DHLP 1&2: Giraph based distributed label propagation algorithms on heterogeneous drug-related networks

Background and Objective: Heterogeneous complex networks are large graphs consisting of different types of nodes and edges. The knowledge extraction from these networks is complicated. Moreover, the scale of these networks is steadily increasing. Thus, scalable methods are required. Methods: In this paper, two distributed label propagation algorithms for heterogeneous networks, namely DHLP-1 and DHLP-2 have been introduced. Biological networks are one type of the heterogeneous complex networks. As a case study, we have measured the efficiency of our proposed DHLP-1 and DHLP-2 algorithms on a biological network consisting of drugs, diseases, and targets. The subject we have studied in this network is drug repositioning but our algorithms can be used as general methods for heterogeneous networks other than the biological network. Results: We compared the proposed algorithms with similar non-distributed versions of them namely MINProp and Heter-LP. The experiments revealed the good performance of the algorithms in terms of running time and accuracy.Comment: Source code available for Apache Giraph on Hadoo

Outlier Detection from Network Data with Subnetwork Interpretation

Detecting a small number of outliers from a set of data observations is always challenging. This problem is more difficult in the setting of multiple network samples, where computing the anomalous degree of a network sample is generally not sufficient. In fact, explaining why the network is exceptional, expressed in the form of subnetwork, is also equally important. In this paper, we develop a novel algorithm to address these two key problems. We treat each network sample as a potential outlier and identify subnetworks that mostly discriminate it from nearby regular samples. The algorithm is developed in the framework of network regression combined with the constraints on both network topology and L1-norm shrinkage to perform subnetwork discovery. Our method thus goes beyond subspace/subgraph discovery and we show that it converges to a global optimum. Evaluation on various real-world network datasets demonstrates that our algorithm not only outperforms baselines in both network and high dimensional setting, but also discovers highly relevant and interpretable local subnetworks, further enhancing our understanding of anomalous networks

A Scalable Approach for Discovering Conserved Active Subnetworks across Species

Overlaying differential changes in gene expression on protein interaction networks has proven to be a useful approach to interpreting the cell's dynamic response to a changing environment. Despite successes in finding active subnetworks in the context of a single species, the idea of overlaying lists of differentially expressed genes on networks has not yet been extended to support the analysis of multiple species' interaction networks. To address this problem, we designed a scalable, cross-species network search algorithm, neXus (Network - cross(X)-species - Search), that discovers conserved, active subnetworks based on parallel differential expression studies in multiple species. Our approach leverages functional linkage networks, which provide more comprehensive coverage of functional relationships than physical interaction networks by combining heterogeneous types of genomic data. We applied our cross-species approach to identify conserved modules that are differentially active in stem cells relative to differentiated cells based on parallel gene expression studies and functional linkage networks from mouse and human. We find hundreds of conserved active subnetworks enriched for stem cell-associated functions such as cell cycle, DNA repair, and chromatin modification processes. Using a variation of this approach, we also find a number of species-specific networks, which likely reflect mechanisms of stem cell function that have diverged between mouse and human. We assess the statistical significance of the subnetworks by comparing them with subnetworks discovered on random permutations of the differential expression data. We also describe several case examples that illustrate the utility of comparative analysis of active subnetworks

TOSNet : a topic-based optimal subnetwork identification in academic networks

Subnetwork identification plays a significant role in analyzing, managing, and comprehending the structure and functions in big networks. Numerous approaches have been proposed to solve the problem of subnetwork identification as well as community detection. Most of the methods focus on detecting communities by considering node attributes, edge information, or both. This study focuses on discovering subnetworks containing researchers with similar or related areas of interest or research topics. A topic- aware subnetwork identification is essential to discover potential researchers on particular research topics and provide qualitywork. Thus, we propose a topic-based optimal subnetwork identification approach (TOSNet). Based on some fundamental characteristics, this paper addresses the following problems: 1)How to discover topic-based subnetworks with a vigorous collaboration intensity? 2) How to rank the discovered subnetworks and single out one optimal subnetwork? We evaluate the performance of the proposed method against baseline methods by adopting the modularity measure, assess the accuracy based on the size of the identified subnetworks, and check the scalability for different sizes of benchmark networks. The experimental findings indicate that our approach shows excellent performance in identifying contextual subnetworks that maintain intensive collaboration amongst researchers for a particular research topic. © 2020 Institute of Electrical and Electronics Engineers Inc.. All rights reserved

Cross-layer design of multi-hop wireless networks

MULTI -hop wireless networks are usually defined as a collection of nodes equipped with radio transmitters, which not only have the capability to communicate each other in a multi-hop fashion, but also to route each others’ data packets. The distributed nature of such networks makes them suitable for a variety of applications where there are no assumed reliable central entities, or controllers, and may significantly improve the scalability issues of conventional single-hop wireless networks. This Ph.D. dissertation mainly investigates two aspects of the research issues related to the efficient multi-hop wireless networks design, namely: (a) network protocols and (b) network management, both in cross-layer design paradigms to ensure the notion of service quality, such as quality of service (QoS) in wireless mesh networks (WMNs) for backhaul applications and quality of information (QoI) in wireless sensor networks (WSNs) for sensing tasks. Throughout the presentation of this Ph.D. dissertation, different network settings are used as illustrative examples, however the proposed algorithms, methodologies, protocols, and models are not restricted in the considered networks, but rather have wide applicability. First, this dissertation proposes a cross-layer design framework integrating a distributed proportional-fair scheduler and a QoS routing algorithm, while using WMNs as an illustrative example. The proposed approach has significant performance gain compared with other network protocols. Second, this dissertation proposes a generic admission control methodology for any packet network, wired and wireless, by modeling the network as a black box, and using a generic mathematical 0. Abstract 3 function and Taylor expansion to capture the admission impact. Third, this dissertation further enhances the previous designs by proposing a negotiation process, to bridge the applications’ service quality demands and the resource management, while using WSNs as an illustrative example. This approach allows the negotiation among different service classes and WSN resource allocations to reach the optimal operational status. Finally, the guarantees of the service quality are extended to the environment of multiple, disconnected, mobile subnetworks, where the question of how to maintain communications using dynamically controlled, unmanned data ferries is investigated

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