scholarly journals Assessing robustness of carotid artery CT angiography radiomics in the identification of culprit lesions in cerebrovascular events

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Elizabeth P. V. Le ◽  
Leonardo Rundo ◽  
Jason M. Tarkin ◽  
Nicholas R. Evans ◽  
Mohammed M. Chowdhury ◽  
...  
Keyword(s):  
Carotid Artery ◽  
Cross Validation ◽  
Area Under The Curve ◽  
Region Of Interest ◽  
Disease Diagnosis ◽  
Machine Learning Algorithms ◽  
Cerebrovascular Events ◽  
Radiological Images ◽  
Carotid Calcification ◽  
Fold Cross Validation

AbstractRadiomics, quantitative feature extraction from radiological images, can improve disease diagnosis and prognostication. However, radiomic features are susceptible to image acquisition and segmentation variability. Ideally, only features robust to these variations would be incorporated into predictive models, for good generalisability. We extracted 93 radiomic features from carotid artery computed tomography angiograms of 41 patients with cerebrovascular events. We tested feature robustness to region-of-interest perturbations, image pre-processing settings and quantisation methods using both single- and multi-slice approaches. We assessed the ability of the most robust features to identify culprit and non-culprit arteries using several machine learning algorithms and report the average area under the curve (AUC) from five-fold cross validation. Multi-slice features were superior to single for producing robust radiomic features (67 vs. 61). The optimal image quantisation method used bin widths of 25 or 30. Incorporating our top 10 non-redundant robust radiomics features into ElasticNet achieved an AUC of 0.73 and accuracy of 69% (compared to carotid calcification alone [AUC: 0.44, accuracy: 46%]). Our results provide key information for introducing carotid CT radiomics into clinical practice. If validated prospectively, our robust carotid radiomic set could improve stroke prediction and target therapies to those at highest risk.

Prediction of K562 Cells Functional Inhibitors Based on Machine Learning Approaches

2020 ◽  
Vol 25 (40) ◽  
pp. 4296-4302 ◽  
Author(s):  
Yuan Zhang ◽  
Zhenyan Han ◽  
Qian Gao ◽  
Xiaoyi Bai ◽  
Chi Zhang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Inclusion Bodies ◽  
Cross Validation ◽  
Independent Set ◽  
K562 Cells ◽  
Machine Learning Algorithms ◽  
Learning Approaches ◽  
Validation Test ◽  
Excess Number ◽  
Fold Cross Validation

Background: β thalassemia is a common monogenic genetic disease that is very harmful to human health. The disease arises is due to the deletion of or defects in β-globin, which reduces synthesis of the β-globin chain, resulting in a relatively excess number of α-chains. The formation of inclusion bodies deposited on the cell membrane causes a decrease in the ability of red blood cells to deform and a group of hereditary haemolytic diseases caused by massive destruction in the spleen. Methods: In this work, machine learning algorithms were employed to build a prediction model for inhibitors against K562 based on 117 inhibitors and 190 non-inhibitors. Results: The overall accuracy (ACC) of a 10-fold cross-validation test and an independent set test using Adaboost were 83.1% and 78.0%, respectively, surpassing Bayes Net, Random Forest, Random Tree, C4.5, SVM, KNN and Bagging. Conclusion: This study indicated that Adaboost could be applied to build a learning model in the prediction of inhibitors against K526 cells.

scholarly journals CT-Based Radiomics Analysis for Preoperative Diagnosis of Pancreatic Mucinous Cystic Neoplasm and Atypical Serous Cystadenomas

2021 ◽  
Vol 11 ◽  
Author(s):  
Tiansong Xie ◽  
Xuanyi Wang ◽  
Zehua Zhang ◽  
Zhengrong Zhou
Keyword(s):  
Predictive Value ◽  
Cross Validation ◽  
Clinical Decision Making ◽  
Area Under The Curve ◽  
Clinical Decision ◽  
Cystic Neoplasm ◽  
Cystic Neoplasms ◽  
Serous Cystadenomas ◽  
Radiological Model ◽  
Fold Cross Validation

