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In the Bayesian Reinforcement Learning (BRL) setting, agents try to maximise the collected rewards while interacting with their environment while using some prior knowledge that is accessed beforehand. Many BRL algorithms have already been proposed, but the benchmarks used to compare them are only relevant for specific cases. The paper addresses this problem, and provides a new BRL comparison methodology along with the corresponding open source library. In this methodology, a comparison criterion that measures the performance of algorithms on large sets of Markov Decision Processes (MDPs) drawn from some probability distributions is defined. In order to enable the comparison of non-anytime algorithms, our methodology also includes a detailed analysis of the computation time requirement of each algorithm. Our library is released with all source code and documentation: it includes three test problems, each of which has two different prior distributions, and seven state-of-the-art RL algorithms. Finally, our library is illustrated by comparing all the available algorithms and the results are discussed. [ABSTRACT FROM AUTHOR]

With the development of computer network bandwidth, packet classification algorithms which are able to deal with large-scale rule sets are in urgent need. Among the existing algorithms, researches on packet classification algorithms based on hierarchical trie have become an important packet classification research branch because of their widely practical use. Although hierarchical trie is beneficial to save large storage space, it has several shortcomings such as the existence of backtracking and empty nodes. This paper proposes a new packet classification algorithm, Hierarchical Trie Algorithm Based on Expectation-Maximization Clustering (HTEMC). Firstly, this paper uses the formalization method to deal with the packet classification problem by means of mapping the rules and data packets into a two-dimensional space. Secondly, this paper uses expectation-maximization algorithm to cluster the rules based on their aggregate characteristics, and thereby diversified clusters are formed. Thirdly, this paper proposes a hierarchical trie based on the results of expectation-maximization clustering. Finally, this paper respectively conducts simulation experiments and real-environment experiments to compare the performances of our algorithm with other typical algorithms, and analyzes the results of the experiments. The hierarchical trie structure in our algorithm not only adopts trie path compression to eliminate backtracking, but also solves the problem of low efficiency of trie updates, which greatly improves the performance of the algorithm. [ABSTRACT FROM AUTHOR]

Computational modeling of engineered gene circuits is an important while challenged task in systems biology. In order to describe and predict the response behaviors of genetic circuits using reliable model parameters, this paper applies an optimal experimental design(OED) method to obtain input signals. In order to obtain informative observations, this study focuses on maximizing Fisher information matrix(FIM)-based optimal criteria and to provide optimal inputs. Furthermore, this paper designs a two-stage optimization with the modified E-optimal criteria and applies harmony search(HS)-based OED algorithm to minimize estimation errors. The proposed optimal identification methodology involves estimation errors and the sample size to pursue a trade-off between estimation accuracy and measurement cost in modeling gene networks. The designed cost function takes two major factors into account, in which experimental costs are proportional to the number of time points. Experiments select two types of synthetic genetic networks to validate the effectiveness of the proposed HS-OED approach. Identification outcomes and analysis indicate the proposed HS-OED method outperforms two candidate OED approaches, with reduced computational effort. [ABSTRACT FROM AUTHOR]

In business replenishment, discount offers of multi-item may either provide different discount schedules with a single discount type, or provide schedules with multiple discount types. The paper investigates the joint effects of multiple discount schemes on the decisions of multi-item joint replenishment. In this paper, a joint replenishment problem (JRP) model, considering three discount (all-unit discount, incremental discount, total volume discount) offers simultaneously, is constructed to determine the basic cycle time and joint replenishment frequencies of multi-item. To solve the proposed problem, a heuristic algorithm is proposed to find the optimal solutions and the corresponding total cost of the JRP model. Numerical experiment is performed to test the algorithm and the computational results of JRPs under different discount combinations show different significance in the replenishment cost reduction. [ABSTRACT FROM AUTHOR]

Finding communities in multilayer networks is a vital step in understanding the structure and dynamics of these layers, where each layer represents a particular type of relationship between nodes in the natural world. However, most community discovery methods for multilayer networks may ignore the interplay between layers or the unique topological structure in a layer. Moreover, most of them can only detect non-overlapping communities. In this paper, we propose a new community discovery method for multilayer networks, which leverages the interplay between layers and the unique topology in a layer to reveal overlapping communities. Through a comprehensive analysis of edge behaviors within and across layers, we first calculate the similarities for edges from the same layer and the cross layers. Then, by leveraging these similarities, we can construct a dendrogram for the multilayer networks that takes both the unique topological structure and the important interplay into consideration. Finally, by introducing a new community density metric for multilayer networks, we can cut the dendrogram to get the overlapping communities for these layers. By applying our method on both synthetic and real-world datasets, we demonstrate that our method has an accurate performance in discovering overlapping communities in multilayer networks. [ABSTRACT FROM AUTHOR]

This paper proposes a novel adaptive Super-Twisting sliding mode control for a microgyroscope under unknown model uncertainties and external disturbances. In order to improve the convergence rate of reaching the sliding surface and the accuracy of regulating and trajectory tracking, a high order Super-Twisting sliding mode control strategy is employed, which not only can combine the advantages of the traditional sliding mode control with the Super-Twisting sliding mode control, but also guarantee that the designed control system can reach the sliding surface and equilibrium point in a shorter finite time from any initial state and avoid chattering problems. In consideration of unknown parameters of micro gyroscope system, an adaptive algorithm based on Lyapunov stability theory is designed to estimate the unknown parameters and angular velocity of microgyroscope. Finally, the effectiveness of the proposed scheme is demonstrated by simulation results. The comparative study between adaptive Super-Twisting sliding mode control and conventional sliding mode control demonstrate the superiority of the proposed method. [ABSTRACT FROM AUTHOR]

