Using Machine Learning Approaches to Predict Target Gene Expression in Rice T-DNA Insertional Mutants

To change the expression of the flanking genes by inserting T-DNA into the genome is commonly used in rice functional gene research. However, whether the expression of a gene of interest is enhanced must be validated experimentally. Consequently, to improve the efficiency of screening activated genes, we established a model to predict gene expression in T-DNA mutants through machine learning methods. We gathered experimental datasets consisting of gene expression data in T-DNA mutants and captured the PROMOTER and MIDDLE sequences for encoding. In first-layer models, support vector machine (SVM) models were constructed with nine features consisting of information about biological function and local and global sequences. Feature encoding based on the PROMOTER sequence was weighted by logistic regression. The second-layer models integrated 16 first-layer models with minimum redundancy maximum relevance (mRMR) feature selection and the LADTree algorithm, which were selected from nine feature selection methods and 65 classified methods, respectively. The accuracy of the final two-layer machine learning model, referred to as TIMgo, was 99.3% based on fivefold cross-validation, and 85.6% based on independent testing. We discovered that the information within the local sequence had a greater contribution than the global sequence with respect to classification. TIMgo had a good predictive ability for target genes within 20 kb from the 35S enhancer. Based on the analysis of significant sequences, the G-box regulatory sequence may also play an important role in the activation mechanism of the 35S enhancer.

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Building a Model for Predicting Target Gene Expression in Rice T-DNA Insertional Mutants by Machine Learning Approaches

10.21203/rs.3.rs-20492/v1 ◽

2020 ◽

Author(s):

Chi-Chou Liao ◽

Liang-Jwu Chen ◽

Shuen-Fang Lo ◽

Chi-Wei Chen ◽

Jia-Jyun Chen ◽

...

Keyword(s):

Gene Expression ◽

Machine Learning ◽

Feature Selection ◽

Target Genes ◽

Predictive Ability ◽

Promoter Sequence ◽

Regulatory Sequence ◽

Learning Approaches ◽

Machine Learning Model ◽

Local Sequence

Abstract Background T-DNA activation-tagging technology is widely used to enhance flanking gene expression near the site of insertion for functional genomics research in rice. However, whether the expression of a gene of interest is enhanced must be validated experimentally. Results In this study, we built a model to predict gene expression in T-DNA mutants by machine learning approaches, thereby improving the efficiency of screening for activated genes. We gathered experimental consisting of gene expression data in T-DNA mutants and captured the PROMOTER and MIDDLE sequences for encoding. In first-layer models, SVM models were constructed with nine features consisting of information about biological function and local and global sequences. Feature-encoding based on the PROMOTER sequence was weighted by logistic regression. The second-layer models integrated 16 first-layer models with feature selection and the algorithm, which were selected from nine feature selection methods and 65 classified methods, respectively. The accuracy of the final two-layer machine learning model, referred to as was 99.3% based on five-fold cross-validation, and 85.6% based on independent-testing. Conclusion We discovered that the information within the local sequence had a greater contribution than the global sequence with respect to classification had a good predictive ability for target genes within 20 from the 35S enhancer. Based on the analysis of significant sequences, the G-box regulatory sequence may also play an important role in the mechanism of activation of the 35S enhancer.

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Computational prediction of implantation outcome after embryo transfer

Health Informatics Journal ◽

10.1177/1460458219892138 ◽

2019 ◽

Vol 26 (3) ◽

pp. 1810-1826 ◽

Cited By ~ 3

Author(s):

Behnaz Raef ◽

Masoud Maleki ◽

Reza Ferdousi

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Prediction Model ◽

Embryo Transfer ◽

Area Under The Curve ◽

Computational Prediction ◽

Support Vector ◽

Human Menopausal Gonadotropin ◽

Optimum Number ◽

Learning Approaches

The aim of this study is to develop a computational prediction model for implantation outcome after an embryo transfer cycle. In this study, information of 500 patients and 1360 transferred embryos, including cleavage and blastocyst stages and fresh or frozen embryos, from April 2016 to February 2018, were collected. The dataset containing 82 attributes and a target label (indicating positive and negative implantation outcomes) was constructed. Six dominant machine learning approaches were examined based on their performance to predict embryo transfer outcomes. Also, feature selection procedures were used to identify effective predictive factors and recruited to determine the optimum number of features based on classifiers performance. The results revealed that random forest was the best classifier (accuracy = 90.40% and area under the curve = 93.74%) with optimum features based on a 10-fold cross-validation test. According to the Support Vector Machine-Feature Selection algorithm, the ideal numbers of features are 78. Follicle stimulating hormone/human menopausal gonadotropin dosage for ovarian stimulation was the most important predictive factor across all examined embryo transfer features. The proposed machine learning-based prediction model could predict embryo transfer outcome and implantation of embryos with high accuracy, before the start of an embryo transfer cycle.

