Colon Cancer Prediction from Gene Expression Profiles Using Kernel Based Support Vector Machine

Background Machine learning (ML) algorithm support vector machine (SVM) performed better than Thrombolysis in Myocardial Infarction (TIMI) score for ASIAN STEMI patients. However, Deep Learning (DL) effectiveness in the multiethnic ASIAN population has yet to be determined. DL has automatic learning of the feature from a given dataset without the need to conduct feature selection. However, the selected features by the algorithm is black box. Identifying features associated with mortality is essential to recognize characteristics of patients with high risk for better patient management. Purpose To develop a DL algorithm for in-hospital mortality in multiethnic STEMI patients using predictors identified from the SVM algorithm. To investigate DL performance constructed using predictors from SVM feature extraction and expert-recommended predictors. Methods We constructed four algorithms; a) DL and SVM algorithms with predictors identified from the SVM variable importance b) DL and SVM using predictors based on expert recommendation. We used registry data from the National Cardiovascular Disease Database of 11397 patient's. Fifty parameters including demographics, cardiovascular risk, medications and clinical variables were considered. The Area under the curve (AUC) is the performance evaluation metric. Algorithms were validated against the TIMI and tested using the same validation data. SVM variable importance with backward elimination was used to select and rank important variables. Results DL algorithms outperform SVM and TIMI on the validation dataset; i) DL with SVM selected predictors (15 predictors, AUC = 0.97), ii) DL with expert-recommended predictors (16 predictors, AUC = 0.96), iii) SVM with selected predictors (15 predictors, AUC = 0.92), iv) SVM with expert-recommended predictors (AUC = 0.89) and TIMI (AUC = 0.82). Common predictors across SVM feature selection, expert-recommendation and TIMI are: age, heart rate, Killip class, fasting blood glucose, systolic blood pressure, comorbid diseases and ST-elevation. SVM feature selection also identified diuretics, PCI and pharmacotherapy drugs as predictors that improve mortality prediction in STEMI patients. Our findings suggest that the TIMI score underestimates patients risk of mortality. DL algorithm using selected predictors classified 35% of nonsurvival patients as high risk (risk probabilities >50%) compared to only 12.7% nonsurvival patients by TIMI (score >5) (Figure below). Conclusions In the ASIAN population, patients with STEMI can be better classified using the DL algorithm compared to the ML and TIMI score. Combining ML feature selection with DL allows the identification of distinct factors in a unique ASIAN population for better mortality prediction than relying solely on an expert recommendation as it is a very subjective approach. Continuous validation on population-specific algorithms using DL and ML is needed before implementing in a real clinical setting. Funding Acknowledgement Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Technology Development Fund 1 TIMI performance on validation setDL performance on validation set

