Supervised, Unsupervised, and Semi-Supervised Feature Selection: A Review on Gene Selection

A review on advancements in feature selection and feature extraction for high-dimensional NGS data analysis

Recent advancements in biomedical technologies and the proliferation of high-dimensional Next Generation Sequencing (NGS) datasets have led to significant growth in the bulk and density of data. The NGS high-dimensional data, characterized by a large number of genomics, transcriptomics, proteomics, and metagenomics features relative to the number of biological samples, presents significant challenges for reducing feature dimensionality. The high dimensionality of NGS data poses significant challenges for data analysis, including increased computational burden, potential overfitting, and difficulty in interpreting results. Feature selection and feature extraction are two pivotal techniques employed to address these challenges by reducing the dimensionality of the data, thereby enhancing model performance, interpretability, and computational efficiency. Feature selection and feature extraction can be categorized into statistical and machine learning methods. The present study conducts a comprehensive and comparative review of various statistical, machine learning, and deep learning-based feature selection and extraction techniques specifically tailored for NGS and microarray data interpretation of humankind. A thorough literature search was performed to gather information on these techniques, focusing on array-based and NGS data analysis. Various techniques, including deep learning architectures, machine learning algorithms, and statistical methods, have been explored for microarray, bulk RNA-Seq, and single-cell, single-cell RNA-Seq (scRNA-Seq) technology-based datasets surveyed here. The study provides an overview of these techniques, highlighting their applications, advantages, and limitations in the context of high-dimensional NGS data. This review provides better insights for readers to apply feature selection and feature extraction techniques to enhance the performance of predictive models, uncover underlying biological patterns, and gain deeper insights into massive and complex NGS and microarray data.

SNP Array for Small-Shrimp (Genus Acetes) Origin Determination Using Machine Learning

Accurate origin determination of seafood is crucial for consumer trust and safety. This study was performed to develop a machine learning-based single-nucleotide polymorphism (SNP) analysis technique to determine the origin of Acetes species in salted small-shrimp products. Mitochondrial DNA (COI and 16S rRNA) analysis revealed genetic variations among species and origins. Eight candidate SNPs were identified, six of which were developed into markers for genotyping analysis. Using the developed markers, an SNP array was created and SNP data from salted small-shrimp samples were obtained. Machine learning analysis using a supervised learning algorithm achieved 100% accuracy in classifying the origin of Acetes based on SNP data. This method offers a reliable method for regulatory bodies to combat food fraud and ensure product integrity. The approach can be further improved by expanding the data set to encompass a wider range of species and origins. This study highlights the potential of SNP analysis and machine learning for ensuring seafood authenticity and promoting sustainable practices.

BiliQML: a supervised machine-learning model to quantify biliary forms from digitized whole slide liver histopathological images

The progress of research focused on cholangiocytes and the biliary tree during development and following injury is hindered by limited available quantitative methodologies. Current techniques include two-dimensional standard histological cell-counting approaches, which are rapidly performed, error prone, and lack architectural context or three-dimensional analysis of the biliary tree in opacified livers, which introduce technical issues along with minimal quantitation. The present study aims to fill these quantitative gaps with a supervised machine-learning model (BiliQML) able to quantify biliary forms in the liver of anti-keratin 19 antibody-stained whole slide images. Training utilized 5,019 researcher-labeled biliary forms, which following feature selection, and algorithm optimization, generated an F score of 0.87. Application of BiliQML on seven separate cholangiopathy models [genetic (Afp-CRE;Pkd1l1null/Fl, Alb-CRE;Rbp-jkfl/fl, and Albumin-CRE;ROSANICD), surgical (bile duct ligation), toxicological (3,5-diethoxycarbonyl-1,4-dihydrocollidine), and therapeutic (Cyp2c70-/- with ileal bile acid transporter inhibition)] allowed for a means to validate the capabilities and utility of this platform. The results from BiliQML quantification revealed biological and pathological differences across these seven diverse models, indicating a highly sensitive, robust, and scalable methodology for the quantification of distinct biliary forms. BiliQML is the first comprehensive machine-learning platform for biliary form analysis, adding much-needed morphologic context to standard immunofluorescence-based histology, and provides clinical and basic science researchers with a novel tool for the characterization of cholangiopathies.NEW & NOTEWORTHY BiliQML is the first comprehensive machine-learning platform for biliary form analysis in whole slide histopathological images. This platform provides clinical and basic science researchers with a novel tool for the improved quantification and characterization of biliary tract disorders.

AI-Based Metamaterial Design

The use of metamaterials in various devices has revolutionized applications in optics, healthcare, acoustics, and power systems. Advancements in these fields demand novel or superior metamaterials that can demonstrate targeted control of electromagnetic, mechanical, and thermal properties of matter. Traditional design systems and methods often require manual manipulations which is time-consuming and resource intensive. The integration of artificial intelligence (AI) in optimizing metamaterial design can be employed to explore variant disciplines and address bottlenecks in design. AI-based metamaterial design can also enable the development of novel metamaterials by optimizing design parameters that cannot be achieved using traditional methods. The application of AI can be leveraged to accelerate the analysis of vast data sets as well as to better utilize limited data sets via generative models. This review covers the transformative impact of AI and AI-based metamaterial design for optics, acoustics, healthcare, and power systems. The current challenges, emerging fields, future directions, and bottlenecks within each domain are discussed.

Synovial fibroblast gene expression is associated with sensory nerve growth and pain in rheumatoid arthritis

It has been presumed that rheumatoid arthritis (RA) joint pain is related to inflammation in the synovium; however, recent studies reveal that pain scores in patients do not correlate with synovial inflammation. We developed a machine-learning approach (graph-based gene expression module identification or GbGMI) to identify an 815-gene expression module associated with pain in synovial biopsy samples from patients with established RA who had limited synovial inflammation at arthroplasty. We then validated this finding in an independent cohort of synovial biopsy samples from patients who had early untreated RA with little inflammation. Single-cell RNA sequencing analyses indicated that most of these 815 genes were most robustly expressed by lining layer synovial fibroblasts. Receptor-ligand interaction analysis predicted cross-talk between human lining layer fibroblasts and human dorsal root ganglion neurons expressing calcitonin gene-related peptide (CGRP+). Both RA synovial fibroblast culture supernatant and netrin-4, which is abundantly expressed by lining fibroblasts and was within the GbGMI-identified pain-associated gene module, increased the branching of pain-sensitive murine CGRP+ dorsal root ganglion neurons in vitro. Imaging of solvent-cleared synovial tissue with little inflammation from humans with RA revealed CGRP+ pain-sensing neurons encasing blood vessels growing into synovial hypertrophic papilla. Together, these findings support a model whereby synovial lining fibroblasts express genes associated with pain that enhance the growth of pain-sensing neurons into regions of synovial hypertrophy in RA.