In this paper, an improved algorithm of wavelet packet-chaos model for life prediction of space relays based on volterra series is proposed. In the proposed method, the high and low frequency time sequence components of performance parameters are obtained by employing the improved wavelet packet transform to decompose the performance parameters of the relay into multiple scales. Then the optimization algorithm of parameters in volterra series is improved, and is used to construct a chaotic forecasting model for the high and low frequency time sequence components gained by the wavelet packet transform. At last, the chaotic forecasting results of the high and low frequency components are combined by taking the wavelet packet reconstruction approach, so as to predict the lifetime of the studied space relay. The algorithm can predict the life curve of the relay accurately and reflect the characteristics of the relay performance with sufficient accuracy. The proposed method is validated via a case study of a space relay. [ABSTRACT FROM AUTHOR]

Saliency detection attracted attention of many researchers and had become a very active area of research. Recently, many saliency detection models have been proposed and achieved excellent performance in various fields. However, most of these models only consider low-level features. This paper proposes a novel saliency detection model using both color and texture features and incorporating higher-level priors. The SLIC superpixel algorithm is applied to form an over-segmentation of the image. Color saliency map and texture saliency map are calculated based on the region contrast method and adaptive weight. Higher-level priors including location prior and color prior are incorporated into the model to achieve a better performance and full resolution saliency map is obtained by using the up-sampling method. Experimental results on three datasets demonstrate that the proposed saliency detection model outperforms the state-of-the-art models. [ABSTRACT FROM AUTHOR]

In this paper, we propose a new approach for learning node embeddings for weighted undirected networks. We perform a random walk on the network to extract the latent structural information and perform node embedding learning under a similarity-based framework. Unlike previous works, we apply a different criterion to capture the proximity information between nodes in a network, and use it for improved modeling of similarities between nodes. We show that the mean commute time (MCT) between two nodes, defined as the average time a random walker takes to reach a target node and return to the source, plays a crucial role in quantifying the actual degree of proximity between two nodes of the network. We then introduce a novel definition of a similarity matrix that is based on the pair-wise mean commute time captured, which enables us to adequately represent the connection of similar nodes. We utilize pseudoinverse of the Laplacian matrix of the graph for calculating such a proximity measure, capturing rich structural information out of the graph for learning more adequate node representations of a network. The results of different experiments on three real-world networks demonstrate that our proposed method outperforms existing related efforts in classification, clustering, visualization as well as link prediction tasks. [ABSTRACT FROM AUTHOR]

Given a real-world graph, how can we measure relevance scores for ranking and link prediction? Random walk with restart (RWR) provides an excellent measure for this and has been applied to various applications such as friend recommendation, community detection, anomaly detection, etc. However, RWR suffers from two problems: 1) using the same restart probability for all the nodes limits the expressiveness of random walk, and 2) the restart probability needs to be manually chosen for each application without theoretical justification. We have two main contributions in this paper. First, we propose R W E R (RWER), a random walk based measure which improves the expressiveness of random walks by using a distinct restart probability for each node. The improved expressiveness leads to superior accuracy for ranking and link prediction. Second, we propose SR (pervised start for RWER), an algorithm for learning the restart probabilities of RWER from a given graph. SR eliminates the need to heuristically and manually select the restart parameter for RWER. Extensive experiments show that our proposed method provides the best performance for ranking and link prediction tasks. [ABSTRACT FROM AUTHOR]

A freight train service network generally involves two categories of trains: unscheduled trains, whose operating frequencies fluctuate with the freight demand, and scheduled trains, which are operated based on regular timetables similar to passenger trains. The timetables for scheduled trains are released to the public once determined, and they are not influenced by the freight demand. Typically, the total capacity of scheduled trains can satisfy the predicted average demand of express cargos. However, in practice, the demand always changes. Therefore, a method to assign the shipments to scheduled and unscheduled train services has become an important issue faced in railway transportation. This paper focuses on the coordinated optimization of rail express cargo assignment in a hybrid train services network. On the premise of fully utilizing the capacity of scheduled train services, we propose a car-to-train assignment model to reasonably assign rail express cargos to scheduled and unscheduled trains. The objective aims to maximize the profit of transporting the rail express cargos. The constraints include the capacity restriction on the service arcs, flow balance constraints, transportation due date constraints and logical relationship constraints among the decision variables. Furthermore, we discuss a linearization technique to convert the nonlinear transportation due date constraint into a linear constraint, making it possible to solve by a standard optimization solver. Finally, an illustrative case study based on the Beijing-Guangzhou Railway Line is carried out to demonstrate the effectiveness and efficiency of the proposed solution approach. [ABSTRACT FROM AUTHOR]

For railway operators, one of many important goals is to improve the utilization efficiency of electric multiple units (EMUs). When operators design EMU circulation plans, EMU type restrictions are critical factors when assigning EMUs to the correct depots for maintenance. However, existing studies only consider that EMUs are maintained at their home depots. However, targeting that problem, in this paper, an optimization model for the EMU circulation planning problem that allows depots to be selected for EMU maintenance is proposed. This model aims at optimizing the number of used EMUs and the number of EMU maintenance tasks and simultaneously incorporates other important constraints, including type restrictions, on EMU maintenance and night accommodation capacity at depots. In order to solve the model, a branch-and-price algorithm is also developed. A case study of a real-world high-speed railway was conducted to compare and analyze the effects of different maintenance location constraints. The results show that the number of EMUs used will decrease under the maintenance sharing scheme, the number of EMU maintenance tasks can be reduced, and the time occupied in EMU maintenance will be released. In addition, the scheme of maintenance resources sharing and increases to mileage limits can effectively decrease the number of EMU maintenance tasks significantly. The model and algorithm can be used as an effective quantitative analysis tool for railway operators' decision-making processes in the EMU circulation planning problem. [ABSTRACT FROM AUTHOR]

