Interval-value Based Particle Swarm Optimization algorithm for cancer-type specific gene selection and sample classification

Microarray technology allows simultaneous measurement of the expression levels of thousands of genes within a biological tissue sample. The fundamental power of microarrays lies within the ability to conduct parallel surveys of gene expression using microarray data. The classification of tissue samples based on gene expression data is an important problem in medical diagnosis of diseases such as cancer. In gene expression data, the number of genes is usually very high compared to the number of data samples. Thus the difficulty that lies with data are of high dimensionality and the sample size is small. This research work addresses the problem by classifying resultant dataset using the existing algorithms such as Support Vector Machine (SVM), K-nearest neighbor (KNN), Interval Valued Classification (IVC) and the improvised Interval Value based Particle Swarm Optimization (IVPSO) algorithm. Thus the results show that the IVPSO algorithm outperformed compared with other algorithms under several performance evaluation functions

Beyond Bag-of-Concepts:Vectors of Locally Aggregated Concepts

Bag-of-Concepts, a model that counts the frequency of clustered word embeddings (i.e., concepts) in a document, has demonstrated the feasibility of leveraging clustered word embeddings to create features for document representation. However, information is lost as the word embeddings themselves are not used in the resulting feature vector. This paper presents a novel text representation method, Vectors of Locally Aggregated Concepts (VLAC). Like Bag-of-Concepts, it clusters word embeddings for its feature generation. However, instead of counting the frequency of clustered word embeddings, VLAC takes each cluster’s sum of residuals with respect to its centroid and concatenates those to create a feature vector. The resulting feature vectors contain more discriminative information than Bag-of-Concepts due to the additional inclusion of these first order statistics. The proposed method is tested on four different data sets for single-label classification and compared with several baselines, including TF-IDF and Bag-of-Concepts. Results indicate that when combining features of VLAC with TF-IDF significant improvements in performance were found regardless of which word embeddings were used.</p