scholarly journals Comparison of SVM and Spectral Embedding in Promoter Biobricks’ Categorizing and Clustering

2019 ◽  
Author(s):  
Shangjie Zou
Keyword(s):  
Machine Learning ◽  
Dna Sequences ◽  
Learning Algorithm ◽  
Source Code ◽  
Laplacian Matrix ◽  
Support Vector ◽  
Inducible Promoters ◽  
Functional Annotations ◽  
Spectral Embedding

AbstractBackgroundIn organisms’ genomes, promoters are short DNA sequences on the upstream of structural genes, with the function of controlling genes’ transcription. Promoters can be roughly divided into two classes: constitutive promoters and inducible promoters. Promoters with clear functional annotations are practical synthetic biology biobricks. Many statistical and machine learning methods have been introduced to predict the functions of candidate promoters. Spectral Eigenmap has been proved to be an effective clustering method to classify biobricks, while support vector machine (SVM) is a powerful machine learning algorithm, especially when dataset is small.MethodsThe two algorithms: spectral embedding and SVM are applied to the same dataset with 375 prokaryotic promoters. For spectral embedding, a Laplacian matrix is built with edit distance, followed by K-Means Clustering. The sequences are represented by numeric vector to serve as dataset for SVM trainning.ResultsSVM achieved a high predicting accuracy of 93.07% in 10-fold cross validation for classification of promoters’ transcriptional functions. Laplacian eigenmap (spectral embedding) based on editing distance may not be capable for extracting discriminative features for this task.AvailabilityCodes, datasets and some important matrices are available on github https://github.com/shangjieZou/Promoter-transcriptional-predictor/tree/source-code

Recognition and Classification of Human Activity by Posture Sensing and Machine Learning

2012 ◽  
Vol 468-471 ◽  
pp. 2916-2919
Author(s):  
Fan Yang ◽  
Yu Chuan Wu
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Human Activity ◽  
Learning Algorithm ◽  
Optimal Parameter ◽  
Support Vector ◽  
Rbf Kernel ◽  
Human Activity Detection ◽  
Near Future

This paper describes how to use a posture sensor to validate human daily activity and by machine learning algorithm - Support Vector Machine (SVM) an outstanding model is built. The optimal parameter σ and c of RBF kernel SVM were obtained by searching automatically. Those kinematic data was carried out through three major steps: wavelet transformation, Principle Component Analysis (PCA) -based dimensionality reduction and k-fold cross-validation, followed by implementing a best classifier to distinguish 6 difference actions. As an activity classifier, the SVM (Support Vector Machine) algorithm is used, and we have achieved over 94.5% of mean accuracy in detecting differential actions. It shows that the verification approach based on the recognition of human activity detection is valuable and will be further explored in the near future.

scholarly journals Extraction of Sea Ice Cover by Sentinel-1 SAR Based on SVM with Unsupervised Generation of Training Data

2020 ◽  
Author(s):  
Xiaoming Li ◽  
Yan Sun ◽  
Qiang Zhang
Keyword(s):  
Machine Learning ◽  
Sea Ice ◽  
Learning Algorithm ◽  
Texture Features ◽  
Open Water ◽  
Ice Cover ◽  
Training Data ◽  
Support Vector ◽  
Training Samples

In this paper, we focus on developing a novel method to extract sea ice cover (i.e., discrimination/classification of sea ice and open water) using Sentinel-1 (S1) cross-polarization (vertical-horizontal, VH or horizontal-vertical, HV) data in extra wide (EW) swath mode based on the machine learning algorithm support vector machine (SVM). The classification basis includes the S1 radar backscatter coefficients and texture features that are calculated from S1 data using the gray level co-occurrence matrix (GLCM). Different from previous methods where appropriate samples are manually selected to train the SVM to classify sea ice and open water, we proposed a method of unsupervised generation of the training samples based on two GLCM texture features, i.e. entropy and homogeneity, that have contrasting characteristics on sea ice and open water. We eliminate the most uncertainty of selecting training samples in machine learning and achieve automatic classification of sea ice and open water by using S1 EW data. The comparison shows good agreement between the SAR-derived sea ice cover using the proposed method and a visual inspection, of which the accuracy reaches approximately 90% - 95% based on a few cases. Besides this, compared with the analyzed sea ice cover data Ice Mapping System (IMS) based on 728 S1 EW images, the accuracy of extracted sea ice cover by using S1 data is more than 80%.