ObjectivesTo investigate the value of CT-based radiomics analysis in preoperatively discriminating pancreatic mucinous cystic neoplasms (MCN) and atypical serous cystadenomas (ASCN).MethodsA total of 103 MCN and 113 ASCN patients who underwent surgery were retrospectively enrolled. A total of 764 radiomics features were extracted from preoperative CT images. The optimal features were selected by Mann-Whitney U test and minimum redundancy and maximum relevance method. The radiomics score (Rad-score) was then built using random forest algorithm. Radiological/clinical features were also assessed for each patient. Multivariable logistic regression was used to construct a radiological model. The performance of the Rad-score and the radiological model was evaluated using 10-fold cross-validation for area under the curve (AUC), sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy.ResultsTen screened optimal features were identified and the Rad-score was then built based on them. The radiological model was built based on four radiological/clinical factors. In the 10-fold cross-validation, the Rad-score was proved to be robust and reliable (average AUC: 0.784, sensitivity: 0.847, specificity: 0.745, PPV: 0.767, NPV: 0.849, accuracy: 0.793). The radiological model performed slightly less well in classification (average AUC: average AUC: 0.734 sensitivity: 0.748, specificity: 0.705, PPV: 0.732, NPV: 0.798, accuracy: 0.728.ConclusionsThe CT-based radiomics analysis provided promising performance for preoperatively discriminating MCN from ASCN and showed good potential in improving diagnostic power, which may serve as a novel tool for guiding clinical decision-making for these patients.

scholarly journals Evaluation and Identification of the Neuroprotective Compounds of Xiaoxuming Decoction by Machine Learning: A Novel Mode to Explore the Combination Rules in Traditional Chinese Medicine Prescription

2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Shilun Yang ◽  
Yanjia Shen ◽  
Wendan Lu ◽  
Yinglin Yang ◽  
Haigang Wang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Cross Validation ◽  
Bayesian Models ◽  
Machine Learning Algorithms ◽  
Therapeutic Effects ◽  
Test Set ◽  
Screening Experiments ◽  
Fold Cross Validation

Xiaoxuming decoction (XXMD), a classic traditional Chinese medicine (TCM) prescription, has been used as a therapeutic in the treatment of stroke in clinical practice for over 1200 years. However, the pharmacological mechanisms of XXMD have not yet been elucidated. The purpose of this study was to develop neuroprotective models for identifying neuroprotective compounds in XXMD against hypoxia-induced and H2O2-induced brain cell damage. In this study, a phenotype-based classification method was designed by machine learning to identify neuroprotective compounds and to clarify the compatibility of XXMD components. Four different single classifiers (AB, kNN, CT, and RF) and molecular fingerprint descriptors were used to construct stacked naïve Bayesian models. Among them, the RF algorithm had a better performance with an average MCC value of 0.725±0.014 and 0.774±0.042 from 5-fold cross-validation and test set, respectively. The probability values calculated by four models were then integrated into a stacked Bayesian model. In total, two optimal models, s-NB-1-LPFP6 and s-NB-2-LPFP6, were obtained. The two validated optimal models revealed Matthews correlation coefficients (MCC) of 0.968 and 0.993 for 5-fold cross-validation and of 0.874 and 0.959 for the test set, respectively. Furthermore, the two models were used for virtual screening experiments to identify neuroprotective compounds in XXMD. Ten representative compounds with potential therapeutic effects against the two phenotypes were selected for further cell-based assays. Among the selected compounds, two compounds significantly inhibited H2O2-induced and Na2S2O4-induced neurotoxicity simultaneously. Together, our findings suggested that machine learning algorithms such as combination Bayesian models were feasible to predict neuroprotective compounds and to preliminarily demonstrate the pharmacological mechanisms of TCM.

