scholarly journals Developing a Novel Machine Learning-Based Classification Scheme for Predicting SPCs in Colorectal Cancer Survivors

2020 ◽  
Vol 10 (4) ◽  
pp. 1355 ◽  
Author(s):  
Wen-Chien Ting ◽  
Horng-Rong Chang ◽  
Chi-Chang Chang ◽  
Chi-Jie Lu
Keyword(s):  
Colorectal Cancer ◽  
Machine Learning ◽  
Risk Factors ◽  
Primary Site ◽  
Multivariate Adaptive Regression Splines ◽  
Support Vector ◽  
Second Primary ◽  
Primary Tumors ◽  
Machine Learning Classification ◽  
Extreme Gradient Boosting

Colorectal cancer is ranked third and fourth in terms of mortality and cancer incidence in the world. While advances in treatment strategies have provided cancer patients with longer survival, potentially harmful second primary cancers can occur. Therefore, second primary colorectal cancer analysis is an important issue with regard to clinical management. In this study, a novel predictive scheme was developed for predicting the risk factors associated with second colorectal cancer in patients with colorectal cancer by integrating five machine learning classification techniques, including support vector machine, random forest, multivariate adaptive regression splines, extreme learning machine, and extreme gradient boosting. A total of 4287 patients in the datasets provided by three hospital tumor registries were used. Our empirical results revealed that this proposed predictive scheme provided promising classification results and the identification of important risk factors for predicting second colorectal cancer based on accuracy, sensitivity, specificity, and area under the curve metrics. Collectively, our clinical findings suggested that the most important risk factors were the combined stage, age at diagnosis, BMI, surgical margins of the primary site, tumor size, sex, regional lymph nodes positive, grade/differentiation, primary site, and drinking behavior. Accordingly, these risk factors should be monitored for the early detection of second primary tumors in order to improve treatment and intervention strategies.

scholarly journals Machine Learning Classification of Inflammatory Bowel Disease in Children Based on a Large Real-World Pediatric Cohort CEDATA-GPGE® Registry

2021 ◽  
Vol 8 ◽  
Author(s):  
Nicolas Schneider ◽  
Keywan Sohrabi ◽  
Henning Schneider ◽  
Klaus-Peter Zimmer ◽  
Patrick Fischer ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Support Vector Machine ◽  
Convolutional Neural Network ◽  
Support Vector ◽  
Machine Learning Classification ◽  
Extreme Gradient Boosting ◽  
Inflammatory Bowel

Introduction: The rising incidence of pediatric inflammatory bowel diseases (PIBD) facilitates the need for new methods of improving diagnosis latency, quality of care and documentation. Machine learning models have shown to be applicable to classifying PIBD when using histological data or extensive serology. This study aims to evaluate the performance of algorithms based on promptly available data more suited to clinical applications.Methods: Data of inflammatory locations of the bowels from initial and follow-up visitations is extracted from the CEDATA-GPGE registry and two follow-up sets are split off containing only input from 2017 and 2018. Pre-processing excludes patients in remission and encodes the categorical data numerically. For classification of PIBD diagnosis, a support vector machine (SVM), a random forest algorithm (RF), extreme gradient boosting (XGBoost), a dense neural network (DNN) and a convolutional neural network (CNN) are employed. As best performer, a convolutional neural network is further improved using grid optimization.Results: The achieved accuracy of the optimized neural network reaches up to 90.57% on data inserted into the registry in 2018. Less performant methods reach 88.78% for the DNN down to 83.94% for the XGBoost. The accuracy of prediction for the 2018 follow-up dataset is higher than those for older datasets. Neural networks yield a higher standard deviation with 3.45 for the CNN compared to 0.83–0.86 of the support vector machine and ensemble methods.Discussion: The displayed accuracy of the convolutional neural network proofs the viability of machine learning classification in PIBD diagnostics using only timely available data.

scholarly journals Aerosol optical depth prediction using machine learning techniques

