Cell and tumor classification using gene expression data: Construction of forests

Papillary Urothelial Neoplasm of Low Malignant Potential: Evolving Terminology and Concepts

In recent years, many studies have shown that microarray gene expression data is useful for disease identification and cancer classification. However, since gene expression data may contain thousands of genes simultaneously, successful microarray classification can be rather difficult. Feature (gene) selection is a frequently used pre-processing technology for successful classification of microarray gene expression data. Selecting a useful gene subset as a classifier not only decreases the computational time and cost, but also increases the classification accuracy. It is therefore imperative to extract only a small number of genes, which are exclusively relevant for the classification of a particular cancer/disease type. In this paper, correlation-based binary particle swarm optimizations is proposed to select the relevant genes, and a K-nearest neighbor with the leave-one-out cross-validation method serves as a classifier to evaluate the classification performance on six published cancer classification data sets. The experimental results show that the proposed method selects fewer gene subsets, while still resulting in higher prediction accuracy than the other literature methods.

A reliable and precise classification of tumors is essential for successful diagnosis and treatment of cancer. cDNA microarrays and high-density oligonucleotide chips are novel biotechnologies increasingly used in cancer research. By allowing the monitoring of expression levels in cells for thousands of genes simultaneously, microarray experiments may lead to a more complete understanding of the molecular variations among tumors and hence to a finer and more informative classification. The ability to successfully distinguish between tumor classes (already known or yet to be discovered) using gene expression data is an important aspect of this novel approach to cancer classification. This article compares the performance of different discrimination methods for the classification of tumors based on gene expression data. The methods include nearest-neighbor classifiers, linear discriminant analysis, and classification trees. Recent machine learning approaches, such as bagging and boosting, are also considered. The discrimination methods are applied to datasets from three recently published cancer gene expression studies.

Gene Expression data comprising more number genes and samples are used for cancer classification. Gene Expression information provides the gene expression level contributing to specific action. Cancer classification is done using the gene expression data. In our work, feature selection methods such as mutual information and genetic algorithm are used for examining cancer microarray Gene expression Data. By using feature selection methods most probable cancer associated genes are selected from large microarray Gene Expression data. The objective of the present work to attain enhanced classification accuracy. We have used the colon cancer dataset contains 2000 gene has 62 types, in which 40 are colon cancer tissue's types and the other 20 are normal types.

Standardized methods for accurate tumor classification are of critical importance for cancer diagnosis and treatment, particularly in diagnostically-challenging cases where site-directed therapies are an option. Molecular diagnostics for tumor classification, subclassification and site of origin determination based on advances in gene expression profiling have translated into clinical practice as complementary approaches to clinicopathological evaluations. In this review, the foundational science of gene expression-based cancer classification, technical and clinical considerations for clinical translation, and an overview of molecular signatures of tumor classification that are available for clinical use will be discussed. Proposed approaches will also be described for further integration of molecular tests for cancer classification into the diagnostic paradigm using a tissue-based strategy as a key component to direct evaluation. Increasing evidence of improved patient outcomes with the application of site and molecularly-targeted cancer therapy through use of molecular tools highlights the growing potential for these gene expression-based diagnostics to positively impact patient management. Looking forward, the availability of adequate tissue will be a significant issue and limiting factor as cancer diagnosis progresses; when the tumor specimen is limited, use of molecular classification may be a reasonable early step in the evaluation, particularly if the tumor is poorly-differentiated and has atypical features.

Rectal cancer: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up.

Constantly improving gene expression profiling technologies are expected to provide understanding and insight into cancer-related cellular processes. Gene expression data is also expected to significantly aid in the development of efficient cancer diagnosis and classification platforms. In this work we examine three sets of gene expression data measured across sets of tumor(s) and normal clinical samples: The first set consists of 2,000 genes, measured in 62 epithelial colon samples (Alon et al., 1999). The second consists of approximately equal to 100,000 clones, measured in 32 ovarian samples (unpublished extension of data set described in Schummer et al. (1999)). The third set consists of approximately equal to 7,100 genes, measured in 72 bone marrow and peripheral blood samples (Golub et al, 1999). We examine the use of scoring methods, measuring separation of tissue type (e.g., tumors from normals) using individual gene expression levels. These are then coupled with high-dimensional classification methods to assess the classification power of complete expression profiles. We present results of performing leave-one-out cross validation (LOOCV) experiments on the three data sets, employing nearest neighbor classifier, SVM (Cortes and Vapnik, 1995), AdaBoost (Freund and Schapire, 1997) and a novel clustering-based classification technique. As tumor samples can differ from normal samples in their cell-type composition, we also perform LOOCV experiments using appropriately modified sets of genes, attempting to eliminate the resulting bias. We demonstrate success rate of at least 90% in tumor versus normal classification, using sets of selected genes, with, as well as without, cellular-contamination-related members. These results are insensitive to the exact selection mechanism, over a certain range.

The 2022 revision of the World Health Organization classification of tumors of the urinary system and male genital organs: advances and challenges

The effectiveness of cancer treatment depends strongly on an accurate diagnosis. In this paper we propose a system for automatic and precise diagnosis of a tumor's origin based on genetic data. This system is based on a combination of coding theory techniques and machine learning algorithms. In particular, tumor classification is described as a multiclass learning setup, where gene expression values serve the system to distinguish between types of tumors. Since multiclass learning is intrinsically complex, the data is divided into several biclass problems whose results are combined with an error correcting linear block code. The robustness of the prediction is increased as errors of the base binary classifiers are corrected by the linear code. Promising results have been achieved with a best case precision of 72% when the system was tested on real data from cancer patients.

