scholarly journals A novel dimension reduction algorithm based on weighted kernel principal analysis for gene expression data

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258326
Author(s):  
Wen Bo Liu ◽  
Sheng Nan Liang ◽  
Xi Wen Qin
Keyword(s):  
Gene Expression ◽  
Machine Learning ◽  
Random Forest ◽  
Dimension Reduction ◽  
Principal Component ◽  
Classification Performance ◽  
Kernel Functions ◽  
Reduction Algorithm ◽  
Expression Data ◽  
Weighted Kernel

Gene expression data has the characteristics of high dimensionality and a small sample size and contains a large number of redundant genes unrelated to a disease. The direct application of machine learning to classify this type of data will not only incur a great time cost but will also sometimes fail to improved classification performance. To counter this problem, this paper proposes a dimension-reduction algorithm based on weighted kernel principal component analysis (WKPCA), constructs kernel function weights according to kernel matrix eigenvalues, and combines multiple kernel functions to reduce the feature dimensions. To further improve the dimensional reduction efficiency of WKPCA, t-class kernel functions are constructed, and corresponding theoretical proofs are given. Moreover, the cumulative optimal performance rate is constructed to measure the overall performance of WKPCA combined with machine learning algorithms. Naive Bayes, K-nearest neighbour, random forest, iterative random forest and support vector machine approaches are used in classifiers to analyse 6 real gene expression dataset. Compared with the all-variable model, linear principal component dimension reduction and single kernel function dimension reduction, the results show that the classification performance of the 5 machine learning methods mentioned above can be improved effectively by WKPCA dimension reduction.

scholarly journals Transformer Oil Quality Assessment Using Random Forest with Feature Engineering

Energies ◽  
2021 ◽  
Vol 14 (7) ◽  
pp. 1809
Author(s):  
Mohammed El Amine Senoussaoui ◽  
Mostefa Brahami ◽  
Issouf Fofana
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Oil Quality ◽  
Principal Component ◽  
Condition Assessment ◽  
Classification Performance ◽  
Transformer Oil ◽  
Classification Model ◽  
Insulation Degradation ◽  
Transformer Oils

Machine learning is widely used as a panacea in many engineering applications including the condition assessment of power transformers. Most statistics attribute the main cause of transformer failure to insulation degradation. Thus, a new, simple, and effective machine-learning approach was proposed to monitor the condition of transformer oils based on some aging indicators. The proposed approach was used to compare the performance of two machine-learning classifiers: J48 decision tree and random forest. The service-aged transformer oils were classified into four groups: the oils that can be maintained in service, the oils that should be reconditioned or filtered, the oils that should be reclaimed, and the oils that must be discarded. From the two algorithms, random forest exhibited a better performance and high accuracy with only a small amount of data. Good performance was achieved through not only the application of the proposed algorithm but also the approach of data preprocessing. Before feeding the classification model, the available data were transformed using the simple k-means method. Subsequently, the obtained data were filtered through correlation-based feature selection (CFsSubset). The resulting features were again retransformed by conducting the principal component analysis and were passed through the CFsSubset filter. The transformation and filtration of the data improved the classification performance of the adopted algorithms, especially random forest. Another advantage of the proposed method is the decrease in the number of the datasets required for the condition assessment of transformer oils, which is valuable for transformer condition monitoring.

scholarly journals 3145 An Evaluation of Machine Learning and Traditional Statistical Methods for Discovery in Large-Scale Translational Data

2019 ◽  
Vol 3 (s1) ◽  
pp. 2-2
Author(s):  
Megan C Hollister ◽  
Jeffrey D. Blume
Keyword(s):  
Gene Expression ◽  
Machine Learning ◽  
Random Forest ◽  
Gene Expression Data ◽  
Large Scale ◽  
Second Generation ◽  
A Priori ◽  
Expression Data ◽  
P Values ◽  
Machine Learning Methods

