Feature Ranking Algorithms Research Articles

Evaluation of an Image-based Classification Model to Identify Glioma Subtypes Using Arterial Spin Labeling Perfusion MRI On the Publicly Available UCSF Glioma Dataset.

Glioma is acomplex cancer comprising various subtypes and mutations, which may have different metabolic characteristics that can potentially be investigated and identified using perfusion imaging. Therefore, the aim of this work was to use radiomics and machine learning analysis of arterial spin labeling MRI data to automatically differentiate glioma subtypes and mutations. Atotal of 495 Arterial Spin Labeling (ASL) perfusion imaging datasets from the UCSF Glioma database were used in this study. These datasets were segmented to delineate the tumor volume and classified according to tumor grade, pathological diagnosis, and IDH status. Perfusion image data was obtained from a3T MRI scanner using pseudo-continuous ASL. High level texture features were extracted for each ASL dataset using PyRadiomics after tumor volume segmentation and then analyzed using amachine learning framework consisting of ReliefF feature ranking and logistic model tree classification algorithms. The results of the evaluation revealed balanced accuracies for the three endpoints ranging from 55.76% (SD = 4.28, 95% CI: 53.90-57.65) for the tumor grade using 25.4 ± 37.21 features, 62.53% (SD = 2.86, 95% CI: 61.27-63.78) for the mutation status with 23.3 ± 29.17 picked features, and 80.97% (SD = 1.83, 95% CI: 80.17-81.78) for the pathological diagnosis which used 47.3 ± 32.72 selected features. Radiomics and machine learning analysis of ASL perfusion data in glioma patients hold potential for aiding in the diagnosis and treatment of glioma, mainly for discerning glioblastoma from astrocytoma, while performance for tumor grading and mutation status appears limited.

Identification of Key Genes in Fetal Gut Development at Single-Cell Level by Exploiting Machine Learning Techniques.

The study of fetal gut development is critical due to its substantial influence on immediate neonatal and long-term adult health. Current research largely focuses on microbiome colonization, gut immunity, and barrier function, alongside the impact of external factors on these phenomena. Limited research has been dedicated to the categorization of developing fetal gut cells. Our study aimed to enhance our understanding of fetal gut development by employing advanced machine-learning techniques on single-cell sequencing data. This dataset consisted of 62,849 samples, each characterized by 33,694 distinct gene features. Four feature ranking algorithms were utilized to sort features according to their significance, resulting in four feature lists. Then, these lists were fed into an incremental feature selection method to extract essential genes, classification rules, and build efficient classifiers. Several important genes were recognized by multiple feature ranking algorithms, such as FGG, MDK, RBP1, RBP2, IGFBP7, and SPON2. These features were key in differentiating specific developing intestinal cells, including epithelial, immune, mesenchymal, and vasculature cells of the colon, duo jejunum, and ileum cells. The classification rules showed special gene expression patterns on some intestinal cell types and the efficient classifiers can be useful tools for identifying intestinal cells.

Identification of gene and protein signatures associated with long-term effects of COVID-19 on the immune system after patient recovery by analyzing single-cell multi-omics data using a machine learning approach

Viral infections significantly impact the immune system, and impact will persist until recovery. However, the influence of severe acute respiratory syndrome coronavirus 2 infection on the homeostatic immune status and secondary immune response in recovered patients remains unclear. To investigate these persistent alterations, we employed five feature-ranking algorithms (LASSO, MCFS, RF, CATBoost, and XGBoost), incremental feature selection, synthetic minority oversampling technique and two classification algorithms (decision tree and k-nearest neighbors) to analyze multi-omics data (surface proteins and transcriptome) from coronavirus disease 2019 (COVID-19) recovered patients and healthy controls post-influenza vaccination. The single-cell multi-omics dataset was divided into five subsets corresponding to five immune cell subtypes: B cells, CD4+ T cells, CD8+ T cells, Monocytes, and Natural Killer cells. Each cell was represented by 28,402 scRNA-seq (RNA) features, 3 Hash Tag Oligo (HTO) features, 138 Cellular indexing of transcriptomes and epitopes by sequencing (CITE) features and 23,569 Single Cell Transform (SCT) features. Some multi-omics markers were identified and effective classifiers were constructed. Our findings indicate a distinct immune status in COVID-19 recovered patients, characterized by low expression of ribosomal protein (RPS26) and high expression of immune cell surface proteins (CD33, CD48). Notably, TMEM176B, a membrane protein, was highly expressed in monocytes of COVID-19 convalescent patients. These observations aid in discerning molecular differences among immune cell subtypes and contribute to understanding the prolonged effects of COVID-19 on the immune system, which is valuable for treating infectious diseases like COVID-19.