2021 ◽  
Author(s):  
Stavros Andreas Logothetis ◽  
Vasileios Salamalikis ◽  
Andreas Kazantzidis
Keyword(s):  
Machine Learning ◽  
Aerosol Optical Depth ◽  
Optical Depth ◽  
Multivariate Adaptive Regression Splines ◽  
Surface Radiation ◽  
Machine Learning Techniques ◽  
Gradient Boosting ◽  
Support Vector ◽  
Climate Projections ◽  
Extreme Gradient Boosting

<p>Aerosol optical depth (AOD) describes adequately aerosols’s burden and extinction within an atmospheric column. AOD can be retrieved using remote sensing instruments such as ground-based sun photometers. Despite the very good quality of ground based AOD measurements, their spatiotemporal coverage is restricted. In this study, an alternative approach of AOD estimation is proposed with the synergy of ground-based measurements and machine learning (ML) techniques, in order to expand and complement the existing spatiotemporal capabilities of AOD data. The ML algorithms which are implemented are: Random Forests, Gradient Boosting Machines, Extreme Gradient Boosting Machines, Support Vector Regression, K-nearest Neighbors Regression, and Multivariate Adaptive Regression Splines. Each model receives as input information the Global Horizontal Irradiance (GHI) as well as water vapor (WV) content in hourly basis and under clear skies. A randomized cross-validation search scheme is implemented to obtain the optimal hyperparameters and avoid overfitting for each ML algorithm. GHI and WV are retrieved from Baseline Surface Radiation Network (BSRN) and NASA’s Modern-Era Retrospective Analysis for Research and Applications-2 (MERRA-2) reanalysis product respectively. AOD estimations are evaluated against AOD from AErosol RObotic NETwork (AERONET) inversion product, using the Level 2.0 Version 3 (L2V3) which provides cloud-screened and quality assured measurements. In total, 29 collocated AERONET-BSRN stations are used spanning from 2000 to 2019. Since, the aerosol pattern is different at each site, the effect of various aerosol types is further investigated. ML-based AOD predictions are adequately good, highlighting the feasibility of ML algorithms on producing AOD data. The results of this study could be useful for direct normal irradiance estimations as well as aerosols radiative effect calculations and climate projections.</p>

scholarly journals Importance of GWAS risk loci and clinical data in predicting asthma using machine-learning approaches

2020 ◽  
Author(s):  
Si-Qiao Liang ◽  
Jian-Xiong Long ◽  
Jingmin Deng ◽  
Xuan Wei ◽  
Mei-Ling Yang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Risk Factors ◽  
Clinical Data ◽  
Genome Wide Association Study ◽  
Prediction Models ◽  
Area Under The Curve ◽  
Gradient Boosting ◽  
Support Vector ◽  
Learning Approaches ◽  
Extreme Gradient Boosting

Abstract Asthma is a serious immune-mediated respiratory airway disease. Its pathological processes involve genetics and the environment, but it remains unclear. To understand the risk factors of asthma, we combined genome-wide association study (GWAS) risk loci and clinical data in predicting asthma using machine-learning approaches. A case–control study with 123 asthma patients and 100 healthy controls was conducted in Zhuang population in Guangxi. GWAS risk loci were detected using polymerase chain reaction, and clinical data were collected. Machine-learning approaches (e.g., extreme gradient boosting [XGBoost], decision tree, support vector machine, and random forest algorithms) were used to identify the major factors that contributed to asthma. A total of 14 GWAS risk loci with clinical data were analyzed on the basis of 10 times of 10-fold cross-validation for all machine-learning models. Using GWAS risk loci or clinical data, the best performances were area under the curve (AUC) values of 64.3% and 71.4%, respectively. Combining GWAS risk loci and clinical data, the XGBoost established the best model with an AUC of 79.7%, indicating that the combination of genetics and clinical data can enable improved performance. We then sorted the importance of features and found that the top six risk factors for predicting asthma were rs3117098, rs7775228, family history, rs2305480, rs4833095, and body mass index. Asthma-prediction models based on GWAS risk loci and clinical data can accurately predict asthma and thus provide insights into the disease pathogenesis of asthma. Further research is required to evaluate more genetic markers and clinical data and predict asthma risk.