With the rising of e-hailing services in urban areas, ride sharing is becoming a common mode of transportation. This paper presents a mathematical model to design an enhanced ridesharing system with meet points and users’ preferable time windows. The introduction of meet points allows ridesharing operators to trade off the benefits of saving en-route delays and the cost of additional walking for some passengers to be collectively picked up or dropped off. This extension to the traditional door-to-door ridesharing problem brings more operation flexibility in urban areas (where potential requests may be densely distributed in neighborhood), and thus could achieve better system performance in terms of reducing the total travel time and increasing the served passengers. We design and implement a Tabu-based meta-heuristic algorithm to solve the proposed mixed integer linear program (MILP). To evaluate the validation and effectiveness of the proposed model and solution algorithm, several scenarios are designed and also resolved to optimality by CPLEX. Results demonstrate that (i) detailed route plan associated with passenger assignment to meet points can be obtained with en-route delay savings; (ii) as compared to CPLEX, the meta-heuristic algorithm bears the advantage of higher computation efficiency and produces good quality solutions with 8%~15% difference from the global optima; and (iii) introducing meet points to ridesharing system saves the total travel time by 2.7%-3.8% for small-scale ridesharing systems. More benefits are expected for ridesharing systems with large size of fleet. This study provides a new tool to efficiently operate the ridesharing system, particularly when the ride sharing vehicles are in short supply during peak hours. Traffic congestion mitigation will also be expected. [ABSTRACT FROM AUTHOR]

Automatic extraction of protein-protein interaction (PPI) pairs from biomedical literature is a widely examined task in biological information extraction. Currently, many kernel based approaches such as linear kernel, tree kernel, graph kernel and combination of multiple kernels has achieved promising results in PPI task. However, most of these kernel methods fail to capture the semantic relation information between two entities. In this paper, we present a special type of tree kernel for PPI extraction which exploits both syntactic (structural) and semantic vectors information known as Distributed Smoothed Tree kernel (DSTK). DSTK comprises of distributed trees with syntactic information along with distributional semantic vectors representing semantic information of the sentences or phrases. To generate robust machine learning model composition of feature based kernel and DSTK were combined using ensemble support vector machine (SVM). Five different corpora (AIMed, BioInfer, HPRD50, IEPA, and LLL) were used for evaluating the performance of our system. Experimental results show that our system achieves better f-score with five different corpora compared to other state-of-the-art systems. [ABSTRACT FROM AUTHOR]

The use of RFID technology in complex and distributed environments often leads to a multi-domain RFID system, in which trust establishment among entities from heterogeneous domains without past interaction or prior agreed policy, is a challenge. The current trust management mechanisms in the literature do not meet the specific requirements in multi-domain RFID systems. Therefore, this paper analyzes the special challenges on trust management in multi-domain RFID systems, and identifies the implications and the requirements of the challenges on the solutions to the trust management of multi-domain RFID systems. A multi-domain trust management model is proposed, which provides a hierarchical trust management framework include a diversity of trust evaluation and establishment approaches. The simulation results and analysis show that the proposed method has excellent ability to deal with the trust relationships, better security, and higher accuracy rate. [ABSTRACT FROM AUTHOR]

Derive the quantitative predictions of constraint-based models require of conversion algorithms to enumerate and construct the skeleton graph conformed by the extreme points of the feasible region, where all constraints in the model are fulfilled. The conversion is problematic when the system of linear constraints is degenerate. This paper describes a conversion algorithm that combines the best of two methods: the incremental slicing of cones that defeats degeneracy and pivoting for a swift traversal of the set of extreme points. An extensive computational practice uncovers two complementary classes of conversion problems. The two classes are distinguished by a practical measure of complexity that involves the input and output sizes. Detailed characterizations of the complexity classes and the corresponding performances of the algorithm are presented. For the benefit of implementors, a simple example illustrates the stages of the exposition. [ABSTRACT FROM AUTHOR]

An effective evaluation of transportation network efficiency could offer guidance for the optimal control of urban traffic. Based on the introduction and related mathematical analysis of three quantitative evaluation methods for transportation network efficiency, this paper compares the information measured by them, including network structure, traffic demand, travel choice behavior and other factors which affect network efficiency. Accordingly, the applicability of various evaluation methods is discussed. Through analyzing different transportation network examples it is obtained that Q-H method could reflect the influence of network structure, traffic demand and user route choice behavior on transportation network efficiency well. In addition, the transportation network efficiency measured by this method and Braess’s Paradox can be explained with each other, which indicates a better evaluation of the real operation condition of transportation network. Through the analysis of the network efficiency calculated by Q-H method, it can also be drawn that a specific appropriate demand is existed to a given transportation network. Meanwhile, under the fixed demand, both the critical network structure that guarantees the stability and the basic operation of the network and a specific network structure contributing to the largest value of the transportation network efficiency can be identified. [ABSTRACT FROM AUTHOR]

Two, partially interwoven, hot topics in the analysis and statistical modeling of neural data, are the development of efficient and informative representations of the time series derived from multiple neural recordings, and the extraction of information about the connectivity structure of the underlying neural network from the recorded neural activities. In the present paper we show that state-space clustering can provide an easy and effective option for reducing the dimensionality of multiple neural time series, that it can improve inference of synaptic couplings from neural activities, and that it can also allow the construction of a compact representation of the multi-dimensional dynamics, that easily lends itself to complexity measures. We apply a variant of the ‘mean-shift’ algorithm to perform state-space clustering, and validate it on an Hopfield network in the glassy phase, in which metastable states are largely uncorrelated from memories embedded in the synaptic matrix. In this context, we show that the neural states identified as clusters’ centroids offer a parsimonious parametrization of the synaptic matrix, which allows a significant improvement in inferring the synaptic couplings from the neural activities. Moving to the more realistic case of a multi-modular spiking network, with spike-frequency adaptation inducing history-dependent effects, we propose a procedure inspired by Boltzmann learning, but extending its domain of application, to learn inter-module synaptic couplings so that the spiking network reproduces a prescribed pattern of spatial correlations; we then illustrate, in the spiking network, how clustering is effective in extracting relevant features of the network’s state-space landscape. Finally, we show that the knowledge of the cluster structure allows casting the multi-dimensional neural dynamics in the form of a symbolic dynamics of transitions between clusters; as an illustration of the potential of such reduction, we define and analyze a measure of complexity of the neural time series. [ABSTRACT FROM AUTHOR]

