Cost-effective upgrade of WDM all-optical networks using overlay fibres and hop reduction links

Fibre overlay is a cost-effective technique to alleviate wavelength blocking in some links of a wavelength-routed optical network by increasing the number of wavelengths in those links. In this letter, we investigate the effects of overlaying fibre in an all-optical network (AON) based on GÉANT2 topology. The constraint-based routing and wavelength assignment (CB-RWA) algorithm locates where cost-efficient upgrades should be implemented. Through numerical examples, we demonstrate that the network capacity improves by 25 per cent by overlaying fibre on 10 per cent of the links, and by 12 per cent by providing hop reduction links comprising 2 per cent of the links. For the upgraded network, we also show the impact of dynamic traffic allocation on the blocking probability. Copyright © 2010 John Wiley & Sons, Ltd.

Energy Aware Cluster-based Multihop Routing Protocol for Sensor Networks

Clustering combined with multihop communication is a promising solution to cope with the energy requirements of large scale Wireless Sensor Networks. In this work, a new cluster based routing protocol referred to as Energy Aware Cluster-based Multihop (EACM) Routing Protocol is introduced, with multihop communication between cluster heads for transmitting messages to the base station and direct communication within clusters. We propose EACM with both static and dynamic clustering. The network is partitioned into near optimal load balanced clusters by using a voting technique, which ensures that the suitability of a node to become a cluster head is determined by all its neighbors. Results show that the new protocol performs better than LEACH on network lifetime and energy dissipation

Multipath policy routing in packet switched networks

Dissertação apresentada para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Mean Squared Residue Based Biclustering Algorithms for the Analysis of Gene Expression Data

Computational Biology is the research are that contributes to the analysis of biological data through the development of algorithms which will address significant research problems.The data from molecular biology includes DNA,RNA ,Protein and Gene expression data.Gene Expression Data provides the expression level of genes under different conditions.Gene expression is the process of transcribing the DNA sequence of a gene into mRNA sequences which in turn are later translated into proteins.The number of copies of mRNA produced is called the expression level of a gene.Gene expression data is organized in the form of a matrix. Rows in the matrix represent genes and columns in the matrix represent experimental conditions.Experimental conditions can be different tissue types or time points.Entries in the gene expression matrix are real values.Through the analysis of gene expression data it is possible to determine the behavioral patterns of genes such as similarity of their behavior,nature of their interaction,their respective contribution to the same pathways and so on. Similar expression patterns are exhibited by the genes participating in the same biological process.These patterns have immense relevance and application in bioinformatics and clinical research.Theses patterns are used in the medical domain for aid in more accurate diagnosis,prognosis,treatment planning.drug discovery and protein network analysis.To identify various patterns from gene expression data,data mining techniques are essential.Clustering is an important data mining technique for the analysis of gene expression data.To overcome the problems associated with clustering,biclustering is introduced.Biclustering refers to simultaneous clustering of both rows and columns of a data matrix. Clustering is a global whereas biclustering is a local model.Discovering local expression patterns is essential for identfying many genetic pathways that are not apparent otherwise.It is therefore necessary to move beyond the clustering paradigm towards developing approaches which are capable of discovering local patterns in gene expression data.A biclusters is a submatrix of the gene expression data matrix.The rows and columns in the submatrix need not be contiguous as in the gene expression data matrix.Biclusters are not disjoint.Computation of biclusters is costly because one will have to consider all the combinations of columans and rows in order to find out all the biclusters.The search space for the biclustering problem is 2 m+n where m and n are the number of genes and conditions respectively.Usually m+n is more than 3000.The biclustering problem is NP-hard.Biclustering is a powerful analytical tool for the biologist.The research reported in this thesis addresses the problem of biclustering.Ten algorithms are developed for the identification of coherent biclusters from gene expression data.All these algorithms are making use of a measure called mean squared residue to search for biclusters.The objective here is to identify the biclusters of maximum size with the mean squared residue lower than a given threshold. All these algorithms begin the search from tightly coregulated submatrices called the seeds.These seeds are generated by K-Means clustering algorithm.The algorithms developed can be classified as constraint based,greedy and metaheuristic.Constarint based algorithms uses one or more of the various constaints namely the MSR threshold and the MSR difference threshold.The greedy approach makes a locally optimal choice at each stage with the objective of finding the global optimum.In metaheuristic approaches particle Swarm Optimization(PSO) and variants of Greedy Randomized Adaptive Search Procedure(GRASP) are used for the identification of biclusters.These algorithms are implemented on the Yeast and Lymphoma datasets.Biologically relevant and statistically significant biclusters are identified by all these algorithms which are validated by Gene Ontology database.All these algorithms are compared with some other biclustering algorithms.Algorithms developed in this work overcome some of the problems associated with the already existing algorithms.With the help of some of the algorithms which are developed in this work biclusters with very high row variance,which is higher than the row variance of any other algorithm using mean squared residue, are identified from both Yeast and Lymphoma data sets.Such biclusters which make significant change in the expression level are highly relevant biologically.