Prediction of attention deficit hyperactivity disorder based on explainable artificial intelligence

Accurate assessment of Attention Deficit Hyperactivity Disorder (ADHD) is crucial for the effective treatment of affected individuals. Traditionally, psychometric tests such as the WISC-IV have been utilized to gather evidence and identify patterns or factors contributing to ADHD diagnosis. However, in recent years, the use of machine learning (ML) models in conjunction with post-hoc eXplainable Artificial Intelligence (XAI) techniques has improved our ability to make precise predictions and provide transparent explanations. The objective of this study is twofold: firstly, to predict the likelihood of an individual receiving an ADHD diagnosis using ML algorithms, and secondly, to offer interpretable insights into the decision-making process of the ML model. The dataset under scrutiny comprises 694 cases collected over the past decade in Spain, including information on age, gender, and WISC-IV test scores. The outcome variable is the professional diagnosis. Diverse ML algorithms representing various learning styles were rigorously evaluated through a stratified 10-fold cross-validation, with performance assessed using key metrics, including accuracy, area under the receiver operating characteristic curve, sensitivity, and specificity. Models were compared using both the full set of initial features and a well-suited wrapper-type feature selection algorithm (Boruta). Following the identification of the most suitable model, Shapley additive values were computed to assign weights to each predictor based on their additive contribution to the outcome and to elucidate the predictions. Strikingly, a reduced set of 8 out of the initial 20 variables produced results comparable to using the full feature set. Among the ML models tested, the Random Forest algorithm outperformed others on most metrics (ACC = 0.90, AUC = 0.94, Sensitivity = 0.91, Specificity = 0.92). Notably, the principal predictors, ranked by importance, included GAI - CPI, WMI, CPI, PSI, VCI, WMI - PSI, PRI, and LN. Individual case examples exhibit variations in predictions depending on unique characteristics, including instances of false positives and negatives. Our ML model adeptly predicted ADHD diagnoses in 90% of cases, with potential for further enhancement by expanding our database. Furthermore, the use of XAI techniques enables the elucidation of salient factors in individual cases, thereby aiding inexperienced professionals in the diagnostic process and facilitating comparison with expert assessments. It is important to note that this tool is designed to support the ADHD diagnostic process, where the medical professional always has the final say in decision-making.

Bi-level gene selection of cancer by combining clustering and sparse learning

The diagnosis of cancer based on gene expression profile data has attracted extensive attention in the field of biomedical science. This type of data usually has the characteristics of high dimensionality and noise. In this paper, a hybrid gene selection method based on clustering and sparse learning is proposed to choose the key genes with high precision. We first propose a filter method, which combines the k-means clustering algorithm and signal-to-noise ratio ranking method, and then, a weighted gene co-expression network has been applied to the reduced data set to identify modules corresponding to biological pathways. Moreover, we choose the key genes by using group bridge and sparse group lasso as wrapper methods. Finally, we conduct some numerical experiments on six cancer datasets. The numerical results show that our proposed method has achieved good performance in gene selection and cancer classification.

Population characteristic exploitation-based multi-orientation multi-objective gene selection for microarray data classification

Gene selection is a process of selecting discriminative genes from microarray data that helps to diagnose and classify cancer samples effectively. Swarm intelligence evolution-based gene selection algorithms can never circumvent the problem that the population is prone to local optima in the process of gene selection. To tackle this challenge, previous research has focused primarily on two aspects: mitigating premature convergence to local optima and escaping from local optima. In contrast to these strategies, this paper introduces a novel perspective by adopting reverse thinking, where the issue of local optima is seen as an opportunity rather than an obstacle. Building on this foundation, we propose MOMOGS-PCE, a novel gene selection approach that effectively exploits the advantageous characteristics of populations trapped in local optima to uncover global optimal solutions. Specifically, MOMOGS-PCE employs a novel population initialization strategy, which involves the initialization of multiple populations that explore diverse orientations to foster distinct population characteristics. The subsequent step involved the utilization of an enhanced NSGA-II algorithm to amplify the advantageous characteristics exhibited by the population. Finally, a novel exchange strategy is proposed to facilitate the transfer of characteristics between populations that have reached near maturity in evolution, thereby promoting further population evolution and enhancing the search for more optimal gene subsets. The experimental results demonstrated that MOMOGS-PCE exhibited significant advantages in comprehensive indicators compared with six competitive multi-objective gene selection algorithms. It is confirmed that the "reverse-thinking" approach not only avoids local optima but also leverages it to uncover superior gene subsets for cancer diagnosis.

Empirical exploration of whale optimisation algorithm for heart disease prediction

Heart Diseases have the highest mortality worldwide, necessitating precise predictive models for early risk assessment. Much existing research has focused on improving model accuracy with single datasets, often neglecting the need for comprehensive evaluation metrics and utilization of different datasets in the same domain (heart disease). This research introduces a heart disease risk prediction approach by harnessing the whale optimization algorithm (WOA) for feature selection and implementing a comprehensive evaluation framework. The study leverages five distinct datasets, including the combined dataset comprising the Cleveland, Long Beach VA, Switzerland, and Hungarian heart disease datasets. The others are the Z-AlizadehSani, Framingham, South African, and Cleveland heart datasets. The WOA-guided feature selection identifies optimal features, subsequently integrated into ten classification models. Comprehensive model evaluation reveals significant improvements across critical performance metrics, including accuracy, precision, recall, F1 score, and the area under the receiver operating characteristic curve. These enhancements consistently outperform state-of-the-art methods using the same dataset, validating the effectiveness of our methodology. The comprehensive evaluation framework provides a robust assessment of the model's adaptability, underscoring the WOA's effectiveness in identifying optimal features in multiple datasets in the same domain.

