Complex Network Analysis and the Applications in Vehicle Delay-Tolerant Networks

Vehicle Delay Tolerant Networks (VDTNs) is a particular kind of Delay Tolerant Networks (DTNs), where vehicles equipped with transmission capabilities are interconnected to form Vehicle NETworks (VNETs). Some applications and services on the top of VDTNs have raised a lot of attention, especially by providing information about weather conditions, road safety, traffic jams, speed limit, and even video streamings without the need of infrastructures. However, due to features such as high vehicle mobility, dynamic scenarios, sparsity of vehicles, short contact durations, disruption and intermittent connectivity and strict requirements for latency, many VDTNs do not present satisfactory performance, because no path exists between a source and its target. In this dissertation, we propose three routing methods to solve the problem as follows. Our first VDTN system focuses on the multi-copy routing in Vehicle Delay Tolerant Networks (VDTNs). Multi-copy routing can balance the network congestion caused by broadcasting and the efficiency limitation in single-copy routing. However, the different copies of each packet search the destination node independently in current multi-copy routing algorithms, which leads to a low utilization of copies since they may search through the same path repeatedly without cooperation. To solve this problem, we propose a fractal Social community based efficient multi-coPy routing in VDTNs, namely SPread. First, we measure social network features in Vehicle NETworks (VNETs). Then, by taking advantage of weak ties and fractal structure feature of the community in VNETs, SPread carefully scatters different copies of each packet to different communities that are close to the destination community, thus ensuring that different copies search the destination community through different weak ties. For the routing of each copy, current routing algorithms either fail to exploit reachability information of nodes to different nodes (centrality based methods) or only use single-hop reachability information (community based methods), e.g., similarity and probability. Here, the reachability of node $i$ to a destination $j$ (a community or a node) means the possibility that a packet can reach $j$ through $i$. In order to overcome above drawbacks, inspired by the personalized PageRank algorithm, we design new algorithms for calculating multi-hop reachability of vehicles to different communities and vehicles dynamically. Therefore, the routing efficiency of each copy can be enhanced. Finally, extensive trace-driven simulation demonstrates the high efficiency of SPread in comparison with state-of-the-art routing algorithms in DTNs. However, in SPread, we only consider the VNETs as complex networks and fail to use the unique location information to improve the routing performance. We believe that the complex network knowledge should be combined with special features of various networks themselves in order to benefit the real application better. Therefore, we further explore the possibility to improve the performance of VDTN system by taking advantage of the special features of VNETs. We first analyze vehicle network traces and observe that i) each vehicle has only a few active sub-areas that it frequently visits, and ii) two frequently encountered vehicles usually encounter each other in their active sub-areas. We then propose Active Area based Routing method (AAR) which consists of two steps based on the two observations correspondingly. AAR first distributes a packet copy to each active sub-area of the target vehicle using a traffic-considered shortest path spreading algorithm, and then in each sub-area, each packet carrier tries to forward the packet to a vehicle that has high encounter frequency with the target vehicle. Furthermore, we propose a Distributed AAR (DAAR) to improve the performance of AAR. Extensive trace-driven simulation demonstrates that AAR produces higher success rates and shorter delay in comparison with the state-of-the-art routing algorithms in VDTNs. Also, DAAR has a higher success rate and a lower average delay compared with AAR since information of dynamic active sub-areas tends to be updated from time to time, while the information of static active sub-areas may be outdated due to the change of vehicles\u27 behaviors. Finally, we try to combine different routing algorithms together and propose a DIstributed Adaptive-Learning routing method for VDTNs, namely DIAL, by taking advantages of the human beings communication feature that most interactions are generated by pairs of people who interacted often previously. DIAL consists of two components: the information fusion based routing method and the adaptive-learning framework. The information fusion based routing method enables DIAL to improve the routing performance by sharing and fusing multiple information without centralized infrastructures. Furthermore, based on the information shared by information fusion based routing method, the adaptive-learning framework enables DIAL to design personalized routing strategies for different vehicle pairs without centralized infrastructures. Therefore, DIAL can not only share and fuse multiple information of each vehicle without centralized infrastructures, but also design each vehicle pair with personalized routing strategy. Extensive trace-driven simulation demonstrates that DIAL has better routing success rate, shorter average delays and the load balance function in comparison with state-of-the-art routing methods which need the help of centralized infrastructures in VDTNs

