Predicting 30-Day Mortality after an Acute Coronary Syndrome (ACS) using Machine Learning Methods for Feature Selection, Classification and Visualisation

Hybrid combinations of feature selection, classification and visualisation using machine learning (ML) methods have the potential for enhanced understanding and 30-day mortality prediction of patients with cardiovascular disease using population-specific data. Identifying a feature selection method with a classifier algorithm that produces high performance in mortality studies is essential and has not been reported before. Feature selection methods such as Boruta, Random Forest (RF), Elastic Net (EN), Recursive Feature Elimination (RFE), learning vector quantization (LVQ), Genetic Algorithm (GA), Cluster Dendrogram (CD), Support Vector Machine (SVM) and Logistic Regression (LR) were combined with RF, SVM, LR, and EN classifiers for 30-day mortality prediction. ML models were constructed using 302 patients and 54 input variables from the Malaysian National Cardiovascular Disease Database. Validation of the best ML model was performed against Thrombolysis in Myocardial Infarction (TIMI) using an additional dataset of 102 patients. The Self-Organising Feature Map (SOM) was used to visualise mortality-related factors post-ACS. The performance of MLmodels using the area under the curve (AUC) ranged from 0.48 to 0.80. The best-performing model (AUC = 0.80) was a hybrid combination of the RF variable importance method, the sequential backward selection and the RF classifier using five predictors (age, triglyceride, creatinine, troponin, and total cholesterol). Comparison with TIMI using an additional dataset resulted in the best ML model outperforming the TIMI score (AUC = 0.75 vs. AUC = 0.60). The findings of this study will provide a basis for developing an online ML-based population-specific risk scoring calculator.

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A Hybrid Approach for Feature Selection Based on Genetic Algorithm and Recursive Feature Elimination

International Journal of Information System Modeling and Design ◽

10.4018/ijismd.2021040102 ◽

2021 ◽

Vol 12 (2) ◽

pp. 17-38

Author(s):

Pooja Rani ◽

Rajneesh Kumar ◽

Anurag Jain ◽

Sunil Kumar Chawla

Keyword(s):

Machine Learning ◽

Genetic Algorithm ◽

Feature Selection ◽

Hybrid Approach ◽

Feature Selection Method ◽

Classification Systems ◽

Recursive Feature Elimination ◽

Support Vector ◽

Sensitivity Specificity ◽

Selection Of

Machine learning has become an integral part of our life in today's world. Machine learning when applied to real-world applications suffers from the problem of high dimensional data. Data can have unnecessary and redundant features. These unnecessary features affect the performance of classification systems used in prediction. Selection of important features is the first step in developing any decision support system. In this paper, the authors have proposed a hybrid feature selection method GARFE by integrating GA (genetic algorithm) and RFE (recursive feature elimination) algorithms. Efficiency of proposed method is analyzed using support vector machine classifier on the scale of accuracy, sensitivity, specificity, precision, F-measure, and execution time parameters. Proposed GARFE method is also compared to eight other feature selection methods. Results demonstrate that the proposed GARFE method has increased the performance of classification systems by removing irrelevant and redundant features.

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Use of Machine Learning to Investigate the Quantitative Checklist for Autism in Toddlers (Q-CHAT) towards Early Autism Screening

Diagnostics ◽

10.3390/diagnostics11030574 ◽

2021 ◽

Vol 11 (3) ◽

pp. 574

Author(s):

Gennaro Tartarisco ◽

Giovanni Cicceri ◽

Davide Di Pietro ◽

Elisa Leonardi ◽

Stefania Aiello ◽

...

Keyword(s):

