MLkit: A machine-learning-powered automatic workflow for classification of cancer samples.

e13583 Background: In the era of data explosion, precision classification of cancer samples based on multi-dimensional medical data provides more insights into disease mechanism and useful hints on clinical treatment associated with tissue of origin, recurrence tendency and prognostic of chemotherapy or immunotherapy. We developed an automatic workflow MLkit to select features from large-scale multi-dimensional medical data and conduct classification through various machine learning techniques. Methods: MLkit is an automatic and one-stop workflow for classification of cancer samples with four modules: preprocessing (missing data remove or imputation and feature standardization), feature selection (unsupervised multi-statistics and supervised multiple machine estimators with recursive feature elimination and cross-validation), modeling (hyper-parameter, performance evaluation and probability calibration) and prediction. Most of current machine learning algorithms were implemented in this workflow, including linear model (logistic regression, ridge regression and stochastic gradient descent), ensemble model (gradient boosting, random forest, xgboost, catboost, lightgmb and stacking), support vector kernel (linear and non-linear), naive Bayes, k-nearest neighbors and multi-layer perceptron neural network. To evaluate the performance of this workflow, we utilized it to fit a model used for prediction of tissue of origin based on 450K DNA methylation data of 2,210 samples from lung, kidney and breast cancer patients collected in TCGA. Results: MLkit performed well in the prediction of tissue of origin for independent validation sets of cancer patients with stable feature selection, automatic hyper-parameters and efficient probability calibration, in which the model achieved AUCs ranged from 0.85 to 0.96. In addition, we also utilized this workflow on extensive real world data and most of results showed superior accuracy and stable performance. Conclusions: MLkit facilitates automated and one-stop classification of cancer samples using machine learning algorithms. It can be operated with simple command line, making it accessible to a broad range of users. The well performance of this workflow based on multi-dimensional medical data can help to improve the discovery of tumor biomarker and optimize clinical follow-up and therapeutic treatment for cancer patients.

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Techniques for Detecting Malware Traffic: A Comprehensive Approach to Feature Selection and Classification

International Journal for Research in Applied Science and Engineering Technology ◽

10.22214/ijraset.2021.39088 ◽

2021 ◽

Vol 9 (12) ◽

pp. 1-10

Author(s):

Harsha A K

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Random Forest ◽

Learning Algorithms ◽

Malware Detection ◽

Machine Learning Algorithms ◽

Gradient Boosting ◽

Support Vector ◽

Steady Increase ◽

Extreme Gradient Boosting

Abstract: Since the advent of encryption, there has been a steady increase in malware being transmitted over encrypted networks. Traditional approaches to detect malware like packet content analysis are inefficient in dealing with encrypted data. In the absence of actual packet contents, we can make use of other features like packet size, arrival time, source and destination addresses and other such metadata to detect malware. Such information can be used to train machine learning classifiers in order to classify malicious and benign packets. In this paper, we offer an efficient malware detection approach using classification algorithms in machine learning such as support vector machine, random forest and extreme gradient boosting. We employ an extensive feature selection process to reduce the dimensionality of the chosen dataset. The dataset is then split into training and testing sets. Machine learning algorithms are trained using the training set. These models are then evaluated against the testing set in order to assess their respective performances. We further attempt to tune the hyper parameters of the algorithms, in order to achieve better results. Random forest and extreme gradient boosting algorithms performed exceptionally well in our experiments, resulting in area under the curve values of 0.9928 and 0.9998 respectively. Our work demonstrates that malware traffic can be effectively classified using conventional machine learning algorithms and also shows the importance of dimensionality reduction in such classification problems. Keywords: Malware Detection, Extreme Gradient Boosting, Random Forest, Feature Selection.