The impact of Bayesian optimization on feature selection

Feature selection is an indispensable step for the analysis of high-dimensional molecular data. Despite its importance, consensus is lacking on how to choose the most appropriate feature selection methods, especially when the performance of the feature selection methods itself depends on hyper-parameters. Bayesian optimization has demonstrated its advantages in automatically configuring the settings of hyper-parameters for various models. However, it remains unclear whether Bayesian optimization can benefit feature selection methods. In this research, we conducted extensive simulation studies to compare the performance of various feature selection methods, with a particular focus on the impact of Bayesian optimization on those where hyper-parameters tuning is needed. We further utilized the gene expression data obtained from the Alzheimer's Disease Neuroimaging Initiative to predict various brain imaging-related phenotypes, where various feature selection methods were employed to mine the data. We found through simulation studies that feature selection methods with hyper-parameters tuned using Bayesian optimization often yield better recall rates, and the analysis of transcriptomic data further revealed that Bayesian optimization-guided feature selection can improve the accuracy of disease risk prediction models. In conclusion, Bayesian optimization can facilitate feature selection methods when hyper-parameter tuning is needed and has the potential to substantially benefit downstream tasks.

Screening ovarian cancer by using risk factors: machine learning assists

BACKGROUND AND AIM

Ovarian cancer (OC) is a prevalent and aggressive malignancy that poses a significant public health challenge. The lack of preventive strategies for OC increases morbidity, mortality, and other negative consequences. Screening OC through risk prediction could be leveraged as a powerful strategy for preventive purposes that have not received much attention. So, this study aimed to leverage machine learning approaches as predictive assistance solutions to screen high-risk groups of OC and achieve practical preventive purposes.

MATERIALS AND METHODS

As this study is data-driven and retrospective in nature, we leveraged 1516 suspicious OC women data from one concentrated database belonging to six clinical settings in Sari City from 2015 to 2019. Six machine learning (ML) algorithms, including XG-Boost, Random Forest (RF), J-48, support vector machine (SVM), K-nearest neighbor (KNN), and artificial neural network (ANN) were leveraged to construct prediction models for OC. To choose the best model for predicting OC, we compared various prediction models built using the area under the receiver characteristic operator curve (AU-ROC).

RESULTS

Current experimental results revealed that the XG-Boost with AU-ROC = 0.93 (0.95 CI = [0.91-0.95]) was recognized as the best-performing model for predicting OC.

CONCLUSIONS

ML approaches possess significant predictive efficiency and interoperability to achieve powerful preventive strategies leveraging OC screening high-risk groups.

Analyzing omics data based on sample network

Identifying valuable features from complex omics data is of great significance for disease diagnosis study. This paper proposes a new feature selection algorithm based on sample network (FS-SN) to mine important information from omics data. The sample network is constructed according to the sample neighbor relationship at the molecular (feature) expression level, and the distinguishing ability of the feature is evaluated based on the topology of the sample network. The sample network established on a feature with a strong discriminating ability tends to have many edges between the same group samples and few edges between the different group samples. At the same time, FS-SN removes redundant features according to the gravitational interaction between features. To show the validation of FS-SN, it was compared on ten public datasets with ERGS, mRMR, ReliefF, ATSD-DN, and INDEED which are efficient in omics data analysis. Experimental results show that FS-SN performed better than the compared methods in accuracy, sensitivity and specificity in most cases. Hence, FS-SN making use of the topology of the sample network is effective for analyzing omics data, it can identify key features that reflect the occurrence and development of diseases, and reveal the underlying biological mechanism.

An embedded feature selection method based on generalized classifier neural network for cancer classification

The selection of relevant genes plays a vital role in classifying high-dimensional microarray gene expression data. Sparse group Lasso and its variants have been employed for gene selection to capture the interactions of genes within a group. Most of the embedded methods are linear sparse learning models that fail to capture the non-linear interactions. Additionally, very less attention is given to solving multi-class problems. The existing methods create overlapping groups, which further increases dimensionality. The paper proposes a neural network-based embedded feature selection method that can represent the non-linear relationship. In an effort toward an explainable model, a generalized classifier neural network (GCNN) is adopted as the model for the proposed embedded feature selection. GCNN has well-defined architecture in terms of the number of layers and neurons within each layer. Each layer has a distinct functionality, eliminating the obscure nature of most neural networks. The paper proposes a feature selection approach called Weighted GCNN (WGCNN) that embeds feature weighting as a part of training the neural network. Since the gene expression data comprises a large number of features, to avoid overfitting of the model a statistical guided dropout is implemented at the input layer. The proposed method works for binary as well as multi-class classification problems likewise. Experimental validation is carried out on seven microarray datasets on three learning models and compared with six state-of-art methods that are popularly employed for feature selection. The WGCNN performs well in terms of the F1 score and the number of features selected.

Dual regularized subspace learning using adaptive graph learning and rank constraint: Unsupervised feature selection on gene expression microarray datasets

High-dimensional problems have increasingly drawn attention in gene selection and analysis. To add insult to injury, usually the number of features is greater than number of samples in microarray gene dataset which leads to an ill-posed underdetermined equation system. Poor performance and high computational time for learning algorithms are consequences of redundant features in high-dimensional data. Feature selection is a noteworthy pre-processing method to ameliorate the curse of dimensionality with aim of maximum relevancy and minimum redundancy information preservation. Likewise, unsupervised feature selection has been important since collecting labels for data is expensive. In this paper, we develop a novel robust unsupervised feature selection to select discriminative subset of features for unlabeled data based on rank constrained and dual regularized nonnegative matrix factorization. The major focus of the proposed technique is to discard redundant features while keeping the informative features. Proposed feature selection technique consists of nonnegative matrix factorization to decompose the data into feature weight matrix and representation matrix, inner product norm as regularization for both feature weight matrix and representation matrix, adaptive structure learning to preserve local information and Schatten-p norm as rank constraint. To demonstrate the effectiveness of the proposed method, numerical studies are conducted on six benchmark microarray datasets. The results show that the proposed technique outperforms eight state-of-art unsupervised feature selection techniques in terms of clustering accuracy and normalized mutual information.

