Combining multiple biomarkers to linearly maximize the diagnostic accuracy under ordered multi-class setting

2021 ◽  
pp. 096228022098758
Author(s):  
Jia Hua ◽  
Lili Tian
Keyword(s):  
Diagnostic Accuracy ◽  
Classification Accuracy ◽  
Medical Diagnosis ◽  
Binary Classification ◽  
Grid Search ◽  
Data Set ◽  
Cancer Data ◽  
Ovarian Cancer Data ◽  
Multiple Biomarkers ◽  
Important Objective

Either in clinical study or biomedical research, it is a common practice to combine multiple biomarkers to improve the overall diagnostic performance. Despite the fact there exist a large number of statistical methods for biomarker combination under binary classification, research on this topic under multi-class setting is sparse. The overall diagnostic accuracy, i.e. the sum of correct classification rates, directly measures the classification accuracy of the combined biomarkers. Hence the overall accuracy can serve as an important objective function for biomarker combination, especially when the combined biomarkers are used for the purpose of making medical diagnosis. In this paper, we address the problem of combining multiple biomarkers to directly maximize the overall diagnostic accuracy by presenting several grid search methods and derivation-based methods. A comprehensive simulation study was conducted to compare the performances of these methods. An ovarian cancer data set is analyzed in the end.

scholarly journals Multi-Classification of Fetal Health Status Using Extreme Learning Machine

2021 ◽  
Vol 5 (2) ◽  
pp. 62-70
Author(s):  
Ömer KASIM
Keyword(s):  
Extreme Learning Machine ◽  
Classification Accuracy ◽  
Binary Classification ◽  
Clinical Decision ◽  
Support Vector ◽  
Data Set ◽  
Multiple Classification ◽  
Learning Machine ◽  
Multi Class Classification ◽  
The University

Cardiotocography (CTG) is used for monitoring the fetal heart rate signals during pregnancy. Evaluation of these signals by specialists provides information about fetal status. When a clinical decision support system is introduced with a system that can automatically classify these signals, it is more sensitive for experts to examine CTG data. In this study, CTG data were analysed with the Extreme Learning Machine (ELM) algorithm and these data were classified as normal, suspicious and pathological as well as benign and malicious. The proposed method is validated with the University of California International CTG data set. The performance of the proposed method is evaluated with accuracy, f1 score, Cohen kappa, precision, and recall metrics. As a result of the experiments, binary classification accuracy was obtained as 99.29%. There was only 1 false positive.  When multi-class classification was performed, the accuracy was obtained as 98.12%.  The amount of false positives was found as 2. The processing time of the training and testing of the ELM algorithm were quite minimized in terms of data processing compared to the support vector machine and multi-layer perceptron. This result proved that a high classification accuracy was obtained by analysing the CTG data both binary and multiple classification.

scholarly journals Hyperparameter Tuning and Pipeline Optimization via Grid Search Method and Tree-Based AutoML in Breast Cancer Prediction

2021 ◽  
Vol 11 (10) ◽  
pp. 978
Author(s):  
Siti Fairuz Mat Radzi ◽  
Muhammad Khalis Abdul Karim ◽  
M Iqbal Saripan ◽  
Mohd Amiruddin Abdul Rahman ◽  
Iza Nurzawani Che Isa ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Model Selection ◽  
Principal Component ◽  
Receiver Operating Curve ◽  
Support Vector ◽  
Grid Search ◽  
Breast Cancer Data ◽  
Data Set ◽  
Cancer Data

Automated machine learning (AutoML) has been recognized as a powerful tool to build a system that automates the design and optimizes the model selection machine learning (ML) pipelines. In this study, we present a tree-based pipeline optimization tool (TPOT) as a method for determining ML models with significant performance and less complex breast cancer diagnostic pipelines. Some features of pre-processors and ML models are defined as expression trees and optimal gene programming (GP) pipelines, a stochastic search system. Features of radiomics have been presented as a guide for the ML pipeline selection from the breast cancer data set based on TPOT. Breast cancer data were used in a comparative analysis of the TPOT-generated ML pipelines with the selected ML classifiers, optimized by a grid search approach. The principal component analysis (PCA) random forest (RF) classification was proven to be the most reliable pipeline with the lowest complexity. The TPOT model selection technique exceeded the performance of grid search (GS) optimization. The RF classifier showed an outstanding outcome amongst the models in combination with only two pre-processors, with a precision of 0.83. The grid search optimized for support vector machine (SVM) classifiers generated a difference of 12% in comparison, while the other two classifiers, naïve Bayes (NB) and artificial neural network—multilayer perceptron (ANN-MLP), generated a difference of almost 39%. The method’s performance was based on sensitivity, specificity, accuracy, precision, and receiver operating curve (ROC) analysis.