Machine Learning in Identifying Marker Genes for Congenital Heart Diseases of Different Cardiac Cell Types.

Congenital heart disease (CHD) represents a spectrum of inborn heart defects influenced by genetic and environmental factors. This study advances the field by analyzing gene expression profiles in 21,034 cardiac fibroblasts, 73,296 cardiomyocytes, and 35,673 endothelial cells, utilizing single-cell level analysis and machine learning techniques. Six CHD conditions: dilated cardiomyopathy (DCM), donor hearts (used as healthy controls), hypertrophic cardiomyopathy (HCM), heart failure with hypoplastic left heart syndrome (HF_HLHS), Neonatal Hypoplastic Left Heart Syndrome (Neo_HLHS), and Tetralogy of Fallot (TOF), were investigated for each cardiac cell type. Each cell sample was represented by 29,266 gene features. These features were first analyzed by six feature-ranking algorithms, resulting in several feature lists. Then, these lists were fed into incremental feature selection, containing two classification algorithms, to extract essential gene features and classification rules and build efficient classifiers. The identified essential genes can be potential CHD markers in different cardiac cell types. For instance, the LASSO identified key genes specific to various heart cell types in CHD subtypes. FOXO3 was found to be up-regulated in cardiac fibroblasts for both Dilated and hypertrophic cardiomyopathy. In cardiomyocytes, distinct genes such as TMTC1, ART3, ARHGAP24, SHROOM3, and XIST were linked to dilated cardiomyopathy, Neo-Hypoplastic Left Heart Syndrome, hypertrophic cardiomyopathy, HF-Hypoplastic Left Heart Syndrome, and Tetralogy of Fallot, respectively. Endothelial cell analysis further revealed COL25A1, NFIB, and KLF7 as significant genes for dilated cardiomyopathy, hypertrophic cardiomyopathy, and Tetralogy of Fallot. LightGBM, Catboost, MCFS, RF, and XGBoost further delineated key genes for specific CHD subtypes, demonstrating the efficacy of machine learning in identifying CHD-specific genes. Additionally, this study developed quantitative rules for representing the gene expression patterns related to CHDs. This research underscores the potential of machine learning in unraveling the molecular complexities of CHD and establishes a foundation for future mechanism-based studies.

A data-centric machine learning approach to improve prediction of glioma grades using low-imbalance TCGA data

Accurate prediction and grading of gliomas play a crucial role in evaluating brain tumor progression, assessing overall prognosis, and treatment planning. In addition to neuroimaging techniques, identifying molecular biomarkers that can guide the diagnosis, prognosis and prediction of the response to therapy has aroused the interest of researchers in their use together with machine learning and deep learning models. Most of the research in this field has been model-centric, meaning it has been based on finding better performing algorithms. However, in practice, improving data quality can result in a better model. This study investigates a data-centric machine learning approach to determine their potential benefits in predicting glioma grades. We report six performance metrics to provide a complete picture of model performance. Experimental results indicate that standardization and oversizing the minority class increase the prediction performance of four popular machine learning models and two classifier ensembles applied on a low-imbalanced data set consisting of clinical factors and molecular biomarkers. The experiments also show that the two classifier ensembles significantly outperform three of the four standard prediction models. Furthermore, we conduct a comprehensive descriptive analysis of the glioma data set to identify relevant statistical characteristics and discover the most informative attributes using four feature ranking algorithms.