OBJECTIVES/SPECIFIC AIMS: To examine and compare the claims in Bzdok, Altman, and Brzywinski under a broader set of conditions by using unbiased methods of comparison. To explore how to accurately use various machine learning and traditional statistical methods in large-scale translational research by estimating their accuracy statistics. Then we will identify the methods with the best performance characteristics. METHODS/STUDY POPULATION: We conducted a simulation study with a microarray of gene expression data. We maintained the original structure proposed by Bzdok, Altman, and Brzywinski. The structure for gene expression data includes a total of 40 genes from 20 people, in which 10 people are phenotype positive and 10 are phenotype negative. In order to find a statistical difference 25% of the genes were set to be dysregulated across phenotype. This dysregulation forced the positive and negative phenotypes to have different mean population expressions. Additional variance was included to simulate genetic variation across the population. We also allowed for within person correlation across genes, which was not done in the original simulations. The following methods were used to determine the number of dysregulated genes in simulated data set: unadjusted p-values, Benjamini-Hochberg adjusted p-values, Bonferroni adjusted p-values, random forest importance levels, neural net prediction weights, and second-generation p-values. RESULTS/ANTICIPATED RESULTS: Results vary depending on whether a pre-specified significance level is used or the top 10 ranked values are taken. When all methods are given the same prior information of 10 dysregulated genes, the Benjamini-Hochberg adjusted p-values and the second-generation p-values generally outperform all other methods. We were not able to reproduce or validate the finding that random forest importance levels via a machine learning algorithm outperform classical methods. Almost uniformly, the machine learning methods did not yield improved accuracy statistics and they depend heavily on the a priori chosen number of dysregulated genes. DISCUSSION/SIGNIFICANCE OF IMPACT: In this context, machine learning methods do not outperform standard methods. Because of this and their additional complexity, machine learning approaches would not be preferable. Of all the approaches the second-generation p-value appears to offer significant benefit for the cost of a priori defining a region of trivially null effect sizes. The choice of an analysis method for large-scale translational data is critical to the success of any statistical investigation, and our simulations clearly highlight the various tradeoffs among the available methods.

Document Preprocessing with TF-IDF to Improve the Polarity Classification Performance of Unstructured Sentiment Analysis

2020 ◽  
pp. 235-242
Author(s):  
Farrikh Alzami ◽  
Erika Devi Udayanti ◽  
Dwi Puji Prabowo ◽  
Rama Aria Megantara
Keyword(s):  
Machine Learning ◽  
Feature Extraction ◽  
Random Forest ◽  
Sentiment Analysis ◽  
Classification Performance ◽  
Document Preparation ◽  
Learning Models ◽  
Polarity Classification ◽  
Negative Sentiment ◽  
Machine Learning Models

Sentiment analysis in terms of polarity classification is very important in everyday life, with the existence of polarity, many people can find out whether the respected document has positive or negative sentiment so that it can help in choosing and making decisions. Sentiment analysis usually done manually. Therefore, an automatic sentiment analysis classification process is needed. However, it is rare to find studies that discuss extraction features and which learning models are suitable for unstructured sentiment analysis types with the Amazon food review case. This research explores some extraction features such as Word Bags, TF-IDF, Word2Vector, as well as a combination of TF-IDF and Word2Vector with several machine learning models such as Random Forest, SVM, KNN and Naïve Bayes to find out a combination of feature extraction and learning models that can help add variety to the analysis of polarity sentiments. By assisting with document preparation such as html tags and punctuation and special characters, using snowball stemming, TF-IDF results obtained with SVM are suitable for obtaining a polarity classification in unstructured sentiment analysis for the case of Amazon food review with a performance result of 87,3 percent.

Cox Survival Analysis of Microarray Gene Expression Data Using Correlation Principal Component Regression

2007 ◽  
Vol 6 (1) ◽  
Author(s):  
Qiang Zhao ◽  
Jianguo Sun
Keyword(s):  
Gene Expression ◽  
Gene Expression Data ◽  
Principal Component Regression ◽  
Predictive Ability ◽  
Principal Component ◽  
Microarray Gene Expression Data ◽  
Expression Data ◽  
Microarray Gene Expression ◽  
New Approach ◽  
Microarray Gene

