02), respectively, which suggested a good calibration performance.ConclusionsOur classification model that integrated age of onset, BMI, and HbA1c could distinguish T1DM from T2DM, which provides a useful tool in assisting physicians in subtyping and precising treatment in diabetes.

Dataset Information

T4SE-XGB: Interpretable Sequence-Based Prediction of Type IV Secreted Effectors Using eXtreme Gradient Boosting Algorithm.

Publications

T4SE-XGB: Interpretable Sequence-Based Prediction of Type IV Secreted Effectors Using eXtreme Gradient Boosting Algorithm.

Similar Datasets

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