Investigating the topology of interacting networks - Theory and application to coupled climate subnetworks

Network theory provides various tools for investigating the structural or functional topology of many complex systems found in nature, technology and society. Nevertheless, it has recently been realised that a considerable number of systems of interest should be treated, more appropriately, as interacting networks or networks of networks. Here we introduce a novel graph-theoretical framework for studying the interaction structure between subnetworks embedded within a complex network of networks. This framework allows us to quantify the structural role of single vertices or whole subnetworks with respect to the interaction of a pair of subnetworks on local, mesoscopic and global topological scales. Climate networks have recently been shown to be a powerful tool for the analysis of climatological data. Applying the general framework for studying interacting networks, we introduce coupled climate subnetworks to represent and investigate the topology of statistical relationships between the fields of distinct climatological variables. Using coupled climate subnetworks to investigate the terrestrial atmosphere's three-dimensional geopotential height field uncovers known as well as interesting novel features of the atmosphere's vertical stratification and general circulation. Specifically, the new measure "cross-betweenness" identifies regions which are particularly important for mediating vertical wind field interactions. The promising results obtained by following the coupled climate subnetwork approach present a first step towards an improved understanding of the Earth system and its complex interacting components from a network perspective

Learnable PINs: Cross-Modal Embeddings for Person Identity

We propose and investigate an identity sensitive joint embedding of face and voice. Such an embedding enables cross-modal retrieval from voice to face and from face to voice. We make the following four contributions: first, we show that the embedding can be learnt from videos of talking faces, without requiring any identity labels, using a form of cross-modal self-supervision; second, we develop a curriculum learning schedule for hard negative mining targeted to this task, that is essential for learning to proceed successfully; third, we demonstrate and evaluate cross-modal retrieval for identities unseen and unheard during training over a number of scenarios and establish a benchmark for this novel task; finally, we show an application of using the joint embedding for automatically retrieving and labelling characters in TV dramas.Comment: To appear in ECCV 201

Know Your Enemy: Stealth Configuration-Information Gathering in SDN

Software Defined Networking (SDN) is a network architecture that aims at providing high flexibility through the separation of the network logic from the forwarding functions. The industry has already widely adopted SDN and researchers thoroughly analyzed its vulnerabilities, proposing solutions to improve its security. However, we believe important security aspects of SDN are still left uninvestigated. In this paper, we raise the concern of the possibility for an attacker to obtain knowledge about an SDN network. In particular, we introduce a novel attack, named Know Your Enemy (KYE), by means of which an attacker can gather vital information about the configuration of the network. This information ranges from the configuration of security tools, such as attack detection thresholds for network scanning, to general network policies like QoS and network virtualization. Additionally, we show that an attacker can perform a KYE attack in a stealthy fashion, i.e., without the risk of being detected. We underline that the vulnerability exploited by the KYE attack is proper of SDN and is not present in legacy networks. To address the KYE attack, we also propose an active defense countermeasure based on network flows obfuscation, which considerably increases the complexity for a successful attack. Our solution offers provable security guarantees that can be tailored to the needs of the specific network under consideratio

Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases.

Using expression profiles from postmortem prefrontal cortex samples of 624 dementia patients and non-demented controls, we investigated global disruptions in the co-regulation of genes in two neurodegenerative diseases, late-onset Alzheimer's disease (AD) and Huntington's disease (HD). We identified networks of differentially co-expressed (DC) gene pairs that either gained or lost correlation in disease cases relative to the control group, with the former dominant for both AD and HD and both patterns replicating in independent human cohorts of AD and aging. When aligning networks of DC patterns and physical interactions, we identified a 242-gene subnetwork enriched for independent AD/HD signatures. This subnetwork revealed a surprising dichotomy of gained/lost correlations among two inter-connected processes, chromatin organization and neural differentiation, and included DNA methyltransferases, DNMT1 and DNMT3A, of which we predicted the former but not latter as a key regulator. To validate the inter-connection of these two processes and our key regulator prediction, we generated two brain-specific knockout (KO) mice and show that Dnmt1 KO signature significantly overlaps with the subnetwork (P = 3.1 × 10(-12)), while Dnmt3a KO signature does not (P = 0.017)

Detection of Epigenomic Network Community Oncomarkers

In this paper we propose network methodology to infer prognostic cancer biomarkers based on the epigenetic pattern DNA methylation. Epigenetic processes such as DNA methylation reflect environmental risk factors, and are increasingly recognised for their fundamental role in diseases such as cancer. DNA methylation is a gene-regulatory pattern, and hence provides a means by which to assess genomic regulatory interactions. Network models are a natural way to represent and analyse groups of such interactions. The utility of network models also increases as the quantity of data and number of variables increase, making them increasingly relevant to large-scale genomic studies. We propose methodology to infer prognostic genomic networks from a DNA methylation-based measure of genomic interaction and association. We then show how to identify prognostic biomarkers from such networks, which we term `network community oncomarkers'. We illustrate the power of our proposed methodology in the context of a large publicly available breast cancer dataset

Information visualization for DNA microarray data analysis: A critical review

Graphical representation may provide effective means of making sense of the complexity and sheer volume of data produced by DNA microarray experiments that monitor the expression patterns of thousands of genes simultaneously. The ability to use ldquoabstractrdquo graphical representation to draw attention to areas of interest, and more in-depth visualizations to answer focused questions, would enable biologists to move from a large amount of data to particular records they are interested in, and therefore, gain deeper insights in understanding the microarray experiment results. This paper starts by providing some background knowledge of microarray experiments, and then, explains how graphical representation can be applied in general to this problem domain, followed by exploring the role of visualization in gene expression data analysis. Having set the problem scene, the paper then examines various multivariate data visualization techniques that have been applied to microarray data analysis. These techniques are critically reviewed so that the strengths and weaknesses of each technique can be tabulated. Finally, several key problem areas as well as possible solutions to them are discussed as being a source for future work