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Tremor Identification Using Machine Learning in Parkinson's Disease

Early Detection of Neurological Disorders Using Machine Learning Systems - Advances in Medical Technologies and Clinical Practice ◽

10.4018/978-1-5225-8567-1.ch008 ◽

2019 ◽

pp. 128-151

Author(s):

Angana Saikia ◽

Vinayak Majhi ◽

Masaraf Hussain ◽

Sudip Paul ◽

Amitava Datta

Keyword(s):

Machine Learning ◽

Parkinson’S Disease ◽

Support Vector Machine ◽

Parkinson's Disease ◽

Discriminant Analysis ◽

Learning Algorithms ◽

The Body ◽

Machine Learning Algorithms ◽

Support Vector

Tremor is an involuntary quivering movement or shake. Characteristically occurring at rest, the classic slow, rhythmic tremor of Parkinson's disease (PD) typically starts in one hand, foot, or leg and can eventually affect both sides of the body. The resting tremor of PD can also occur in the jaw, chin, mouth, or tongue. Loss of dopamine leads to the symptoms of Parkinson's disease and may include a tremor. For some people, a tremor might be the first symptom of PD. Various studies have proposed measurable technologies and the analysis of the characteristics of Parkinsonian tremors using different techniques. Various machine-learning algorithms such as a support vector machine (SVM) with three kernels, a discriminant analysis, a random forest, and a kNN algorithm are also used to classify and identify various kinds of tremors. This chapter focuses on an in-depth review on identification and classification of various Parkinsonian tremors using machine learning algorithms.

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Evaluating Variable Selection and Machine Learning Algorithms for Estimating Forest Heights by Combining Lidar and Hyperspectral Data

ISPRS International Journal of Geo-Information ◽

10.3390/ijgi9090507 ◽

2020 ◽

Vol 9 (9) ◽

pp. 507

Author(s):

Sanjiwana Arjasakusuma ◽

Sandiaga Swahyu Kusuma ◽

Stuart Phinn

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Learning Algorithms ◽

Principal Component ◽

Hyperspectral Data ◽

Machine Learning Algorithms ◽

Gradient Boosting ◽

Support Vector ◽

Forest Height ◽

Extreme Gradient Boosting

Machine learning has been employed for various mapping and modeling tasks using input variables from different sources of remote sensing data. For feature selection involving high- spatial and spectral dimensionality data, various methods have been developed and incorporated into the machine learning framework to ensure an efficient and optimal computational process. This research aims to assess the accuracy of various feature selection and machine learning methods for estimating forest height using AISA (airborne imaging spectrometer for applications) hyperspectral bands (479 bands) and airborne light detection and ranging (lidar) height metrics (36 metrics), alone and combined. Feature selection and dimensionality reduction using Boruta (BO), principal component analysis (PCA), simulated annealing (SA), and genetic algorithm (GA) in combination with machine learning algorithms such as multivariate adaptive regression spline (MARS), extra trees (ET), support vector regression (SVR) with radial basis function, and extreme gradient boosting (XGB) with trees (XGbtree and XGBdart) and linear (XGBlin) classifiers were evaluated. The results demonstrated that the combinations of BO-XGBdart and BO-SVR delivered the best model performance for estimating tropical forest height by combining lidar and hyperspectral data, with R2 = 0.53 and RMSE = 1.7 m (18.4% of nRMSE and 0.046 m of bias) for BO-XGBdart and R2 = 0.51 and RMSE = 1.8 m (15.8% of nRMSE and −0.244 m of bias) for BO-SVR. Our study also demonstrated the effectiveness of BO for variables selection; it could reduce 95% of the data to select the 29 most important variables from the initial 516 variables from lidar metrics and hyperspectral data.