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Diagnostic Performance of 2D and 3D T2WI-Based Radiomics Features With Machine Learning Algorithms to Distinguish Solid Solitary Pulmonary Lesion

Frontiers in Oncology ◽

10.3389/fonc.2021.683587 ◽

2021 ◽

Vol 11 ◽

Author(s):

Qi Wan ◽

Jiaxuan Zhou ◽

Xiaoying Xia ◽

Jianfeng Hu ◽

Peng Wang ◽

...

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Diagnostic Performance ◽

Feature Selection Method ◽

Machine Learning Algorithms ◽

Support Vector ◽

Learning Approaches ◽

Selection Methods ◽

Linear Discriminant ◽

2D And 3D

ObjectiveTo evaluate the performance of 2D and 3D radiomics features with different machine learning approaches to classify SPLs based on magnetic resonance(MR) T2 weighted imaging (T2WI).Material and MethodsA total of 132 patients with pathologically confirmed SPLs were examined and randomly divided into training (n = 92) and test datasets (n = 40). A total of 1692 3D and 1231 2D radiomics features per patient were extracted. Both radiomics features and clinical data were evaluated. A total of 1260 classification models, comprising 3 normalization methods, 2 dimension reduction algorithms, 3 feature selection methods, and 10 classifiers with 7 different feature numbers (confined to 3–9), were compared. The ten-fold cross-validation on the training dataset was applied to choose the candidate final model. The area under the receiver operating characteristic curve (AUC), precision-recall plot, and Matthews Correlation Coefficient were used to evaluate the performance of machine learning approaches.ResultsThe 3D features were significantly superior to 2D features, showing much more machine learning combinations with AUC greater than 0.7 in both validation and test groups (129 vs. 11). The feature selection method Analysis of Variance(ANOVA), Recursive Feature Elimination(RFE) and the classifier Logistic Regression(LR), Linear Discriminant Analysis(LDA), Support Vector Machine(SVM), Gaussian Process(GP) had relatively better performance. The best performance of 3D radiomics features in the test dataset (AUC = 0.824, AUC-PR = 0.927, MCC = 0.514) was higher than that of 2D features (AUC = 0.740, AUC-PR = 0.846, MCC = 0.404). The joint 3D and 2D features (AUC=0.813, AUC-PR = 0.926, MCC = 0.563) showed similar results as 3D features. Incorporating clinical features with 3D and 2D radiomics features slightly improved the AUC to 0.836 (AUC-PR = 0.918, MCC = 0.620) and 0.780 (AUC-PR = 0.900, MCC = 0.574), respectively.ConclusionsAfter algorithm optimization, 2D feature-based radiomics models yield favorable results in differentiating malignant and benign SPLs, but 3D features are still preferred because of the availability of more machine learning algorithmic combinations with better performance. Feature selection methods ANOVA and RFE, and classifier LR, LDA, SVM and GP are more likely to demonstrate better diagnostic performance for 3D features in the current study.

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Ensemble Machine Learning Approaches for Proteogenomic Cancer Studies

10.21203/rs.3.rs-101902/v1 ◽

2020 ◽

Author(s):