Issues and solutions in biomarker evaluation when subclasses are involved under binary classification

2020 ◽  
pp. 096228022093807
Author(s):  
Yingdong Feng ◽  
Lili Tian
Keyword(s):  
Binary Classification ◽  
Control Group ◽  
Case Group ◽  
Data Set ◽  
Cancer Data ◽  
Main Class ◽  
Area Under Roc Curve ◽  
Pooling Strategy ◽  
Diagnostic Framework ◽  
Biomarker Evaluation

In practice, it is common to evaluate biomarkers in binary classification settings (e.g. non-cancer vs. cancer) where one or both main classes involve multiple subclasses. For example, non-cancer class might consist of healthy subjects and benign cases, while cancer class might consist of subjects at early and late stages. The standard practice is pooling within each main class, i.e. all non-cancer subclasses are pooled together to create a control group, and all cancer subclasses are pooled together to create a case group. Based on the pooled data, the area under ROC curve ( AUC) and other characteristics are estimated under binary classification for the purpose of biomarker evaluation. Despite the popularity of this pooling strategy in practice, its validity and implication in biomarker evaluation have never been carefully inspected. This paper aims to demonstrate that pooling strategy can be seriously misleading in biomarker evaluation. Furthermore, we present a new diagnostic framework as well as new accuracy measures appropriate for biomaker evaluation under such settings. In the end, an ovarian cancer data set is analyzed.

scholarly journals Classification of standing and sitting phases based on in-socket piezoelectric sensors in a transfemoral amputee

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Tawfik Yahya ◽  
Nur Azah Hamzaid ◽  
Sadeeq Ali ◽  
Farahiyah Jasni ◽  
Hanie Nadia Shasmin
Keyword(s):  
Time Domain ◽  
Classification Accuracy ◽  
Sensory System ◽  
Metabolic Energy ◽  
Support Vector ◽  
Data Set ◽  
Transfemoral Amputee ◽  
Sit To Stand ◽  
Optimal Classifier ◽  
The Impact

AbstractA transfemoral prosthesis is required to assist amputees to perform the activity of daily living (ADL). The passive prosthesis has some drawbacks such as utilization of high metabolic energy. In contrast, the active prosthesis consumes less metabolic energy and offers better performance. However, the recent active prosthesis uses surface electromyography as its sensory system which has weak signals with microvolt-level intensity and requires a lot of computation to extract features. This paper focuses on recognizing different phases of sitting and standing of a transfemoral amputee using in-socket piezoelectric-based sensors. 15 piezoelectric film sensors were embedded in the inner socket wall adjacent to the most active regions of the agonist and antagonist knee extensor and flexor muscles, i. e. region with the highest level of muscle contractions of the quadriceps and hamstring. A male transfemoral amputee wore the instrumented socket and was instructed to perform several sitting and standing phases using an armless chair. Data was collected from the 15 embedded sensors and went through signal conditioning circuits. The overlapping analysis window technique was used to segment the data using different window lengths. Fifteen time-domain and frequency-domain features were extracted and new feature sets were obtained based on the feature performance. Eight of the common pattern recognition multiclass classifiers were evaluated and compared. Regression analysis was used to investigate the impact of the number of features and the window lengths on the classifiers’ accuracies, and Analysis of Variance (ANOVA) was used to test significant differences in the classifiers’ performances. The classification accuracy was calculated using k-fold cross-validation method, and 20% of the data set was held out for testing the optimal classifier. The results showed that the feature set (FS-5) consisting of the root mean square (RMS) and the number of peaks (NP) achieved the highest classification accuracy in five classifiers. Support vector machine (SVM) with cubic kernel proved to be the optimal classifier, and it achieved a classification accuracy of 98.33 % using the test data set. Obtaining high classification accuracy using only two time-domain features would significantly reduce the processing time of controlling a prosthesis and eliminate substantial delay. The proposed in-socket sensors used to detect sit-to-stand and stand-to-sit movements could be further integrated with an active knee joint actuation system to produce powered assistance during energy-demanding activities such as sit-to-stand and stair climbing. In future, the system could also be used to accurately predict the intended movement based on their residual limb’s muscle and mechanical behaviour as detected by the in-socket sensory system.