BackgroundMachine learning (ML) algorithm support vector machine (SVM) performed better than Thrombolysis in Myocardial Infarction (TIMI) score for ASIAN STEMI patients. However, Deep Learning (DL) effectiveness in the multiethnic ASIAN population has yet to be determined. DL has automatic learning of the feature from a given dataset without the need to conduct feature selection. However, the selected features by the algorithm is black box. Identifying features associated with mortality is essential to recognize characteristics of patients with high risk for better patient management.PurposeTo develop a DL algorithm for in-hospital mortality in multiethnic STEMI patients using predictors identified from the SVM algorithm. To investigate DL performance constructed using predictors from SVM feature extraction and expert-recommended predictors.MethodsWe constructed four algorithms; a) DL and SVM algorithms with predictors identified from the SVM variable importance b) DL and SVM using predictors based on expert recommendation. We used registry data from the National Cardiovascular Disease Database of 11397 patient's. Fifty parameters including demographics, cardiovascular risk, medications and clinical variables were considered. The Area under the curve (AUC) is the performance evaluation metric. Algorithms were validated against the TIMI and tested using the same validation data. SVM variable importance with backward elimination was used to select and rank important variables.ResultsDL algorithms outperform SVM and TIMI on the validation dataset; i) DL with SVM selected predictors (15 predictors, AUC = 0.97), ii) DL with expert-recommended predictors (16 predictors, AUC = 0.96), iii) SVM with selected predictors (15 predictors, AUC = 0.92), iv) SVM with expert-recommended predictors (AUC = 0.89) and TIMI (AUC = 0.82). Common predictors across SVM feature selection, expert-recommendation and TIMI are: age, heart rate, Killip class, fasting blood glucose, systolic blood pressure, comorbid diseases and ST-elevation. SVM feature selection also identified diuretics, PCI and pharmacotherapy drugs as predictors that improve mortality prediction in STEMI patients. Our findings suggest that the TIMI score underestimates patients risk of mortality. DL algorithm using selected predictors classified 35% of nonsurvival patients as high risk (risk probabilities >50%) compared to only 12.7% nonsurvival patients by TIMI (score >5) (Figure below).ConclusionsIn the ASIAN population, patients with STEMI can be better classified using the DL algorithm compared to the ML and TIMI score. Combining ML feature selection with DL allows the identification of distinct factors in a unique ASIAN population for better mortality prediction than relying solely on an expert recommendation as it is a very subjective approach. Continuous validation on population-specific algorithms using DL and ML is needed before implementing in a real clinical setting.Funding AcknowledgementType of funding sources: Public grant(s) – National budget only. Main funding source(s): Technology Development Fund 1TIMI performance on validation setDL performance on validation set

This paper aims to develop a new idea for the classification of power quality disturbances. The method is based on Stockwell’s-Transform (ST) and Type-2 Fuzzy Kernel Support Vector Machine (T2FK-SVM). Through the introduction of ST and its properties, we propose a classification plan for nine types of power quality disturbances. Firstly, features of disturbance signals extracted through the ST. Secondly, features extracted by using the ST are applied as input to T2FK-SVM classifier for automatic classification of the power quality (PQ) disturbances. Design of Kernel is a main part of many kernel based methods such as Support Vector Machine (SVM), so by using of Type-2 Fuzzy sets as a kernel of SVM, the total accuracy of classification enhanced.This method can reduce the features of the disturbance signals significantly, and so less time and memory is required for classification by the T2FK-SVM method. Six single event and two complex event as well normal voltage selected as reference are considered for the classification. The simulation results showed accurate classification, fast learning and execution in the detection and classification of PQ events. Results are compared with other methods and the robustness of proposed method evaluated under noisy conditions. Finally, proposed method is also implemented on real time PQ disturbances to confirm the validity of this method in practical conditions.

Machine learning-based receiver operating characteristic (ROC) curves for crisp and fuzzy classification of DNA microarrays in cancer research

This study deals with the linear, polynomial, and radial basis function (RBF) kernel-based support vector machines (SVM) applied to the classification of breast cancer. It checks the efficiency of different kernel-based techniques for distinguishing benign and malignant tumors against medical datasets. This analysis is conducted on the public Wisconsin Breast Cancer Dataset borrowed from the UCI Machine Learning Repository, which consists of 569 cases, 357 benign and 212 malignant. It aims to develop the assessment necessary for each Kernel based on its accuracy, precision, recall, computational efficiency, F1 score, and area under the curve (AUC). The outcome reveals that, in general, the polynomial Kernel will provide top-ranking results across the various features, thereby enhancing accuracy (96.84%), specificity (97.76%), and AUC (0.9966) compared to the linear and RBF kernels for use in disease classifications of cancers. These findings indicate that the polynomial kernel adeptly captures complex, non-linear data relationships, making it a strong candidate for developing more accurate SVM-based breast cancer detection models.

