A heuristic gene regulatory networks model for cardiac function and pathology
- Authors: Zarnegar, Armita , Vamplew, Peter , Stranieri, Andrew , Jelinek, Herbert
- Date: 2016
- Type: Text , Conference proceedings
- Relation: 2016 Computing in Cardiology Conference (CinC); Vancouver; 11-14th Sept, 2016
- Full Text: false
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- Description: Genome-wide association studies (GWAS) and next-generation sequencing (NGS) has led to an increase in information about the human genome and cardiovascular disease. Understanding the role of genes in cardiac function and pathology requires modeling gene interactions and identification of regulatory genes as part of a gene regulatory network (GRN). Feature selection and data reduction not sufficient and require domain knowledge to deal with large data. We propose three novel innovations in constructing a GRN based on heuristics. A 2D Visualised Co-regulation function. Post-processing to identify gene-gene interactions. Finally a threshold algorithm is applied to identify the hub genes that provide the backbone of the GRN. The 2D Visualized Co-regulation function performed significantly better compared to the Pearson's correlation for measuring pairwise associations (t=3.46, df=5, p=0.018). The F-measure, improved from 0.11 to 0.12. The hub network provided a 60% improvement to that reported in the literature. The performance of the hub network was then also compared against ARACNe and performed significantly better (p=0.024). We conclude that a heuristics approach in developing GRNs has potential to improve our understanding of gene regulation and interaction in diverse biological function and disease.
Texture image classification using pixel N-grams
- Authors: Kulkarni, Pradnya , Stranieri, Andrew , Ugon, Julien
- Date: 2016
- Type: Text , Conference proceedings
- Relation: 2016 IEEE International Conference on Signal and Image Processing (ICSIP); Beijing, China; 13-15 Aug, 2016 p. 137-141
- Full Text: false
- Reviewed:
- Description: Various statistical methods such as co-occurrence matrix, local binary patterns and spectral approaches such as Gabor filters have been used for generating global features for image classification. However, global image features fail to distinguish between local variations within an image. Bag-of-visual-words (BoVW) model do capture local variations in an image, but typically do not consider spatial relationships between the visual words. Here, a novel image representation ‘Pixel N-grams’, inspired from the character N-gram concept in text retrieval has been applied for texture classification purpose. Texture is an important property for image classification. Experiments on the benchmark texture database (UIUC) demonstrates that the overall classification accuracy resulting from Pixel N-gram approach (89.5%) is comparable with that achieved using BoVW approach (84.4%) with the added advantage of simplicity and reduced computational cost.