scholarly journals Klasifikasi rempah rimpang berdasarkan ciri warna rgb dan tekstur glcm menggunakan algoritma naive bayes

2020 ◽  
Vol 16 (3) ◽  
pp. 156
Author(s):  
Nadya P. Batubara ◽  
Didit Widiyanto ◽  
Nurul Chamidah
Keyword(s):  
Image Enhancement ◽  
Cross Validation ◽  
Naive Bayes ◽  
Region Of Interest ◽  
Naïve Bayes ◽  
Grey Level ◽  
Occurrence Matrix ◽  
Fold Cross Validation

Abstrak. Pada penelitian ini akan membahas bagaimana cara mengklasifikasikan beberapa jenis rempah berdasarkan algoritma Naïve Bayes dengan menggunakan ekstraksi ciri warna RGB dan tekstur GLCM. Tahapan dalam proses klasifikasi citra digital pada penelitian ini yaitu praproses citra, segmentasi, ekstraksi ciri, klasifikasi dan uji performa Proses yang dilakukan pada penelitian ini adalah mengubah RGB to Grayscale untuk mendapatkan citra abunya, setelah mengubah citra menjadi Grayscale. Setelah melakukan image enhancement, citra di segmentasi dengan thresholding menggunakan metode Otsu. Setelah mendapatkan hasil dari segmentasi dilakukan RoI (Region of Interest) yang menghasilkan perkalian pixel. Setelah itu dilakukan ekstraksi ciri dengan menggunakan GLCM (Grey Level Co-occurrence Matrix) dan ekstraksi fitur RGB (Red, green, blue) yang di ekstrak ke dalam GLCM. Setelah mendapatkan hasil dari ekstraksi ciri maka dilakukan klasifikasi menggunakan algoritma Naïve Bayes. Tahapan terakhir pada penelitian ini adalah uji performa menggunakan K-fold cross validation dengan K=10 dan mendapatkan hasil akurasi sebesar 52%. Kata Kunci: Rempah-rempah, Naïve Bsayes, RGB, GLCM.

A Binary Classifier for the Prediction of EC Numbers of Enzymes

2019 ◽  
Vol 16 (5) ◽  
pp. 383-391 ◽  
Author(s):  
Hao Cui ◽  
Lei Chen
Keyword(s):  
Cross Validation ◽  
Enzyme Commission ◽  
Matthews Correlation Coefficient ◽  
Learning Algorithm ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Binary Classifier ◽  
Two Samples ◽  
Functional Classes ◽  
Fold Cross Validation

Background: Identification of Enzyme Commission (EC) number of enzymes is quite important for understanding the metabolic processes that produce enough energy to sustain life. Previous studies mainly focused on predicting six main functional classes or sub-functional classes, i.e., the first two digits of the EC number. Objective: In this study, a binary classifier was proposed to identify the full EC number (four digits) of enzymes. Methods: Enzymes and their known EC numbers were paired as positive samples and negative samples were randomly produced that were as many as positive samples. The associations between any two samples were evaluated by integrating the linkages between enzymes and EC numbers. The classic machining learning algorithm, Support Vector Machine (SVM), was adopted as the prediction engine. Results: The five-fold cross-validation test on five datasets indicated that the overall accuracy, Matthews correlation coefficient and F1-measure were about 0.786, 0.576 and 0.771, respectively, suggesting the utility of the proposed classifier. In addition, the effectiveness of the classifier was elaborated by comparing it with other classifiers that were based on other classic machine learning algorithms. Conclusion: The proposed classifier was quite effective for prediction of EC number of enzymes and was specially designed for dealing with the problem addressed in this study by testing it on five datasets containing randomly produced samples.

scholarly journals K-Fold Cross Validation for Selection of Cardiovascular Disease Diagnosis Features by Applying Rule-Based Datamining