This study employs a dataset acquired from an Algorithm Introductory Class at a Brazilian university, where students were evaluated on "21st Century Skills" and engaged in an online environment allowing social interactions via postings and comments. Extensively generating pertinent inferences from this heterogeneous dataset—which consists of qualitative reactions to student postings as well as quantitative skill assessments—is challenging. Particularly in an interactive, online learning setting, conventional grading methods might not fairly represent a student's aptitudes range. Therefore, a good model is required to investigate these complex interactions and project student development. makes advantage of a Deep SVM architecture by combining Residual Deep Belief Networks (DBNs) for feature extraction with Kernel-based Support Vector Machines (KSVM) for classification. This work provides a novel approach combining Residual Deep Belief Network (DBN) for feature extraction with Kernel Support Vector Machine (KSVM) for classification. Application of residual DBN for feature extraction offers a complete mechanism to control and assess the high-dimensional data generated by grading assessments and online activity of students. The study combines many data sources—online interactions and traditional grades—into a logical framework. For the training dataset, the proposed KSVM achieves an accuracy of 91.4%, which is higher than e-LION (85.3%), OLAP-DGCNN (88.7%), SEt-VDCNN (90.2%), and BR2-2 T-MICE (84.9%).

Feature selection is referred to the process of obtaining a subset from an original feature set according to certain feature selection criterion, which selects the relevant features of the dataset. It plays a role in compressing the data processing scale, where the redundant and irrelevant features are removed. Feature selection techniques show that more information is not always good in machine learning applications. Apply different algorithms for the data at hand and with baseline classification performance values we can select a final feature selection algorithm. In this paper, we propose a hybrid classification model, which has correlation based filter feature selection algorithm and Machine learning as classifiers. The objective of this study is to select relevant features and analyze the outperform machine learning algorithms in order to train our model, predict and compare their classification performance. In this method, features are ordered according to their Absolute correlation value with respect to the class attribute. Then top K Features are selected from ordered list of features to form a reduced dataset. This proposed classifier model is applied to our smart meter datasets. To measure the performance of these selected features; seven benchmark classifier are used; Random Forest (RF), Logistic Regression (LR), k-Nearest Neighbor (kNN), Naive Bayes (NB), Decision Tree (DT), Linear Discriminant Analysis (LDA) and Support Vector Machine (SVM). This paper then analyzes the performance of all classifiers with feature selection in term of accuracy, sensitivity, F-Measure, Specificity, Precision, and MCC. From our experiment, we found that Random Forest classifier performed higher than other used classifiers.

Credit risk analysis forms an important criterion for the endurance of the banking sector. Understanding credit liability of customer enhances the security stability of the banker. This research is aimed at comparing the predictive accuracy of data mining techniques with feature selection and extraction techniques in the default of credit card clients and suggesting the most efficient technique for analyzing credit card default. Customer's default payments in Taiwan were used as the dataset. Machine Learning classification algorithms like K-nearest neighbor(KNN), Naive Bayesian(NB), Decision Tree(DT) and Support Vector Machines(SVM) were applied to the dataset. Feature filter methods like information gain (IG), gain ratio (GR) and chi-square (CS) and Wrapper based methods like Best First search(BFS) and Hill Climbing search (HCS) were used to identify minimum features required. Feature extraction methods such as Principal Component Analysis(PCA) and Linear Discriminant Anal-ysis(LDA) were also applied. The minimum features of feature selection algorithms along with PCA and LDA were then applied to Base classifiers and their accuracies were tabulated and compared. SVM with feature selection and extraction techniques had the best predictive accuracy.