Protein complex detection with semi-supervised learning in protein interaction networks

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions (PPIs) play fundamental roles in nearly all biological processes. The systematic analysis of PPI networks can enable a great understanding of cellular organization, processes and function. In this paper, we investigate the problem of protein complex detection from noisy protein interaction data, i.e., finding the subsets of proteins that are closely coupled via protein interactions. However, protein complexes are likely to overlap and the interaction data are very noisy. It is a great challenge to effectively analyze the massive data for biologically meaningful protein complex detection.</p> <p>Results</p> <p>Many people try to solve the problem by using the traditional unsupervised graph clustering methods. Here, we stand from a different point of view, redefining the properties and features for protein complexes and designing a “semi-supervised” method to analyze the problem. In this paper, we utilize the neural network with the “semi-supervised” mechanism to detect the protein complexes. By retraining the neural network model recursively, we could find the optimized parameters for the model, in such a way we can successfully detect the protein complexes. The comparison results show that our algorithm could identify protein complexes that are missed by other methods. We also have shown that our method achieve better precision and recall rates for the identified protein complexes than other existing methods. In addition, the framework we proposed is easy to be extended in the future.</p> <p>Conclusions</p> <p>Using a weighted network to represent the protein interaction network is more appropriate than using a traditional unweighted network. In addition, integrating biological features and topological features to represent protein complexes is more meaningful than using dense subgraphs. Last, the “semi-supervised” learning model is a promising model to detect protein complexes with more biological and topological features available.</p

Subgroup discovery for structured target concepts

The main object of study in this thesis is subgroup discovery, a theoretical framework for finding subgroups in data—i.e., named sub-populations— whose behaviour with respect to a specified target concept is exceptional when compared to the rest of the dataset. This is a powerful tool that conveys crucial information to a human audience, but despite past advances has been limited to simple target concepts. In this work we propose algorithms that bring this framework to novel application domains. We introduce the concept of representative subgroups, which we use not only to ensure the fairness of a sub-population with regard to a sensitive trait, such as race or gender, but also to go beyond known trends in the data. For entities with additional relational information that can be encoded as a graph, we introduce a novel measure of robust connectedness which improves on established alternative measures of density; we then provide a method that uses this measure to discover which named sub-populations are more well-connected. Our contributions within subgroup discovery crescent with the introduction of kernelised subgroup discovery: a novel framework that enables the discovery of subgroups on i.i.d. target concepts with virtually any kind of structure. Importantly, our framework additionally provides a concrete and efficient tool that works out-of-the-box without any modification, apart from specifying the Gramian of a positive definite kernel. To use within kernelised subgroup discovery, but also on any other kind of kernel method, we additionally introduce a novel random walk graph kernel. Our kernel allows the fine tuning of the alignment between the vertices of the two compared graphs, during the count of the random walks, while we also propose meaningful structure-aware vertex labels to utilise this new capability. With these contributions we thoroughly extend the applicability of subgroup discovery and ultimately re-define it as a kernel method.Der Hauptgegenstand dieser Arbeit ist die Subgruppenentdeckung (Subgroup Discovery), ein theoretischer Rahmen für das Auffinden von Subgruppen in Daten—d. h. benannte Teilpopulationen—deren Verhalten in Bezug auf ein bestimmtes Targetkonzept im Vergleich zum Rest des Datensatzes außergewöhnlich ist. Es handelt sich hierbei um ein leistungsfähiges Instrument, das einem menschlichen Publikum wichtige Informationen vermittelt. Allerdings ist es trotz bisherigen Fortschritte auf einfache Targetkonzepte beschränkt. In dieser Arbeit schlagen wir Algorithmen vor, die diesen Rahmen auf neuartige Anwendungsbereiche übertragen. Wir führen das Konzept der repräsentativen Untergruppen ein, mit dem wir nicht nur die Fairness einer Teilpopulation in Bezug auf ein sensibles Merkmal wie Rasse oder Geschlecht sicherstellen, sondern auch über bekannte Trends in den Daten hinausgehen können. Für Entitäten mit zusätzlicher relationalen Information, die als Graph kodiert werden kann, führen wir ein neuartiges Maß für robuste Verbundenheit ein, das die etablierten alternativen Dichtemaße verbessert; anschließend stellen wir eine Methode bereit, die dieses Maß verwendet, um herauszufinden, welche benannte Teilpopulationen besser verbunden sind. Unsere Beiträge in diesem Rahmen gipfeln in der Einführung der kernelisierten Subgruppenentdeckung: ein neuartiger Rahmen, der die Entdeckung von Subgruppen für u.i.v. Targetkonzepten mit praktisch jeder Art von Struktur ermöglicht. Wichtigerweise, unser Rahmen bereitstellt zusätzlich ein konkretes und effizientes Werkzeug, das ohne jegliche Modifikation funktioniert, abgesehen von der Angabe des Gramian eines positiv definitiven Kernels. Für den Einsatz innerhalb der kernelisierten Subgruppentdeckung, aber auch für jede andere Art von Kernel-Methode, führen wir zusätzlich einen neuartigen Random-Walk-Graph-Kernel ein. Unser Kernel ermöglicht die Feinabstimmung der Ausrichtung zwischen den Eckpunkten der beiden unter-Vergleich-gestelltenen Graphen während der Zählung der Random Walks, während wir auch sinnvolle strukturbewusste Vertex-Labels vorschlagen, um diese neue Fähigkeit zu nutzen. Mit diesen Beiträgen erweitern wir die Anwendbarkeit der Subgruppentdeckung gründlich und definieren wir sie im Endeffekt als Kernel-Methode neu