Machine Learning ◽

High Performance ◽

Behavioral Science ◽

Autistic Traits ◽

Classification Performance ◽

Recursive Feature Elimination ◽

Diagnostic Tools ◽

Support Vector ◽

K Nearest Neighbors ◽

Autism Screening

In the past two decades, several screening instruments were developed to detect toddlers who may be autistic both in clinical and unselected samples. Among others, the Quantitative CHecklist for Autism in Toddlers (Q-CHAT) is a quantitative and normally distributed measure of autistic traits that demonstrates good psychometric properties in different settings and cultures. Recently, machine learning (ML) has been applied to behavioral science to improve the classification performance of autism screening and diagnostic tools, but mainly in children, adolescents, and adults. In this study, we used ML to investigate the accuracy and reliability of the Q-CHAT in discriminating young autistic children from those without. Five different ML algorithms (random forest (RF), naïve Bayes (NB), support vector machine (SVM), logistic regression (LR), and K-nearest neighbors (KNN)) were applied to investigate the complete set of Q-CHAT items. Our results showed that ML achieved an overall accuracy of 90%, and the SVM was the most effective, being able to classify autism with 95% accuracy. Furthermore, using the SVM–recursive feature elimination (RFE) approach, we selected a subset of 14 items ensuring 91% accuracy, while 83% accuracy was obtained from the 3 best discriminating items in common to ours and the previously reported Q-CHAT-10. This evidence confirms the high performance and cross-cultural validity of the Q-CHAT, and supports the application of ML to create shorter and faster versions of the instrument, maintaining high classification accuracy, to be used as a quick, easy, and high-performance tool in primary-care settings.

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Radiogenomic modeling predicts survival-associated prognostic groups in glioblastoma

Neuro-Oncology Advances ◽

10.1093/noajnl/vdab004 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Nicholas Nuechterlein ◽

Beibin Li ◽

Abdullah Feroze ◽

Eric C Holland ◽

Linda Shapiro ◽

...

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Molecular Subtypes ◽

Feature Selection Method ◽

Area Under The Curve ◽

Selection Method ◽

Recursive Feature Elimination ◽

Signal Abnormality ◽

Mri Features ◽

Mri Scans

Abstract Background Combined whole-exome sequencing (WES) and somatic copy number alteration (SCNA) information can separate isocitrate dehydrogenase (IDH)1/2-wildtype glioblastoma into two prognostic molecular subtypes, which cannot be distinguished by epigenetic or clinical features. The potential for radiographic features to discriminate between these molecular subtypes has yet to be established. Methods Radiologic features (n = 35 340) were extracted from 46 multisequence, pre-operative magnetic resonance imaging (MRI) scans of IDH1/2-wildtype glioblastoma patients from The Cancer Imaging Archive (TCIA), all of whom have corresponding WES/SCNA data. We developed a novel feature selection method that leverages the structure of extracted MRI features to mitigate the dimensionality challenge posed by the disparity between a large number of features and the limited patients in our cohort. Six traditional machine learning classifiers were trained to distinguish molecular subtypes using our feature selection method, which was compared to least absolute shrinkage and selection operator (LASSO) feature selection, recursive feature elimination, and variance thresholding. Results We were able to classify glioblastomas into two prognostic subgroups with a cross-validated area under the curve score of 0.80 (±0.03) using ridge logistic regression on the 15-dimensional principle component analysis (PCA) embedding of the features selected by our novel feature selection method. An interrogation of the selected features suggested that features describing contours in the T2 signal abnormality region on the T2-weighted fluid-attenuated inversion recovery (FLAIR) MRI sequence may best distinguish these two groups from one another. Conclusions We successfully trained a machine learning model that allows for relevant targeted feature extraction from standard MRI to accurately predict molecularly-defined risk-stratifying IDH1/2-wildtype glioblastoma patient groups.

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A Machine Learning Approach to EEG-based Prediction of Human Affective States Using Recursive Feature Elimination Method

MATEC Web of Conferences ◽

10.1051/matecconf/202133504001 ◽

2021 ◽

Vol 335 ◽

pp. 04001

Author(s):

Didar Dadebayev ◽

Goh Wei Wei ◽

Tan Ee Xion

Keyword(s):