Nonlinear Feature Selection Neural Network via Structured Sparse Regularization

Feature selection is an important and effective data preprocessing method, which can remove the noise and redundant features while retaining the relevant and discriminative features in high-dimensional data. In real-world applications, the relationships between data samples and their labels are usually nonlinear. However, most of the existing feature selection models focus on learning a linear transformation matrix, which cannot capture such a nonlinear structure in practice and will degrade the performance of downstream tasks. To address the issue, we propose a novel nonlinear feature selection method to select those most relevant and discriminative features in high-dimensional dataset. Specifically, our method learns the nonlinear structure of high-dimensional data by a neural network with cross entropy loss function, and then using the structured sparsity norm such as l2,p -norm to regularize the weights matrix connecting the input layer and the first hidden layer of the neural network model to learn weight of each feature. Therefore, a structural sparse weights matrix is obtained by conducting nonlinear learning based on a neural network with structured sparsity regularization. Then, we use the gradient descent method to achieve the optimal solution of the proposed model. Evaluating the experimental results on several synthetic datasets and real-world datasets shows the effectiveness and superiority of the proposed nonlinear feature selection model.

Exploring patient medication adherence and data mining methods in clinical big data: A contemporary review

BACKGROUND

Increasingly, patient medication adherence data are being consolidated from claims databases and electronic health records (EHRs). Such databases offer an indirect avenue to gauge medication adherence in our data-rich healthcare milieu. The surge in data accessibility, coupled with the pressing need for its conversion to actionable insights, has spotlighted data mining, with machine learning (ML) emerging as a pivotal technique. Nonadherence poses heightened health risks and escalates medical costs. This paper elucidates the synergistic interaction between medical database mining for medication adherence and the role of ML in fostering knowledge discovery.

METHODS

We conducted a comprehensive review of EHR applications in the realm of medication adherence, leveraging ML techniques. We expounded on the evolution and structure of medical databases pertinent to medication adherence and harnessed both supervised and unsupervised ML paradigms to delve into adherence and its ramifications.

RESULTS

Our study underscores the applications of medical databases and ML, encompassing both supervised and unsupervised learning, for medication adherence in clinical big data. Databases like SEER and NHANES, often underutilized due to their intricacies, have gained prominence. Employing ML to excavate patient medication logs from these databases facilitates adherence analysis. Such findings are pivotal for clinical decision-making, risk stratification, and scholarly pursuits, aiming to elevate healthcare quality.

CONCLUSION

Advanced data mining in the era of big data has revolutionized medication adherence research, thereby enhancing patient care. Emphasizing bespoke interventions and research could herald transformative shifts in therapeutic modalities.

Machine learning in the identification of prognostic DNA methylation biomarkers among patients with cancer: A systematic review of epigenome-wide studies

BACKGROUND

DNA methylation biomarkers have great potential in improving prognostic classification systems for patients with cancer. Machine learning (ML)-based analytic techniques might help overcome the challenges of analyzing high-dimensional data in relatively small sample sizes. This systematic review summarizes the current use of ML-based methods in epigenome-wide studies for the identification of DNA methylation signatures associated with cancer prognosis.

METHODS

We searched three electronic databases including PubMed, EMBASE, and Web of Science for articles published until 2 January 2023. ML-based methods and workflows used to identify DNA methylation signatures associated with cancer prognosis were extracted and summarized. Two authors independently assessed the methodological quality of included studies by a seven-item checklist adapted from 'A Tool to Assess Risk of Bias and Applicability of Prediction Model Studies (PROBAST)' and from the 'Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK). Different ML methods and workflows used in included studies were summarized and visualized by a sunburst chart, a bubble chart, and Sankey diagrams, respectively.

RESULTS

Eighty-three studies were included in this review. Three major types of ML-based workflows were identified. 1) unsupervised clustering, 2) supervised feature selection, and 3) deep learning-based feature transformation. For the three workflows, the most frequently used ML techniques were consensus clustering, least absolute shrinkage and selection operator (LASSO), and autoencoder, respectively. The systematic review revealed that the performance of these approaches has not been adequately evaluated yet and that methodological and reporting flaws were common in the identified studies using ML techniques.

CONCLUSIONS

There is great heterogeneity in ML-based methodological strategies used by epigenome-wide studies to identify DNA methylation markers associated with cancer prognosis. In theory, most existing workflows could not handle the high multi-collinearity and potentially non-linearity interactions in epigenome-wide DNA methylation data. Benchmarking studies are needed to compare the relative performance of various approaches for specific cancer types. Adherence to relevant methodological and reporting guidelines are urgently needed.

Application note: TDbasedUFE and TDbasedUFEadv: bioconductor packages to perform tensor decomposition based unsupervised feature extraction

Motivation

Tensor decomposition (TD)-based unsupervised feature extraction (FE) has proven effective for a wide range of bioinformatics applications ranging from biomarker identification to the identification of disease-causing genes and drug repositioning. However, TD-based unsupervised FE failed to gain widespread acceptance due to the lack of user-friendly tools for non-experts.

Results

We developed two bioconductor packages-TDbasedUFE and TDbasedUFEadv-that enable researchers unfamiliar with TD to utilize TD-based unsupervised FE. The packages facilitate the identification of differentially expressed genes and multiomics analysis. TDbasedUFE was found to outperform two state-of-the-art methods, such as DESeq2 and DIABLO.

Availability and implementation

TDbasedUFE and TDbasedUFEadv are freely available as R/Bioconductor packages, which can be accessed at https://bioconductor.org/packages/TDbasedUFE and https://bioconductor.org/packages/TDbasedUFEadv, respectively.

Applications, functions, and accuracy of artificial intelligence in restorative dentistry: A literature review

OBJECTIVE

The applications of artificial intelligence (AI) are increasing in restorative dentistry; however, the AI performance is unclear for dental professionals. The purpose of this narrative review was to evaluate the applications, functions, and accuracy of AI in diverse aspects of restorative dentistry including caries detection, tooth preparation margin detection, tooth restoration design, metal structure casting, dental restoration/implant detection, removable partial denture design, and tooth shade determination.

OVERVIEW

An electronic search was performed on Medline/PubMed, Embase, Web of Science, Cochrane, Scopus, and Google Scholar databases. English-language articles, published from January 1, 2000, to March 1, 2022, relevant to the aforementioned aspects were selected using the key terms of artificial intelligence, machine learning, deep learning, artificial neural networks, convolutional neural networks, clustering, soft computing, automated planning, computational learning, computer vision, and automated reasoning as inclusion criteria. A manual search was also performed. Therefore, 157 articles were included, reviewed, and discussed.

CONCLUSIONS

Based on the current literature, the AI models have shown promising performance in the mentioned aspects when being compared with traditional approaches in terms of accuracy; however, as these models are still in development, more studies are required to validate their accuracy and apply them to routine clinical practice.

