scholarly journals Performance of Genotypic Tools for Prediction of Tropism in HIV-1 Subtype C V3 Loop Sequences

Intervirology ◽  
2015 ◽  
Vol 58 (1) ◽  
pp. 1-5 ◽  
Author(s):  
Soham Gupta ◽  
Ujjwal Neogi ◽  
Hiresave Srinivasa ◽  
Anita Shet
Keyword(s):  
Machine Learning ◽  
False Positive Rate ◽  
Machine Learning Algorithms ◽  
Clinical Settings ◽  
V3 Loop ◽  
Subtype C ◽  
Positive Rate ◽  
Good Concordance ◽  
Hiv 1 ◽  
Tropism Prediction

Currently, there is no consensus on the genotypic tools to be used for tropism analysis in HIV-1 subtype C strains. Thus, the aim of the study was to evaluate the performance of the different V3 loop-based genotypic algorithms available. We compiled a dataset of 645 HIV-1 subtype C V3 loop sequences of known coreceptor phenotypes (531 R5-tropic/non-syncytium-inducing and 114 X4-tropic/R5X4-tropic/syncytium-inducing sequences) from the Los Alamos database (http://www.hiv.lanl.gov/) and previously published literature. Coreceptor usage was predicted based on this dataset using different software-based machine-learning algorithms as well as simple classical rules. All the sophisticated machine-learning methods showed a good concordance of above 85%. Geno2Pheno (false-positive rate cutoff of 5-15%) and CoRSeqV3-C were found to have a high predicting capability in determining both HIV-1 subtype C X4-tropic and R5-tropic strains. The current sophisticated genotypic tropism tools based on V3 loop perform well for tropism prediction in HIV-1 subtype C strains and can be used in clinical settings.

Machine Learning for Automated Polyp Detection in Computed Tomography Colonography

2012 ◽  
pp. 830-850
Author(s):  
Abhilash Alexander Miranda ◽  
Olivier Caelen ◽  
Gianluca Bontempi
Keyword(s):  
Machine Learning ◽  
Computed Tomography ◽  
False Positive ◽  
False Positive Rate ◽  
Learning Algorithms ◽  
Colorectal Polyps ◽  
Machine Learning Algorithms ◽  
Computed Tomography Colonography ◽  
Positive Rate ◽  
Independent Features

This chapter presents a comprehensive scheme for automated detection of colorectal polyps in computed tomography colonography (CTC) with particular emphasis on robust learning algorithms that differentiate polyps from non-polyp shapes. The authors’ automated CTC scheme introduces two orientation independent features which encode the shape characteristics that aid in classification of polyps and non-polyps with high accuracy, low false positive rate, and low computations making the scheme suitable for colorectal cancer screening initiatives. Experiments using state-of-the-art machine learning algorithms viz., lazy learning, support vector machines, and naïve Bayes classifiers reveal the robustness of the two features in detecting polyps at 100% sensitivity for polyps with diameter greater than 10 mm while attaining total low false positive rates, respectively, of 3.05, 3.47 and 0.71 per CTC dataset at specificities above 99% when tested on 58 CTC datasets. The results were validated using colonoscopy reports provided by expert radiologists.

scholarly journals Early Weed Detection Using Image Processing and Machine Learning Techniques in an Australian Chilli Farm

Agriculture ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 387
Author(s):  
Nahina Islam ◽  
Md Mamunur Rashid ◽  
Santoso Wibowo ◽  
Cheng-Yuan Xu ◽  
Ahsan Morshed ◽  
...  
Keyword(s):  
Machine Learning ◽  
False Positive Rate ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Weed Detection ◽  
Learning Techniques ◽  
Positive Rate ◽  
Uav Images

This paper explores the potential of machine learning algorithms for weed and crop classification from UAV images. The identification of weeds in crops is a challenging task that has been addressed through orthomosaicing of images, feature extraction and labelling of images to train machine learning algorithms. In this paper, the performances of several machine learning algorithms, random forest (RF), support vector machine (SVM) and k-nearest neighbours (KNN), are analysed to detect weeds using UAV images collected from a chilli crop field located in Australia. The evaluation metrics used in the comparison of performance were accuracy, precision, recall, false positive rate and kappa coefficient. MATLAB is used for simulating the machine learning algorithms; and the achieved weed detection accuracies are 96% using RF, 94% using SVM and 63% using KNN. Based on this study, RF and SVM algorithms are efficient and practical to use, and can be implemented easily for detecting weed from UAV images.