The deployment of large number of femtocell base stations allows us to extend the coverage and efficiently utilize resources in a low cost manner. However, the small cell size of femtocell networks can result in frequent handovers to the mobile user, and consequently throughput degradation. Thus, in this paper, we propose predictive association control schemes to improve the system’s effective throughput. Our design focuses on reducing handover frequency without impacting on throughput. The proposed schemes determine handover decisions that contribute most to the network throughput and are proper for distributed implementations. The simulation results show significant gains compared with existing methods in terms of handover frequency and network throughput perspective. [ABSTRACT FROM AUTHOR]

Recently, Pulse Coupled Oscillator (PCO)-based travelling waves have attracted substantial attention by researchers in wireless sensor network (WSN) synchronization. Because WSNs are generally artificial occurrences that mimic natural phenomena, the PCO utilizes firefly synchronization of attracting mating partners for modelling the WSN. However, given that sensor nodes are unable to receive messages while transmitting data packets (due to deafness), the PCO model may not be efficient for sensor network modelling. To overcome this limitation, this paper proposed a new scheme called the Travelling Wave Pulse Coupled Oscillator (TWPCO). For this, the study used a self-organizing scheme for energy-efficient WSNs that adopted travelling wave biologically inspired network systems based on phase locking of the PCO model to counteract deafness. From the simulation, it was found that the proposed TWPCO scheme attained a steady state after a number of cycles. It also showed superior performance compared to other mechanisms, with a reduction in the total energy consumption of 25%. The results showed that the performance improved by 13% in terms of data gathering. Based on the results, the proposed scheme avoids the deafness that occurs in the transmit state in WSNs and increases the data collection throughout the transmission states in WSNs. [ABSTRACT FROM AUTHOR]

Node importance degree is a vital index in distribution network reconfiguration because it reflects the robustness of the network structure by evaluating node importance. Since the traditional reconfiguration ignores this index, the reconstructed network structure may be vulnerable which would reduce the security and stability of the distribution systems. This paper presents a novel reconfiguration strategy considering the node importance. The optimization objectives are the improvement of the node importance degree and the reduction of power loss. To balance the objectives, the reconfiguration mathematical model is formulated as a compound objective function with weight coefficients. Then the quantum particle swarm algorithm is employed to address this compound objective optimization problem. The strategy can model different scenarios network reconfiguration by adjusting the weight vector based on the tendencies of the utility decision maker. Illustrative examples verify the effectiveness of the proposed strategy. [ABSTRACT FROM AUTHOR]

Railway and metro transport systems (RS) are becoming one of the popular choices of transportation among people, especially those who live in urban cities. Urbanization and increasing population due to rapid development of economy in many cities are leading to a bigger demand for urban rail transit. Despite being a popular variant of Traveling Salesman Problem (TSP), it appears that the universal formula or techniques to solve the problem are yet to be found. This paper aims to develop an optimization algorithm for optimum route selection to multiple destinations in RS before returning to the starting point. Bee foraging behaviour is examined to generate a reliable algorithm in railway TSP. The algorithm is then verified by comparing the results with the exact solutions in 10 test cases, and a numerical case study is designed to demonstrate the application with large size sample. It is tested to be efficient and effective in railway route planning as the tour can be completed within a certain period of time by using minimal resources. The findings further support the reliability of the algorithm and capability to solve the problems with different complexity. This algorithm can be used as a method to assist business practitioners making better decision in route planning. [ABSTRACT FROM AUTHOR]

The detection of the singleton attractors is of great significance for the systematic study of genetic regulatory network. In this paper, we design an algorithm to compute the singleton attractors and pre-images of the strong-inhibition Boolean networks which is a biophysically plausible gene model. Our algorithm can not only identify accurately the singleton attractors, but also find easily the pre-images of the network. Based on extensive computational experiments, we show that the computational time of the algorithm is proportional to the number of the singleton attractors, which indicates the algorithm has much advantage in finding the singleton attractors for the networks with high average degree and less inhibitory interactions. Our algorithm may shed light on understanding the function and structure of the strong-inhibition Boolean networks. [ABSTRACT FROM AUTHOR]

A large-scale multiple surveillance system for infectious disease outbreaks has been in operation in England and Wales since the early 1990s. Changes to the statistical algorithm at the heart of the system were proposed and the purpose of this paper is to compare two new algorithms with the original algorithm. Test data to evaluate performance are created from weekly counts of the number of cases of each of more than 2000 diseases over a twenty-year period. The time series of each disease is separated into one series giving the baseline (background) disease incidence and a second series giving disease outbreaks. One series is shifted forward by twelve months and the two are then recombined, giving a realistic series in which it is known where outbreaks have been added. The metrics used to evaluate performance include a scoring rule that appropriately balances sensitivity against specificity and is sensitive to variation in probabilities near 1. In the context of disease surveillance, a scoring rule can be adapted to reflect the size of outbreaks and this was done. Results indicate that the two new algorithms are comparable to each other and better than the algorithm they were designed to replace. [ABSTRACT FROM AUTHOR]

Manual offline analysis, of a scanning electron microscopy (SEM) image, is a time consuming process and requires continuous human intervention and efforts. This paper presents an image processing based method for automated offline analyses of SEM images. To this end, our strategy relies on a two-stage process, viz. texture analysis and quantification. The method involves a preprocessing step, aimed at the noise removal, in order to avoid false edges. For texture analysis, the proposed method employs a state of the art Curvelet transform followed by segmentation through a combination of entropy filtering, thresholding and mathematical morphology (MM). The quantification is carried out by the application of a box-counting algorithm, for fractal dimension (FD) calculations, with the ultimate goal of measuring the parameters, like surface area and perimeter. The perimeter is estimated indirectly by counting the boundary boxes of the filled shapes. The proposed method, when applied to a representative set of SEM images, not only showed better results in image segmentation but also exhibited a good accuracy in the calculation of surface area and perimeter. The proposed method outperforms the well-known Watershed segmentation algorithm. [ABSTRACT FROM AUTHOR]

