Enhancing instance-based classification with local density: a new algorithm for classifying unbalanced biomedical data

A Density-Based Random Forest for Imbalanced Data Classification

Many machine learning problem domains, such as the detection of fraud, spam, outliers, and anomalies, tend to involve inherently imbalanced class distributions of samples. However, most classification algorithms assume equivalent sample sizes for each class. Therefore, imbalanced classification datasets pose a significant challenge in prediction modeling. Herein, we propose a density-based random forest algorithm (DBRF) to improve the prediction performance, especially for minority classes. DBRF is designed to recognize boundary samples as the most difficult to classify and then use a density-based method to augment them. Subsequently, two different random forest classifiers were constructed to model the augmented boundary samples and the original dataset dependently, and the final output was determined using a bagging technique. A real-world material classification dataset and 33 open public imbalanced datasets were used to evaluate the performance of DBRF. On the 34 datasets, DBRF could achieve improvements of 2–15% over random forest in terms of the F1-measure and G-mean. The experimental results proved the ability of DBRF to solve the problem of classifying objects located on the class boundary, including objects of minority classes, by taking into account the density of objects in space.

Automatic detection of erythemato-squamous diseases using k-means clustering

A new approach based on the implementation of k-means clustering is presented for automated detection of erythemato-squamous diseases. The purpose of clustering techniques is to find a structure for the given data by finding similarities between data according to data characteristics. The studied domain contained records of patients with known diagnosis. The k-means clustering algorithm's task was to classify the data points, in this case the patients with attribute data, to one of the five clusters. The algorithm was used to detect the five erythemato-squamous diseases when 33 features defining five disease indications were used. The purpose is to determine an optimum classification scheme for this problem. The present research demonstrated that the features well represent the erythemato-squamous diseases and the k-means clustering algorithm's task achieved high classification accuracies for only five erythemato-squamous diseases.

Genomic sweeping for hypermethylated genes

MOTIVATION

Genes silenced by the aberrent methylation of nearby CpG islands can contribute to the onset or progression of cancer and represent potential biomarkers for diagnosis and prognosis. Relatively few have thus far been validated as hypermethylated in cancer among over 14,000 candidates with promoter region CpG islands. A descriptive set of genes known to be unmethylated in cancer does not exist. This lack of a negative set and a large number of candidates necessitated the development of a new approach to identify novel genes hypermethylated in cancer.

RESULTS

We developed a general method, cluster_boost, that in an imbalanced data setting predicts new minority class members given limited known samples and a large set of unlabeled samples. Synthetic datasets modeled after the hypermethylated genes data show that cluster_boost can successfully identify minority samples within unlabeled data. Using genome sequence features, cluster_boost predicted candidate hypermethylated genes among 14,000 genes of unknown status. In primary ovarian cancers, we determined the methylation status for 15 genes with different levels of support for being hypermethlyated. Results indicate cluster_boost can accurately identify novel genes hypermethylated in cancer.

AVAILABILITY

Software and datasets are freely available at http://labs.genome.duke.edu/FureyLab/cluster_boost.php.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.