2019 ◽  
Vol 1 (2) ◽  
pp. 23-35
Author(s):  
Dwi Normawati ◽  
Dewi Pramudi Ismi
Keyword(s):  
Coronary Heart Disease ◽  
Feature Selection ◽  
Heart Disease ◽  
Rough Set ◽  
Cross Validation ◽  
Rough Set Theory ◽  
Disease Diagnosis ◽  
Classification Performance ◽  
Rule Based ◽  
Fold Cross Validation

Coronary heart disease is a disease that often causes human death, occurs when there is atherosclerosis blocking blood flow to the heart muscle in the coronary arteries. The doctor's referral method for diagnosing coronary heart disease is coronary angiography, but it is invasive, high risk and expensive. The purpose of this study is to analyze the effect of implementing the k-Fold Cross Validation (CV) dataset on the rule-based feature selection to diagnose coronary heart disease, using the Cleveland heart disease dataset. The research conducted a feature selection using a medical expert-based (MFS) and computer-based method, namely the Variable Precision Rough Set (VPRS), which is the development of the Rough Set theory. Evaluation of classification performance using the k-Fold method of 10-Fold, 5-Fold and 3-Fold. The results of the study are the number of attributes of the feature selection results are different in each Fold, both for the VPRS and MFS methods, for accuracy values obtained from the average accuracy resulting from 10-Fold, 5-Fold and 3-Fold. The result was the highest accuracy value in the VPRS method 76.34% with k = 5, while the MTF accuracy was 71.281% with k = 3. So, the k-fold implementation for this case is less effective, because the division of data is still structured, according to the order of records that apply in each fold, while the amount of testing data is too small and too structured. This affects the results of the accuracy because the testing rules are not thoroughly represented

scholarly journals Identifying the Main Risk Factors for CVD Prediction Using Machine Learning Algorithms

2021 ◽  
Author(s):  
Luis Rolando Guarneros-Nolasco ◽  
Nancy Aracely Cruz-Ramos ◽  
Giner Alor-Hernández ◽  
Lisbeth Rodríguez-Mazahua ◽  
José Luis Sánchez-Cervantes
Keyword(s):  
Machine Learning ◽  
Cross Validation ◽  
Performance Metrics ◽  
Learning Algorithms ◽  
Predictive Performance ◽  
Machine Learning Algorithms ◽  
Algorithm Performance ◽  
Body Regions ◽  
Risks Factors ◽  
Fold Cross Validation

CVDs are a leading cause of death globally. In CVDs, the heart is unable to deliver enough blood to other body regions. Since effective and accurate diagnosis of CVDs is essential for CVD prevention and treatment, machine learning (ML) techniques can be effectively and reliably used to discern patients suffering from a CVD from those who do not suffer from any heart condition. Namely, machine learning algorithms (MLAs) play a key role in the diagnosis of CVDs through predictive models that allow us to identify the main risks factors influencing CVD development. In this study, we analyze the performance of ten MLAs on two datasets for CVD prediction and two for CVD diagnosis. Algorithm performance is analyzed on top-two and top-four dataset attributes/features with respect to five performance metrics –accuracy, precision, recall, f1-score, and roc-auc – using the train-test split technique and k-fold cross-validation. Our study identifies the top two and four attributes from each CVD diagnosis/prediction dataset. As our main findings, the ten MLAs exhibited appropriate diagnosis and predictive performance; hence, they can be successfully implemented for improving current CVD diagnosis efforts and help patients around the world, especially in regions where medical staff is lacking.

scholarly journals COVID-DenseNet: A Deep Learning Architecture to Detect COVID-19 from Chest Radiology Images

2020 ◽  
Author(s):  
Laboni Sarker ◽  
Md. Mohaiminul Islam ◽  
Tanveer Hannan ◽  
Zakaria Ahmed
Keyword(s):  
Deep Learning ◽  
Cross Validation ◽  
Critical Factors ◽  
Effective Screening ◽  
Average Accuracy ◽  
Radiological Images ◽  
Learning Technique ◽  
Chest Radiology ◽  
Fold Cross Validation ◽  
Radiology Image