Yulan Liang ◽

Amin Gharipour ◽

Erik Kelemen ◽

Arpad Kelemen

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Prediction Accuracy ◽

Performance Criteria ◽

Stable Set ◽

Support Vector ◽

Kappa Statistics ◽

Learning Approaches ◽

Ensemble Machine Learning ◽

Homogeneous Ensemble

Abstract Background: The identification of important proteins is critical for medical diagnosis and prognosis in common diseases. Diverse sets of computational tools were developed for omics data reductions and protein selections. However, standard statistical models with single feature selection involve the multi-testing burden of low power with the available limited samples. Furthermore, high correlations among proteins with high redundancy and moderate effects often lead to unstable selections and cause reproducibility issues. Ensemble feature selection in machine learning may identify a stable set of disease biomarkers that could improve the prediction performance of subsequent classification models, and thereby simplify their interpretability. In this study, we developed a three-stage homogeneous ensemble feature selection approach for both identifying proteins and improving prediction accuracy. This approach was implemented and applied to ovarian cancer proteogenomics data sets: 1) binary putative homologous recombination deficiency positive or negative; and 2) multiple mRNA classes (differentiated, proliferative, immunoreactive, mesenchymal, and unknown). We conducted and compared various machine learning approaches with homogeneous ensemble feature selection including random forest, support vector machine, and neural network for predicting both binary and multiple class outcomes. Various performance criteria including sensitivity, specificity, kappa statistics were used to assess the prediction consistency and accuracy. Results: With the proposed three-stage homogeneous ensemble feature selection approaches, prediction accuracy can be improved with the limited sample through continuously reducing errors and redundancy, i.e. Treebag provided 83% prediction accuracy (85% sensitivity and 81% specificity) for binary ovarian outcomes. For mRNA multi-classes classification, our approach provided even better accuracy with increased sample size. Conclusions: Despite the different prediction accuracies from various models, homogeneous ensemble feature selection proposed identified consistent sets of top ranked important markers out of 9606 proteins linked to the binary disease and multiple mRNA class outcomes.

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Insight to Gene Expression From Promoter Libraries With the Machine Learning Workflow Exp2Ipynb

Frontiers in Bioinformatics ◽

10.3389/fbinf.2021.747428 ◽

2021 ◽

Vol 1 ◽

Author(s):

Ulf W. Liebal ◽

Sebastian Köbbing ◽

Linux Netze ◽

Artur M. Schweidtmann ◽

Alexander Mitsos ◽

...

Keyword(s):

Gene Expression ◽

Machine Learning ◽

Promoter Sequence ◽

Strain Engineering ◽

Machine Learning Algorithms ◽

Gradient Boosting ◽

Support Vector ◽

Reporter System ◽

Regulate Protein ◽

Multiple Promoter

Metabolic engineering relies on modifying gene expression to regulate protein concentrations and reaction activities. The gene expression is controlled by the promoter sequence, and sequence libraries are used to scan expression activities and to identify correlations between sequence and activity. We introduce a computational workflow called Exp2Ipynb to analyze promoter libraries maximizing information retrieval and promoter design with desired activity. We applied Exp2Ipynb to seven prokaryotic expression libraries to identify optimal experimental design principles. The workflow is open source, available as Jupyter Notebooks and covers the steps to 1) generate a statistical overview to sequence and activity, 2) train machine-learning algorithms, such as random forest, gradient boosting trees and support vector machines, for prediction and extraction of feature importance, 3) evaluate the performance of the estimator, and 4) to design new sequences with a desired activity using numerical optimization. The workflow can perform regression or classification on multiple promoter libraries, across species or reporter proteins. The most accurate predictions in the sample libraries were achieved when the promoters in the library were recognized by a single sigma factor and a unique reporter system. The prediction confidence mostly depends on sample size and sequence diversity, and we present a relationship to estimate their respective effects. The workflow can be adapted to process sequence libraries from other expression-related problems and increase insight to the growing application of high-throughput experiments, providing support for efficient strain engineering.

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A Topical Survey: Applications of Machine Learning in Medical Issues

Journal of Computational and Theoretical Nanoscience ◽

10.1166/jctn.2020.9334 ◽

2020 ◽

Vol 17 (11) ◽

pp. 5010-5019

Author(s):