Heart disease is still one of the top causes of death globally, demanding early and effective prediction tools. Traditional predictive models frequently have limitations because they rely on single‐source statistics, which may not represent the entire scenario of a patient's complex health profile. Feature selection is an essential preprocessing step in machine learning that improves model efficiency by eliminating irrelevant or redundant features. This study evaluates the impact of feature selection on six classification modelsNaïve Bayes, Logistic Regression, Decision Tree, K‐Nearest Neighbors (KNN), Support Vector Machine (SVM), and Random Forestacross four datasets. Performance was assessed using accuracy, precision, recall, F1‐score, and area under the curve (AUC) before and after feature selection. The results indicate that feature selection had varying effects across different models and datasets. In Dataset‐01, Random Forest maintained its strong performance (98.70% accuracy) even after feature selection, while SVM and KNN saw noticeable drops, with accuracy decreasing from 88.96% to 79.87% and 87.01% to 81.17% respectively. For Dataset‐02, SVM showed improvement, increasing from 80.00% to 85.00%, while Naïve Bayes and KNN also improved, reaching 82.50% and 82.50% accuracy, respectively. In Dataset‐03, Logistic Regression and KNN experienced declines, with accuracy dropping from 88.76% to 83.71% and 91.57% to 87.08%, respectively, while Random Forest fell from 97.75% to 91.57%. Dataset‐04 showed mixed results, with Logistic Regression improving from 86.67% to 91.11%, but KNN and Random Forest dropping from 97.78% to 84.44% and 91.11% to 82.22%, respectively. These findings suggest that while feature selection enhances performance for some models, it can negatively impact others, particularly those reliant on a larger feature set. Future research should explore adaptive feature selection techniques to optimize model performance across diverse datasets.

Undernutrition among children under the age of five is a major public health concern, especially in developing countries. This study aimed to use machine learning (ML) algorithms to predict undernutrition and identify its associated factors. Secondary data analysis of the 2017 Multiple Indicator Cluster Survey (MICS) was performed using R and Python. The main outcomes of interest were undernutrition (stunting: height-for-age (HAZ) < -2 SD; wasting: weight-for-height (WHZ) < -2 SD; and underweight: weight-for-age (WAZ) < -2 SD). Seven ML algorithms were trained and tested: linear discriminant analysis (LDA), logistic model, support vector machine (SVM), random forest (RF), least absolute shrinkage and selection operator (LASSO), ridge regression, and extreme gradient boosting (XGBoost). The ML models were evaluated using the accuracy, confusion matrix, and area under the curve (AUC) receiver operating characteristics (ROC). In total, 8564 children were included in the final analysis. The average age of the children was 926 days, and the majority were females. The weighted prevalence rates of stunting, wasting, and underweight were 17%, 7%, and 12%, respectively. The accuracies of all the ML models for wasting were (LDA: 84%; Logistic: 95%; SVM: 92%; RF: 94%; LASSO: 96%; Ridge: 84%, XGBoost: 98%), stunting (LDA: 86%; Logistic: 86%; SVM: 98%; RF: 88%; LASSO: 86%; Ridge: 86%, XGBoost: 98%), and for underweight were (LDA: 90%; Logistic: 92%; SVM: 98%; RF: 89%; LASSO: 92%; Ridge: 88%, XGBoost: 98%). The AUC values of the wasting models were (LDA: 99%; Logistic: 100%; SVM: 72%; RF: 94%; LASSO: 99%; Ridge: 59%, XGBoost: 100%), for stunting were (LDA: 89%; Logistic: 90%; SVM: 100%; RF: 92%; LASSO: 90%; Ridge: 89%, XGBoost: 100%), and for underweight were (LDA: 95%; Logistic: 96%; SVM: 100%; RF: 94%; LASSO: 96%; Ridge: 82%, XGBoost: 82%). Age, weight, length/height, sex, region of residence and ethnicity were important predictors of wasting, stunting and underweight. The XGBoost model was the best model for predicting wasting, stunting, and underweight. The findings showed that different ML algorithms could be useful for predicting undernutrition and identifying important predictors for targeted interventions among children under five years in Ghana.