Understanding the fire prediction capabilities of fuel models is vital to forest fire management. Various fuel models have been developed in the Great Xing'an Mountains in Northeast China. However, the performances of these fuel models have not been tested for historical occurrences of wildfires. Consequently, the applicability of these models requires further investigation. Thus, this paper aims to develop standard fuel models. Seven vegetation types were combined into three fuel models according to potential fire behaviors which were clustered using Euclidean distance algorithms. Fuel model parameter sensitivity was analyzed by the Morris screening method. Results showed that the fuel model parameters 1-hour time-lag loading, dead heat content, live heat content, 1-hour time-lag SAV(Surface Area-to-Volume), live shrub SAV, and fuel bed depth have high sensitivity. Two main sensitive fuel parameters: 1-hour time-lag loading and fuel bed depth, were determined as adjustment parameters because of their high spatio-temporal variability. The FARSITE model was then used to test the fire prediction capabilities of the combined fuel models (uncalibrated fuel models). FARSITE was shown to yield an unrealistic prediction of the historical fire. However, the calibrated fuel models significantly improved the capabilities of the fuel models to predict the actual fire with an accuracy of 89%. Validation results also showed that the model can estimate the actual fires with an accuracy exceeding 56% by using the calibrated fuel models. Therefore, these fuel models can be efficiently used to calculate fire behaviors, which can be helpful in forest fire management. [ABSTRACT FROM AUTHOR]

In view of the fact that the current online virtual network embedding algorithms do not consider the fragment resources generated in the embedding process deeply enough, resulting in the problem that the acceptance ratio and the revenue to cost ratio are both low, a mathematical model for virtual network reconfiguration is constructed and a heuristic algorithm for fragment-aware virtual network reconfiguration (FA-VNR) is proposed. The FA-VNR algorithm selects the set of virtual nodes to be migrated according to the fragment degrees of the physical nodes, and selects the best virtual node migration scheme according to the reduction of the fragment degrees of the physical nodes as well as the reduction of the embedding cost of the embedded virtual networks. Extensive simulation results show that the proposed FA-VNR algorithm not only can obviously improve the acceptance ratio and the revenue to cost ratio of the current online virtual network embedding algorithm, but also has better optimization effect than the existing virtual network reconfiguration algorithm. [ABSTRACT FROM AUTHOR]

The main purpose of this study is to propose, then analyze, and later test a spectral gradient algorithm for solving a convex minimization problem. The considered problem covers the matrix ℓ2,1-norm regularized least squares which is widely used in multi-task learning for capturing the joint feature among each task. To solve the problem, we firstly minimize a quadratic approximated model of the objective function to derive a search direction at current iteration. We show that this direction descends automatically and reduces to the original spectral gradient direction if the regularized term is removed. Secondly, we incorporate a nonmonotone line search along this direction to improve the algorithm’s numerical performance. Furthermore, we show that the proposed algorithm converges to a critical point under some mild conditions. The attractive feature of the proposed algorithm is that it is easily performable and only requires the gradient of the smooth function and the objective function’s values at each and every step. Finally, we operate some experiments on synthetic data, which verifies that the proposed algorithm works quite well and performs better than the compared ones. [ABSTRACT FROM AUTHOR]

Identifying communities or clusters in networked systems has received much attention across the physical and social sciences. Most of this work focuses on single layer or one-mode networks, including social networks between people or hyperlinks between websites. Multilayer or multi-mode networks, such as affiliation networks linking people to organizations, receive much less attention in this literature. Common strategies for discovering the community structure of multi-mode networks identify the communities of each mode simultaneously. Here I show that this combined approach is ineffective at discovering community structures when there are an unequal number of communities between the modes of a multi-mode network. I propose a dual-projection alternative for detecting communities in multi-mode networks that overcomes this shortcoming. The evaluation of synthetic networks with known community structures reveals that the dual-projection approach outperforms the combined approach when there are a different number of communities in the various modes. At the same time, results show that the dual-projection approach is as effective as the combined strategy when the number of communities is the same between the modes. [ABSTRACT FROM AUTHOR]

Academic prestige is difficult to quantify in objective terms. Network theory offers the opportunity to use a mathematical formalism to model both the prestige associated with an academic and the relationships between academic colleagues. Early attempts using this line of reasoning have focused on intellectual genealogy as constituted by supervisor student networks. The process of examination is critical in many areas of study but has not played a part in existing models. A network theoretical “social” model is proposed as a tool to explore and understand the dynamics of prestige in the academic hierarchy. It is observed that such a model naturally gives rise to the idea that the prestige associated with a node in the graph (the prestige of an individual academic) can be viewed as a dynamic quantity that evolves with time based on both local and non-local changes in the properties in the network. The toy model studied here includes both supervisor-student and examiner-student relationships. This gives an insight into some of the key features of academic genealogies and naturally leads to a proposed model for “prestige propagation” on academic networks. This propagation is not solely directed forward in time (from teacher to progeny) but sometimes also flows in the other direction. As collaborators do well, this reflects well on those with whom they choose to collaborate and those that taught them. Furthermore, prestige as a quantity continues to be dynamic even after the end of a relationship or career. Given that time ordering of relationships on the network are implicit but that measures such as betweenness are independent of this implicit time dependence: the success of a PhD student later in their career can improve the prestige of their doctoral supervisor. Thus, prestige can be interpreted to have dynamics that flow both forward and backward in time. [ABSTRACT FROM AUTHOR]