Machine Learning Approach for Predicting Lane-Change Maneuvers using the SHRP2 Naturalistic Driving Study Data

2021 ◽  
pp. 036119812110035
Author(s):  
Anik Das ◽  
Mohamed M. Ahmed
Keyword(s):  
Machine Learning ◽  
Prediction Accuracy ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Lane Change ◽  
Adaptive Boosting ◽  
Extreme Gradient Boosting ◽  
Naturalistic Driving Study ◽  
Naturalistic Driving ◽  
Change Prediction

Accurate lane-change prediction information in real time is essential to safely operate Autonomous Vehicles (AVs) on the roadways, especially at the early stage of AVs deployment, where there will be an interaction between AVs and human-driven vehicles. This study proposed reliable lane-change prediction models considering features from vehicle kinematics, machine vision, driver, and roadway geometric characteristics using the trajectory-level SHRP2 Naturalistic Driving Study and Roadway Information Database. Several machine learning algorithms were trained, validated, tested, and comparatively analyzed including, Classification And Regression Trees (CART), Random Forest (RF), eXtreme Gradient Boosting (XGBoost), Adaptive Boosting (AdaBoost), Support Vector Machine (SVM), K Nearest Neighbor (KNN), and Naïve Bayes (NB) based on six different sets of features. In each feature set, relevant features were extracted through a wrapper-based algorithm named Boruta. The results showed that the XGBoost model outperformed all other models in relation to its highest overall prediction accuracy (97%) and F1-score (95.5%) considering all features. However, the highest overall prediction accuracy of 97.3% and F1-score of 95.9% were observed in the XGBoost model based on vehicle kinematics features. Moreover, it was found that XGBoost was the only model that achieved a reliable and balanced prediction performance across all six feature sets. Furthermore, a simplified XGBoost model was developed for each feature set considering the practical implementation of the model. The proposed prediction model could help in trajectory planning for AVs and could be used to develop more reliable advanced driver assistance systems (ADAS) in a cooperative connected and automated vehicle environment.

scholarly journals Machine learning models to identify low adherence to influenza vaccination among Korean adults with cardiovascular disease

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Moojung Kim ◽  
Young Jae Kim ◽  
Sung Jin Park ◽  
Kwang Gi Kim ◽  
Pyung Chun Oh ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cardiovascular Disease ◽  
Influenza Vaccination ◽  
Machine Learning Techniques ◽  
Gradient Boosting ◽  
Support Vector ◽  
Age Group ◽  
Learning Models ◽  
Extreme Gradient Boosting ◽  
Machine Learning Models

Abstract Background Annual influenza vaccination is an important public health measure to prevent influenza infections and is strongly recommended for cardiovascular disease (CVD) patients, especially in the current coronavirus disease 2019 (COVID-19) pandemic. The aim of this study is to develop a machine learning model to identify Korean adult CVD patients with low adherence to influenza vaccination Methods Adults with CVD (n = 815) from a nationally representative dataset of the Fifth Korea National Health and Nutrition Examination Survey (KNHANES V) were analyzed. Among these adults, 500 (61.4%) had answered "yes" to whether they had received seasonal influenza vaccinations in the past 12 months. The classification process was performed using the logistic regression (LR), random forest (RF), support vector machine (SVM), and extreme gradient boosting (XGB) machine learning techniques. Because the Ministry of Health and Welfare in Korea offers free influenza immunization for the elderly, separate models were developed for the < 65 and ≥ 65 age groups. Results The accuracy of machine learning models using 16 variables as predictors of low influenza vaccination adherence was compared; for the ≥ 65 age group, XGB (84.7%) and RF (84.7%) have the best accuracies, followed by LR (82.7%) and SVM (77.6%). For the < 65 age group, SVM has the best accuracy (68.4%), followed by RF (64.9%), LR (63.2%), and XGB (61.4%). Conclusions The machine leaning models show comparable performance in classifying adult CVD patients with low adherence to influenza vaccination.

scholarly journals A Machine Learning Decision Support System (DSS) for Neuroendocrine Tumor Patients Treated with Somatostatin Analog (SSA) Therapy