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FEASIBILITY OF MACHINE LEARNING METHODS FOR SEPARATING WOOD AND LEAF POINTS FROM TERRESTRIAL LASER SCANNING DATA

ISPRS Annals of Photogrammetry Remote Sensing and Spatial Information Sciences ◽

10.5194/isprs-annals-iv-2-w4-157-2017 ◽

2017 ◽

Vol IV-2/W4 ◽

pp. 157-164 ◽

Cited By ~ 6

Author(s):

D. Wang ◽

M. Hollaus ◽

N. Pfeifer

Keyword(s):

Machine Learning ◽

Laser Scanning ◽

Learning Algorithms ◽

Terrestrial Laser Scanning ◽

Gaussian Mixture ◽

Machine Learning Algorithms ◽

Support Vector ◽

Area Index ◽

Training Samples

Classification of wood and leaf components of trees is an essential prerequisite for deriving vital tree attributes, such as wood mass, leaf area index (LAI) and woody-to-total area. Laser scanning emerges to be a promising solution for such a request. Intensity based approaches are widely proposed, as different components of a tree can feature discriminatory optical properties at the operating wavelengths of a sensor system. For geometry based methods, machine learning algorithms are often used to separate wood and leaf points, by providing proper training samples. However, it remains unclear how the chosen machine learning classifier and features used would influence classification results. To this purpose, we compare four popular machine learning classifiers, namely Support Vector Machine (SVM), Na¨ıve Bayes (NB), Random Forest (RF), and Gaussian Mixture Model (GMM), for separating wood and leaf points from terrestrial laser scanning (TLS) data. Two trees, an <i>Erytrophleum fordii</i> and a <i>Betula pendula</i> (silver birch) are used to test the impacts from classifier, feature set, and training samples. Our results showed that RF is the best model in terms of accuracy, and local density related features are important. Experimental results confirmed the feasibility of machine learning algorithms for the reliable classification of wood and leaf points. It is also noted that our studies are based on isolated trees. Further tests should be performed on more tree species and data from more complex environments.

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A Machine Learning Approach for One-Stop Learning

Data Mining and Knowledge Discovery Technologies ◽

10.4018/978-1-59904-960-1.ch013 ◽

2008 ◽

pp. 333-357 ◽

Cited By ~ 1

Author(s):

Marco A. Alvarez ◽

SeungJin Lim

Keyword(s):

Machine Learning ◽

Learning Algorithms ◽

Machine Learning Algorithms ◽

Support Vector ◽

Learning Approach ◽

Internet Users ◽

Machine Learning Approach ◽

Supervised Learning Algorithms ◽

One Stop ◽

The Subject

Current search engines impose an overhead to motivated students and Internet users who employ the Web as a valuable resource for education. The user, searching for good educational materials for a technical subject, often spends extra time to filter irrelevant pages or ends up with commercial advertisements. It would be ideal if, given a technical subject by user who is educationally motivated, suitable materials with respect to the given subject are automatically identified by an affordable machine processing of the recommendation set returned by a search engine for the subject. In this scenario, the user can save a significant amount of time in filtering out less useful Web pages, and subsequently the user’s learning goal on the subject can be achieved more efficiently without clicking through numerous pages. This type of convenient learning is called One-Stop Learning (OSL). In this paper, the contributions made by Lim and Ko in (Lim and Ko, 2006) for OSL are redefined and modeled using machine learning algorithms. Four selected supervised learning algorithms: Support Vector Machine (SVM), AdaBoost, Naive Bayes and Neural Networks are evaluated using the same data used in (Lim and Ko, 2006). The results presented in this paper are promising, where the highest precision (98.9%) and overall accuracy (96.7%) obtained by using SVM is superior to the results presented by Lim and Ko. Furthermore, the machine learning approach presented here, demonstrates that the small set of features used to represent each Web page yields a good solution for the OSL problem.

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Invisible experience to real-time assessment in elite tennis athlete training: Sport-specific movement classification based on wearable MEMS sensor data

Proceedings of the Institution of Mechanical Engineers Part P Journal of Sports Engineering and Technology ◽

10.1177/17543371211050312 ◽

2021 ◽

pp. 175433712110503

Author(s):

Mingyue Wu ◽

Ran Wang ◽

Yang Hu ◽

Mengjiao Fan ◽

Yufan Wang ◽

...