Chapala Maharana ◽

Bijan Bihari Mishra ◽

Ch. Sanjeev Kumar Dash

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Image Segmentation ◽

Learning Algorithms ◽

Disease Diagnosis ◽

Lesion Detection ◽

Machine Learning Algorithms ◽

Support Vector ◽

Learning Approaches ◽

Medical Issues

Computational Intelligence methods have replaced almost all real world applications with high accuracy within the given time period. Machine Learning approaches like classification, feature selection, feature extraction have solved many problems of different domain. They use different ML models implemented with suitable ML tool or combination of tools from NN (Neural Network), SVM (Support Vector Machine), DL (Deep Learning), ELM (Extreme Learning Machine). The model is used for training with known data along with ML algorithms (fuzzy logic, genetic algorithm) to optimize the accuracy for different medical issues for example gene expression and image segmentation for information extraction and disease diagnosis, health monitoring, disease treatment. Most of the medical problems are solved using recent advances in AI (Artificial Intelligence) technologies with the biomedical systems development (e.g., Knowledge based Decision Support Systems) and AI technologies with medical informatics science. AI based methods like machine learning algorithms implemented models are increasingly found in real life applications ex. healthcare, natural calamity detection and forecasting. There are the expert systems handled by experts for knowledge gain which is used in decision making applications. The ML models are found in different medical applications like disease diagnosis (ex. cancer prediction, diabetics disease prediction) and for treatment of diseases (ex. in diabetics disease the reduction in mean glucose concentration following intermittent gastric feeds). The feature selection ML method is used for EEG classification for detection of the severity of the disease in heart related diseases and for identification of genes in different disorder like autism disorder. The ML models are found in health record systems. There are other applications of ML approaches found in image segmentation, tissue extraction, image fragmentation for disease diagnosis (ex. lesion detection in breast cancer for malignancy) and then treatment of those diseases. ML models are found in mobile health treatment, treatment of psychology patients, treatment of dumb patients etc. Medical data handling is the vital part of health care systems for the development of AI systems which can again be solved by machine learning approaches. The ML approaches for medical issues have used ensemble methods or combinations of machine learning tools and machine learning algorithms to optimize the result with good accuracy value at a faster rate.

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Tree-based homogeneous ensemble model with feature selection for diabetic retinopathy prediction

Jurnal Teknologi dan Sistem Komputer ◽

10.14710/jtsiskom.2020.13669 ◽

2020 ◽

Vol 8 (4) ◽

pp. 297-303

Author(s):

Tamunopriye Ene Dagogo-George ◽

Hammed Adeleye Mojeed ◽

Abdulateef Oluwagbemiga Balogun ◽

Modinat Abolore Mabayoje ◽

Shakirat Aderonke Salihu

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Diabetic Retinopathy ◽

Ensemble Methods ◽

Predictive Performance ◽

Ensemble Classification ◽

Support Vector ◽

Learning Approaches ◽

Vector Machines ◽

Homogeneous Ensemble

Diabetic Retinopathy (DR) is a condition that emerges from prolonged diabetes, causing severe damages to the eyes. Early diagnosis of this disease is highly imperative as late diagnosis may be fatal. Existing studies employed machine learning approaches with Support Vector Machines (SVM) having the highest performance on most analyses and Decision Trees (DT) having the lowest. However, SVM has been known to suffer from parameter and kernel selection problems, which undermine its predictive capability. Hence, this study presents homogenous ensemble classification methods with DT as the base classifier to optimize predictive performance. Boosting and Bagging ensemble methods with feature selection were employed, and experiments were carried out using Python Scikit Learn libraries on DR datasets extracted from UCI Machine Learning repository. Experimental results showed that Bagged and Boosted DT were better than SVM. Specifically, Bagged DT performed best with accuracy 65.38 %, f-score 0.664, and AUC 0.731, followed by Boosted DT with accuracy 65.42 %, f-score 0.655, and AUC 0.724 when compared to SVM (accuracy 65.16 %, f-score 0.652, and AUC 0.721). These results indicate that DT's predictive performance can be optimized by employing the homogeneous ensemble methods to outperform SVM in predicting DR.

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Application of Machine Learning Approaches for the Design and Study of Anticancer Drugs

Current Drug Targets ◽

10.2174/1389450119666180809122244 ◽

2019 ◽

Vol 20 (5) ◽

pp. 488-500 ◽

Cited By ~ 6

Author(s):

Yan Hu ◽

Yi Lu ◽

Shuo Wang ◽

Mengying Zhang ◽

Xiaosheng Qu ◽

...

Keyword(s):

Machine Learning ◽

Drug Design ◽

Anticancer Drugs ◽

Nearest Neighbor ◽

Cost Effective ◽

Support Vector ◽

Learning Approaches ◽

K Nearest Neighbor ◽

Activity Prediction ◽

Linear Discriminant

Background: Globally the number of cancer patients and deaths are continuing to increase yearly, and cancer has, therefore, become one of the world's highest causes of morbidity and mortality. In recent years, the study of anticancer drugs has become one of the most popular medical topics. Objective: In this review, in order to study the application of machine learning in predicting anticancer drugs activity, some machine learning approaches such as Linear Discriminant Analysis (LDA), Principal components analysis (PCA), Support Vector Machine (SVM), Random forest (RF), k-Nearest Neighbor (kNN), and Naïve Bayes (NB) were selected, and the examples of their applications in anticancer drugs design are listed. Results: Machine learning contributes a lot to anticancer drugs design and helps researchers by saving time and is cost effective. However, it can only be an assisting tool for drug design. Conclusion: This paper introduces the application of machine learning approaches in anticancer drug design. Many examples of success in identification and prediction in the area of anticancer drugs activity prediction are discussed, and the anticancer drugs research is still in active progress. Moreover, the merits of some web servers related to anticancer drugs are mentioned.