Design of novel multi filter union feature selection framework for breast cancer dataset

2021 ◽  
pp. 1063293X2110160
Author(s):  
Dinesh Morkonda Gunasekaran ◽  
Prabha Dhandayudam
Keyword(s):  
Breast Cancer ◽  
Feature Selection ◽  
Care Center ◽  
Feature Selection Method ◽  
Selection Method ◽  
Cancer Center ◽  
Breast Cancer Dataset ◽  
Data Set ◽  
Health Care Center ◽  
Cancer Data

Nowadays women are commonly diagnosed with breast cancer. Feature based Selection method plays an important step while constructing a classification based framework. We have proposed Multi filter union (MFU) feature selection method for breast cancer data set. The feature selection process based on random forest algorithm and Logistic regression (LG) algorithm based union model is used for selecting important features in the dataset. The performance of the data analysis is evaluated using optimal features subset from selected dataset. The experiments are computed with data set of Wisconsin diagnostic breast cancer center and next the real data set from women health care center. The result of the proposed approach shows high performance and efficient when comparing with existing feature selection algorithms.

scholarly journals Leveraging Road Characteristics and Contributor Behaviour for Assessing Road Type Quality in OSM

2021 ◽  
Vol 10 (7) ◽  
pp. 436
Author(s):  
Amerah Alghanim ◽  
Musfira Jilani ◽  
Michela Bertolotto ◽  
Gavin McArdle
Keyword(s):  
Machine Learning ◽  
Spatial Data ◽  
Classification Accuracy ◽  
Supervised Machine Learning ◽  
Machine Learning Techniques ◽  
Data Set ◽  
Semantic Inference ◽  
Road Type ◽  
The Impact

Volunteered Geographic Information (VGI) is often collected by non-expert users. This raises concerns about the quality and veracity of such data. There has been much effort to understand and quantify the quality of VGI. Extrinsic measures which compare VGI to authoritative data sources such as National Mapping Agencies are common but the cost and slow update frequency of such data hinder the task. On the other hand, intrinsic measures which compare the data to heuristics or models built from the VGI data are becoming increasingly popular. Supervised machine learning techniques are particularly suitable for intrinsic measures of quality where they can infer and predict the properties of spatial data. In this article we are interested in assessing the quality of semantic information, such as the road type, associated with data in OpenStreetMap (OSM). We have developed a machine learning approach which utilises new intrinsic input features collected from the VGI dataset. Specifically, using our proposed novel approach we obtained an average classification accuracy of 84.12%. This result outperforms existing techniques on the same semantic inference task. The trustworthiness of the data used for developing and training machine learning models is important. To address this issue we have also developed a new measure for this using direct and indirect characteristics of OSM data such as its edit history along with an assessment of the users who contributed the data. An evaluation of the impact of data determined to be trustworthy within the machine learning model shows that the trusted data collected with the new approach improves the prediction accuracy of our machine learning technique. Specifically, our results demonstrate that the classification accuracy of our developed model is 87.75% when applied to a trusted dataset and 57.98% when applied to an untrusted dataset. Consequently, such results can be used to assess the quality of OSM and suggest improvements to the data set.

The strong prognostic value of KELIM, a model-based parameter from CA 125 kinetics in ovarian cancer: Data from CALYPSO trial (a GINECO-GCIG study)

2013 ◽  
Vol 130 (2) ◽  
pp. 289-294 ◽  
Author(s):  
Benoit You ◽  
Olivier Colomban ◽  
Mark Heywood ◽  
Chee Lee ◽  
Margaret Davy ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Prognostic Value ◽  
Ca 125 ◽  
Cancer Data ◽  
Model Based ◽  
Ovarian Cancer Data

Detection of COVID-19 cases through X-ray images using hybrid deep neural network

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Rajit Nair ◽  
Santosh Vishwakarma ◽  
Mukesh Soni ◽  
Tejas Patel ◽  
Shubham Joshi
Keyword(s):  
Real Time ◽  
Binary Classification ◽  
Data Set ◽  
Content Type ◽  
X Ray ◽  
Internal Parameters ◽  
Average Accuracy ◽  
Chest X Ray ◽  
Multi Class Classification