CLINICAL SIGNIFICANCE

AI with its specific functions has shown successful applications with acceptable accuracy in diverse aspects of restorative dentistry. The understanding of these functions may lead to novel applications with optimal accuracy for AI in restorative dentistry.

GeNetOntology: identifying affected gene ontology terms via grouping, scoring, and modeling of gene expression data utilizing biological knowledge-based machine learning

Introduction: Identifying significant sets of genes that are up/downregulated under specific conditions is vital to understand disease development mechanisms at the molecular level. Along this line, in order to analyze transcriptomic data, several computational feature selection (i.e., gene selection) methods have been proposed. On the other hand, uncovering the core functions of the selected genes provides a deep understanding of diseases. In order to address this problem, biological domain knowledge-based feature selection methods have been proposed. Unlike computational gene selection approaches, these domain knowledge-based methods take the underlying biology into account and integrate knowledge from external biological resources. Gene Ontology (GO) is one such biological resource that provides ontology terms for defining the molecular function, cellular component, and biological process of the gene product. Methods: In this study, we developed a tool named GeNetOntology which performs GO-based feature selection for gene expression data analysis. In the proposed approach, the process of Grouping, Scoring, and Modeling (G-S-M) is used to identify significant GO terms. GO information has been used as the grouping information, which has been embedded into a machine learning (ML) algorithm to select informative ontology terms. The genes annotated with the selected ontology terms have been used in the training part to carry out the classification task of the ML model. The output is an important set of ontologies for the two-class classification task applied to gene expression data for a given phenotype. Results: Our approach has been tested on 11 different gene expression datasets, and the results showed that GeNetOntology successfully identified important disease-related ontology terms to be used in the classification model. Discussion: GeNetOntology will assist geneticists and scientists to identify a range of disease-related genes and ontologies in transcriptomic data analysis, and it will also help doctors design diagnosis platforms and improve patient treatment plans.

Review of feature selection approaches based on grouping of features

With the rapid development in technology, large amounts of high-dimensional data have been generated. This high dimensionality including redundancy and irrelevancy poses a great challenge in data analysis and decision making. Feature selection (FS) is an effective way to reduce dimensionality by eliminating redundant and irrelevant data. Most traditional FS approaches score and rank each feature individually; and then perform FS either by eliminating lower ranked features or by retaining highly-ranked features. In this review, we discuss an emerging approach to FS that is based on initially grouping features, then scoring groups of features rather than scoring individual features. Despite the presence of reviews on clustering and FS algorithms, to the best of our knowledge, this is the first review focusing on FS techniques based on grouping. The typical idea behind FS through grouping is to generate groups of similar features with dissimilarity between groups, then select representative features from each cluster. Approaches under supervised, unsupervised, semi supervised and integrative frameworks are explored. The comparison of experimental results indicates the effectiveness of sequential, optimization-based (i.e., fuzzy or evolutionary), hybrid and multi-method approaches. When it comes to biological data, the involvement of external biological sources can improve analysis results. We hope this work's findings can guide effective design of new FS approaches using feature grouping.

Phenomics and Robust Multiomics Data for Cardiovascular Disease Subtyping

The complex landscape of cardiovascular diseases encompasses a wide range of related pathologies arising from diverse molecular mechanisms and exhibiting heterogeneous phenotypes. This variety of manifestations poses significant challenges in the development of treatment strategies. The increasing availability of precise phenotypic and multiomics data of cardiovascular disease patient populations has spurred the development of a variety of computational disease subtyping techniques to identify distinct subgroups with unique underlying pathogeneses. In this review, we outline the essential components of computational approaches to select, integrate, and cluster omics and clinical data in the context of cardiovascular disease research. We delve into the challenges faced during different stages of the analysis, including feature selection and extraction, data integration, and clustering algorithms. Next, we highlight representative applications of subtyping pipelines in heart failure and coronary artery disease. Finally, we discuss the current challenges and future directions in the development of robust subtyping approaches that can be implemented in clinical workflows, ultimately contributing to the ongoing evolution of precision medicine in health care.

Robust microarray data feature selection using a correntropy based distance metric learning approach

Classification of high-dimensional microarray data is a challenge in bioinformatics and genetic data processing. One of the challenging issues of feature selection is the presence of outliers. The Euclidean distance metric is sensitive to outliers. In this study, a distance metric learning based feature selection approach that uses the correntropy function as the discrimination metric is proposed. For this purpose, the metric learning problem is formulated as an optimization problem and solved using the Lagrange method. The output of the approach signifies the most important and robust features. After feature selection, different classification methods such as SVM, decision trees, and NN classifiers are used to investigate the classification accuracy of the proposed method as well as precision, recall, and F-measure. Experiments are carried out on 13 high-dimensional datasets and show that the proposed method outperforms the previous models in terms of accuracy and robustness.

An Efficient Iterative Approach to Explainable Feature Learning

This article introduces a new iterative approach to explainable feature learning. During each iteration, new features are generated, first by applying arithmetic operations on the input set of features. These are then evaluated in terms of probability distribution agreements between values of samples belonging to different classes. Finally, a graph-based approach for feature selection is proposed, which allows for selecting high-quality and uncorrelated features to be used in feature generation during the next iteration. As shown by the results, the proposed method improved the accuracy of all tested classifiers, where the best accuracies were achieved using random forest. In addition, the method turned out to be insensitive to both of the input parameters, while superior performances in comparison to the state of the art were demonstrated on nine out of 15 test sets and achieving comparable results in the others. Finally, we demonstrate the explainability of the learned feature representation for knowledge discovery.

TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa

Bacterial biofilms are a source of infectious human diseases and are heavily linked to antibiotic resistance. Pseudomonas aeruginosa is a multidrug-resistant bacterium widely present and implicated in several hospital-acquired infections. Over the last years, the development of new drugs able to inhibit Pseudomonas aeruginosa by interfering with its ability to form biofilms has become a promising strategy in drug discovery. Identifying molecules able to interfere with biofilm formation is difficult, but further developing these molecules by rationally improving their activity is particularly challenging, as it requires knowledge of the specific protein target that is inhibited. This work describes the development of a machine learning multitechnique consensus workflow to predict the protein targets of molecules with confirmed inhibitory activity against biofilm formation by Pseudomonas aeruginosa. It uses a specialized database containing all the known targets implicated in biofilm formation by Pseudomonas aeruginosa. The experimentally confirmed inhibitors available on ChEMBL, together with chemical descriptors, were used as the input features for a combination of nine different classification models, yielding a consensus method to predict the most likely target of a ligand. The implemented algorithm is freely available at https://github.com/BioSIM-Research-Group/TargIDe under licence GNU General Public Licence (GPL) version 3 and can easily be improved as more data become available.