VISUAL SEMANTIC SEGMENTATION AND ITS APPLICATIONS

This dissertation addresses the difficulties of semantic segmentation when dealing with an extensive collection of images and 3D point clouds. Due to the ubiquity of digital cameras that help capture the world around us, as well as the advanced scanning techniques that are able to record 3D replicas of real cities, the sheer amount of visual data available presents many opportunities for both academic research and industrial applications. But the mere quantity of data also poses a tremendous challenge. In particular, the problem of distilling useful information from such a large repository of visual data has attracted ongoing interests in the fields of computer vision and data mining. Structural Semantics are fundamental to understanding both natural and man-made objects. Buildings, for example, are like languages in that they are made up of repeated structures or patterns that can be captured in images. In order to find these recurring patterns in images, I present an unsupervised frequent visual pattern mining approach that goes beyond co-location to identify spatially coherent visual patterns, regardless of their shape, size, locations and orientation. First, my approach categorizes visual items from scale-invariant image primitives with similar appearance using a suite of polynomial-time algorithms that have been designed to identify consistent structural associations among visual items, representing frequent visual patterns. After detecting repetitive image patterns, I use unsupervised and automatic segmentation of the identified patterns to generate more semantically meaningful representations. The underlying assumption is that pixels capturing the same portion of image patterns are visually consistent, while pixels that come from different backdrops are usually inconsistent. I further extend this approach to perform automatic segmentation of foreground objects from an Internet photo collection of landmark locations. New scanning technologies have successfully advanced the digital acquisition of large-scale urban landscapes. In addressing semantic segmentation and reconstruction of this data using LiDAR point clouds and geo-registered images of large-scale residential areas, I develop a complete system that simultaneously uses classification and segmentation methods to first identify different object categories and then apply category-specific reconstruction techniques to create visually pleasing and complete scene models

Big networks : a survey

A network is a typical expressive form of representing complex systems in terms of vertices and links, in which the pattern of interactions amongst components of the network is intricate. The network can be static that does not change over time or dynamic that evolves through time. The complication of network analysis is different under the new circumstance of network size explosive increasing. In this paper, we introduce a new network science concept called a big network. A big networks is generally in large-scale with a complicated and higher-order inner structure. This paper proposes a guideline framework that gives an insight into the major topics in the area of network science from the viewpoint of a big network. We first introduce the structural characteristics of big networks from three levels, which are micro-level, meso-level, and macro-level. We then discuss some state-of-the-art advanced topics of big network analysis. Big network models and related approaches, including ranking methods, partition approaches, as well as network embedding algorithms are systematically introduced. Some typical applications in big networks are then reviewed, such as community detection, link prediction, recommendation, etc. Moreover, we also pinpoint some critical open issues that need to be investigated further. © 2020 Elsevier Inc