Coronavirus disease (COVID-19) is a pandemic infectious disease that has a severe risk of spreading rapidly. The quick identification and isolation of the affected persons is the very first step to fight against this virus. In this regard, chest radiology images have been proven to be an effective screening approach of COVID-19 affected patients. A number of AI based solutions have been developed to make the screening of radiological images faster and more accurate in detecting COVID-19. In this study, we are proposing a deep learning based approach using Densenet-121 to effectively detect COVID-19 patients. We incorporated transfer learning technique to leverage the information regarding radiology image learned by another model (CheXNet) which was trained on a huge Radiology dataset of 112,120 images. We trained and tested our model on COVIDx dataset containing 13,800 chest radiography images across 13,725 patients. To check the robustness of our model, we performed both two-class and three-class classifications and achieved 96.49% and 93.71% accuracy respectively. To further validate the consistency of our performance, we performed patient-wise k-fold cross-validation and achieved an average accuracy of 92.91% for three class task. Moreover, we performed an interpretability analysis using Grad-CAM to highlight the most important image regions in making a prediction. Besides ensuring trustworthiness, this explainability can also provide new insights about the critical factors regarding COVID-19. Finally, we developed a website that takes chest radiology images as input and generates probabilities of the presence of COVID-19 or pneumonia and a heatmap highlighting the probable infected regions. Code and models' weights are availabe.

scholarly journals Perbandingan Prediksi Kualitas Kopi Arabika dengan Menggunakan Algoritma SGD, Random Forest dan Naive Bayes

2020 ◽  
Vol 4 (2) ◽  
pp. 1-9
Author(s):  
Veronica Sari ◽  
◽  
Feranandah Firdausi ◽  
Yufis Azhar ◽  
◽  
...  
Keyword(s):  
Random Forest ◽  
Gradient Descent ◽  
Cross Validation ◽  
Naive Bayes ◽  
Area Under The Curve ◽  
Naïve Bayes ◽  
Stochastic Gradient ◽  
Stochastic Gradient Descent ◽  
Quality Institute ◽  
Fold Cross Validation

Classification is one of the techniques that exist in data mining and is useful for grouping a data based on the attachment of the data with the sample data. The dataset that is used in this study is the coffee dataset taken from Dataset Coffee Quality Institute on the GitHub platform. The attributes that contained in the dataset are Aroma, Aftertaste, Flavor, Acidity, Balance, Body, Uniformity, Sweetness, Clean Cup, and Copper points. There are 3 classification methods that are used in this study, Stochastic Gradient Descent, Random Forest and Naive Bayes. The aim of this study is to find out which algorithm is the most effective to predict the coffee quality in the dataset. After that, the prediction results will be tested using K-Fold Cross Validation and Area Under the Curve (AUC) method. The results show that Stochastic Gradient Descent obtained the best accuracy results compared to the other two methods with an accuracy of 98% and increased to 99% after tested using K-fold Cross Validation and AUC method.

scholarly journals Research of Machine Learning algorithms using K-fold cross validation

2019 ◽  
Vol 8 (6S) ◽  
pp. 215-218
Keyword(s):  
Machine Learning ◽  
Cross Validation ◽  
Research Area ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Breast Cancer Dataset ◽  
Cancer Dataset ◽  
Validation Data ◽  
Machine Learning Classification ◽  
Fold Cross Validation

In machine learning, Classification is one of the most important research area. Classification allocates the given input to a known category. In this paper different machine algorithms like Logistic regression (LR), Decision tree (DT), Support vector machine (SVM), K nearest neighbors (KNN) were implemented on UCI breast cancer dataset with preprocessing. The models were trained and tested with k-fold cross validation data. Accuracy and run time execution of each classifier are implemented in python.

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