A filter-based feature selection approach for identifying potential biomarkers for lung cancer

ClearF++: Improved Supervised Feature Scoring Using Feature Clustering in Class-Wise Embedding and Reconstruction

Feature selection methods are essential for accurate disease classification and identifying informative biomarkers. While information-theoretic methods have been widely used, they often exhibit limitations such as high computational costs. Our previously proposed method, ClearF, addresses these issues by using reconstruction error from low-dimensional embeddings as a proxy for the entropy term in the mutual information. However, ClearF still has limitations, including a nontransparent bottleneck layer selection process, which can result in unstable feature selection. To address these limitations, we propose ClearF++, which simplifies the bottleneck layer selection and incorporates feature-wise clustering to enhance biomarker detection. We compare its performance with other commonly used methods such as MultiSURF and IFS, as well as ClearF, across multiple benchmark datasets. Our results demonstrate that ClearF++ consistently outperforms these methods in terms of prediction accuracy and stability, even with limited samples. We also observe that employing the Deep Embedded Clustering (DEC) algorithm for feature-wise clustering improves performance, indicating its suitability for handling complex data structures with limited samples. ClearF++ offers an improved biomarker prioritization approach with enhanced prediction performance and faster execution. Its stability and effectiveness with limited samples make it particularly valuable for biomedical data analysis.

Ensemble filters with harmonize PSO-SVM algorithm for optimal hearing disorder prediction

Discovering a hearing disorder at an earlier intervention is critical for reducing the effects of hearing loss and the approaches to increase the remaining hearing ability can be implemented to achieve the successful development of human communication. Recently, the explosive dataset features have increased the complexity for audiologists to decide the proper treatment for the patient. In most cases, data with irrelevant features and improper classifier parameters causes a crucial influence on the audiometry system in terms of accuracy. This is due to the dependent processes of these two, where the classification accuracy performance could be worsened if both processes are conducted independently. Although the filter algorithm is capable of eliminating irrelevant features, it still lacks the ability to consider feature reliance and results in a poor selection of significant features. Improper kernel parameter settings may also contribute to poor accuracy performance. In this paper, an ensemble filters feature selection based on Information Gain (IG), Gain Ratio (GR), Chi-squared (CS), and Relief-F (RF) with harmonize optimization of Particle Swarm Optimization (PSO) and Support Vector Machine (SVM) is presented to mitigate these problems. Ensemble filters are utilized so that the initial top dominant features relevant for classification can be considered. Then, PSO and SVM are optimized simultaneously to achieve the optimal solution. The results on a standard Audiology dataset show that the proposed method produces 96.50% accuracy with optimal solution compared to classical SVM, which signifies the proposed method is effective in handling high dimensional data for hearing disorder prediction.

LargeMetabo: an out-of-the-box tool for processing and analyzing large-scale metabolomic data

Large-scale metabolomics is a powerful technique that has attracted widespread attention in biomedical studies focused on identifying biomarkers and interpreting the mechanisms of complex diseases. Despite a rapid increase in the number of large-scale metabolomic studies, the analysis of metabolomic data remains a key challenge. Specifically, diverse unwanted variations and batch effects in processing many samples have a substantial impact on identifying true biological markers, and it is a daunting challenge to annotate a plethora of peaks as metabolites in untargeted mass spectrometry-based metabolomics. Therefore, the development of an out-of-the-box tool is urgently needed to realize data integration and to accurately annotate metabolites with enhanced functions. In this study, the LargeMetabo package based on R code was developed for processing and analyzing large-scale metabolomic data. This package is unique because it is capable of (1) integrating multiple analytical experiments to effectively boost the power of statistical analysis; (2) selecting the appropriate biomarker identification method by intelligent assessment for large-scale metabolic data and (3) providing metabolite annotation and enrichment analysis based on an enhanced metabolite database. The LargeMetabo package can facilitate flexibility and reproducibility in large-scale metabolomics. The package is freely available from https://github.com/LargeMetabo/LargeMetabo.

A New Algorithm for Cancer Biomarker Gene Detection Using Harris Hawks Optimization

This paper presents two novel swarm intelligence algorithms for gene selection, HHO-SVM and HHO-KNN. Both of these algorithms are based on Harris Hawks Optimization (HHO), one in conjunction with support vector machines (SVM) and the other in conjunction with k-nearest neighbors (k-NN). In both algorithms, the goal is to determine a small gene subset that can be used to classify samples with a high degree of accuracy. The proposed algorithms are divided into two phases. To obtain an accurate gene set and to deal with the challenge of high-dimensional data, the redundancy analysis and relevance calculation are conducted in the first phase. To solve the gene selection problem, the second phase applies SVM and k-NN with leave-one-out cross-validation. A performance evaluation was performed on six microarray data sets using the two proposed algorithms. A comparison of the two proposed algorithms with several known algorithms indicates that both of them perform quite well in terms of classification accuracy and the number of selected genes.