scholarly journals Malicious Intrusion Detection Using Machine Learning Schemes

2019 ◽  
Vol 8 (6) ◽  
pp. 4194-4198
Keyword(s):  
Machine Learning ◽  
Wireless Networks ◽  
Intrusion Detection ◽  
False Positive Rate ◽  
Feature Selection Method ◽  
Training Model ◽  
True Positive Rate ◽  
Machine Learning Algorithms ◽  
Detection Mechanism ◽  
Positive Rate

Wireless networks are continuously facing challenges in the field of Information Security. This leads to major researches in the area of Intrusion detection. The working of Intrusion detection is performed mainly by signature based detection and anomaly based detection. Anomaly based detection is based on the behavior of the network. One of the major challenge in this domain is to identify and detect the malicious node in wireless networks. The intrusion detection mechanism has to analyse the behavior of the node in the network by means of the several features possessed by each node. Intelligent schemes are the need of the hour in such scenario. This paper has taken a standard dataset for studying the features of the wireless node and reduced the features by applying the most efficient Correlation Attribute feature selection method. The machine learning algorithms are applied to obtain an effective training model which is then applied on the testing dataset to validate the model. The accuracy of the model is determined by the performance parameters such as true positive rate, false positive rate and ROC area. Neural network, bagging and decision tree algorithm RepTree are giving promising results in comparison with other classification algorithms.

scholarly journals Reducing Pseudo-error Rate of Industrial Machine Vision Systems with Machine Learning Methods

2019 ◽  
Vol 12 (4) ◽  
pp. 294-305
Author(s):  
Balázs Szűcs ◽  
Áron Ballagi
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Machine Vision ◽  
Error Rate ◽  
Materials Science ◽  
False Positive Rate ◽  
Machine Learning Algorithms ◽  
Positive Rate ◽  
Industrial Use ◽  
Industrial Machine

Nowadays machine learning and artificial neural networks are hot topic. These methods gains more and more ground in everyday life. In addition to everyday usage, an increasing emphasis placed on industrial use. In the field of research and development, materials science, robotics and thanks to the spread of Industry 4.0 and digitalization, more and more machine learning based systems introduced in production. This paper gives examples of possible ways of using machine learning algorithms in manufacturing, as well as reducing pseudo-error (false positive) rate of machine vision quality control systems. Even the simplest algorithms and models can be very effective on real-world problems. With the usage of convolutional neural networks, the pseudo-error rate of the examined system reducible.

scholarly journals LC-MS Peak Assignment Based on Unanimous Selection by Six Machine Learning Algorithms

2021 ◽  
Author(s):  
Hiroaki Ito ◽  
Takashi Matsui ◽  
Ryo Konno ◽  
Makoto Itakura ◽  
Yoshio Kodera
Keyword(s):  
Machine Learning ◽  
Learning Algorithm ◽  
False Positive Rate ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Weak Signals ◽  
Accuracy And Precision ◽  
Peak Assignment ◽  
Positive Rate ◽  
Assignment Strategy

Abstract Recent Mass spectrometry (MS)-based techniques enable deep proteome coverage with relative quantitative analysis, resulting in increased identification of very weak signals accompanied by increased data size of liquid chromatography (LC)–MS/MS spectra. However, the identification of weak signals using an assignment strategy with poorer performance resulted in imperfect quantification with misidentification of peaks and ratio distortions. Manually annotating a large number of signals within a very large dataset is not a realistic approach. In this study, therefore, we utilized machine learning algorithms to successfully extract a higher number of peptide peaks with high accuracy and precision. Our strategy evaluated each peak identified using six different algorithms; peptide peaks identified by all six algorithms (i.e., unanimously selected) were subsequently assigned as true peaks, which resulted in a reduction in the false-positive rate. Hence, exact and highly quantitative peptide peaks were obtained, providing better performance than obtained applying the conventional criteria or using a single machine learning algorithm.