Ensemble feature ranking approach for software fault prediction

Software fault prediction, which aims to find and fix probable flaws before they appear in real-world settings, is an essential component of software quality assurance. This article provides a thorough analysis of the use of feature ranking algorithms for successful software failure prediction. In order to choose and prioritise the software metrics or qualities most important to fault prediction models, feature ranking approaches are essential. The proposed focus on applying an ensemble feature ranking algorithm to a specific software fault dataset, addressing the challenge posed by the dataset’s high dimensionality. In this extensive study, we examined the effectiveness of multiple machine learning classifiers on six different software projects: jedit, ivy, prop, xerces, tomcat, and poi, utilising feature selection strategies. In order to evaluate classifier performance under two scenarios—one with the top 10 features and another with the top 15 features—our study sought to determine the most relevant features for each project. SVM consistently performed well across the six datasets, achieving noteworthy results like 98.74% accuracy on “jedit” (top 10 features) and 91.88% on “tomcat” (top 10 features). Random Forest achieving 89.20% accuracy on the top 15 features, on “ivy.” In contrast, NB repeatedly recording the lowest accuracy rates, such as 51.58% on “poi” and 50.45% on “xerces” (the top 15 features). These findings highlight SVM and RF as the top performers, whereas NB was consistently the least successful classifier. The findings suggest that the choice of feature ranking algorithm has a substantial impact on the fault prediction models’ predictive accuracy and effectiveness. When using various ranking systems, the research also analyses the trade-offs between computing complexity and forecast accuracy.

Integrating machine learning and feature analysis for predicting and managing thermal deformation in machine tools

This study develops a method to predict and compensate for thermal deformation in machine tools, focusing on selecting temperature-sensitive points, establishing a predictive model, and detecting temperature anomalies. Optimal sensing points were identified using feature ranking algorithms and Partial Dependence Plots, improving Z-axis deformation identification. The research also evaluated various machine learning models for Z-axis deformation prediction, notably optimizing Gaussian Process Regression for superior accuracy. Additionally, anomaly detection in temperature sensors was addressed using One-Dimensional Convolutional Neural Networks and Long Short-Term Memory Networks, enhancing system reliability and robustness. This approach offers a comprehensive solution for thermal deformation in machine tools, contributing to the field's precision and efficiency.

Data-driven learning-based classification model for mitigating false data injection attacks on dynamic line rating systems

The increasing need to explore electric power grid expansion technologies like dynamic line rating (DLR) systems and their dependence on real-time weather data for system planning necessitates research into false data injection attacks (FDIA) on cyber-physical power systems (CPS). This study aims to develop a robust machine learning model to mitigate FDIA in DLR systems, focusing on statistical data processing, feature ranking, selection, training, validation and evaluation. It synthesises z-score and other statistical analyses with minimum redundancy maximum relevance (MR-MR) feature ranking and selection algorithm to improve model performance and generalisation of binary generalised linear model logistic regression (BGLM-LR) and other machine learning classification algorithms. The resulting models formed with BGLM-LR, Gaussian naïve Bayes (GNB), linear support vector machine (LSVM), wide neural network (WNN), and decision tree (DT) were trained and tested with 10-year hourly DLR history data features. The evaluation of the models on unseen data revealed enhanced validation and testing accuracies after the MR-MR feature ranking and selection. BGLM-LR, GNB, LSVM, and WNN showed promising performance for mitigating FDIA. However, the study identifies DT’s limitations as overfitting and lacking generalisation in FDIA mitigation. z-score-MR-MR-BGLM-LR and z-score-MR-MR-LSVM models exhibited outstanding performances with zero false negative rates highlighting the significance of feature ranking and selection. Still, the z-score-MR-MR-BGLM-LR combination exhibits the highest marginal improvement from training to testing, the lowest training and validation time and a perfect area under curve (AUC) of the receiver operating characteristics making it the best choice in mitigating FDIA when computational resources are limited.

Exploring Prognostic Gene Factors in Breast Cancer via Machine Learning.