Classification of P2P Traffic Based on a Heteromorphic Ensemble Learning Model

2014 ◽  
Vol 687-691 ◽  
pp. 2693-2697
Author(s):  
Li Ding ◽  
Li Mao ◽  
Xiao Feng Wang
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Ensemble Learning ◽  
Classification Accuracy ◽  
Learning Algorithm ◽  
Learning Model ◽  
Support Vector ◽  
Machine Learning Algorithm ◽  
Data Environment

One single machine learning algorithm presents shortcomings when the data environment changes in the process of application. This article puts forward a heteromorphic ensemble learning model made up of bayes, support vector machine (SVM) and decision tree which classifies P2P traffic by voting principle. The experiment shows that the model can significantly improve the classification accuracy, and has a good stability.

scholarly journals Forecasting of Breast Cancer and Diabetes Using Ensemble Learning

2019 ◽  
Vol 1 (1) ◽  
pp. 1-5 ◽  
Author(s):  
Shraboni Rudra ◽  
Minhaz Uddin ◽  
Mohammed Minhajul Alam
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Learning Algorithm ◽  
Combine Method ◽  
Diabetes Patient ◽  
Support Vector ◽  
Classification Of Diseases ◽  
The Cost ◽  
Very High

Machine learning algorithm plays an important role in our life. It is the subset of Artificial intelligence. Recently, everyone tries to use AI or try to invent something related to    AI for making life easier. In the medical field, Machine learning is used for the recognition and classification of diseases. It can classify cancer, diabetes or other diseases more accurately from datasets. So, we propose a model which is the combination of Support vector machine and Ad boost. This combine method is known as Ensemble learner. In this paper, we are predicting diabetes and breast cancer. We have used SVM for classification purpose then have applied Ad boost for boosting purposes. The number of a diabetes patient is increasing very rapidly. It causes many other diseases like kidney failure; Eye disorder etc. No medicines are invented to prevent diabetes fully.  Breast cancer is increasing very rapidly between women. The cost of breast cancer treatment is very high. More researches are running on diabetes and breast cancer. We proposed our model to predict the diseases more accurately rather than the previous models.

scholarly journals Amrita-CEN-Senti-DB:Twitter Dataset for Sentimental Analysis and Application of Classical Machine Learning and Deep Learning

2020 ◽  
Author(s):  
vinayakumar R
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Language Processing ◽  
Learning Algorithm ◽  
Support Vector ◽  
Text Data ◽  
Inverse Document Frequency ◽  
Logistics Regression ◽  
Document Frequency

<p><b>Social media is a platform in which tons and tons of text are generated each and every day. The data is so large that cannot be easily understood, so this has paved a path to a new field in the information technology which is natural language processing. In this paper, the text data which is used for the classification is tweets that determines the state of the person according of the sentiments which is positive, negative and neutral. Emotions are the way of expression of the person’s feelings which has a high influence on the decision making tasks. Here we have proposed the text representation, Term Frequency Inverse Document Frequency (tfidf), Keras embedding along with the machine learning and deep learning algorithms for the purpose of the classification of the sentiments, out of which Logistics Regression machine learning based methods out performs well when the features is taken in the limited amount as the features increases Support Vector Machine (SVM) which is also one of the machine learning algorithm out performs well making a benchmark accuracy for this dataset as the 75.8%. For the research purpose the dataset has been made publically available.</b><b></b></p>

scholarly journals Amrita-CEN-Senti-DB:Twitter Dataset for Sentimental Analysis and Application of Classical Machine Learning and Deep Learning

2020 ◽  
Author(s):  
vinayakumar R
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Language Processing ◽  
Learning Algorithm ◽  
Support Vector ◽  
Text Data ◽  
Inverse Document Frequency ◽  
Logistics Regression ◽  
Document Frequency

