Network-based approaches to explore complex biological systems towards network medicine

Network medicine relies on different types of networks: from the molecular level of protein–protein interactions to gene regulatory network and correlation studies of gene expression. Among network approaches based on the analysis of the topological properties of protein–protein interaction (PPI) networks, we discuss the widespread DIAMOnD (disease module detection) algorithm. Starting from the assumption that PPI networks can be viewed as maps where diseases can be identified with localized perturbation within a specific neighborhood (i.e., disease modules), DIAMOnD performs a systematic analysis of the human PPI network to uncover new disease-associated genes by exploiting the connectivity significance instead of connection density. The past few years have witnessed the increasing interest in understanding the molecular mechanism of post-transcriptional regulation with a special emphasis on non-coding RNAs since they are emerging as key regulators of many cellular processes in both physiological and pathological states. Recent findings show that coding genes are not the only targets that microRNAs interact with. In fact, there is a pool of different RNAs—including long non-coding RNAs (lncRNAs) —competing with each other to attract microRNAs for interactions, thus acting as competing endogenous RNAs (ceRNAs). The framework of regulatory networks provides a powerful tool to gather new insights into ceRNA regulatory mechanisms. Here, we describe a data-driven model recently developed to explore the lncRNA-associated ceRNA activity in breast invasive carcinoma. On the other hand, a very promising example of the co-expression network is the one implemented by the software SWIM (switch miner), which combines topological properties of correlation networks with gene expression data in order to identify a small pool of genes—called switch genes—critically associated with drastic changes in cell phenotype. Here, we describe SWIM tool along with its applications to cancer research and compare its predictions with DIAMOnD disease genes

Model-based clustering with data correction for removing artifacts in gene expression data

The NIH Library of Integrated Network-based Cellular Signatures (LINCS) contains gene expression data from over a million experiments, using Luminex Bead technology. Only 500 colors are used to measure the expression levels of the 1,000 landmark genes measured, and the data for the resulting pairs of genes are deconvolved. The raw data are sometimes inadequate for reliable deconvolution leading to artifacts in the final processed data. These include the expression levels of paired genes being flipped or given the same value, and clusters of values that are not at the true expression level. We propose a new method called model-based clustering with data correction (MCDC) that is able to identify and correct these three kinds of artifacts simultaneously. We show that MCDC improves the resulting gene expression data in terms of agreement with external baselines, as well as improving results from subsequent analysis.Comment: 28 page

Clustering Optimisation Techniques in Mobile Networks

The use of mobile phones has exploded over the past years, abundantly through the introduction of smartphones and the rapidly expanding use of mobile data. This has resulted in a spiraling problem of ensuring quality of service for users of mobile networks. Hence, mobile carriers and service providers need to determine how to prioritise expansion decisions and optimise network faults to ensure customer satisfaction and optimal network performance. To assist in that decision-making process, this research employs data mining classification of different Key Performance Indicator datasets to develop a monitoring scheme for mobile networks as a means of identifying the causes of network malfunctions. Then, the data are clustered to observe the characteristics of the technical areas with the use of k-means clustering. The data output is further trained with decision tree classification algorithms. The end result was that this method of network optimisation allowed for significantly improved fault detection performance

Clustering Optimisation Techniques in Mobile Networks

The use of mobile phones has exploded over the past years, abundantly through the introduction of smartphones and the rapidly expanding use of mobile data. This has resulted in a spiraling problem of ensuring quality of service for users of mobile networks. Hence, mobile carriers and service providers need to determine how to prioritise expansion decisions and optimise network faults to ensure customer satisfaction and optimal network performance. To assist in that decision-making process, this research employs data mining classification of different Key Performance Indicator datasets to develop a monitoring scheme for mobile networks as a means of identifying the causes of network malfunctions. Then, the data are clustered to observe the characteristics of the technical areas with the use of k-means clustering. The data output is further trained with decision tree classification algorithms. The end result was that this method of network optimisation allowed for significantly improved fault detection performance

Clustering Optimisation Techniques in Mobile Networks

The use of mobile phones has exploded over the past years, abundantly through the introduction of smartphones and the rapidly expanding use of mobile data. This has resulted in a spiraling problem of ensuring quality of service for users of mobile networks. Hence, mobile carriers and service providers need to determine how to prioritise expansion decisions and optimise network faults to ensure customer satisfaction and optimal network performance. To assist in that decision-making process, this research employs data mining classification of different Key Performance Indicator datasets to develop a monitoring scheme for mobile networks as a means of identifying the causes of network malfunctions. Then, the data are clustered to observe the characteristics of the technical areas with the use of k-means clustering. The data output is further trained with decision tree classification algorithms. The end result was that this method of network optimisation allowed for significantly improved fault detection performance

Clustering Optimisation Techniques in Mobile Networks

The use of mobile phones has exploded over the past years, abundantly through the introduction of smartphones and the rapidly expanding use of mobile data. This has resulted in a spiraling problem of ensuring quality of service for users of mobile networks. Hence, mobile carriers and service providers need to determine how to prioritise expansion decisions and optimise network faults to ensure customer satisfaction and optimal network performance. To assist in that decision-making process, this research employs data mining classification of different Key Performance Indicator datasets to develop a monitoring scheme for mobile networks as a means of identifying the causes of network malfunctions. Then, the data are clustered to observe the characteristics of the technical areas with the use of k-means clustering. The data output is further trained with decision tree classification algorithms. The end result was that this method of network optimisation allowed for significantly improved fault detection performance

Clustering Optimisation Techniques in Mobile Networks

The use of mobile phones has exploded over the past years, abundantly through the introduction of smartphones and the rapidly expanding use of mobile data. This has resulted in a spiraling problem of ensuring quality of service for users of mobile networks. Hence, mobile carriers and service providers need to determine how to prioritise expansion decisions and optimise network faults to ensure customer satisfaction and optimal network performance. To assist in that decision-making process, this research employs data mining classification of different Key Performance Indicator datasets to develop a monitoring scheme for mobile networks as a means of identifying the causes of network malfunctions. Then, the data are clustered to observe the characteristics of the technical areas with the use of k-means clustering. The data output is further trained with decision tree classification algorithms. The end result was that this method of network optimisation allowed for significantly improved fault detection performance