Community detection algorithms have been widely used to study the organization of complex networks like the brain. These techniques provide a partition of brain regions (or nodes) into clusters (or communities), where nodes within a community are densely interconnected with one another. In their simplest application, community detection algorithms are agnostic to the presence of community hierarchies: clusters embedded within clusters of other clusters. To address this limitation, we exercise a multi-scale extension of a common community detection technique, and we apply the tool to synthetic graphs and to graphs derived from human neuroimaging data, including structural and functional imaging data. Our multi-scale community detection algorithm links a graph to copies of itself across neighboring topological scales, thereby becoming sensitive to conserved community organization across levels of the hierarchy. We demonstrate that this method is sensitive to topological inhomogeneities of the graph’s hierarchy by providing a local measure of community stability and inter-scale reliability across topological scales. We compare the brain’s structural and functional network architectures, and we demonstrate that structural graphs display a more prominent hierarchical community organization than functional graphs. Finally, we build an explicitly multimodal multiplex graph that combines both structural and functional connectivity in a single model, and we identify the topological scales where resting state functional connectivity and underlying structural connectivity show similar versus unique hierarchical community architecture. Together, our results demonstrate the advantages of the multi-scale community detection algorithm in studying hierarchical community structure in brain graphs, and they illustrate its utility in modeling multimodal neuroimaging data. [ABSTRACT FROM AUTHOR]

The cloud-based media streaming service is a promising paradigm for multimedia applications. It is attractive to media streaming service providers, who wish to deploy their media server clusters in a media cloud at reduced cost. Since the real-time live streaming service is both a bandwidth-intensive and quality-sensitive application, how to optimize the internal bandwidth utilization of a data center network (DCN) as well as guarantee the external bandwidth of the real-time live streaming application, is a key issue of deploying virtual machine (VM)-hosted media server cluster in a media cloud. Therefore, in this study, we propose an external-bandwidth-guaranteed media server cluster deployment scheme in media cloud. The approach simultaneously considers the outside bandwidth requirement of a tree-based media server cluster for live streaming and the intra-bandwidth consumption of a DCN. The proposed scheme models the optimal problem as a new terminal-Steiner-tree-like problem and provides an approximate algorithm for placing the media servers. Our evaluation results show that the proposed scheme guarantees the external bandwidth requirement of a real-time live streaming application, at the same time, greatly reduces the intra-bandwidth utilization of a media cloud with different DCN structures. [ABSTRACT FROM AUTHOR]

Many link prediction methods have been developed to infer unobserved links or predict missing links based on the observed network structure that is always incomplete and subject to interfering noise. Thus, the performance of existing methods is usually limited in that their computation depends only on input graph structures, and they do not consider external information. The effects of social influence and homophily suggest that both network structure and node attribute information should help to resolve the task of link prediction. This work proposes SASNMF, a link prediction unified framework based on non-negative matrix factorization that considers not only graph structure but also the internal and external auxiliary information, which refers to both the node attributes and the structural latent feature information extracted from the network. Furthermore, three different combinations of internal and external information are proposed and input into the framework to solve the link prediction problem. Extensive experimental results on thirteen real networks, five node attribute networks and eight non-attribute networks show that the proposed framework has competitive performance compared with benchmark methods and state-of-the-art methods, indicating the superiority of the presented algorithm. [ABSTRACT FROM AUTHOR]

Organizational processes vary. Practitioners have developed simple frameworks to differentiate them. Surprisingly, the academic literature on process management does not–it typically strives for one method to manage all processes. We draw on organizational information-processing theory to systematically develop a new, theoretically motivated classification model for organizational processes. We validate this model using survey data from 141 process practitioners of a global corporation. We derive three distinct types of processes and demonstrate that an understanding of process variety based on process dimensions can differentiate processes better than existing frameworks used in practice. Our findings can enable process managers to make informed decisions and serve as a basis for contingent process management. [ABSTRACT FROM AUTHOR]

Identifying hierarchies and rankings of nodes in directed graphs is fundamental in many applications such as social network analysis, biology, economics, and finance. A recently proposed method identifies the hierarchy by finding the ordered partition of nodes which minimises a score function, termed agony. This function penalises the links violating the hierarchy in a way depending on the strength of the violation. To investigate the resolution of ranking hierarchies we introduce an ensemble of random graphs, the Ranked Stochastic Block Model. We find that agony may fail to identify hierarchies when the structure is not strong enough and the size of the classes is small with respect to the whole network. We analytically characterise the resolution threshold and we show that an iterated version of agony can partly overcome this resolution limit. [ABSTRACT FROM AUTHOR]

For a broad range of research and practical applications it is important to understand the allegiances, communities and structure of key players in society. One promising direction towards extracting this information is to exploit the rich relational data in digital social networks (the social graph). As global social networks (e.g., Facebook and Twitter) are very large, most approaches make use of distributed computing systems for this purpose. Distributing graph processing requires solving many difficult engineering problems, which has lead some researchers to look at single-machine solutions that are faster and easier to maintain. In this article, we present an approach for analyzing full social networks on a standard laptop, allowing for interactive exploration of the communities in the locality of a set of user specified query vertices. The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates the edge weights between vertices in a derived graph. Local communities can be constructed by selecting vertices that are connected to the query vertices with high edge weights in the derived graph. This compression is robust to noise and allows for interactive queries of local communities in real-time, which we define to be less than the average human reaction time of 0.25s. We achieve single-machine real-time performance by compressing the neighborhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing. These techniques reduce query times from hours using industrial desktop machines operating on the full graph to milliseconds on standard laptops. Our method allows exploration of strongly associated regions (i.e., communities) of large graphs in real-time on a laptop. It has been deployed in software that is actively used by social network analysts and offers another channel for media owners to monetize their data, helping them to continue to provide free services that are valued by billions of people globally. [ABSTRACT FROM AUTHOR]