Feature Selection ◽

Fractal Dimension ◽

Emotion Recognition ◽

Affective Computing ◽

Feature Selection Method ◽

Recursive Feature Elimination ◽

Support Vector ◽

Emotional States ◽

Affective States ◽

Emotion Classification

Emotion recognition, as a branch of affective computing, has attracted great attention in the last decades as it can enable more natural brain-computer interface systems. Electroencephalography (EEG) has proven to be an effective modality for emotion recognition, with which user affective states can be tracked and recorded, especially for primitive emotional events such as arousal and valence. Although brain signals have been shown to correlate with emotional states, the effectiveness of proposed models is somewhat limited. The challenge is improving accuracy, while appropriate extraction of valuable features might be a key to success. This study proposes a framework based on incorporating fractal dimension features and recursive feature elimination approach to enhance the accuracy of EEG-based emotion recognition. The fractal dimension and spectrum-based features to be extracted and used for more accurate emotional state recognition. Recursive Feature Elimination will be used as a feature selection method, whereas the classification of emotions will be performed by the Support Vector Machine (SVM) algorithm. The proposed framework will be tested with a widely used public database, and results are expected to demonstrate higher accuracy and robustness compared to other studies. The contributions of this study are primarily about the improvement of the EEG-based emotion classification accuracy. There is a potential restriction of how generic the results can be as different EEG dataset might yield different results for the same framework. Therefore, experimenting with different EEG dataset and testing alternative feature selection schemes can be very interesting for future work.

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Diagnostic Performance of 2D and 3D T2WI-Based Radiomics Features With Machine Learning Algorithms to Distinguish Solid Solitary Pulmonary Lesion

Frontiers in Oncology ◽

10.3389/fonc.2021.683587 ◽

2021 ◽

Vol 11 ◽

Author(s):

Qi Wan ◽

Jiaxuan Zhou ◽

Xiaoying Xia ◽

Jianfeng Hu ◽

Peng Wang ◽

...

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Diagnostic Performance ◽

Feature Selection Method ◽

Machine Learning Algorithms ◽

Support Vector ◽

Learning Approaches ◽

Selection Methods ◽

Linear Discriminant ◽

2D And 3D

ObjectiveTo evaluate the performance of 2D and 3D radiomics features with different machine learning approaches to classify SPLs based on magnetic resonance(MR) T2 weighted imaging (T2WI).Material and MethodsA total of 132 patients with pathologically confirmed SPLs were examined and randomly divided into training (n = 92) and test datasets (n = 40). A total of 1692 3D and 1231 2D radiomics features per patient were extracted. Both radiomics features and clinical data were evaluated. A total of 1260 classification models, comprising 3 normalization methods, 2 dimension reduction algorithms, 3 feature selection methods, and 10 classifiers with 7 different feature numbers (confined to 3–9), were compared. The ten-fold cross-validation on the training dataset was applied to choose the candidate final model. The area under the receiver operating characteristic curve (AUC), precision-recall plot, and Matthews Correlation Coefficient were used to evaluate the performance of machine learning approaches.ResultsThe 3D features were significantly superior to 2D features, showing much more machine learning combinations with AUC greater than 0.7 in both validation and test groups (129 vs. 11). The feature selection method Analysis of Variance(ANOVA), Recursive Feature Elimination(RFE) and the classifier Logistic Regression(LR), Linear Discriminant Analysis(LDA), Support Vector Machine(SVM), Gaussian Process(GP) had relatively better performance. The best performance of 3D radiomics features in the test dataset (AUC = 0.824, AUC-PR = 0.927, MCC = 0.514) was higher than that of 2D features (AUC = 0.740, AUC-PR = 0.846, MCC = 0.404). The joint 3D and 2D features (AUC=0.813, AUC-PR = 0.926, MCC = 0.563) showed similar results as 3D features. Incorporating clinical features with 3D and 2D radiomics features slightly improved the AUC to 0.836 (AUC-PR = 0.918, MCC = 0.620) and 0.780 (AUC-PR = 0.900, MCC = 0.574), respectively.ConclusionsAfter algorithm optimization, 2D feature-based radiomics models yield favorable results in differentiating malignant and benign SPLs, but 3D features are still preferred because of the availability of more machine learning algorithmic combinations with better performance. Feature selection methods ANOVA and RFE, and classifier LR, LDA, SVM and GP are more likely to demonstrate better diagnostic performance for 3D features in the current study.

