ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks.

BACKGROUND:The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the complexity of genomic function relates to these states remains a challenge. To address this, we have developed a novel computational method, ManiNetCluster, which simultaneously aligns and clusters gene networks (e.g., co-expression) to systematically reveal the links of genomic function between different conditions. Specifically, ManiNetCluster employs manifold learning to uncover and match local and non-linear structures among networks, and identifies cross-network functional links. RESULTS:We demonstrated that ManiNetCluster better aligns the orthologous genes from their developmental expression profiles across model organisms than state-of-the-art methods (p-value <2.2×10-16). This indicates the potential non-linear interactions of evolutionarily conserved genes across species in development. Furthermore, we applied ManiNetCluster to time series transcriptome data measured in the green alga Chlamydomonas reinhardtii to discover the genomic functions linking various metabolic processes between the light and dark periods of a diurnally cycling culture. We identified a number of genes putatively regulating processes across each lighting regime. CONCLUSIONS:ManiNetCluster provides a novel computational tool to uncover the genes linking various functions from different networks, providing new insight on how gene functions coordinate across different conditions. ManiNetCluster is publicly available as an R package at https://github.com/daifengwanglab/ManiNetCluster

Gray Image extraction using Fuzzy Logic

Fuzzy systems concern fundamental methodology to represent and process uncertainty and imprecision in the linguistic information. The fuzzy systems that use fuzzy rules to represent the domain knowledge of the problem are known as Fuzzy Rule Base Systems (FRBS). On the other hand image segmentation and subsequent extraction from a noise-affected background, with the help of various soft computing methods, are relatively new and quite popular due to various reasons. These methods include various Artificial Neural Network (ANN) models (primarily supervised in nature), Genetic Algorithm (GA) based techniques, intensity histogram based methods etc. providing an extraction solution working in unsupervised mode happens to be even more interesting problem. Literature suggests that effort in this respect appears to be quite rudimentary. In the present article, we propose a fuzzy rule guided novel technique that is functional devoid of any external intervention during execution. Experimental results suggest that this approach is an efficient one in comparison to different other techniques extensively addressed in literature. In order to justify the supremacy of performance of our proposed technique in respect of its competitors, we take recourse to effective metrics like Mean Squared Error (MSE), Mean Absolute Error (MAE), Peak Signal to Noise Ratio (PSNR).Comment: 8 pages, 5 figures, Fuzzy Rule Base, Image Extraction, Fuzzy Inference System (FIS), Membership Functions, Membership values,Image coding and Processing, Soft Computing, Computer Vision Accepted and published in IEEE. arXiv admin note: text overlap with arXiv:1206.363

The Impacts of Privacy Rules on Users' Perception on Internet of Things (IoT) Applications: Focusing on Smart Home Security Service

Department of Management EngineeringAs communication and information technologies advance, the Internet of Things (IoT) has changed the way people live. In particular, as smart home security services have been widely commercialized, it is necessary to examine consumer perception. However, there is little research that explains the general perception of IoT and smart home services. This article will utilize communication privacy management theory and privacy calculus theory to investigate how options to protect privacy affect how users perceive benefits and costs and how those perceptions affect individuals??? intentions to use of smart home service. Scenario-based experiments were conducted, and perceived benefits and costs were treated as formative second-order constructs. The results of PLS analysis in the study showed that smart home options to protect privacy decreased perceived benefits and increased perceived costs. In addition, the perceived benefits and perceived costs significantly affected the intention to use smart home security services. This research contributes to the field of IoT and smart home research and gives practitioners notable guidelines.ope