Breast cancer remains the most prevalent cancer in women. To date, its underlying molecular mechanisms have not been fully uncovered. The determination of gene factors is important to improve our understanding on breast cancer, which can correlate the specific gene expression and tumor staging. However, the knowledge in this regard is still far from complete. Thus, this study aimed to explore these knowledge gaps by analyzing existing gene expression profile data from 3149 breast cancer samples, where each sample was represented by the expression of 19,644 genes and classified into Nottingham histological grade (NHG) classes (Grade 1, 2, and 3). To this end, a machine learning-based framework was designed. First, the profile data were analyzed by using seven feature ranking algorithms to evaluate the importance of features (genes). Seven feature lists were generated, each of which sorted features in accordance with feature importance evaluated from a special aspect. Then, the incremental feature selection method was applied to each list to determine essential features for classification and building efficient classifiers. Consequently, overlapping genes, such as AURKA, CBX2, and MYBL2, were deemed as potentially related to breast cancer malignancy and prognosis, indicating that such genes were identified to be important by multiple feature ranking algorithms. In addition, the study formulated classification rules to reflect special gene expression patterns for three NHG classes. Some genes and rules were analyzed and supported by recent literature, providing new references for studying breast cancer.

Keyword Pool Generation for Web Text Collecting: A Framework Integrating Sample and Semantic Information

Keyword pools are used as search queries to collect web texts, largely determining the size and coverage of the samples and provide a data base for subsequent text mining. However, how to generate a refined keyword pool with high similarity and some expandability is a challenge. Currently, keyword pools for search queries aimed at collecting web texts either lack an objective generation method and evaluation system, or have a low utilization rate of sample semantic information. Therefore, this paper proposed a keyword generation framework that integrates sample and semantic information to construct a complete and objective keyword pool generation and evaluation system. The framework includes a data phase and a modeling phase, and its core is in the modeling phase, where both feature ranking and model performance are considered. A regression model about a topic vector and word vectors is constructed for the first time based on word embedding, and keyword pools are generated from the perspective of model performance. In addition, two keyword generation methods, Recursive Feature Introduction (RFI) and Recursive Feature Introduction and Elimination (RFIE), are also proposed in this paper. Different feature ranking algorithms, keyword generation methods and regression models are compared in the experiments. The results show that: (1) When using RFI to generate keywords, the regression model using ranked features has better prediction performance than the baseline model, and the number of generated keywords is refiner, and the prediction performance of the regression model using tree-based ranked features is significantly better than that of the one using SHAP-based ranked features. (2) The prediction performance of the regression model using RFI with tree-based ranked features is significantly better than that using Recursive Feature Elimination (RFE) with tree-based one. (3) All four regression models using RFI/RFE with SHAP- based/tree-based ranked features have significantly higher average similarity scores and cumulative advantages than the baseline model (the model using RFI with unranked features). (4) Light Gradient Boosting Machine (LGBM) using RFI with SHAP-based ranked features has significantly better prediction performance, higher average similarity scores, and cumulative advantages. In conclusion, our framework can generate a keyword pool that is more similar to the topic, and more refined and expandable, which provides certain research ideas for expanding the research sample size while ensuring the coverage of topics in web text collecting.

Machine learning based method for analyzing vibration and noise in large cruise ships.

Cruise ships are distinguished as special passenger ships, transporting passengers to various ports and giving importance to comfort. High comfort can attract lots of passengers and generate substantial profits. Vibration and noise are the most important indicators for assessing the comfort of cruise ships. Existing methods for analyzing vibration and noise data have shown limitations in uncovering essential information and discerning critical disparities in vibration and noise levels across different ship districts. Conversely, the rapid development in machine learning present an opportunity to leverage sophisticated algorithms for a more insightful examination of vibration and noise aboard cruise ships. This study designed a machine learning-driven approach to analyze the vibration and noise data. Drawing data from China's first large-scale cruise ship, encompassing 127 noise samples, this study sets up a classification task, where decks were assigned as labels and frequencies served as features. Essential information was extracted by investigating this problem. Several machine learning algorithms, including feature ranking, selection, and classification algorithms, were adopted in this method. One or two essential noise frequencies related to each of the decks, except the 10th deck, were obtained, which were partly validated by the traditional statistical methods. Such findings were helpful in reducing and controlling the vibration and noise in cruise ships. Furthermore, the study develops a classifier to distinguish noise samples, which utilizes random forest as the classification algorithm with eight optimal frequency features identified by LightGBM. This classifier yielded a Matthews correlation coefficient of 0.3415. This study gives a new direction for investigating vibration and noise in ships.