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Machine Learning-Enriched Lamb Wave Approaches for Automated Damage Detection

Sensors ◽

10.3390/s20061790 ◽

2020 ◽

Vol 20 (6) ◽

pp. 1790

Author(s):

Zi Zhang ◽

Hong Pan ◽

Xingyu Wang ◽

Zhibin Lin

Keyword(s):

Machine Learning ◽

Feature Extraction ◽

Feature Selection ◽

Damage Detection ◽

Lamb Wave ◽

Lamb Waves ◽

Feature Selection Method ◽

Support Vector ◽

Time Frequency ◽

Damage States

Lamb wave approaches have been accepted as efficiently non-destructive evaluations in structural health monitoring for identifying damage in different states. Despite significant efforts in signal process of Lamb waves, physics-based prediction is still a big challenge due to complexity nature of the Lamb wave when it propagates, scatters and disperses. Machine learning in recent years has created transformative opportunities for accelerating knowledge discovery and accurately disseminating information where conventional Lamb wave approaches cannot work. Therefore, the learning framework was proposed with a workflow from dataset generation, to sensitive feature extraction, to prediction model for lamb-wave-based damage detection. A total of 17 damage states in terms of different damage type, sizes and orientations were designed to train the feature extraction and sensitive feature selection. A machine learning method, support vector machine (SVM), was employed for the learning model. A grid searching (GS) technique was adopted to optimize the parameters of the SVM model. The results show that the machine learning-enriched Lamb wave-based damage detection method is an efficient and accuracy wave to identify the damage severity and orientation. Results demonstrated that different features generated from different domains had certain levels of sensitivity to damage, while the feature selection method revealed that time-frequency features and wavelet coefficients exhibited the highest damage-sensitivity. These features were also much more robust to noise. With increase of noise, the accuracy of the classification dramatically dropped.

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Implementasi teknik seleksi fitur pada klasifikasi malware Android menggunakan support vector machine (SVM)

Repositor ◽

10.22219/repositor.v1i1.1 ◽

2019 ◽

Vol 1 (1) ◽

pp. 1

Author(s):

Hendra Saputra ◽

Setio Basuki ◽

Mahar Faiqurahman

Keyword(s):

Machine Learning ◽

Support Vector Machine ◽

Feature Selection ◽

Feature Selection Method ◽

Selection Method ◽

Support Vector ◽

Chi Square ◽

Android Malware ◽

Correlation Based Feature Selection ◽

Selection Of

AbstrakPertumbuhan Malware Android telah meningkat secara signifikan seiring dengan majunya jaman dan meninggkatnya keragaman teknik dalam pengembangan Android. Teknik Machine Learning adalah metode yang saat ini bisa kita gunakan dalam memodelkan pola fitur statis dan dinamis dari Malware Android. Dalam tingkat keakurasian dari klasifikasi jenis Malware peneliti menghubungkan antara fitur aplikasi dengan fitur yang dibutuhkan dari setiap jenis kategori Malware. Kategori jenis Malware yang digunakan merupakan jenis Malware yang banyak beredar saat ini. Untuk mengklasifikasi jenis Malware pada penelitian ini digunakan Support Vector Machine (SVM). Jenis SVM yang akan digunakan adalah class SVM one against one menggunakan Kernel RBF. Fitur yang akan dipakai dalam klasifikasi ini adalah Permission dan Broadcast Receiver. Untuk meningkatkan akurasi dari hasil klasifikasi pada penelitian ini digunakan metode Seleksi Fitur. Seleksi Fitur yang digunakan ialah Correlation-based Feature Selection (CSF), Gain Ratio (GR) dan Chi-Square (CHI). Hasil dari Seleksi Fitur akan di evaluasi bersama dengan hasil yang tidak menggunakan Seleksi Fitur. Akurasi klasifikasi Seleksi Fitur CFS menghasilkan akurasi sebesar 90.83% , GR dan CHI sebesar 91.25% dan data yang tidak menggunakan Seleksi Fitur sebesar 91.67%. Hasil dari pengujian menunjukan bahwa Permission dan Broadcast Receiver bisa digunakan dalam mengklasifikasi jenis Malware, akan tetapi metode Seleksi Fitur yang digunakan mempunyai akurasi yang berada sedikit dibawah data yang tidak menggunakan Seleksi Fitur. Kata kunci: klasifikasi malware android, seleksi fitur, SVM dan multi class SVM one agains one Abstract Android Malware has growth significantly along with the advance of the times and the increasing variety of technique in the development of Android. Machine Learning technique is a method that now we can use in the modeling the pattern of a static and dynamic feature of Android Malware. In the level of accuracy of the Malware type classification, the researcher connect between the application feature with the feature required by each types of Malware category. The category of malware used is a type of Malware that many circulating today, to classify the type of Malware in this study used Support Vector Machine (SVM). The SVM type wiil be used is class SVM one against one using the RBF Kernel. The feature will be used in this classification are the Permission and Broadcast Receiver. To improve the accuracy of the classification result in this study used Feature Selection method. Selection of feature used are Correlation-based Feature Selection (CFS), Gain Ratio (GR) and Chi-Square (CHI). Result from Feature Selection will be evaluated together with result that not use Feature Selection. Accuracy Classification Feature Selection CFS result accuracy of 90.83%, GR and CHI of 91.25% and data that not use Feature Selection of 91.67%. The result of testing indicate that permission and broadcast receiver can be used in classyfing type of Malware, but the Feature Selection method that used have accuracy is a little below the data that are not using Feature Selection. Keywords: Classification Android Malware, Feature Selection, SVM and Multi Class SVM one against one