A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization

BACKGROUND

In the field of genomics and personalized medicine, it is a key issue to find biomarkers directly related to the diagnosis of specific diseases from high-throughput gene microarray data. Feature selection technology can discover biomarkers with disease classification information.

RESULTS

We use support vector machines as classifiers and use the five-fold cross-validation average classification accuracy, recall, precision and F1 score as evaluation metrics to evaluate the identified biomarkers. Experimental results show classification accuracy above 0.93, recall above 0.92, precision above 0.91, and F1 score above 0.94 on eight microarray datasets.

METHOD

This paper proposes a two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization (EF-BDBA), which can effectively reduce the dimension of microarray data and obtain optimal biomarkers. In the first stage, we propose an ensemble filter feature selection method. The method combines an improved fast correlation-based filter algorithm with Fisher score. obviously redundant and irrelevant features can be filtered out to initially reduce the dimensionality of the microarray data. In the second stage, the optimal feature subset is selected using an improved binary differential evolution incorporating an improved binary African vultures optimization algorithm. The African vultures optimization algorithm has excellent global optimization ability. It has not been systematically applied to feature selection problems, especially for gene microarray data. We combine it with a differential evolution algorithm to improve population diversity.

CONCLUSION

Compared with traditional feature selection methods and advanced hybrid methods, the proposed method achieves higher classification accuracy and identifies excellent biomarkers while retaining fewer features. The experimental results demonstrate the effectiveness and advancement of our proposed algorithmic model.

Improved intelligent water drop-based hybrid feature selection method for microarray data processing

Classifying microarray datasets, which usually contains many noise genes that degrade the performance of classifiers and decrease classification accuracy rate, is a competitive research topic. Feature selection (FS) is one of the most practical ways for finding the most optimal subset of genes that increases classification's accuracy for diagnostic and prognostic prediction of tumor cancer from the microarray datasets. This means that we always need to develop more efficient FS methods, that select only optimal or close-to-optimal subset of features to improve classification performance. In this paper, we propose a hybrid FS method for microarray data processing, that combines an ensemble filter with an Improved Intelligent Water Drop (IIWD) algorithm as a wrapper by adding one of three local search (LS) algorithms: Tabu search (TS), Novel LS algorithm (NLSA), or Hill Climbing (HC) in each iteration from IWD, and using a correlation coefficient filter as a heuristic undesirability (HUD) for next node selection in the original IWD algorithm. The effects of adding three different LS algorithms to the proposed IIWD algorithm have been evaluated through comparing the performance of the proposed ensemble filter-IIWD-based wrapper without adding any LS algorithms named (PHFS-IWD) FS method versus its performance when adding a specific LS algorithm from (TS, NLSA or HC) in FS methods named, (PHFS-IWDTS, PHFS-IWDNLSA, and PHFS-IWDHC), respectively. Naïve Bayes(NB) classifier with five microarray datasets have been deployed for evaluating and comparing the proposed hybrid FS methods. Results show that using LS algorithms in each iteration from the IWD algorithm improves F-score value with an average equal to 5% compared with PHFS-IWD. Also, PHFS-IWDNLSA improves the F-score value with an average of 4.15% over PHFS-IWDTS, and 5.67% over PHFS-IWDHC while PHFS-IWDTS outperformed PHFS-IWDHC with an average of increment equal to 1.6%. On the other hand, the proposed hybrid-based FS methods improve accuracy with an average equal to 8.92% in three out of five datasets and decrease the number of genes with a percentage of 58.5% in all five datasets compared with six of the most recent state-of-the-art FS methods.

Enhancing spatial resolution of GRACE-derived groundwater storage anomalies in Urmia catchment using machine learning downscaling methods

The Urmia lake in north-west Iran has dried up to perilously low levels in the past two decades. In this study, we investigate the drivers behind the decline in lake water level with the help of in-situ and remote sensing data. We use total water storage (TWS) changes from the gravity recovery and climate experiment (GRACE) satellite mission. TWS from GRACE includes all the water storage compartments in a column and is the only remote sensing product that can help in estimating groundwater storage (GWS) changes. The coarse spatial (approx. 300 km) resolution of GRACE does not allow us to identify local changes that may have led to the Urmia lake disaster. In this study, we tackle the poor resolution of the GRACE data by employing three machine learning (ML) methods including random forest (RF), support vector regression (SVR) and multi-layer perceptron (MLP). The methods predict the groundwater storage anomaly (GWSA), derived from GRACE, as a function of hydro-climatic variables such as precipitation, evapotranspiration, land surface temperature (LST) and normalized difference vegetation index (NDVI) on a finer scale of 0.25° × 0.25°. We found that i) The RF model exhibited highest R (0.98), highest NSE (0.96) and lowest RMSE (18.36 mm) values. ii) The RF downscaled data indicated that the exploitation of groundwater resources in the aquifers is the main driver of groundwater storage and changes in the regional ecosystem, which has been corroborated by few other studies as well. The impact of precipitation and evapotranspiration on the GWSA was found to be rather weak, indicating that the anthropogenic derivers had the most significant impact on the GWSA changes. iii) We generally observed a significant negative trend in GWSA, having also significant positive correlations with the well data. However, over regions with dam construction significant negative correlations were found.

Sudden cardiac death multiparametric classification system for Chagas heart disease's patients based on clinical data and 24-hours ECG monitoring

About 6.5 million people are infected with Chagas disease (CD) globally, and WHO estimates that $ > million people worldwide suffer from ChHD. Sudden cardiac death (SCD) represents one of the leading causes of death worldwide and affects approximately 65% of ChHD patients at a rate of 24 per 1000 patient-years, much greater than the SCD rate in the general population. Its occurrence in the specific context of ChHD needs to be better exploited. This paper provides the first evidence supporting the use of machine learning (ML) methods within non-invasive tests: patients' clinical data and cardiac restitution metrics (CRM) features extracted from ECG-Holter recordings as an adjunct in the SCD risk assessment in ChHD. The feature selection (FS) flows evaluated 5 different groups of attributes formed from patients' clinical and physiological data to identify relevant attributes among 57 features reported by 315 patients at HUCFF-UFRJ. The FS flow with FS techniques (variance, ANOVA, and recursive feature elimination) and Naive Bayes (NB) model achieved the best classification performance with 90.63% recall (sensitivity) and 80.55% AUC. The initial feature set is reduced to a subset of 13 features (4 Classification; 1 Treatment; 1 CRM; and 7 Heart Tests). The proposed method represents an intelligent diagnostic support system that predicts the high risk of SCD in ChHD patients and highlights the clinical and CRM data that most strongly impact the final outcome.