Statistical analysis of microarray gene expression data has recently attracted a great deal of attention. One problem of interest is to relate genes to survival outcomes of patients with the purpose of building regression models for the prediction of future patients' survival based on their gene expression data. For this, several authors have discussed the use of the proportional hazards or Cox model after reducing the dimension of the gene expression data. This paper presents a new approach to conduct the Cox survival analysis of microarray gene expression data with the focus on models' predictive ability. The method modifies the correlation principal component regression (Sun, 1995) to handle the censoring problem of survival data. The results based on simulated data and a set of publicly available data on diffuse large B-cell lymphoma show that the proposed method works well in terms of models' robustness and predictive ability in comparison with some existing partial least squares approaches. Also, the new approach is simpler and easy to implement.

scholarly journals Machine learning, transcriptome, and genotyping chip analyses provide insights into SNP markers identifying flower color in Platycodon grandiflorus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Go-Eun Yu ◽  
Younhee Shin ◽  
Sathiyamoorthy Subramaniyam ◽  
Sang-Ho Kang ◽  
Si-Myung Lee ◽  
...  
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Feature Selection Method ◽  
Flower Color ◽  
Classification Performance ◽  
Snp Markers ◽  
Rna Seq ◽  
Color Classification ◽  
Dna Pcr ◽  
Selection Of

AbstractBellflower is an edible ornamental gardening plant in Asia. For predicting the flower color in bellflower plants, a transcriptome-wide approach based on machine learning, transcriptome, and genotyping chip analyses was used to identify SNP markers. Six machine learning methods were deployed to explore the classification potential of the selected SNPs as features in two datasets, namely training (60 RNA-Seq samples) and validation (480 Fluidigm chip samples). SNP selection was performed in sequential order. Firstly, 96 SNPs were selected from the transcriptome-wide SNPs using the principal compound analysis (PCA). Then, 9 among 96 SNPs were later identified using the Random forest based feature selection method from the Fluidigm chip dataset. Among six machines, the random forest (RF) model produced higher classification performance than the other models. The 9 SNP marker candidates selected for classifying the flower color classification were verified using the genomic DNA PCR with Sanger sequencing. Our results suggest that this methodology could be used for future selection of breeding traits even though the plant accessions are highly heterogeneous.

scholarly journals A method of gene expression data transfer from cell lines to cancer patients for machine-learning prediction of drug efficiency

Cell Cycle ◽  
2018 ◽  
Vol 17 (4) ◽  
pp. 486-491 ◽  
Author(s):  
Nicolas Borisov ◽  
Victor Tkachev ◽  
Maria Suntsova ◽  
Olga Kovalchuk ◽  
Alex Zhavoronkov ◽  
...  
Keyword(s):  
Gene Expression ◽  
Machine Learning ◽  
Cancer Patients ◽  
Cell Lines ◽  
Gene Expression Data ◽  
Data Transfer ◽  
Expression Data ◽  
Drug Efficiency

scholarly journals Phybrata Sensors and Machine Learning for Enhanced Neurophysiological Diagnosis and Treatment

Sensors ◽  
2021 ◽  
Vol 21 (21) ◽  
pp. 7417
Author(s):  
Alex J. Hope ◽  
Utkarsh Vashisth ◽  
Matthew J. Parker ◽  
Andreas B. Ralston ◽  
Joshua M. Roper ◽  
...  
Keyword(s):  
Machine Learning ◽  
Time Series ◽  
Random Forest ◽  
Binary Classification ◽  
Classification Performance ◽  
Support Vector ◽  
Use Case ◽  
Signal Features ◽  
Test Population