Machine Learning for Automated Polyp Detection in Computed Tomography Colonography

2010 ◽  
pp. 54-77
Author(s):  
Abhilash Alexander Miranda ◽  
Olivier Caelen ◽  
Gianluca Bontempi
Keyword(s):  
Machine Learning ◽  
Computed Tomography ◽  
False Positive ◽  
False Positive Rate ◽  
Learning Algorithms ◽  
Colorectal Polyps ◽  
Machine Learning Algorithms ◽  
Computed Tomography Colonography ◽  
Positive Rate ◽  
Independent Features

This chapter presents a comprehensive scheme for automated detection of colorectal polyps in computed tomography colonography (CTC) with particular emphasis on robust learning algorithms that differentiate polyps from non-polyp shapes. The authors’ automated CTC scheme introduces two orientation independent features which encode the shape characteristics that aid in classification of polyps and non-polyps with high accuracy, low false positive rate, and low computations making the scheme suitable for colorectal cancer screening initiatives. Experiments using state-of-the-art machine learning algorithms viz., lazy learning, support vector machines, and naïve Bayes classifiers reveal the robustness of the two features in detecting polyps at 100% sensitivity for polyps with diameter greater than 10 mm while attaining total low false positive rates, respectively, of 3.05, 3.47 and 0.71 per CTC dataset at specificities above 99% when tested on 58 CTC datasets. The results were validated using colonoscopy reports provided by expert radiologists.

Comparative Study of Various Machine Learning Algorithms for Prediction of Insomnia

2019 ◽  
pp. 234-257 ◽  
Author(s):  
Ravinder Ahuja ◽  
Vishal Vivek ◽  
Manika Chandna ◽  
Shivani Virmani ◽  
Alisha Banga
Keyword(s):  
Machine Learning ◽  
Heart Diseases ◽  
False Positive Rate ◽  
Learning Algorithms ◽  
True Positive Rate ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Mobility Problem ◽  
Positive Rate ◽  
F Measure

An early diagnosis of insomnia can prevent further medical aids such as anger issues, heart diseases, anxiety, depression, and hypertension. Fifteen machine learning algorithms have been applied and 14 leading factors have been taken into consideration for predicting insomnia. Seven performance parameters (accuracy, kappa, the true positive rate, false positive rate, precision, f-measure, and AUC) are used and for implementation. The authors have used python language. The support vector machine is giving higher performance out of all algorithms giving accuracy 91.6%, f-measure is 92.13, and kappa is 0.83. Further, SVM is applied on another dataset of 100 patients and giving accuracy 92%. In addition, an analysis of the variable importance of CART, C5.0, decision tree, random forest, adaptive boost, and XG boost is calculated. The analysis shows that insomnia primarily depends on the factors, which are the vision problem, mobility problem, and sleep disorder. This chapter mainly finds the usages and effectiveness of machine learning algorithms in Insomnia diseases prediction.

scholarly journals Landslide Susceptibility Assessment by Novel Hybrid Machine Learning Algorithms

2019 ◽  
Vol 11 (16) ◽  
pp. 4386 ◽  
Author(s):  
Pham ◽  
Shirzadi ◽  
Shahabi ◽  
Omidvar ◽  
Singh ◽  
...  
Keyword(s):  
Machine Learning ◽  
Characteristic Curve ◽  
False Positive Rate ◽  
Spatial Prediction ◽  
Machine Learning Algorithms ◽  
Ensemble Model ◽  
Power Prediction ◽  
Landslide Occurrence ◽  
Positive Rate ◽  
Hybrid Machine

: Landslides have multidimensional effects on the socioeconomic as well as environmental conditions of the impacted areas. The aim of this study is the spatial prediction of landslide using hybrid machine learning models including bagging (BA), random subspace (RS) and rotation forest (RF) with alternating decision tree (ADTree) as base classifier in the northern part of the Pithoragarh district, Uttarakhand, Himalaya, India. To construct the database, ten conditioning factors and a total of 103 landslide locations with a ratio of 70/30 were used. The significant factors were determined by chi-square attribute evaluation (CSEA) technique. The validity of the hybrid models was assessed by true positive rate (TP Rate), false positive rate (FP Rate), recall (sensitivity), precision, F-measure and area under the receiver operatic characteristic curve (AUC). Results concluded that land cover was the most important factor while curvature had no effect on landslide occurrence in the study area and it was removed from the modelling process. Additionally, results indicated that although all ensemble models enhanced the power prediction of the ADTree classifier (AUCtraining = 0.859; AUCvalidation = 0.813); however, the RS ensemble model (AUCtraining = 0.883; AUCvalidation = 0.842) outperformed and outclassed the RF (AUCtraining = 0.871; AUCvalidation = 0.840), and the BA (AUCtraining = 0.865; AUCvalidation = 0.836) ensemble model. The obtained results would be helpful for recognizing the landslide prone areas in future to better manage and decrease the damage and negative impacts on the environment.