Diagnostics ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 804
Author(s):  
Jasminka Hasic Telalovic ◽  
Serena Pillozzi ◽  
Rachele Fabbri ◽  
Alice Laffi ◽  
Daniele Lavacchi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Single Agent ◽  
Predictive Biomarkers ◽  
Progression Free Survival ◽  
Primary Site ◽  
Somatostatin Analog ◽  
Support Vector ◽  
Classification Models ◽  
First Line Therapy ◽  
Bayes Algorithm

The application of machine learning (ML) techniques could facilitate the identification of predictive biomarkers of somatostatin analog (SSA) efficacy in patients with neuroendocrine tumors (NETs). We collected data from 74 patients with a pancreatic or gastrointestinal NET who received SSA as first-line therapy. We developed three classification models to predict whether the patient would experience a progressive disease (PD) after 12 or 18 months based on clinic-pathological factors at the baseline. The dataset included 70 samples and 15 features. We initially developed three classification models with accuracy ranging from 55% to 70%. We then compared ten different ML algorithms. In all but one case, the performance of the Multinomial Naïve Bayes algorithm (80%) was the highest. The support vector machine classifier (SVC) had a higher performance for the recall metric of the progression-free outcome (97% vs. 94%). Overall, for the first time, we documented that the factors that mainly influenced progression-free survival (PFS) included age, the number of metastatic sites and the primary site. In addition, the following factors were also isolated as important: adverse events G3–G4, sex, Ki67, metastatic site (liver), functioning NET, the primary site and the stage. In patients with advanced NETs, ML provides a predictive model that could potentially be used to differentiate prognostic groups and to identify patients for whom SSA therapy as a single agent may not be sufficient to achieve a long-lasting PFS.

scholarly journals Comparison of Ensemble Machine Learning Methods for Soil Erosion Pin Measurements

2021 ◽  
Vol 10 (1) ◽  
pp. 42
Author(s):  
Kieu Anh Nguyen ◽  
Walter Chen ◽  
Bor-Shiun Lin ◽  
Uma Seeboonruang
Keyword(s):  
Machine Learning ◽  
Soil Erosion ◽  
Ensemble Methods ◽  
Machine Learning Algorithms ◽  
Multivariate Adaptive Regression Splines ◽  
Gradient Boosting ◽  
Support Vector ◽  
Ensemble Machine Learning ◽  
Boosting Method ◽  
Bagging Method

Although machine learning has been extensively used in various fields, it has only recently been applied to soil erosion pin modeling. To improve upon previous methods of quantifying soil erosion based on erosion pin measurements, this study explored the possible application of ensemble machine learning algorithms to the Shihmen Reservoir watershed in northern Taiwan. Three categories of ensemble methods were considered in this study: (a) Bagging, (b) boosting, and (c) stacking. The bagging method in this study refers to bagged multivariate adaptive regression splines (bagged MARS) and random forest (RF), and the boosting method includes Cubist and gradient boosting machine (GBM). Finally, the stacking method is an ensemble method that uses a meta-model to combine the predictions of base models. This study used RF and GBM as the meta-models, decision tree, linear regression, artificial neural network, and support vector machine as the base models. The dataset used in this study was sampled using stratified random sampling to achieve a 70/30 split for the training and test data, and the process was repeated three times. The performance of six ensemble methods in three categories was analyzed based on the average of three attempts. It was found that GBM performed the best among the ensemble models with the lowest root-mean-square error (RMSE = 1.72 mm/year), the highest Nash-Sutcliffe efficiency (NSE = 0.54), and the highest index of agreement (d = 0.81). This result was confirmed by the spatial comparison of the absolute differences (errors) between model predictions and observations using GBM and RF in the study area. In summary, the results show that as a group, the bagging method and the boosting method performed equally well, and the stacking method was third for the erosion pin dataset considered in this study.