<p><b>Social media is a platform in which tons and tons of text are generated each and every day. The data is so large that cannot be easily understood, so this has paved a path to a new field in the information technology which is natural language processing. In this paper, the text data which is used for the classification is tweets that determines the state of the person according of the sentiments which is positive, negative and neutral. Emotions are the way of expression of the person’s feelings which has a high influence on the decision making tasks. Here we have proposed the text representation, Term Frequency Inverse Document Frequency (tfidf), Keras embedding along with the machine learning and deep learning algorithms for the purpose of the classification of the sentiments, out of which Logistics Regression machine learning based methods out performs well when the features is taken in the limited amount as the features increases Support Vector Machine (SVM) which is also one of the machine learning algorithm out performs well making a benchmark accuracy for this dataset as the 75.8%. For the research purpose the dataset has been made publically available.</b><b></b></p>

scholarly journals Predictive Modelling of Employee Turnover in Indian IT Industry Using Machine Learning Techniques

2019 ◽  
Vol 23 (1) ◽  
pp. 12-21 ◽  
Author(s):  
Shikha N. Khera ◽  
Divya
Keyword(s):  
Machine Learning ◽  
Learning Algorithm ◽  
Confusion Matrix ◽  
Predictive Modelling ◽  
Supervised Machine Learning ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
It Industry ◽  
Knowledge Based ◽  
Employee Attrition

Information technology (IT) industry in India has been facing a systemic issue of high attrition in the past few years, resulting in monetary and knowledge-based loses to the companies. The aim of this research is to develop a model to predict employee attrition and provide the organizations opportunities to address any issue and improve retention. Predictive model was developed based on supervised machine learning algorithm, support vector machine (SVM). Archival employee data (consisting of 22 input features) were collected from Human Resource databases of three IT companies in India, including their employment status (response variable) at the time of collection. Accuracy results from the confusion matrix for the SVM model showed that the model has an accuracy of 85 per cent. Also, results show that the model performs better in predicting who will leave the firm as compared to predicting who will not leave the company.

scholarly journals Machine learning algorithm improved automated droplet classification of ddPCR for detection of BRAF V600E in paraffin-embedded samples

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Gabriel A. Colozza-Gama ◽  
Fabiano Callegari ◽  
Nikola Bešič ◽  
Ana C. de J. Paviza ◽  
Janete M. Cerutti
Keyword(s):  
Machine Learning ◽  
Sanger Sequencing ◽  
Learning Algorithm ◽  
Absolute Quantification ◽  
Braf V600e Mutation ◽  
Braf V600e ◽  
Driver Genes ◽  
Quantitative Classification ◽  
Cancer Driver

AbstractSomatic mutations in cancer driver genes can help diagnosis, prognosis and treatment decisions. Formalin-fixed paraffin-embedded (FFPE) specimen is the main source of DNA for somatic mutation detection. To overcome constraints of DNA isolated from FFPE, we compared pyrosequencing and ddPCR analysis for absolute quantification of BRAF V600E mutation in the DNA extracted from FFPE specimens and compared the results to the qualitative detection information obtained by Sanger Sequencing. Sanger sequencing was able to detect BRAF V600E mutation only when it was present in more than 15% total alleles. Although the sensitivity of ddPCR is higher than that observed for Sanger, it was less consistent than pyrosequencing, likely due to droplet classification bias of FFPE-derived DNA. To address the droplet allocation bias in ddPCR analysis, we have compared different algorithms for automated droplet classification and next correlated these findings with those obtained from pyrosequencing. By examining the addition of non-classifiable droplets (rain) in ddPCR, it was possible to obtain better qualitative classification of droplets and better quantitative classification compared to no rain droplets, when considering pyrosequencing results. Notable, only the Machine learning k-NN algorithm was able to automatically classify the samples, surpassing manual classification based on no-template controls, which shows promise in clinical practice.

scholarly journals Early Prediction of Seven-Day Mortality in Intensive Care Unit Using a Machine Learning Model: Results from the SPIN-UTI Project