Microarray analysis and gene expression profile have been widely used in tumor classification, survival analysis and ER statues of breast cancer. Sample discrimination as well as identification of significant genes have been the focus of most previous studies. The aim of this research is to propose a fuzzy model to predict the relapse time of breast cancer by using breast cancer dataset published by van't Veer. Fuzzy rule mining based on support vector machine has been used in a hybrid method with rule pruning and shown its ability to divide the samples in many subgroups. To handle the existence of uncertainties in linguistic variables and fuzzy sets, the TSK model of Interval type-2 fuzzy logic system has been used and a new simple method is also developed to consider the uncertainties of the rules which have been optimized by genetic algorithm. B632 validation method is applied to estimate the error of the model. The results with 95 % confidence interval show a reasonable accuracy in prediction.

Multi-class cancer classification based on microarray data is described. A generalized output-coding scheme based on One Versus One (OVO) combined with Latent Variable Model (LVM) is used. Results from the proposed One Versus One (OVO) outputcoding strategy is compared with the results obtained from the generalized One Versus All (OVA) method and their efficiencies of using them for multi-class tumor classification have been studied. This comparative study was done using two microarray gene expression data: Global Cancer Map (GCM) dataset and brain cancer (BC) dataset. Primary feature selection was based on fold change and penalized t-statistics. Evaluation was conducted with varying feature numbers. The OVO coding strategy worked quite well with the BC data, while both OVO and OVA results seemed to be similar for the GCM data. The selection of output coding methods for combining binary classifiers for multi-class tumor classification depends on the number of tumor types considered, the discrepancies between the tumor samples used for training as well as the heterogeneity of expression within the cancer subtypes used as training data.

BackgroundUsing DNA microarrays, we have developed two novel models for tumor classification and target gene prediction. First, gene expression profiles are summarized by optimally selected Self-Organizing Maps (SOMs), followed by tumor sample classification by Fuzzy C-means clustering. Then, the prediction of marker genes is accomplished by either manual feature selection (visualizing the weighted/mean SOM component plane) or automatic feature selection (by pair-wise Fisher's linear discriminant).ResultsThe proposed models were tested on four published datasets: (1) Leukemia (2) Colon cancer (3) Brain tumors and (4) NCI cancer cell lines. The models gave class prediction with markedly reduced error rates compared to other class prediction approaches, and the importance of feature selection on microarray data analysis was also emphasized.ConclusionsOur models identify marker genes with predictive potential, often better than other available methods in the literature. The models are potentially useful for medical diagnostics and may reveal some insights into cancer classification. Additionally, we illustrated two limitations in tumor classification from microarray data related to the biology underlying the data, in terms of (1) the class size of data, and (2) the internal structure of classes. These limitations are not specific for the classification models used.

Feature subset selection (FSS) methods play an important role for cancer classification using microarray gene expression data. In this scenario, it is extremely important to select genes by taking into account the possible interactions with other gene subsets. This paper shows that, by accumulating the evidence in favour (or against) each gene along a search process, the obtained gene subsets may constitute better solutions, either in terms of size or in predictive accuracy, or in both, at a negligible overhead in computational cost.

Tumor classification is crucial to the clinical diagnosis and proper treatment of cancers. In recent years, sparse representation-based classifier (SRC) has been proposed for tumor classification. The employed dictionary plays an important role in sparse representation-based or sparse coding-based classification. However, sparse representation-based tumor classification models have not used the employed dictionary, thereby limiting their performance. Furthermore, this sparse representation model assumes that the coding residual follows a Gaussian or Laplacian distribution, which may not effectively describe the coding residual in practical tumor classification. In the present study, we formulated a novel effective cancer classification technique, namely, Fisher discrimination regularized robust coding (FDRRC), by combining the Fisher discrimination dictionary learning method with the regularized robust coding (RRC) model, which searches for a maximum a posteriori solution to coding problems by assuming that the coding residual and representation coefficient are independent and identically distributed. The proposed FDRRC model is extensively evaluated on various tumor datasets and shows superior performance compared with various state-of-the-art tumor classification methods in a variety of classification tasks.

Microarray gene expression data are often classified by cell line or tumor type to assist in the diagnosis and prediction of human cancer. While microarray analysis demonstrates potential, choosing the most suitable machine learning approach is crucial for accurate cancer diagnosis and prediction. In this beginner’s guide, we outline how to select an optimal machine learning model for cancer phenotype prediction by comparing various existing methods. This study used three well-known machine learning methods: linear discriminant analysis, support vector machines, and random forest. To assess prediction performance, several performance metrics were considered, including model prediction accuracy (AC), the area under the curve (AUC), F-measure, the receiver operating characteristic (ROC) curve, and the precision-recall curve (PRC). Microarray gene expression data from two cancer types, leukemia and colon cancer were analysed. A cross-validation process with 100 resampling iterations was implemented to compute average performance measures (APM), ensuring the reliability of the results. Findings emphasize the significance of selecting the right machine learning model for accurate predictions of new samples. The methods employed provided satisfactory results, validated by various APM for both leukemia and colon cancer datasets. Notably, the random forest classifier exhibited the best performance in cancer prediction. International Journal of Statistical Sciences, Vol. 25(2), November, 2025, pp 47-57