The ability to predict what courses a student may enroll in the coming semester plays a pivotal role in the allocation of learning resources, which is a hot topic in the domain of educational data mining. In this study, we propose an innovative approach to characterize students’ cross-college course enrollments by leveraging a novel contextual graph. Specifically, different kinds of variables, such as students, courses, colleges and diplomas, as well as various types of variable relations, are utilized to depict the context of each variable, and then a representation learning algorithm node2vec is applied to extracting sophisticated graph-based features for the enrollment analysis. In this manner, the relations between any pair of variables can be measured quantitatively, which enables the variable type to transform from nominal to ratio. These graph-based features are examined by the random forest algorithm, and experiments on 24,663 students, 1,674 courses and 417,590 enrollment records demonstrate that the contextual graph can successfully improve analyzing the cross-college course enrollments, where three of the graph-based features have significantly stronger impacts on prediction accuracy than the others. Besides, the empirical results also indicate that the student’s course preference is the most important factor in predicting future course enrollments, which is consistent to the previous studies that acknowledge the course interest is a key point for course recommendations. [ABSTRACT FROM AUTHOR]

Network propagation is an important and widely used algorithm in systems biology, with applications in protein function prediction, disease gene prioritization, and patient stratification. However, up to this point it has required significant expertise to run. Here we extend the popular network analysis program Cytoscape to perform network propagation as an integrated function. Such integration greatly increases the access to network propagation by putting it in the hands of biologists and linking it to the many other types of network analysis and visualization available through Cytoscape. We demonstrate the power and utility of the algorithm by identifying mutations conferring resistance to Vemurafenib. [ABSTRACT FROM AUTHOR]

High dimensional data are commonly encountered in various scientific fields and pose great challenges to modern statistical analysis. To address this issue different penalized regression procedures have been introduced in the litrature, but these methods cannot cope with the problem of outliers and leverage points in the heavy tailed high dimensional data. For this purppose, a new Robust Adaptive Lasso (RAL) method is proposed which is based on pearson residuals weighting scheme. The weight function determines the compatibility of each observations and downweight it if they are inconsistent with the assumed model. It is observed that RAL estimator can correctly select the covariates with non-zero coefficients and can estimate parameters, simultaneously, not only in the presence of influential observations, but also in the presence of high multicolliearity. We also discuss the model selection oracle property and the asymptotic normality of the RAL. Simulations findings and real data examples also demonstrate the better performance of the proposed penalized regression approach. [ABSTRACT FROM AUTHOR]

Sparse coding performs well in image classification. However, robust target recognition requires a lot of comprehensive template images and the sparse learning process is complex. We incorporate sparsity into a template matching concept to construct a local sparse structure matching (LSSM) model for general infrared target recognition. A local structure preserving sparse coding (LSPSc) formulation is proposed to simultaneously preserve the local sparse and structural information of objects. By adding a spatial local structure constraint into the classical sparse coding algorithm, LSPSc can improve the stability of sparse representation for targets and inhibit background interference in infrared images. Furthermore, a kernel LSPSc (K-LSPSc) formulation is proposed, which extends LSPSc to the kernel space to weaken the influence of the linear structure constraint in nonlinear natural data. Because of the anti-interference and fault-tolerant capabilities, both LSPSc- and K-LSPSc-based LSSM can implement target identification based on a simple template set, which just needs several images containing enough local sparse structures to learn a sufficient sparse structure dictionary of a target class. Specifically, this LSSM approach has stable performance in the target detection with scene, shape and occlusions variations. High performance is demonstrated on several datasets, indicating robust infrared target recognition in diverse environments and imaging conditions. [ABSTRACT FROM AUTHOR]

Inferring epidemiological parameters such as the R0 from time-scaled phylogenies is a timely challenge. Most current approaches rely on likelihood functions, which raise specific issues that range from computing these functions to finding their maxima numerically. Here, we present a new regression-based Approximate Bayesian Computation (ABC) approach, which we base on a large variety of summary statistics intended to capture the information contained in the phylogeny and its corresponding lineage-through-time plot. The regression step involves the Least Absolute Shrinkage and Selection Operator (LASSO) method, which is a robust machine learning technique. It allows us to readily deal with the large number of summary statistics, while avoiding resorting to Markov Chain Monte Carlo (MCMC) techniques. To compare our approach to existing ones, we simulated target trees under a variety of epidemiological models and settings, and inferred parameters of interest using the same priors. We found that, for large phylogenies, the accuracy of our regression-ABC is comparable to that of likelihood-based approaches involving birth-death processes implemented in BEAST2. Our approach even outperformed these when inferring the host population size with a Susceptible-Infected-Removed epidemiological model. It also clearly outperformed a recent kernel-ABC approach when assuming a Susceptible-Infected epidemiological model with two host types. Lastly, by re-analyzing data from the early stages of the recent Ebola epidemic in Sierra Leone, we showed that regression-ABC provides more realistic estimates for the duration parameters (latency and infectiousness) than the likelihood-based method. Overall, ABC based on a large variety of summary statistics and a regression method able to perform variable selection and avoid overfitting is a promising approach to analyze large phylogenies. [ABSTRACT FROM AUTHOR]

We consider a dynamical model of distress propagation on complex networks, which we apply to the study of financial contagion in networks of banks connected to each other by direct exposures. The model that we consider is an extension of the DebtRank algorithm, recently introduced in the literature. The mechanics of distress propagation is very simple: When a bank suffers a loss, distress propagates to its creditors, who in turn suffer losses, and so on. The original DebtRank assumes that losses are propagated linearly between connected banks. Here we relax this assumption and introduce a one-parameter family of non-linear propagation functions. As a case study, we apply this algorithm to a data-set of 183 European banks, and we study how the stability of the system depends on the non-linearity parameter under different stress-test scenarios. We find that the system is characterized by a transition between a regime where small shocks can be amplified and a regime where shocks do not propagate, and that the overall stability of the system increases between 2008 and 2013. [ABSTRACT FROM AUTHOR]