PurposeNoninvasive, accurate and novel approaches to predict patients who will achieve pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) could assist treatment strategies. The aim of this study was to explore the application of machine learning (ML) based peritumoral ultrasound radiomics signature (PURS), compared with intratumoral radiomics (IURS) and clinicopathologic factors, for early prediction of pCR.MethodsWe analyzed 358 locally advanced breast cancer patients (250 in the training set and 108 in the test set), who accepted NAC and post NAC surgery at our institution. The clinical and pathological data were analyzed using the independent t test and the Chi-square test to determine the factors associated with pCR. The PURS and IURS of baseline breast tumors were extracted by using 3D-slicer and PyRadiomics software. Five ML classifiers including linear discriminant analysis (LDA), support vector machine (SVM), random forest (RF), logistic regression (LR), and adaptive boosting (AdaBoost) were applied to construct radiomics predictive models. The performance of PURS, IURS models and clinicopathologic predictors were assessed with respect to sensitivity, specificity, accuracy and the areas under the curve (AUCs).ResultsNinety-seven patients achieved pCR. The clinicopathologic predictors obtained an AUC of 0.759. Among PURS models, the RF classifier achieved better efficacy (AUC of 0.889) than LR (0.849), AdaBoost (0.823), SVM (0.746) and LDA (0.732). The RF classifier also obtained a maximum AUC of 0.931 than 0.920 (AdaBoost), 0.875 (LR), 0.825 (SVM), and 0.798 (LDA) in IURS models in the test set. The RF based PURS yielded higher predictive ability (AUC 0.889; 95% CI 0.814, 0.947) than clinicopathologic factors (AUC 0.759; 95% CI 0.657, 0.861; p < 0.05), but lower efficacy compared with IURS (AUC 0.931; 95% CI 0.865, 0.980; p < 0.05).ConclusionThe peritumoral US radiomics, as a novel potential biomarker, can assist clinical therapy decisions.

Objective: Using methylation characteristics of human genes to construct machine learning predictive models for screening cervical cancer and precancerous lesions. Methods: Human DNA methylation detection was performed on 224 cervical exfoliated cell specimens from the Cancer Hospital of the Chinese Academy of Medical Sciences, Tianjin Central Hospital of Gynecology Obstetrics, Xinmi Maternal and Child Health Hospital of Henan Province, West China Second Affiliated Hospital of Sichuan University, and Heping Hospital Affiliated to Changzhi Medical College collected during April 2014 and March 2015. The hypermethylated gene fragments related to cervical cancer were selected by high-density, high-association, and hypermethylated gene fragment screening and the LASSO regression algorithm. Taking cervical intraepithelial neoplasia grade 2 (CIN2) or more severe lesions as the research outcome, machine learning predictive models based on the random forest (RF), naive Bayes (NB), and support vector machine (SVM) algorithm, respectively, were constructed. A total of 144 outpatient specimens were used as the training set and 80 cervical exfoliated cell specimens from women participating in the cervical cancer screening program were used as the test set to verify the predictive models. Using histological diagnosis results as the gold standard, the detection efficacy for CIN2 or more severe lesions of the three machine learning predictive models were compared with that of the human papilloma virus (HPV) detection and cytological diagnosis. Results: In the training set of 144 cases, there were 34 cases of HPV positivity, with a positive rate of 23.61%. Cytologically, there were 37 cases diagnosed as no intraepithelial lesion or malignancy (NILM), and 107 cases diagnosed as atypical squamous cells of undetermined significance (ASC-US) or above. Histologically, there were 28 cases without cervical intraepithelial neoplasia or benign cervical lesions, 31 cases of CIN1, 18 cases of CIN2, 31 cases of CIN3, and 36 cases of squamous cell carcinoma. Seven hypermethylated gene fragments were selected from 45 genes, and three machine learning prediction models based on the RF, NB, and SVM algorithm, respectively, were constructed. In the validation set of 80 cases, there were 28 cases of HPV positivity, with a positive rate of 35.00%. Cytologically, there were 65 cases diagnosed as NILM and 15 cases as ASC-US or above. Histologically, there were 39 cases without cervical intraepithelial neoplasia or benign cervical lesions, 10 cases of CIN1, 10 cases of CIN2, 11 cases of CIN3, and 10 cases of squamous cell carcinoma. In the validation set, the area under the curve (AUC) values of the RF model, NB model, SVM model, HPV detection, and cytological diagnosis of CIN2 or above were 0.90, 0.88, 0.82, 0.68, and 0.45, respectively. The DeLong test showed that there was no statistically significant difference in the AUC values between the RF, NB, and SVM models (all P＞0.05), and the AUC values of the RF and NB models were higher than that of HPV detection (both P＜0.01), and the AUC values of the RF, NB, and SVM models were higher than that of cytological diagnosis (all P＜0.01). Compared with the NB model, the sensitivity of the RF model was similar (80.65% vs. 77.42%), but the specificity of the NB model was much higher than that of the RF model (93.88% vs. 73.47%). Conclusion: Among the machine learning prediction models for cervical cancer and precancerous lesions constructed based on human DNA methylation, the NB model has good predictive performance for CIN2 and above lesions, and may be used for screening of cervical cancer and precancerous lesions.