scholarly journals Detecting Smoking Events Using Accelerometer Data Collected Via Smartwatch Technology: Validation Study (Preprint)

2017 ◽  
Author(s):  
Casey A Cole ◽  
Dien Anshari ◽  
Victoria Lambert ◽  
James F Thrasher ◽  
Homayoun Valafar
Keyword(s):  
Machine Learning ◽  
False Positive ◽  
False Positive Rate ◽  
Smoking Behavior ◽  
Observation Time ◽  
Machine Learning Algorithms ◽  
Accelerometer Data ◽  
Convenience Sample ◽  
Study Protocols ◽  
Positive Rate

BACKGROUND Smoking is the leading cause of preventable death in the world today. Ecological research on smoking in context currently relies on self-reported smoking behavior. Emerging smartwatch technology may more objectively measure smoking behavior by automatically detecting smoking sessions using robust machine learning models. OBJECTIVE This study aimed to examine the feasibility of detecting smoking behavior using smartwatches. The second aim of this study was to compare the success of observing smoking behavior with smartwatches to that of conventional self-reporting. METHODS A convenience sample of smokers was recruited for this study. Participants (N=10) recorded 12 hours of accelerometer data using a mobile phone and smartwatch. During these 12 hours, they engaged in various daily activities, including smoking, for which they logged the beginning and end of each smoking session. Raw data were classified as either smoking or nonsmoking using a machine learning model for pattern recognition. The accuracy of the model was evaluated by comparing the output with a detailed description of a modeled smoking session. RESULTS In total, 120 hours of data were collected from participants and analyzed. The accuracy of self-reported smoking was approximately 78% (96/123). Our model was successful in detecting 100 of 123 (81%) smoking sessions recorded by participants. After eliminating sessions from the participants that did not adhere to study protocols, the true positive detection rate of the smartwatch based-detection increased to more than 90%. During the 120 hours of combined observation time, only 22 false positive smoking sessions were detected resulting in a 2.8% false positive rate. CONCLUSIONS Smartwatch technology can provide an accurate, nonintrusive means of monitoring smoking behavior in natural contexts. The use of machine learning algorithms for passively detecting smoking sessions may enrich ecological momentary assessment protocols and cessation intervention studies that often rely on self-reported behaviors and may not allow for targeted data collection and communications around smoking events.

scholarly journals LC–MS peak assignment based on unanimous selection by six machine learning algorithms

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hiroaki Ito ◽  
Takashi Matsui ◽  
Ryo Konno ◽  
Makoto Itakura ◽  
Yoshio Kodera
Keyword(s):  
Machine Learning ◽  
Learning Algorithm ◽  
False Positive Rate ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Weak Signals ◽  
Accuracy And Precision ◽  
Positive Rate ◽  
Assignment Strategy ◽  
Performance Results

AbstractRecent mass spectrometry (MS)-based techniques enable deep proteome coverage with relative quantitative analysis, resulting in increased identification of very weak signals accompanied by increased data size of liquid chromatography (LC)–MS/MS spectra. However, the identification of weak signals using an assignment strategy with poorer performance results in imperfect quantification with misidentification of peaks and ratio distortions. Manually annotating a large number of signals within a very large dataset is not a realistic approach. In this study, therefore, we utilized machine learning algorithms to successfully extract a higher number of peptide peaks with high accuracy and precision. Our strategy evaluated each peak identified using six different algorithms; peptide peaks identified by all six algorithms (i.e., unanimously selected) were subsequently assigned as true peaks, which resulted in a reduction in the false-positive rate. Hence, exact and highly quantitative peptide peaks were obtained, providing better performance than obtained applying the conventional criteria or using a single machine learning algorithm.

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