A non-uniform quantization scheme for visualization of CT images.

Medical science heavily depends on image acquisition and post-processing for accurate diagnosis and treatment planning. The introduction of noise degrades the visual quality of the medical images during the capturing process, which may result in false perception. Therefore, medical image enhancement is an essential topic of research for the improvement of image quality. In this paper, a clustering-based contrast enhancement technique is presented for computed tomography (CT) images. Our approach uses the recursive splitting of data into clusters targeting the maximum error reduction in each cluster. This leads to grouping similar pixels in every cluster, maximizing inter-cluster and minimizing intra-cluster similarities. A suitable number of clusters can be chosen to represent high precision data with the desired bit-depth. We use 256 clusters to convert 16-bit CT scans to 8-bit images suitable for visualization on standard low dynamic range displays. We compare our method with several existing contrast enhancement algorithms and show that the proposed technique provides better results in terms of execution efficiency and quality of enhanced images.

A hierarchical integration deep flexible neural forest framework for cancer subtype classification by integrating multi-omics data.

BACKGROUND: Cancer subtype classification attains the great importance for accurate diagnosis and personalized treatment of cancer. Latest developments in high-throughput sequencing technologies have rapidly produced multi-omics data of the same cancer sample. Many computational methods have been proposed to classify cancer subtypes, however most of them generate the model by only employing gene expression data. It has been shown that integration of multi-omics data contributes to cancer subtype classification. RESULTS: A new hierarchical integration deep flexible neural forest framework is proposed to integrate multi-omics data for cancer subtype classification named as HI-DFNForest. Stacked autoencoder (SAE) is used to learn high-level representations in each omics data, then the complex representations are learned by integrating all learned representations into a layer of autoencoder. Final learned data representations (from the stacked autoencoder) are used to classify patients into different cancer subtypes using deep flexible neural forest (DFNForest) model.Cancer subtype classification is verified on BRCA, GBM and OV data sets from TCGA by integrating gene expression, miRNA expression and DNA methylation data. These results demonstrated that integrating multiple omics data improves the accuracy of cancer subtype classification than only using gene expression data and the proposed framework has achieved better performance compared with other conventional methods. CONCLUSION: The new hierarchical integration deep flexible neural forest framework(HI-DFNForest) is an effective method to integrate multi-omics data to classify cancer subtypes.

Clustering by fast search and merge of local density peaks for gene expression microarray data.

Clustering is an unsupervised approach to classify elements based on their similarity, and it is used to find the intrinsic patterns of data. There are enormous applications of clustering in bioinformatics, pattern recognition, and astronomy. This paper presents a clustering approach based on the idea that density wise single or multiple connected regions make a cluster, in which density maxima point represents the center of the corresponding density region. More precisely, our approach firstly finds the local density regions and subsequently merges the density connected regions to form the meaningful clusters. This idea empowers the clustering procedure, in which outliers are automatically detected, higher dense regions are intuitively determined and merged to form clusters of arbitrary shape, and clusters are identified regardless the dimensionality of space in which they are embedded. Extensive experiments are performed on several complex data sets to analyze and compare our approach with the state-of-the-art clustering methods. In addition, we benchmarked the algorithm on gene expression microarray data sets for cancer subtyping; to distinguish normal tissues from tumor; and to classify multiple tissue data sets.