Considering the roles of protein complexes in many biological processes in the cell, detection of protein complexes from available protein-protein interaction (PPI) networks is a key challenge in the post genome era. Despite high dynamicity of cellular systems and dynamic interaction between proteins in a cell, most computational methods have focused on static networks which cannot represent the inherent dynamicity of protein interactions. Recently, some researchers try to exploit the dynamicity of PPI networks by constructing a set of dynamic PPI subnetworks correspondent to each time-point (column) in a gene expression data. However, many genes can participate in multiple biological processes and cellular processes are not necessarily related to every sample, but they might be relevant only for a subset of samples. So, it is more interesting to explore each subnetwork based on a subset of genes and conditions (i.e., biclusters) in a gene expression data. Here, we present a new method, called BiCAMWI to employ dynamicity in detecting protein complexes. The preprocessing phase of the proposed method is based on a novel genetic algorithm that extracts some sets of genes that are co-regulated under some conditions from input gene expression data. Each extracted gene set is called bicluster. In the detection phase of the proposed method, then, based on the biclusters, some dynamic PPI subnetworks are extracted from input static PPI network. Protein complexes are identified by applying a detection method on each dynamic PPI subnetwork and aggregating the results. Experimental results confirm that BiCAMWI effectively models the dynamicity inherent in static PPI networks and achieves significantly better results than state-of-the-art methods. So, we suggest BiCAMWI as a more reliable method for protein complex detection. [ABSTRACT FROM AUTHOR]

Exploration and exploitation are two essential components for any optimization algorithm. Much exploration leads to oscillation and premature convergence while too much exploitation slows down the optimization algorithm and the optimizer may be stuck in local minima. Therefore, balancing the rates of exploration and exploitation at the optimization lifetime is a challenge. This study evaluates the impact of using chaos-based control of exploration/exploitation rates against using the systematic native control. Three modern algorithms were used in the study namely grey wolf optimizer (GWO), antlion optimizer (ALO) and moth-flame optimizer (MFO) in the domain of machine learning for feature selection. Results on a set of standard machine learning data using a set of assessment indicators prove advance in optimization algorithm performance when using variational repeated periods of declined exploration rates over using systematically decreased exploration rates. [ABSTRACT FROM AUTHOR]

Navigability, an ability to find a logarithmically short path between elements using only local information, is one of the most fascinating properties of real-life networks. However, the exact mechanism responsible for the formation of navigation properties remained unknown. We show that navigability can be achieved by using only two ingredients present in the majority of networks: network growth and local homophily, giving a persuasive answer how the navigation appears in real-life networks. A very simple algorithm produces hierarchical self-similar optimally wired navigable small world networks with exponential degree distribution by using only local information. Adding preferential attachment produces a scale-free network which has shorter greedy paths, but worse (power law) scaling of the information extraction locality (algorithmic complexity of a search). Introducing saturation of the preferential attachment leads to truncated scale-free degree distribution that offers a good tradeoff between these parameters and can be useful for practical applications. Several features of the model are observed in real-life networks, in particular in the brain neural networks, supporting the earlier suggestions that they are navigable. [ABSTRACT FROM AUTHOR]

The General Unified Threshold model of Survival (GUTS) provides a consistent mathematical framework for survival analysis. However, the calibration of GUTS models is computationally challenging. We present a novel algorithm and its fast implementation in our R package, GUTS, that help to overcome these challenges. We show a step-by-step application example consisting of model calibration and uncertainty estimation as well as making probabilistic predictions and validating the model with new data. Using self-defined wrapper functions, we show how to produce informative text printouts and plots without effort, for the inexperienced as well as the advanced user. The complete ready-to-run script is available as supplemental material. We expect that our software facilitates novel re-analysis of existing survival data as well as asking new research questions in a wide range of sciences. In particular the ability to quickly quantify stressor thresholds in conjunction with dynamic compensating processes, and their uncertainty, is an improvement that complements current survival analysis methods. [ABSTRACT FROM AUTHOR]

The article raised a user-friendly interactive approach-Attraction Propagation (AP) in segmentation of colorectal polyps. Compared with other interactive approaches, the AP relied on only one foreground seed to get different shapes of polyps, and it can be compatible with pre-processing stage of Computer-Aided Diagnosis (CAD) under the systematically procedure of Optical Colonoscopy (OC). The experimental design was based on challenging distinct datasets that totally includes 1691 OC images, and the results demonstrated that no matter in accuracy or calculating speed, the AP performed better than the state-of-the-art. [ABSTRACT FROM AUTHOR]

Thanks to the proliferation of online social networks, it has become conventional for researchers to communicate and collaborate with each other. Meanwhile, one critical challenge arises, that is, how to find the most relevant and potential collaborators for each researcher? In this work, we propose a novel collaborator recommendation model called CCRec, which combines the information on researchers’ publications and collaboration network to generate better recommendation. In order to effectively identify the most potential collaborators for researchers, we adopt a topic clustering model to identify the academic domains, as well as a random walk model to compute researchers’ feature vectors. Using DBLP datasets, we conduct benchmarking experiments to examine the performance of CCRec. The experimental results show that CCRec outperforms other state-of-the-art methods in terms of precision, recall and F1 score. [ABSTRACT FROM AUTHOR]

We present the software library marathon, which is designed to support the analysis of sampling algorithms that are based on the Markov-Chain Monte Carlo principle. The main application of this library is the computation of properties of so-called state graphs, which represent the structure of Markov chains. We demonstrate applications and the usefulness of marathon by investigating the quality of several bounding methods on four well-known Markov chains for sampling perfect matchings and bipartite graphs. In a set of experiments, we compute the total mixing time and several of its bounds for a large number of input instances. We find that the upper bound gained by the famous canonical path method is often several magnitudes larger than the total mixing time and deteriorates with growing input size. In contrast, the spectral bound is found to be a precise approximation of the total mixing time. [ABSTRACT FROM AUTHOR]

As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. In order to build accurate large-scale models of subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature will be essential. In the current work, we present a multi-scale utility called LipidWrapper capable of creating curved membrane models with geometries derived from various sources, both experimental and theoretical. To demonstrate its utility, we use LipidWrapper to examine an important mechanism of influenza virulence. A copy of the program can be downloaded free of charge under the terms of the open-source FreeBSD License from http://nbcr.ucsd.edu/lipidwrapper. LipidWrapper has been tested on all major computer operating systems. [ABSTRACT FROM AUTHOR]