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Classification of Crop Residue Cover in High-Resolution RGB Images Using Machine Learning

Journal of the ASABE ◽

10.13031/ja.14572 ◽

2022 ◽

Vol 65 (1) ◽

pp. 75-86

Author(s):

Parth C. Upadhyay ◽

John A. Lory ◽

Guilherme N. DeSouza ◽

Timotius A. P. Lagaunne ◽

Christine M. Spinka

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Feature Selection Method ◽

Texture Features ◽

Ground Truth ◽

Selection Method ◽

Support Vector ◽

Svm Classifier ◽

Aerial Vehicle ◽

Rgb Images

HighlightsA machine learning framework estimated residue cover in RGB images taken at three resolutions from 88 locations.The best results primarily used texture features, the RFE-SVM feature selection method, and the SVM classifier.Accounting for shadows and plants plus modifying and optimizing the texture features may improve performance.An automated system developed using machine learning is a viable strategy to estimate residue cover from RGB images obtained with handheld or UAV platforms.Abstract. Maintaining plant residue on the soil surface contributes to sustainable cultivation of arable land. Applying machine learning methods to RGB images of residue could overcome the subjectivity of manual methods. The objectives of this study were to use supervised machine learning while identifying the best feature selection method, the best classifier, and the most effective image feature types for classifying residue levels in RGB imagery. Imagery was collected from 88 locations in 40 row-crop fields in five Missouri counties between early May and late June in 2018 and 2019 using a tripod-mounted camera (0.014 cm pixel-1 ground sampling distance, GSD) and an unmanned aerial vehicle (UAV, 0.05 and 0.14 GSD). At each field location, 50 contiguous 0.3 × 0.2 m region of interest (ROI) images were extracted from the imagery, resulting in a dataset of 4,400 ROI images at each GSD. Residue percentages for ground truth were estimated using a bullseye grid method (n = 100 points) based on the 0.014 GSD images. Representative color, texture, and shape features were extracted and evaluated using four feature selection methods and two classifiers. Recursive feature elimination using support vector machine (RFE-SVM) was the best feature selection method, and the SVM classifier performed best for classifying the amount of residue as a three-class problem. The best features for this application were associated with texture, with local binary pattern (LBP) features being the most prevalent for all three GSDs. Shape features were irrelevant. The three residue classes were correctly identified with 88%, 84%, and 81% 10-fold cross-validation scores for the 2018 training data and 81%, 69%, and 65% accuracy for the 2019 testing data in decreasing resolution order. Converting image-wise data (0.014 GSD) to location residue estimates using a Bayesian model showed good agreement with the location-based ground truth (r2 = 0.90). This initial assessment documents the use of RGB images to match other methods of estimating residue, with potential to replace or be used as a quality control for line-transect assessments. Keywords: Feature selection, Soil erosion, Support vector machine, Texture features, Unmanned aerial vehicle.

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Analysis of Expression Pattern of snoRNAs in Different Cancer Types with Machine Learning Algorithms

International Journal of Molecular Sciences ◽

10.3390/ijms20092185 ◽

2019 ◽

Vol 20 (9) ◽

pp. 2185 ◽

Cited By ~ 18

Author(s):

Xiaoyong Pan ◽

Lei Chen ◽

Kai-Yan Feng ◽

Xiao-Hua Hu ◽

Yu-Hang Zhang ◽

...