Classification of COVID-19 Patients into Clinically Relevant Subsets by a Novel Machine Learning Pipeline Using Transcriptomic Features

The persistent impact of the COVID-19 pandemic and heterogeneity in disease manifestations point to a need for innovative approaches to identify drivers of immune pathology and predict whether infected patients will present with mild/moderate or severe disease. We have developed a novel iterative machine learning pipeline that utilizes gene enrichment profiles from blood transcriptome data to stratify COVID-19 patients based on disease severity and differentiate severe COVID cases from other patients with acute hypoxic respiratory failure. The pattern of gene module enrichment in COVID-19 patients overall reflected broad cellular expansion and metabolic dysfunction, whereas increased neutrophils, activated B cells, T-cell lymphopenia, and proinflammatory cytokine production were specific to severe COVID patients. Using this pipeline, we also identified small blood gene signatures indicative of COVID-19 diagnosis and severity that could be used as biomarker panels in the clinical setting.

Feature extraction of linear separability using robust autoencoder with distance metric

This paper proposes a robust autoencoder with Wasserstein distance metric to extract the linear separability features from the input data. To minimize the difference between the reconstructed feature space and the original feature space, using Wasserstein distance realizes a homeomorphic transformation of the original feature space, i.e., the so-called the reconstruction of feature space. The autoencoder is used for features extraction of linear separability in the reconstructed feature space. Experiment results on real datasets show that the proposed method reaches up 0.9777 and 0.7112 on the low-dimensional and high-dimensional datasets in extracted accuracies, respectively, and also outperforms competitors. Results also confirm that compared with feature metric-based methods and deep network architectures-based method, the linear separabilities of those features extracted by distance metric-based methods win over them. More importantly, the linear separabilities of those features obtained by evaluating distance similarity of the data are better than those obtained by evaluating feature importance of data. We also demonstrate that the data distribution in the feature space reconstructed by a homeomorphic transformation can be closer to the original data distribution.

SEQENS: An ensemble method for relevant gene identification in microarray data

This paper describes an ensemble feature identification algorithm called SEQENS, and measures its capability to identify the relevant variables in a case-control study using a genetic expression microarray dataset. SEQENS uses Sequential Feature Search on multiple sample splitting to select variables showing stronger relation with the target, and a variable relevance ranking is finally produced. Although designed for feature identification, SEQENS could also serve as a basis for feature selection (classifier optimisation). Cliff, a ranking evaluation metric is also presented and used to assess the feature identification algorithms when a groundtruth of relevant variables is available. To test performance, three types of synthetic groundtruths emulating fictitious diseases are generated from ten randomly chosen variables following different target pattern distributions using the E-MTAB-3732 dataset. Several sample-to-dimensionality ratios ranging from 300 to 3,000 observations and 854 to 54,675 variables are explored. SEQENS is compared with other feature selection or identification state-of-the-art methods. On average, the proposed algorithm identifies better the relevant genes and exhibits a stronger stability. The algorithm is available to the community.

PCLassoLog: A protein complex-based, group Lasso-logistic model for cancer classification and risk protein complex discovery

Risk gene identification has attracted much attention in the past two decades. Since most genes need to be translated into proteins and cooperate with other proteins to form protein complexes to carry out cellular functions, which significantly extends the functional diversity of individual proteins, revealing the molecular mechanism of cancer from a comprehensive perspective needs to shift from identifying individual risk genes toward identifying risk protein complexes. Here, we embed protein complexes into the regularized learning framework and propose a protein complex-based, group Lasso-logistic model (PCLassoLog) to discover risk protein complexes. Experiments on deep proteomic data of two cancer types show that PCLassoLog yields superior predictive performance on independent datasets. More importantly, PCLassoLog identifies risk protein complexes that not only contain individual risk proteins but also incorporate close partners that synergize with them. Furthermore, selection probabilities are calculated and two other protein complex-based models are proposed to complement PCLassoLog in identifying reliable risk protein complexes. Based on PCLassoLog, a pan-cancer analysis is performed to identify risk protein complexes in 12 cancer types. Finally, PCLassoLog is used to discover risk protein complexes associated with gene mutation. We implement all protein complex-based models as an R package PCLassoReg, which may serve as an effective tool to discover risk protein complexes in various contexts.

High-dimensional genomic feature selection with the ordered stereotype logit model

For many high-dimensional genomic and epigenomic datasets, the outcome of interest is ordinal. While these ordinal outcomes are often thought of as the observed cutpoints of some latent continuous variable, some ordinal outcomes are truly discrete and are comprised of the subjective combination of several factors. The nonlinear stereotype logistic model, which does not assume proportional odds, was developed for these 'assessed' ordinal variables. It has previously been extended to the frequentist high-dimensional feature selection setting, but the Bayesian framework provides some distinct advantages in terms of simultaneous uncertainty quantification and variable selection. Here, we review the stereotype model and Bayesian variable selection methods and demonstrate how to combine them to select genomic features associated with discrete ordinal outcomes. We compared the Bayesian and frequentist methods in terms of variable selection performance. We additionally applied the Bayesian stereotype method to an acute myeloid leukemia RNA-sequencing dataset to further demonstrate its variable selection abilities by identifying features associated with the European LeukemiaNet prognostic risk score.

Identification of key biomarkers for STAD using filter feature selection approaches

Gastric cancer (GC) is the fifth most common cancer and the third leading cause of cancer death worldwide. Discovery of diagnostic biomarkers prompts the early detection of GC. In this study, we used limma method combined with joint mutual information (JMI), a machine learning algorithm, to identify a signature of 11 genes that performed well in distinguishing tumor and normal samples in a stomach adenocarcinoma cohort. Other two GC datasets were used to validate the classifying performances. Several of the candidate genes were correlated with GC tumor progression and survival. Overall, we highlight the application of feature selection approaches in the analysis of high-dimensional biological data, which will improve study accuracies and reduce workloads for the researchers when identifying potential tumor biomarkers.