Keyword(s):

Machine Learning ◽

Real Time ◽

Learning Algorithms ◽

Machine Learning Algorithms ◽

Support Vector ◽

Test Accuracy ◽

Z Score ◽

Mems Sensor ◽

Score Normalization

This study examined the reliability of a tennis stroke classification and assessment platform consisting of a single low-cost MEMS sensor in a wrist-worn wearable device, smartphone, and computer. The data that was collected was transmitted via Bluetooth and analyzed by machine learning algorithms. Twelve right-handed male elite tennis athletes participated in the study, and each athlete performed 150 strokes. The results from three machine learning algorithms regarding their recognition and classification of the real-time data stream were compared. Stroke recognition and classification went through pre-processing, segmentation, feature extraction, and classification with Support Vector Machine (SVM), including SVM without normalization, SVM with Min–Max, SVM with Z-score normalization, K-nearest neighbor (K-NN), and Naive Bayes (NB) machine learning algorithms. During the data training process, 10-fold cross-validation was used to avoid overfitting and suitable parameters were found within the SVM classifiers. The best classifier was achieved when C = 1 using the RBF kernel function. Different machine learning algorithms’ classification of unique stroke types yielded highly reliable clusters within each stroke type with the highest test accuracy of 99% achieved by SVM with Min–Max normalization and 98.4% achieved using SVM with a Z-score normalization classifier.

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Tremor Identification Using Machine Learning in Parkinson's Disease

Research Anthology on Diagnosing and Treating Neurocognitive Disorders ◽

10.4018/978-1-7998-3441-0.ch018 ◽

2021 ◽

pp. 341-365

Author(s):

Angana Saikia ◽

Vinayak Majhi ◽

Masaraf Hussain ◽

Sudip Paul ◽

Amitava Datta

Keyword(s):

Machine Learning ◽

Parkinson’S Disease ◽

Support Vector Machine ◽

Parkinson's Disease ◽

Discriminant Analysis ◽

Learning Algorithms ◽

The Body ◽

Machine Learning Algorithms ◽

Support Vector

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A Novel Ensemble Stacking Classification of Genetic Variations Using Machine Learning Algorithms

International Journal of Image and Graphics ◽

10.1142/s0219467823500158 ◽

2021 ◽

Author(s):

Jahnavi Yeturu ◽

Poongothai Elango ◽

S. P. Raja ◽

P. Nagendra Kumar

Keyword(s):

Machine Learning ◽

Heart Diseases ◽

Learning Algorithms ◽

Genetic Mutation ◽

Machine Learning Algorithms ◽

Support Vector ◽

Genetic Mutations ◽

Validation Data ◽

Data Set

Genetics is the clinical review of congenital mutation, where the principal advantage of analyzing genetic mutation of humans is the exploration, analysis, interpretation and description of the genetic transmitted and inherited effect of several diseases such as cancer, diabetes and heart diseases. Cancer is the most troublesome and disordered affliction as the proportion of cancer sufferers is growing massively. Identification and discrimination of the mutations that impart to the enlargement of tumor from the unbiased mutations is difficult, as majority tumors of cancer are able to exercise genetic mutations. The genetic mutations are systematized and categorized to sort the cancer by way of medical observations and considering clinical studies. At the present time, genetic mutations are being annotated and these interpretations are being accomplished either manually or using the existing primary algorithms. Evaluation and classification of each and every individual genetic mutation was basically predicated on evidence from documented content built on medical literature. Consequently, as a means to build genetic mutations, basically, depending on the clinical evidences persists a challenging task. There exist various algorithms such as one hot encoding technique is used to derive features from genes and their variations, TF-IDF is used to extract features from the clinical text data. In order to increase the accuracy of the classification, machine learning algorithms such as support vector machine, logistic regression, Naive Bayes, etc., are experimented. A stacking model classifier has been developed to increase the accuracy. The proposed stacking model classifier has obtained the log loss 0.8436 and 0.8572 for cross-validation data set and test data set, respectively. By the experimentation, it has been proved that the proposed stacking model classifier outperforms the existing algorithms in terms of log loss. Basically, minimum log loss refers to the efficient model. Here the log loss has been reduced to less than 1 by using the proposed stacking model classifier. The performance of these algorithms can be gauged on the basis of the various measures like multi-class log loss.