2021 ◽  
Vol 10 (5) ◽  
pp. 992
Author(s):  
Martina Barchitta ◽  
Andrea Maugeri ◽  
Giuliana Favara ◽  
Paolo Marco Riela ◽  
Giovanni Gallo ◽  
...  
Keyword(s):  
Machine Learning ◽  
Intensive Care ◽  
Intensive Care Units ◽  
Learning Algorithm ◽  
Area Under The Curve ◽  
Support Vector ◽  
Icu Admission ◽  
Risk Of Death ◽  
Saps Ii ◽  
Svm Algorithm

Patients in intensive care units (ICUs) were at higher risk of worsen prognosis and mortality. Here, we aimed to evaluate the ability of the Simplified Acute Physiology Score (SAPS II) to predict the risk of 7-day mortality, and to test a machine learning algorithm which combines the SAPS II with additional patients’ characteristics at ICU admission. We used data from the “Italian Nosocomial Infections Surveillance in Intensive Care Units” network. Support Vector Machines (SVM) algorithm was used to classify 3782 patients according to sex, patient’s origin, type of ICU admission, non-surgical treatment for acute coronary disease, surgical intervention, SAPS II, presence of invasive devices, trauma, impaired immunity, antibiotic therapy and onset of HAI. The accuracy of SAPS II for predicting patients who died from those who did not was 69.3%, with an Area Under the Curve (AUC) of 0.678. Using the SVM algorithm, instead, we achieved an accuracy of 83.5% and AUC of 0.896. Notably, SAPS II was the variable that weighted more on the model and its removal resulted in an AUC of 0.653 and an accuracy of 68.4%. Overall, these findings suggest the present SVM model as a useful tool to early predict patients at higher risk of death at ICU admission.

scholarly journals Machine learning-based ability to classify psychosis and early stages of disease through parenting and attachment-related variables is associated with social cognition

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Linda A. Antonucci ◽  
Alessandra Raio ◽  
Giulio Pergola ◽  
Barbara Gelao ◽  
Marco Papalino ◽  
...  
Keyword(s):  
Machine Learning ◽  
Social Cognition ◽  
Attachment Style ◽  
Learning Algorithm ◽  
Early Recognition ◽  
Emotion Perception ◽  
First Episode ◽  
Support Vector ◽  
Significant Group ◽  
Early Stages

Abstract Background Recent views posited that negative parenting and attachment insecurity can be considered as general environmental factors of vulnerability for psychosis, specifically for individuals diagnosed with psychosis (PSY). Furthermore, evidence highlighted a tight relationship between attachment style and social cognition abilities, a key PSY behavioral phenotype. The aim of this study is to generate a machine learning algorithm based on the perceived quality of parenting and attachment style-related features to discriminate between PSY and healthy controls (HC) and to investigate its ability to track PSY early stages and risk conditions, as well as its association with social cognition performance. Methods Perceived maternal and paternal parenting, as well as attachment anxiety and avoidance scores, were trained to separate 71 HC from 34 PSY (20 individuals diagnosed with schizophrenia + 14 diagnosed with bipolar disorder with psychotic manifestations) using support vector classification and repeated nested cross-validation. We then validated this model on independent datasets including individuals at the early stages of disease (ESD, i.e. first episode of psychosis or depression, or at-risk mental state for psychosis) and with familial high risk for PSY (FHR, i.e. having a first-degree relative suffering from psychosis). Then, we performed factorial analyses to test the group x classification rate interaction on emotion perception, social inference and managing of emotions abilities. Results The perceived parenting and attachment-based machine learning model discriminated PSY from HC with a Balanced Accuracy (BAC) of 72.2%. Slightly lower classification performance was measured in the ESD sample (HC-ESD BAC = 63.5%), while the model could not discriminate between FHR and HC (BAC = 44.2%). We observed a significant group x classification interaction in PSY and HC from the discovery sample on emotion perception and on the ability to manage emotions (both p = 0.02). The interaction on managing of emotion abilities was replicated in the ESD and HC validation sample (p = 0.03). Conclusion Our results suggest that parenting and attachment-related variables bear significant classification power when applied to both PSY and its early stages and are associated with variability in emotion processing. These variables could therefore be useful in psychosis early recognition programs aimed at softening the psychosis-associated disability.

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