Unsupervised Feature Selection via Orthogonal Basis Clustering and Local Structure Preserving

Due to the "curse of dimensionality" issue, how to discard redundant features and select informative features in high-dimensional data has become a critical problem, hence there are many research studies dedicated to solving this problem. Unsupervised feature selection technique, which does not require any prior category information to conduct with, has gained a prominent place in preprocessing high-dimensional data among all feature selection techniques, and it has been applied to many neural networks and learning systems related applications, e.g., pattern classification. In this article, we propose an efficient method for unsupervised feature selection via orthogonal basis clustering and reliable local structure preserving, which is referred to as OCLSP briefly. Our OCLSP method consists of an orthogonal basis clustering together with an adaptive graph regularization, which realizes the functionality of simultaneously achieving excellent cluster separation and preserving the local information of data. Besides, we exploit an efficient alternative optimization algorithm to solve the challenging optimization problem of our proposed OCLSP method, and we perform a theoretical analysis of its computational complexity and convergence. Eventually, we conduct comprehensive experiments on nine real-world datasets to test the validity of our proposed OCLSP method, and the experimental results demonstrate that our proposed OCLSP method outperforms many state-of-the-art unsupervised feature selection methods in terms of clustering accuracy and normalized mutual information, which indicates that our proposed OCLSP method has a strong ability in identifying more important features.

Data driven identification of international cutting edge science and technologies using SpaCy

Difficulties in collecting, processing, and identifying massive data have slowed research on cutting-edge science and technology hotspots. Promoting these technologies will not be successful without an effective data-driven method to identify cutting-edge technologies. This paper proposes a data-driven model for identifying global cutting-edge science technologies based on SpaCy. In this model, we collected data released by 17 well-known American technology media websites from July 2019 to July 2020 using web crawling with Python. We combine graph-based neural network learning with active learning as the research method in this paper. Next, we introduced a ten-fold cross-check to train the model through machine learning with repeated experiments. The experimental results show that this model performed very well in entity recognition tasks with an F value of 98.11%. The model provides an information source for cutting-edge technology identification. It can promote innovations in cutting-edge technologies through its effective identification and tracking and explore more efficient scientific and technological research work modes.

A Comprehensive Review of Feature Selection and Feature Selection Stability in Machine Learning

Feature selection is a data preprocessing method used to reduce the number of features in the datasets. Feature selection techniques search the entire feature space to find an optimal feature set that is free of redundant and irrelevant features. Reducing the dimensionality of a dataset by removing redundant and irrelevant features has a pivotal role in improving the performance, i.e., accuracy, of inductive learners and building simple models. Thus, feature selection is an imperative task of machine learning. The apparent need for feature selection raised considerable interest and became an important research topic in a wide range of fields, including bioinformatics, text classification, image recognition, and computer vision. As a result, a large pool of feature selection methods has been proposed, and a considerable amount of literature has been published on feature selection. The quality of feature selection algorithms is measured not only by the performance of the features they prefer but also by their stability. Therefore, this study focuses on two topics: feature selection and feature selection stability. In the pages that follow, general concepts and methods of feature selection are discussed and then an overview of feature selection stability and stability measures are given.

Feature Selection Boosted by Unselected Features

Feature selection aims to select strongly relevant features and discard the rest. Recently, embedded feature selection methods, which incorporate feature weights learning into the training process of a classifier, have attracted much attention. However, traditional embedded methods merely focus on the combinatorial optimality of all selected features. They sometimes select the weakly relevant features with satisfactory combination abilities and leave out some strongly relevant features, thereby degrading the generalization performance. To address this issue, we propose a novel embedded framework for feature selection, termed feature selection boosted by unselected features (FSBUF). Specifically, we introduce an extra classifier for unselected features into the traditional embedded model and jointly learn the feature weights to maximize the classification loss of unselected features. As a result, the extra classifier recycles the unselected strongly relevant features to replace the weakly relevant features in the selected feature subset. Our final objective can be formulated as a minimax optimization problem, and we design an effective gradient-based algorithm to solve it. Furthermore, we theoretically prove that the proposed FSBUF is able to improve the generalization ability of traditional embedded feature selection methods. Extensive experiments on synthetic and real-world data sets exhibit the comprehensibility and superior performance of FSBUF.

Chemometrics for Raman Spectroscopy Harmonization

Raman spectroscopy is used in a wide variety of fields, and in a plethora of different configurations. Raman spectra of simple analytes can often be analyzed using univariate approaches and interpreted in a straightforward manner. For more complex spetral data such as time series or line profiles (1D), Raman maps (2D), or even volumes (3D), multivariate data analysis (MVDA) becomes a requirement. Even though there are some existing standards for creation, implementation, and validation of methods and models employed in industry and academics, further research and development in the field must contribute to their improvement. This review will cover, in broad terms, existing techniques as well as new developments for MVDA for Raman spectroscopic data, and in particular the use associated with instrumentation and data calibration. Chemometric models are often generated via fusion of analytical data from different sources, which enhances model discrimination and prediction abilities as compared to models derived from a single data source. For Raman spectroscopy, raw or unprocessed data is rarely ever used. Instead, spectra are usually corrected and manipulated,¹ often by case-specific rather than universal methods. Calibration models can be used to characterize qualitatively and/or quantitatively samples measured with the same instrumentation that was used to create the model. However, regular validation is required to ensure that aging or incorrect maintenance of the instrument does not alter the model's predictions, particularly when applied in regulated fields such as pharmaceuticals. Furthermore, a model transfer may be required for different reasons, such as replacement or significant repair of the instrumentation. Modeling can also be used to consistently harmonize Raman spectroscopic data across several instrumental designs, accounting for variations in the resulting spectrum induced by different components. Data for Raman harmonization models should be processed in a protocolled manner, and the original data accessible to allow for model reconstruction or transfer when new data is added. Important processing steps will be the calibration of the spectral axes and instrument dependent effects, such as spectral resolution. In addition, data fusion and model transfer are essential for allowing new instrumentation to build on existing models to harmonize their own data. Ideally, an open access database would be created and maintained, for the purpose of allowing for continued harmonization of new Raman instruments using an outlined and accepted protocol.