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Prediction of Cardiovascular Disease using Machine Learning Algorithms

International Journal of Engineering and Advanced Technology - Regular Issue ◽

10.35940/ijeat.b3986.029320 ◽

2020 ◽

Vol 9 (3) ◽

pp. 2404-2414

Keyword(s):

Machine Learning ◽

Cardiovascular Disease ◽

Logistic Regression ◽

Human Life ◽

Learning Algorithms ◽

Machine Learning Algorithms ◽

Support Vector ◽

Noise Data ◽

The Individual

Background/Aim: Healthcare is an unavoidable assignment to be done in human life. Cardiovascular sickness is a general class for a scope of infections that are influencing heart and veins. The early strategies for estimating the cardiovascular sicknesses helped in settling on choices about the progressions to have happened in high-chance patients which brought about the decrease of their dangers. Methods: In the proposed research, we have considered informational collection from kaggle and it doesn't require information pre-handling systems like the expulsion of noise data, evacuation of missing information, filling default esteems if applicable and classification of attributes for prediction and decision making at different levels. The performance of the diagnosis model is obtained by using methods like classification, accuracy, sensitivity and specificity analysis. This paper proposes a prediction model to predict whether a people have a cardiovascular disease or not and to provide an awareness or diagnosis on that. This is done by comparing the accuracies of applying rules to the individual results of Support Vector Machine, Random forest, Naive Bayes classifier and logistic regression on the dataset taken in a region to present an accurate model of predicting cardiovascular disease. Results: The machine learning algorithms under study were able to predict cardiovascular disease in patients with accuracy between 58.71% and 77.06%. Conclusions: It was shown that Logistic Regression has better Accuracy (77.06 %) when compared to different Machine-learning Algorithms.

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Survival prediction for bladder cancer using machine learning: development of BlaCaSurv online survival prediction application

10.1101/2020.11.13.20231191 ◽

2020 ◽

Author(s):

Ashis Kumar Das ◽

Shiba Mishra ◽

Devi Kalyan Mishra ◽

Saji Saraswathy Gopalan

Keyword(s):

Machine Learning ◽

Bladder Cancer ◽

Cancer Patients ◽

Web Application ◽

Learning Algorithms ◽

Machine Learning Algorithms ◽

Gradient Boosting ◽

Support Vector ◽

Survival Prediction ◽

Common Cause

AbstractBackgroundBladder cancer is the most common cancer of the urinary system among the American population and it is the fourth most common cause of cancer morbidity and the eight most common cause of cancer mortality among men. Using machine learning algorithms, we predict the five-year survival among bladder cancer patients and deploy the best performing algorithm as a web application for survival prediction.MethodsMicroscopically confirmed adult bladder cancer patients were included from the Surveillance Epidemiology and End Results (SEER) database (2000-2017) and randomly split into training and test datasets (70/30 ratio). Five machine learning algorithms (logistic regression, support vector machine, gradient boosting, random forest, and K nearest neighbor) were trained on features to predict five-year survival. The algorithms were compared with performance metrics and the best performing algorithm was deployed as a web application.ResultsA total of 52,529 patients were included in our study. The gradient boosting algorithm was the best performer in terms of predictive ability and discrimination. It was deployed as the survival prediction web application named BlaCaSurv (https://blacasurv.herokuapp.com/).ConclusionsWe tested several machine learning algorithms and developed a web application for predicting five-year survival for bladder cancer patients. This application can be used as a supplementary prognostic tool to clinical decision making.

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