Using machine learning approaches for multi-omics data analysis: A review

With the development of modern high-throughput omic measurement platforms, it has become essential for biomedical studies to undertake an integrative (combined) approach to fully utilise these data to gain insights into biological systems. Data from various omics sources such as genetics, proteomics, and metabolomics can be integrated to unravel the intricate working of systems biology using machine learning-based predictive algorithms. Machine learning methods offer novel techniques to integrate and analyse the various omics data enabling the discovery of new biomarkers. These biomarkers have the potential to help in accurate disease prediction, patient stratification and delivery of precision medicine. This review paper explores different integrative machine learning methods which have been used to provide an in-depth understanding of biological systems during normal physiological functioning and in the presence of a disease. It provides insight and recommendations for interdisciplinary professionals who envisage employing machine learning skills in multi-omics studies.

A Novel Biomarker Identification Approach for Gastric Cancer Using Gene Expression and DNA Methylation Dataset

As one type of complex disease, gastric cancer has high mortality rate, and there are few effective treatments for patients in advanced stage. With the development of biological technology, a large amount of multiple-omics data of gastric cancer are generated, which enables computational method to discover potential biomarkers of gastric cancer. That will be very important to detect gastric cancer at earlier stages and thus assist in providing timely treatment. However, most of biological data have the characteristics of high dimension and low sample size. It is hard to process directly without feature selection. Besides, only using some omic data, such as gene expression data, provides limited evidence to investigate gastric cancer associated biomarkers. In this research, gene expression data and DNA methylation data are integrated to analyze gastric cancer, and a feature selection approach is proposed to identify the possible biomarkers of gastric cancer. After the original data are pre-processed, the mutual information (MI) is applied to select some top genes. Then, fold change (FC) and T-test are adopted to identify differentially expressed genes (DEG). In particular, false discover rate (FDR) is introduced to revise p_value to further screen genes. For chosen genes, a deep neural network (DNN) model is utilized as the classifier to measure the quality of classification. The experimental results show that the approach can achieve superior performance in terms of accuracy and other metrics. Biological analysis for chosen genes further validates the effectiveness of the approach.

Classification, Categorization, and Algorithms for Articular Cartilage Defects

There is a critical unmet need in the clinical implementation of valid preventative and therapeutic strategies for patients with articular cartilage pathology based on the significant gap in understanding of the relationships between diagnostic data, disease progression, patient-related variables, and symptoms. In this article, the current state of classification and categorization for articular cartilage pathology is discussed with particular focus on machine learning methods and the authors propose a bedside-bench-bedside approach with highly quantitative techniques as a solution to these hurdles. Leveraging computational learning with available data toward articular cartilage pathology patient phenotyping holds promise for clinical research and will likely be an important tool to identify translational solutions into evidence-based clinical applications to benefit patients. Recommendations for successful implementation of these approaches include using standardized definitions of articular cartilage, to include characterization of depth, size, location, and number; using measurements that minimize subjectivity or validated patient-reported outcome measures; considering not just the articular cartilage pathology but the whole joint, and the patient perception and perspective. Application of this approach through a multistep process by a multidisciplinary team of clinicians and scientists holds promise for validating disease mechanism-based phenotypes toward clinically relevant understanding of articular cartilage pathology for evidence-based application to orthopaedic practice.

ClearF: a supervised feature scoring method to find biomarkers using class-wise embedding and reconstruction

BACKGROUND

Feature selection or scoring methods for the detection of biomarkers are essential in bioinformatics. Various feature selection methods have been developed for the detection of biomarkers, and several studies have employed information-theoretic approaches. However, most of these methods generally require a long processing time. In addition, information-theoretic methods discretize continuous features, which is a drawback that can lead to the loss of information.

RESULTS

In this paper, a novel supervised feature scoring method named ClearF is proposed. The proposed method is suitable for continuous-valued data, which is similar to the principle of feature selection using mutual information, with the added advantage of a reduced computation time. The proposed score calculation is motivated by the association between the reconstruction error and the information-theoretic measurement. Our method is based on class-wise low-dimensional embedding and the resulting reconstruction error. Given multi-class datasets such as a case-control study dataset, low-dimensional embedding is first applied to each class to obtain a compressed representation of the class, and also for the entire dataset. Reconstruction is then performed to calculate the error of each feature and the final score for each feature is defined in terms of the reconstruction errors. The correlation between the information theoretic measurement and the proposed method is demonstrated using a simulation. For performance validation, we compared the classification performance of the proposed method with those of various algorithms on benchmark datasets.

CONCLUSIONS

The proposed method showed higher accuracy and lower execution time than the other established methods. Moreover, an experiment was conducted on the TCGA breast cancer dataset, and it was confirmed that the genes with the highest scores were highly associated with subtypes of breast cancer.