Concussion injuries remain a significant public health challenge. A significant unmet clinical need remains for tools that allow related physiological impairments and longer-term health risks to be identified earlier, better quantified, and more easily monitored over time. We address this challenge by combining a head-mounted wearable inertial motion unit (IMU)-based physiological vibration acceleration (“phybrata”) sensor and several candidate machine learning (ML) models. The performance of this solution is assessed for both binary classification of concussion patients and multiclass predictions of specific concussion-related neurophysiological impairments. Results are compared with previously reported approaches to ML-based concussion diagnostics. Using phybrata data from a previously reported concussion study population, four different machine learning models (Support Vector Machine, Random Forest Classifier, Extreme Gradient Boost, and Convolutional Neural Network) are first investigated for binary classification of the test population as healthy vs. concussion (Use Case 1). Results are compared for two different data preprocessing pipelines, Time-Series Averaging (TSA) and Non-Time-Series Feature Extraction (NTS). Next, the three best-performing NTS models are compared in terms of their multiclass prediction performance for specific concussion-related impairments: vestibular, neurological, both (Use Case 2). For Use Case 1, the NTS model approach outperformed the TSA approach, with the two best algorithms achieving an F1 score of 0.94. For Use Case 2, the NTS Random Forest model achieved the best performance in the testing set, with an F1 score of 0.90, and identified a wider range of relevant phybrata signal features that contributed to impairment classification compared with manual feature inspection and statistical data analysis. The overall classification performance achieved in the present work exceeds previously reported approaches to ML-based concussion diagnostics using other data sources and ML models. This study also demonstrates the first combination of a wearable IMU-based sensor and ML model that enables both binary classification of concussion patients and multiclass predictions of specific concussion-related neurophysiological impairments.

scholarly journals Inference of Genetic Networks From Time-Series and Static Gene Expression Data: Combining a Random-Forest-Based Inference Method With Feature Selection Methods

2020 ◽  
Vol 11 ◽  
Author(s):  
Shuhei Kimura ◽  
Ryo Fukutomi ◽  
Masato Tokuhisa ◽  
Mariko Okada
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Random Forest ◽  
Gene Expression Data ◽  
Computational Cost ◽  
Expression Data ◽  
Selection Methods ◽  
Inference Method ◽  
Combined Application ◽  
Inference Methods

Several researchers have focused on random-forest-based inference methods because of their excellent performance. Some of these inference methods also have a useful ability to analyze both time-series and static gene expression data. However, they are only of use in ranking all of the candidate regulations by assigning them confidence values. None have been capable of detecting the regulations that actually affect a gene of interest. In this study, we propose a method to remove unpromising candidate regulations by combining the random-forest-based inference method with a series of feature selection methods. In addition to detecting unpromising regulations, our proposed method uses outputs from the feature selection methods to adjust the confidence values of all of the candidate regulations that have been computed by the random-forest-based inference method. Numerical experiments showed that the combined application with the feature selection methods improved the performance of the random-forest-based inference method on 99 of the 100 trials performed on the artificial problems. However, the improvement tends to be small, since our combined method succeeded in removing only 19% of the candidate regulations at most. The combined application with the feature selection methods moreover makes the computational cost higher. While a bigger improvement at a lower computational cost would be ideal, we see no impediments to our investigation, given that our aim is to extract as much useful information as possible from a limited amount of gene expression data.

Logic Learning Machine and standard supervised methods for Hodgkin’s lymphoma prognosis using gene expression data and clinical variables

2016 ◽  
Vol 24 (1) ◽  
pp. 54-65 ◽  
Author(s):  
Stefano Parodi ◽  
Chiara Manneschi ◽  
Damiano Verda ◽  
Enrico Ferrari ◽  
Marco Muselli
Keyword(s):  
Gene Expression ◽  
Machine Learning ◽  
Support Vector Machine ◽  
Decision Tree ◽  
Hodgkin’S Lymphoma ◽  
Hodgkin's Lymphoma ◽  
Support Vector ◽  
Expression Data ◽  
Clinical Variables ◽  
Learning Machine

This study evaluates the performance of a set of machine learning techniques in predicting the prognosis of Hodgkin’s lymphoma using clinical factors and gene expression data. Analysed samples from 130 Hodgkin’s lymphoma patients included a small set of clinical variables and more than 54,000 gene features. Machine learning classifiers included three black-box algorithms ( k-nearest neighbour, Artificial Neural Network, and Support Vector Machine) and two methods based on intelligible rules (Decision Tree and the innovative Logic Learning Machine method). Support Vector Machine clearly outperformed any of the other methods. Among the two rule-based algorithms, Logic Learning Machine performed better and identified a set of simple intelligible rules based on a combination of clinical variables and gene expressions. Decision Tree identified a non-coding gene ( XIST) involved in the early phases of X chromosome inactivation that was overexpressed in females and in non-relapsed patients. XIST expression might be responsible for the better prognosis of female Hodgkin’s lymphoma patients.

Sign in / Sign up

Export Citation Format

Share Document