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Expression Pattern ◽

Learning Algorithms ◽

Expression Patterns ◽

Feature Selection Method ◽

Machine Learning Algorithms ◽

Support Vector ◽

Feature List ◽

Cancer Types

Small nucleolar RNAs (snoRNAs) are a new type of functional small RNAs involved in the chemical modifications of rRNAs, tRNAs, and small nuclear RNAs. It is reported that they play important roles in tumorigenesis via various regulatory modes. snoRNAs can both participate in the regulation of methylation and pseudouridylation and regulate the expression pattern of their host genes. This research investigated the expression pattern of snoRNAs in eight major cancer types in TCGA via several machine learning algorithms. The expression levels of snoRNAs were first analyzed by a powerful feature selection method, Monte Carlo feature selection (MCFS). A feature list and some informative features were accessed. Then, the incremental feature selection (IFS) was applied to the feature list to extract optimal features/snoRNAs, which can make the support vector machine (SVM) yield best performance. The discriminative snoRNAs included HBII-52-14, HBII-336, SNORD123, HBII-85-29, HBII-420, U3, HBI-43, SNORD116, SNORA73B, SCARNA4, HBII-85-20, etc., on which the SVM can provide a Matthew’s correlation coefficient (MCC) of 0.881 for predicting these eight cancer types. On the other hand, the informative features were fed into the Johnson reducer and repeated incremental pruning to produce error reduction (RIPPER) algorithms to generate classification rules, which can clearly show different snoRNAs expression patterns in different cancer types. The analysis results indicated that extracted discriminative snoRNAs can be important for identifying cancer samples in different types and the expression pattern of snoRNAs in different cancer types can be partly uncovered by quantitative recognition rules.

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Machine Learning and Feature Selection Methods for EGFR Mutation Status Prediction in Lung Cancer

Applied Sciences ◽

10.3390/app11073273 ◽

2021 ◽

Vol 11 (7) ◽

pp. 3273

Author(s):

Joana Morgado ◽

Tania Pereira ◽

Francisco Silva ◽

Cláudia Freitas ◽

Eduardo Negrão ◽

...

Keyword(s):

Machine Learning ◽

Lung Cancer ◽

Feature Selection ◽

Egfr Mutation ◽

Feature Selection Method ◽

Principal Component ◽

Image Features ◽

Support Vector ◽

Selection Methods ◽

Mutation Status

The evolution of personalized medicine has changed the therapeutic strategy from classical chemotherapy and radiotherapy to a genetic modification targeted therapy, and although biopsy is the traditional method to genetically characterize lung cancer tumor, it is an invasive and painful procedure for the patient. Nodule image features extracted from computed tomography (CT) scans have been used to create machine learning models that predict gene mutation status in a noninvasive, fast, and easy-to-use manner. However, recent studies have shown that radiomic features extracted from an extended region of interest (ROI) beyond the tumor, might be more relevant to predict the mutation status in lung cancer, and consequently may be used to significantly decrease the mortality rate of patients battling this condition. In this work, we investigated the relation between image phenotypes and the mutation status of Epidermal Growth Factor Receptor (EGFR), the most frequently mutated gene in lung cancer with several approved targeted-therapies, using radiomic features extracted from the lung containing the nodule. A variety of linear, nonlinear, and ensemble predictive classification models, along with several feature selection methods, were used to classify the binary outcome of wild-type or mutant EGFR mutation status. The results show that a comprehensive approach using a ROI that included the lung with nodule can capture relevant information and successfully predict the EGFR mutation status with increased performance compared to local nodule analyses. Linear Support Vector Machine, Elastic Net, and Logistic Regression, combined with the Principal Component Analysis feature selection method implemented with 70% of variance in the feature set, were the best-performing classifiers, reaching Area Under the Curve (AUC) values ranging from 0.725 to 0.737. This approach that exploits a holistic analysis indicates that information from more extensive regions of the lung containing the nodule allows a more complete lung cancer characterization and should be considered in future radiogenomic studies.

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