Quantitative Operating Principles of Yeast Metabolism during Adaptation to Heat Stress

Microorganisms evolved adaptive responses to survive stressful challenges in ever-changing environments. Understanding the relationships between the physiological/metabolic adjustments allowing cellular stress adaptation and gene expression changes being used by organisms to achieve such adjustments may significantly impact our ability to understand and/or guide evolution. Here, we studied those relationships during adaptation to various stress challenges in Saccharomyces cerevisiae, focusing on heat stress responses. We combined dozens of independent experiments measuring whole-genome gene expression changes during stress responses with a simplified kinetic model of central metabolism. We identified alternative quantitative ranges for a set of physiological variables in the model (production of ATP, trehalose, NADH, etc.) that are specific for adaptation to either heat stress or desiccation/rehydration. Our approach is scalable to other adaptive responses and could assist in developing biotechnological applications to manipulate cells for medical, biotechnological, or synthetic biology purposes.

The adaptive computer-aided diagnosis system based on tumor sizes for the classification of breast tumors detected at screening ultrasound

Screening ultrasound (US) is increasingly used as a supplement to mammography in women with dense breasts, and more than 80% of cancers detected by US alone are 1cm or smaller. An adaptive computer-aided diagnosis (CAD) system based on tumor size was proposed to classify breast tumors detected at screening US images using quantitative morphological and textural features. In the present study, a database containing 156 tumors (78 benign and 78 malignant) was separated into two subsets of different tumor sizes (<1cm and ⩾1cm) to explore the improvement in the performance of the CAD system. After adaptation, the accuracies, sensitivities, specificities and Az values of the CAD for the entire database increased from 73.1% (114/156), 73.1% (57/78), 73.1% (57/78), and 0.790 to 81.4% (127/156), 83.3% (65/78), 79.5% (62/78), and 0.852, respectively. In the data subset of tumors larger than 1cm, the performance improved from 66.2% (51/77), 68.3% (28/41), 63.9% (23/36), and 0.703 to 81.8% (63/77), 85.4% (35/41), 77.8% (28/36), and 0.855, respectively. The proposed CAD system can be helpful to classify breast tumors detected at screening US.

multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles

Clustering is carried out to identify patterns in transcriptomics profiles to determine clinically relevant subgroups of patients. Feature (gene) selection is a critical and an integral part of the process. Currently, there are many feature selection and clustering methods to identify the relevant genes and perform clustering of samples. However, choosing an appropriate methodology is difficult. In addition, extensive feature selection methods have not been supported by the available packages. Hence, we developed an integrative R-package called multiClust that allows researchers to experiment with the choice of combination of methods for gene selection and clustering with ease. Using multiClust, we identified the best performing clustering methodology in the context of clinical outcome. Our observations demonstrate that simple methods such as variance-based ranking perform well on the majority of data sets, provided that the appropriate number of genes is selected. However, different gene ranking and selection methods remain relevant as no methodology works for all studies.

A comparative analysis of swarm intelligence techniques for feature selection in cancer classification

Feature selection in cancer classification is a central area of research in the field of bioinformatics and used to select the informative genes from thousands of genes of the microarray. The genes are ranked based on T-statistics, signal-to-noise ratio (SNR), and F-test values. The swarm intelligence (SI) technique finds the informative genes from the top-m ranked genes. These selected genes are used for classification. In this paper the shuffled frog leaping with Lévy flight (SFLLF) is proposed for feature selection. In SFLLF, the Lévy flight is included to avoid premature convergence of shuffled frog leaping (SFL) algorithm. The SI techniques such as particle swarm optimization (PSO), cuckoo search (CS), SFL, and SFLLF are used for feature selection which identifies informative genes for classification. The k-nearest neighbour (k-NN) technique is used to classify the samples. The proposed work is applied on 10 different benchmark datasets and examined with SI techniques. The experimental results show that the results obtained from k-NN classifier through SFLLF feature selection method outperform PSO, CS, and SFL.

A graph-theoretic approach for identifying non-redundant and relevant gene markers from microarray data using multiobjective binary PSO

The purpose of feature selection is to identify the relevant and non-redundant features from a dataset. In this article, the feature selection problem is organized as a graph-theoretic problem where a feature-dissimilarity graph is shaped from the data matrix. The nodes represent features and the edges represent their dissimilarity. Both nodes and edges are given weight according to the feature's relevance and dissimilarity among the features, respectively. The problem of finding relevant and non-redundant features is then mapped into densest subgraph finding problem. We have proposed a multiobjective particle swarm optimization (PSO)-based algorithm that optimizes average node-weight and average edge-weight of the candidate subgraph simultaneously. The proposed algorithm is applied for identifying relevant and non-redundant disease-related genes from microarray gene expression data. The performance of the proposed method is compared with that of several other existing feature selection techniques on different real-life microarray gene expression datasets.