Identification of key genes associated with persistent immune changes and secondary immune activation responses induced by influenza vaccination after COVID-19 recovery by machine learning methods

COVID-19 is hypothesized to exert enduring effects on the immune systems of patients, leading to alterations in immune-related gene expression. This study aimed to scrutinize the persistent implications of SARS-CoV-2 infection on gene expression and its influence on subsequent immune activation responses. We designed a machine learning-based approach to analyze transcriptomic data from both healthy individuals and patients who had recovered from COVID-19. Patients were categorized based on their influenza vaccination status and then compared with healthy controls. The initial sample set encompassed 86 blood samples from healthy controls and 72 blood samples from recuperated COVID-19 patients prior to influenza vaccination. The second sample set included 123 blood samples from healthy controls and 106 blood samples from recovered COVID-19 patients who had been vaccinated against influenza. For each sample, the dataset captured expression levels of 17,060 genes. Above two sample sets were first analyzed by seven feature ranking algorithms, yielding seven feature lists for each dataset. Then, each list was fed into the incremental feature selection method, incorporating three classic classification algorithms, to extract essential genes, classification rules and build efficient classifiers. The genes and rules were analyzed in this study. The main findings included that NEXN and ZNF354A were highly expressed in recovered COVID-19 patients, whereas MKI67 and GZMB were highly expressed in patients with secondary immune activation post-COVID-19 recovery. These pivotal genes could provide valuable insights for future health monitoring of COVID-19 patients and guide the creation of continued treatment regimens.

Identification of key gene expression associated with quality of life after recovery from COVID-19.

Post-acute sequelae of COVID-19 (PASC) is a persistent complication of severe acute respiratory syndrome coronavirus 2 infection that includes symptoms, such as fatigue, cognitive impairment, and respiratory distress. These symptoms severely affect the quality of life of patients after their recovery from COVID-19. In this study, a group of machine learning algorithms analyzed the whole blood RNA-seq data from patients with different PASC levels. The purpose of this analysis was to identify the gene markers associated with PASC and the special expression patterns for different PASC levels. By comparing the quality of life of patients after the acute phase of COVID-19 and before the disease, samples in the dataset were divided into three groups, namely, "Better," "The Same," and "Worse." Each patient was represented by the expression levels of 58,929 genes. The machine learning-based workflow included six feature-ranking algorithms, incremental feature selection (IFS), and four classification algorithms. The feature ranking algorithms were in charge of assessing feature importance, whereas IFS with classification algorithms were used to extract essential genes and to construct efficient classifiers and classification rules. The expression of top genes in the results was associated with the immune response to viral infection, which is supported by the published literature. For example, patients with low CCDC18 expression and high CPED1 expression had good quality of life, whereas those with low CDC16 expression had poor quality of life.

Identifying genes associated with resistance to KRAS G12C inhibitors via machine learning methods