The right and left-hand motor imagery (MI) analysis based on the electroencephalogram (EEG) signal can directly link the central nervous system to a computer or a device. This study aims to identify a set of robust and nonlinear effective brain connectivity features quantified by transfer entropy (TE) to characterize the relationship between brain regions from EEG signals and create a hierarchical feature selection and classification for discrimination of right and lefthand MI tasks. TE is calculated among EEG channels as the distinctive, effective connectivity features. TE is a model-free method that can measure nonlinear effective connectivity and analyze multivariate dependent directed information flow among neural EEG channels. Then four feature subset selection methods namely relief-F, Fisher, Laplacian, and local learningbased clustering (LLCFS) algorithms are used to choose the most significant effective connectivity features and reduce redundant information. Finally, support vector machine (SVM) and linear discriminant analysis (LDA) methods are used for classification. Results show that the best performance in 29 healthy subjects and 60 trials is achieved using the TE method via the Relief-F algorithm as feature selection and support vector machine (SVM) classification with 91.02% accuracy. The TE index and a hierarchical feature selection and classification can be useful for the discrimination of right- and left-hand MI tasks from multichannel EEG signals. Effective connectivity features were extracted from electroencephalogram (EEG) to analyze relationships between regions.Four feature selection methods used to select most significant effective features.Support vector machine (SVM) used for discrimination of right and left hand motor imagery (MI) task. In this study, we investigated brain activity using effective connectivity during MI task based on EEG signals. The motor imagery task can accomplish the same goal as motor execution, since they are both activated by the same brain area. Transfer entropy, coherence, and Granger casualty were employed to extract the features. Differential patterns of activity between the left vs. right MI task showed activity around the motor area rather than other areas. In order to reduce redundant information and select the most significant effective connectivity features, four feature subset selection algorithms are used: Relief-F, Fisher, Laplacian, and learning-based clustering feature selection (LLCFS). Then, support vector machine (SVM) and linear discriminant analysis (LDA) are used to classify left and right hand MI task. Comparison of three different connectivity methods showed that TE index had the highest classification accuracy, and could be useful for the discrimination of right and left hand MI tasks from multichannel EEG signals.

This paper discusses a flaw detection system that uses automated long range ultrasonic detectors modeled on a successful pattern recognition method. The procedure has three stages: 1. a variety of feature extraction methods to better represent the signals; 2. feature ranking based on feature selection; and 3. classification using a kernel-based support vector machine (SVM). The results of analysis indicate that the proposed algorithm is successful at detecting flaws.

Identification of voice disorders has been a vital role in our life nowadays. Acoustic analysis can be useful tool to diagnose voice disorders as a complementary technique to other medicine methods such as Laryngoscopy and Stroboscopy. In this paper, we scrutinized feature reduction techniques such as principal component analysis (PCA) and linear discriminant analysis (LDA) as feature subset extraction methods and individual feature selection (IFS), forward feature selection (FFS), backward feature selection (BFS) and branch and bound feature selection (BBFS) as feature subset selection procedures. Performance of each method is evaluated by different classifiers. Between feature selection methods, individual feature selection followed by SVM classifier shows the best recognition rate of 91.55% and AUC of 95.80% among these methods. The experimental results demonstrated that highest performance could be achieved by recognition rate of 94.26% and AUC of 97.94% using linear discriminant analysis along with support vector machine as a classifier. Also this mixture has lowest order of computational complexity in comparison with other architectures.