Machine Learning and Network-Based Models to Identify Genetic Risk Factors to the Progression and Survival of Colorectal Cancer

2021 ◽  
pp. 104539
Author(s):  
Md. Jakir Hossain ◽  
Utpala Nanda Chowdhury ◽  
M. Babul Islam ◽  
Shahadat Uddin ◽  
Mohammad Boshir Ahmed ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Machine Learning ◽  
Risk Factors ◽  
Genetic Risk ◽  
Genetic Risk Factors

scholarly journals Prediction of Hanwoo Cattle Phenotypes from Genotypes Using Machine Learning Methods

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2066
Author(s):  
Swati Srivastava ◽  
Bryan Irvine Lopez ◽  
Himansu Kumar ◽  
Myoungjin Jang ◽  
Han-Ha Chai ◽  
...  
Keyword(s):  
Machine Learning ◽  
Support Vector ◽  
Learning Methods ◽  
Eye Muscle ◽  
Important Species ◽  
Machine Learning Methods ◽  
Extreme Gradient Boosting ◽  
Boosting Method ◽  
Predictive Correlation ◽  
Hanwoo Cattle

Hanwoo was originally raised for draft purposes, but the increase in local demand for red meat turned that purpose into full-scale meat-type cattle rearing; it is now considered one of the most economically important species and a vital food source for Koreans. The application of genomic selection in Hanwoo breeding programs in recent years was expected to lead to higher genetic progress. However, better statistical methods that can improve the genomic prediction accuracy are required. Hence, this study aimed to compare the predictive performance of three machine learning methods, namely, random forest (RF), extreme gradient boosting method (XGB), and support vector machine (SVM), when predicting the carcass weight (CWT), marbling score (MS), backfat thickness (BFT) and eye muscle area (EMA). Phenotypic and genotypic data (53,866 SNPs) from 7324 commercial Hanwoo cattle that were slaughtered at the age of around 30 months were used. The results showed that the boosting method XGB showed the highest predictive correlation for CWT and MS, followed by GBLUP, SVM, and RF. Meanwhile, the best predictive correlation for BFT and EMA was delivered by GBLUP, followed by SVM, RF, and XGB. Although XGB presented the highest predictive correlations for some traits, we did not find an advantage of XGB or any machine learning methods over GBLUP according to the mean squared error of prediction. Thus, we still recommend the use of GBLUP in the prediction of genomic breeding values for carcass traits in Hanwoo cattle.

scholarly journals Explainable machine learning can outperform Cox regression predictions and provide insights in breast cancer survival

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arturo Moncada-Torres ◽  
Marissa C. van Maaren ◽  
Mathijs P. Hendriks ◽  
Sabine Siesling ◽  
Gijs Geleijnse
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Explicit Knowledge ◽  
Cox Regression ◽  
Metastatic Breast ◽  
Gradient Boosting ◽  
Support Vector ◽  
Netherlands Cancer Registry ◽  
Extreme Gradient Boosting ◽  
The Impact

AbstractCox Proportional Hazards (CPH) analysis is the standard for survival analysis in oncology. Recently, several machine learning (ML) techniques have been adapted for this task. Although they have shown to yield results at least as good as classical methods, they are often disregarded because of their lack of transparency and little to no explainability, which are key for their adoption in clinical settings. In this paper, we used data from the Netherlands Cancer Registry of 36,658 non-metastatic breast cancer patients to compare the performance of CPH with ML techniques (Random Survival Forests, Survival Support Vector Machines, and Extreme Gradient Boosting [XGB]) in predicting survival using the $$c$$ c -index. We demonstrated that in our dataset, ML-based models can perform at least as good as the classical CPH regression ($$c$$ c -index $$\sim \,0.63$$ ∼ 0.63 ), and in the case of XGB even better ($$c$$ c -index $$\sim 0.73$$ ∼ 0.73 ). Furthermore, we used Shapley Additive Explanation (SHAP) values to explain the models’ predictions. We concluded that the difference in performance can be attributed to XGB’s ability to model nonlinearities and complex interactions. We also investigated the impact of specific features on the models’ predictions as well as their corresponding insights. Lastly, we showed that explainable ML can generate explicit knowledge of how models make their predictions, which is crucial in increasing the trust and adoption of innovative ML techniques in oncology and healthcare overall.

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