BackgroundTargeted therapy has revolutionized cancer treatment, greatly improving patient outcomes and quality of life. Lung cancer, specifically non-small cell lung cancer, is frequently driven by the G12C mutation at the KRAS locus. The development of KRAS inhibitors has been a breakthrough in the field of cancer research, given the crucial role of KRAS mutations in driving tumor growth and progression. However, over half of patients with cancer bypass inhibition show limited response to treatment. The mechanisms underlying tumor cell resistance to this treatment remain poorly understood. MethodsTo address above gap in knowledge, we conducted a study aimed to elucidate the differences between tumor cells that respond positively to KRAS (G12C) inhibitor therapy and those that do not. Specifically, we analyzed single-cell gene expression profiles from KRAS G12C-mutant tumor cell models (H358, H2122, and SW1573) treated with KRAS G12C (ARS-1620) inhibitor, which contained 4297 cells that continued to proliferate under treatment and 3315 cells that became quiescent. Each cell was represented by the expression levels on 8687 genes. We then designed an innovative machine learning based framework, incorporating seven feature ranking algorithms and four classification algorithms to identify essential genes and establish quantitative rules. ResultsOur analysis identified some top-ranked genes, including H2AFZ, CKS1B, TUBA1B, RRM2, and BIRC5, that are known to be associated with the progression of multiple cancers. ConclusionAbove genes were relevant to tumor cell resistance to targeted therapy. This study provides important insights into the molecular mechanisms underlying tumor cell resistance to KRAS inhibitor treatment.

Identification of Colon Immune Cell Marker Genes Using Machine Learning Methods.

Immune cell infiltration that occurs at the site of colon tumors influences the course of cancer. Different immune cell compositions in the microenvironment lead to different immune responses and different therapeutic effects. This study analyzed single-cell RNA sequencing data in a normal colon with the aim of screening genetic markers of 25 candidate immune cell types and revealing quantitative differences between them. The dataset contains 25 classes of immune cells, 41,650 cells in total, and each cell is expressed by 22,164 genes at the expression level. They were fed into a machine learning-based stream. The five feature ranking algorithms (last absolute shrinkage and selection operator, light gradient boosting machine, Monte Carlo feature selection, minimum redundancy maximum relevance, and random forest) were first used to analyze the importance of gene features, yielding five feature lists. Then, incremental feature selection and two classification algorithms (decision tree and random forest) were combined to filter the most important genetic markers from each list. For different immune cell subtypes, their marker genes, such as KLRB1 in CD4 T cells, RPL30 in B cell IGA plasma cells, and JCHAIN in IgG producing B cells, were identified. They were confirmed to be differentially expressed in different immune cells and involved in immune processes. In addition, quantitative rules were summarized by using the decision tree algorithm to distinguish candidate immune cell types. These results provide a reference for exploring the cell composition of the colon cancer microenvironment and for clinical immunotherapy.

Accurate breast cancer diagnosis using a stable feature ranking algorithm

BackgroundBreast cancer (BC) is one of the most common cancers among women. Since diverse features can be collected, how to stably select the powerful ones for accurate BC diagnosis remains challenging.MethodsA hybrid framework is designed for successively investigating both feature ranking (FR) stability and cancer diagnosis effectiveness. Specifically, on 4 BC datasets (BCDR-F03, WDBC, GSE10810 and GSE15852), the stability of 23 FR algorithms is evaluated via an advanced estimator (S), and the predictive power of the stable feature ranks is further tested by using different machine learning classifiers.ResultsExperimental results identify 3 algorithms achieving good stability (S ge 0.55) on the four datasets and generalized Fisher score (GFS) leading to state-of-the-art performance. Moreover, GFS ranks suggest that shape features are crucial in BC image analysis (BCDR-F03 and WDBC) and that using a few genes can well differentiate benign and malignant tumor cases (GSE10810 and GSE15852).ConclusionsThe proposed framework recognizes a stable FR algorithm for accurate BC diagnosis. Stable and effective features could deepen the understanding of BC diagnosis and related decision-making applications.