Translational medicine as a permanent glue and force of clinical medicine and public health: perspectives (1) from 2012 Sino-American symposium on clinical and translational medicine

Abstracts

Health systems globally face challenges and opportunities in balancing quality, access, and cost, where clinical and translational medicine (CTM) should play more important and powerful roles in the identification, development and validation of solutions and strategies. Strategic collaboration can gather global strengths and resources and improve health systems, care delivery, regulations and policies. CTM-driven innovation and development has the potential to achieve step-change improvements across three dimensions. Thus, we have the reasons to believe that CTM will play even more roles in the development of new diagnostics, therapies, healthcare, and policies and SAS-CTM will become more and more important platform to obtain the latest development in CTM internationally and explore new opportunities in the international collaborations.

Identifying dysregulated pathways in cancers from pathway interaction networks

Background

Cancers, a group of multifactorial complex diseases, are generally caused by mutation of multiple genes or dysregulation of pathways. Identifying biomarkers that can characterize cancers would help to understand and diagnose cancers. Traditional computational methods that detect genes differentially expressed between cancer and normal samples fail to work due to small sample size and independent assumption among genes. On the other hand, genes work in concert to perform their functions. Therefore, it is expected that dysregulated pathways will serve as better biomarkers compared with single genes.

Results

In this paper, we propose a novel approach to identify dysregulated pathways in cancer based on a pathway interaction network. Our contribution is three-fold. Firstly, we present a new method to construct pathway interaction network based on gene expression, protein-protein interactions and cellular pathways. Secondly, the identification of dysregulated pathways in cancer is treated as a feature selection problem, which is biologically reasonable and easy to interpret. Thirdly, the dysregulated pathways are identified as subnetworks from the pathway interaction networks, where the subnetworks characterize very well the functional dependency or crosstalk between pathways. The benchmarking results on several distinct cancer datasets demonstrate that our method can obtain more reliable and accurate results compared with existing state of the art methods. Further functional analysis and independent literature evidence also confirm that our identified potential pathogenic pathways are biologically reasonable, indicating the effectiveness of our method.

Conclusions

Dysregulated pathways can serve as better biomarkers compared with single genes. In this work, by utilizing pathway interaction networks and gene expression data, we propose a novel approach that effectively identifies dysregulated pathways, which can not only be used as biomarkers to diagnose cancers but also serve as potential drug targets in the future.

Potential significance of telocytes in the pathogenesis of lung diseases

Multiple cells play critical roles in the pathogenesis of lung diseases, even though the exact mechanisms are still not clear. Telocytes are characterized by telopodes, which are thin and long prolongations, and a small amount of cytoplasm rich with mitochondria, as shown by immune-positive staining against CD34, c-kit and vimentin. Telocytes have been found in many organs of mammals, including the trachea and lung. This report summarizes the latest findings associated with telocytes, with a special focus on the lung, and demonstrates that telocytes exist in the smooth muscle layer under cartilage and bronchiole in the lung, and also in the interstitial space of alveoli. Telocytes have a mediate connection with epithelial cells and direct connection with smooth muscle cells both in blood vessels and bronchiole in the lung. Telocytes also have a close relationship with other cell types, such as immune cells and stem cells. Telopodes appear with dichotomous branching and alternation of podom and podomer, forming a 3D network structure with complex homo- and hetero-cellular junctions. All characteristics of telocytes in lung tissue indicate that telocytes may play a potential, but important, role in the pathogenesis of lung diseases.

Evaluation of SLOG/TCI-III pediatric system on target control infusion of propofol

Background

The target-controlled infusion-III (SLOG/TCI-III) system was derived from a model set up by the local pediatric population for target control infusion of propofol.

Methods

The current study aimed at evaluating the difference between target concentrations of propofol and performance, which was measured using the SLOG/TCI-III system in children. Thirty children fulfilling the I-II criteria according to American Society of Anesthesiology were enrolled in the study. The target plasma concentration of propofol was fed into the SLOG/TCI-III system and compared with the measured concentrations of propofol. Blood samples were collected and analyzed by high performance liquid chromatography with fluorescence detector. The performance error (PE) was determined for each measured blood propofol concentration. The performances of the TCI-III system were determined by the median performance error (MDPE), the median absolute performance error (MDAPE), and Wobble (the median absolute deviation of each PE from the MDPE), respectively.

Results

Concentration against target concentration showed good linear correlation: concentration = 1.3428 target concentration - 0.2633 (r = 0.8667). The MDPE and MDAPE of the pediatric system were 10 and 22%, respectively, and the median value for Wobble was 24%. MDPE and MDAPE were less than 15 and 30%, respectively.

Conclusions

The performance of TCI-III system seems to be in the accepted limits for clinical practice in children.