Purpose The latest 2019 coronavirus (COVID-2019), which first appeared in December 2019 in Wuhan's city in China, rapidly spread around the world and became a pandemic. It has had a devastating impact on daily lives, the public's health and the global economy. The positive cases must be identified as soon as possible to avoid further dissemination of this disease and swift care of patients affected. The need for supportive diagnostic instruments increased, as no specific automated toolkits are available. The latest results from radiology imaging techniques indicate that these photos provide valuable details on the virus COVID-19. User advanced artificial intelligence (AI) technologies and radiological imagery can help diagnose this condition accurately and help resolve the lack of specialist doctors in isolated areas. In this research, a new paradigm for automatic detection of COVID-19 with bare chest X-ray images is displayed. Images are presented. The proposed model DarkCovidNet is designed to provide correct binary classification diagnostics (COVID vs no detection) and multi-class (COVID vs no results vs pneumonia) classification. The implemented model computed the average precision for the binary and multi-class classification of 98.46% and 91.352%, respectively, and an average accuracy of 98.97% and 87.868%. The DarkNet model was used in this research as a classifier for a real-time object detection method only once. A total of 17 convolutionary layers and different filters on each layer have been implemented. This platform can be used by the radiologists to verify their initial application screening and can also be used for screening patients through the cloud. Design/methodology/approach This study also uses the CNN-based model named Darknet-19 model, and this model will act as a platform for the real-time object detection system. The architecture of this system is designed in such a way that they can be able to detect real-time objects. This study has developed the DarkCovidNet model based on Darknet architecture with few layers and filters. So before discussing the DarkCovidNet model, look at the concept of Darknet architecture with their functionality. Typically, the DarkNet architecture consists of 5 pool layers though the max pool and 19 convolution layers. Assume as a convolution layer, and as a pooling layer. Findings The work discussed in this paper is used to diagnose the various radiology images and to develop a model that can accurately predict or classify the disease. The data set used in this work is the images bases on COVID-19 and non-COVID-19 taken from the various sources. The deep learning model named DarkCovidNet is applied to the data set, and these have shown signification performance in the case of binary classification and multi-class classification. During the multi-class classification, the model has shown an average accuracy 98.97% for the detection of COVID-19, whereas in a multi-class classification model has achieved an average accuracy of 87.868% during the classification of COVID-19, no detection and Pneumonia. Research limitations/implications One of the significant limitations of this work is that a limited number of chest X-ray images were used. It is observed that patients related to COVID-19 are increasing rapidly. In the future, the model on the larger data set which can be generated from the local hospitals will be implemented, and how the model is performing on the same will be checked. Originality/value Deep learning technology has made significant changes in the field of AI by generating good results, especially in pattern recognition. A conventional CNN structure includes a convolution layer that extracts characteristics from the input using the filters it applies, a pooling layer that reduces calculation efficiency and the neural network's completely connected layer. A CNN model is created by integrating one or more of these layers, and its internal parameters are modified to accomplish a specific mission, such as classification or object recognition. A typical CNN structure has a convolution layer that extracts features from the input with the filters it applies, a pooling layer to reduce the size for computational performance and a fully connected layer, which is a neural network. A CNN model is created by combining one or more such layers, and its internal parameters are adjusted to accomplish a particular task, such as classification or object recognition.

scholarly journals Integrative Genomics with Mediation Analysis in a Survival Context

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Szilárd Nemes ◽  
Toshima Z. Parris ◽  
Anna Danielsson ◽  
Zakaria Einbeigi ◽  
Gunnar Steineck ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Genomic Analysis ◽  
Mrna Levels ◽  
Integrative Genomics ◽  
Asymptotic Results ◽  
Data Set ◽  
Cancer Data ◽  
Dna And Rna ◽  
Altered Gene

DNA copy number aberrations (DCNA) and subsequent altered gene expression profiles may have a major impact on tumor initiation, on development, and eventually on recurrence and cancer-specific mortality. However, most methods employed in integrative genomic analysis of the two biological levels, DNA and RNA, do not consider survival time. In the present note, we propose the adoption of a survival analysis-based framework for the integrative analysis of DCNA and mRNA levels to reveal their implication on patient clinical outcome with the prerequisite that the effect of DCNA on survival is mediated by mRNA levels. The specific aim of the paper is to offer a feasible framework to test the DCNA-mRNA-survival pathway. We provide statistical inference algorithms for mediation based on asymptotic results. Furthermore, we illustrate the applicability of the method in an integrative genomic analysis setting by using a breast cancer data set consisting of 141 invasive breast tumors. In addition, we provide implementation in R.

Using Stratified Sample and Grid Search to Improve Disease Prediction Accuracy of SVM

2013 ◽  
Vol 295-298 ◽  
pp. 644-647 ◽  
Author(s):  
Yu Kai Yao ◽  
Hong Mei Cui ◽  
Ming Wei Len ◽  
Xiao Yun Chen
Keyword(s):  
Data Mining ◽  
Support Vector Machine ◽  
Classification Accuracy ◽  
Prediction Accuracy ◽  
Support Vector ◽  
Disease Prediction ◽  
Data Mining Algorithm ◽  
Grid Search ◽  
Mining Algorithm ◽  
Stratified Sample

SVM (Support Vector Machine) is a powerful data mining algorithm, and is mainly used to finish classification or regression tasks. In this literature, SVM is used to conduct disease prediction. We focus on integrating with stratified sample and grid search technology to improve the classification accuracy of SVM, thus, we propose an improved algorithm named SGSVM: Stratified sample and Grid search based SVM. To testify the performance of SGSVM, heart-disease data from UCI are used in our experiment, and the results show SGSVM has obvious improvement in classification accuracy, and this is very valuable especially in disease prediction.

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