Genetics Information with Functional Brain Networks for Dementia Classification

Mild cognitive impairment (MCI) precedes the Alzheimer’s disease (AD) continuum, making it crucial for therapeutic care to identify patients with MCI at risk of progression. We aim to create generalized models to identify patients with MCI who advance to AD using high-dimensional-data resting state functional magnetic resonance imaging (rs-fMRI) brain networks and gene expression. Studies that integrate genetic traits with brain imaging for clinical examination are limited, compared with most current research methodologies, employing separate or multi-imaging features for disease prognosis. Healthy controls (HCs) and the two phases of MCI (convertible and stable MCI) along with AD can be effectively diagnosed using genetic markers. The rs-fMRI-based brain functional connectome provides various information regarding brain networks and is utilized in combination with genetic factors to distinguish people with AD from HCs. The most discriminating network nodes are identified using the least absolute shrinkage and selection operator (LASSO). The most common brain areas for nodal detection in patients with AD are the middle temporal, inferior temporal, lingual, hippocampus, amygdala, and middle frontal gyri. The highest degree of discriminative power is demonstrated by the nodal graph metrics. Similarly, we propose an ensemble feature-ranking algorithm for high-dimensional genetic information. We use a multiple-kernel learning support vector machine to efficiently merge multipattern data. Using the suggested technique to distinguish AD from HCs produced combined features with a leave-one-out cross-validation (LOOCV) classification accuracy of 93.07% and area under the curve (AUC) of 95.13%, making it the most state-of-the-art technique in terms of diagnostic accuracy. Therefore, our proposed approach has high accuracy and is clinically relevant and efficient for identifying AD.

Identification of dynamic gene expression profiles during sequential vaccination with ChAdOx1/BNT162b2 using machine learning methods.

To date, COVID-19 remains a serious global public health problem. Vaccination against SARS-CoV-2 has been adopted by many countries as an effective coping strategy. The strength of the body's immune response in the face of viral infection correlates with the number of vaccinations and the duration of vaccination. In this study, we aimed to identify specific genes that may trigger and control the immune response to COVID-19 under different vaccination scenarios. A machine learning-based approach was designed to analyze the blood transcriptomes of 161 individuals who were classified into six groups according to the dose and timing of inoculations, including I-D0, I-D2-4, I-D7 (day 0, days 2-4, and day 7 after the first dose of ChAdOx1, respectively) and II-D0, II-D1-4, II-D7-10 (day 0, days 1-4, and days 7-10 after the second dose of BNT162b2, respectively). Each sample was represented by the expression levels of 26,364 genes. The first dose was ChAdOx1, whereas the second dose was mainly BNT162b2 (Only four individuals received a second dose of ChAdOx1). The groups were deemed as labels and genes were considered as features. Several machine learning algorithms were employed to analyze such classification problem. In detail, five feature ranking algorithms (Lasso, LightGBM, MCFS, mRMR, and PFI) were first applied to evaluate the importance of each gene feature, resulting in five feature lists. Then, the lists were put into incremental feature selection method with four classification algorithms to extract essential genes, classification rules and build optimal classifiers. The essential genes, namely, NRF2, RPRD1B, NEU3, SMC5, and TPX2, have been previously associated with immune response. This study also summarized expression rules that describe different vaccination scenarios to help determine the molecular mechanism of vaccine-induced antiviral immunity.

Identification of Smoking-Associated Transcriptome Aberration in Blood with Machine Learning Methods.

Long-term cigarette smoking causes various human diseases, including respiratory disease, cancer, and gastrointestinal (GI) disorders. Alterations in gene expression and variable splicing processes induced by smoking are associated with the development of diseases. This study applied advanced machine learning methods to identify the isoforms with important roles in distinguishing smokers from former smokers based on the expression profile of isoforms from current and former smokers collected in one previous study. These isoforms were deemed as features, which were first analyzed by the Boruta to select features highly correlated with the target variables. Then, the selected features were evaluated by four feature ranking algorithms, resulting in four feature lists. The incremental feature selection method was applied to each list for obtaining the optimal feature subsets and building high-performance classification models. Furthermore, a series of classification rules were accessed by decision tree with the highest performance. Eventually, the rationality of the mined isoforms (features) and classification rules was verified by reviewing previous research. Features such as isoforms ENST00000464835 (expressed by LRRN3), ENST00000622663 (expressed by SASH1), and ENST00000284311 (expressed by GPR15), and pathways (cytotoxicity mediated by natural killer cell and cytokine-cytokine receptor interaction) revealed by the enrichment analysis, were highly relevant to smoking response, suggesting the robustness of our analysis pipeline.

Fseval: A Benchmarking Framework for Feature Selection and Feature Ranking Algorithms

fseval: A Benchmarking Framework for Feature Selection and Feature Ranking Algorithms