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An Improved Machine Learning-Based Employees Attrition Prediction Framework with Emphasis on Feature Selection

Mathematics ◽

10.3390/math9111226 ◽

2021 ◽

Vol 9 (11) ◽

pp. 1226

Author(s):

Saeed Najafi-Zangeneh ◽

Naser Shams-Gharneh ◽

Ali Arjomandi-Nezhad ◽

Sarfaraz Hashemkhani Zolfani

Keyword(s):

Machine Learning ◽

Feature Selection ◽

Standard Deviation ◽

Analytical Formula ◽

Feature Selection Method ◽

Selection Method ◽

Performance Measure ◽

Learning Approaches ◽

Training Costs ◽

Professional Employees

Companies always seek ways to make their professional employees stay with them to reduce extra recruiting and training costs. Predicting whether a particular employee may leave or not will help the company to make preventive decisions. Unlike physical systems, human resource problems cannot be described by a scientific-analytical formula. Therefore, machine learning approaches are the best tools for this aim. This paper presents a three-stage (pre-processing, processing, post-processing) framework for attrition prediction. An IBM HR dataset is chosen as the case study. Since there are several features in the dataset, the “max-out” feature selection method is proposed for dimension reduction in the pre-processing stage. This method is implemented for the IBM HR dataset. The coefficient of each feature in the logistic regression model shows the importance of the feature in attrition prediction. The results show improvement in the F1-score performance measure due to the “max-out” feature selection method. Finally, the validity of parameters is checked by training the model for multiple bootstrap datasets. Then, the average and standard deviation of parameters are analyzed to check the confidence value of the model’s parameters and their stability. The small standard deviation of parameters indicates that the model is stable and is more likely to generalize well.

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A Comparison of Feature Selection and Forecasting Machine Learning Algorithms for Predicting Glycaemia in Type 1 Diabetes Mellitus

Applied Sciences ◽

10.3390/app11041742 ◽

2021 ◽

Vol 11 (4) ◽

pp. 1742

Author(s):

Ignacio Rodríguez-Rodríguez ◽

José-Víctor Rodríguez ◽

Wai Lok Woo ◽

Bo Wei ◽

Domingo-Javier Pardo-Quiles

Keyword(s):

Diabetes Mellitus ◽

Machine Learning ◽

Type 1 Diabetes ◽

Feature Selection ◽

Blood Glucose ◽

Type 1 Diabetes Mellitus ◽

Support Vector ◽

Chronic Hyperglycemia ◽

Predictive Algorithms

Type 1 diabetes mellitus (DM1) is a metabolic disease derived from falls in pancreatic insulin production resulting in chronic hyperglycemia. DM1 subjects usually have to undertake a number of assessments of blood glucose levels every day, employing capillary glucometers for the monitoring of blood glucose dynamics. In recent years, advances in technology have allowed for the creation of revolutionary biosensors and continuous glucose monitoring (CGM) techniques. This has enabled the monitoring of a subject’s blood glucose level in real time. On the other hand, few attempts have been made to apply machine learning techniques to predicting glycaemia levels, but dealing with a database containing such a high level of variables is problematic. In this sense, to the best of the authors’ knowledge, the issues of proper feature selection (FS)—the stage before applying predictive algorithms—have not been subject to in-depth discussion and comparison in past research when it comes to forecasting glycaemia. Therefore, in order to assess how a proper FS stage could improve the accuracy of the glycaemia forecasted, this work has developed six FS techniques alongside four predictive algorithms, applying them to a full dataset of biomedical features related to glycaemia. These were harvested through a wide-ranging passive monitoring process involving 25 patients with DM1 in practical real-life scenarios. From the obtained results, we affirm that Random Forest (RF) as both predictive algorithm and FS strategy offers the best average performance (Root Median Square Error, RMSE = 18.54 mg/dL) throughout the 12 considered predictive horizons (up to 60 min in steps of 5 min), showing Support Vector Machines (SVM) to have the best accuracy as a forecasting algorithm when considering, in turn, the average of the six FS techniques applied (RMSE = 20.58 mg/dL).

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