Performance evaluation of routing protocols for MANETs with known connectivity patterns using evolving graphs

The assessment of routing protocols for mobile wireless networks is a difficult task, because of the networks` dynamic behavior and the absence of benchmarks. However, some of these networks, such as intermittent wireless sensors networks, periodic or cyclic networks, and some delay tolerant networks (DTNs), have more predictable dynamics, as the temporal variations in the network topology can be considered as deterministic, which may make them easier to study. Recently, a graph theoretic model-the evolving graphs-was proposed to help capture the dynamic behavior of such networks, in view of the construction of least cost routing and other algorithms. The algorithms and insights obtained through this model are theoretically very efficient and intriguing. However, there is no study about the use of such theoretical results into practical situations. Therefore, the objective of our work is to analyze the applicability of the evolving graph theory in the construction of efficient routing protocols in realistic scenarios. In this paper, we use the NS2 network simulator to first implement an evolving graph based routing protocol, and then to use it as a benchmark when comparing the four major ad hoc routing protocols (AODV, DSR, OLSR and DSDV). Interestingly, our experiments show that evolving graphs have the potential to be an effective and powerful tool in the development and analysis of algorithms for dynamic networks, with predictable dynamics at least. In order to make this model widely applicable, however, some practical issues still have to be addressed and incorporated into the model, like adaptive algorithms. We also discuss such issues in this paper, as a result of our experience.

Improving availability of mobile networks using a cluster routing protocol with redundant cluster head

We show a cluster based routing protocol in order to improve the convergence of the clusters and of the network it is proposed to use a backup cluster head. The use of a event discrete simulator is used for the implementation and the simulation of a hierarchical routing protocol called the Backup Cluster Head Protocol (BCHP). Finally it is shown that the BCHP protocol improves the convergence and availability of the network through a comparative analysis with the Ad Hoc On Demand Distance Vector (AODV)[1] routing protocol and Cluster Based Routing Protocol (CBRP)[2]

The Balanced Cross-Layer Design Routing Algorithm in Wireless Sensor Networks Using Fuzzy Logic

Recently, the cross-layer design for the wireless sensor network communication protocol has become more and more important and popular. Considering the disadvantages of the traditional cross-layer routing algorithms, in this paper we propose a new fuzzy logic-based routing algorithm, named the Balanced Cross-layer Fuzzy Logic (BCFL) routing algorithm. In BCFL, we use the cross-layer parameters’ dispersion as the fuzzy logic inference system inputs. Moreover, we give each cross-layer parameter a dynamic weight according the value of the dispersion. For getting a balanced solution, the parameter whose dispersion is large will have small weight, and vice versa. In order to compare it with the traditional cross-layer routing algorithms, BCFL is evaluated through extensive simulations. The simulation results show that the new routing algorithm can handle the multiple constraints without increasing the complexity of the algorithm and can achieve the most balanced performance on selecting the next hop relay node. Moreover, the Balanced Cross-layer Fuzzy Logic routing algorithm can adapt to the dynamic changing of the network conditions and topology effectively.

A Survey on Underwater Acoustic Sensor Network Routing Protocols

Underwater acoustic sensor networks (UASNs) have become more and more important in ocean exploration applications, such as ocean monitoring, pollution detection, ocean resource management, underwater device maintenance, etc. In underwater acoustic sensor networks, since the routing protocol guarantees reliable and effective data transmission from the source node to the destination node, routing protocol design is an attractive topic for researchers. There are many routing algorithms have been proposed in recent years. To present the current state of development of UASN routing protocols, we review herein the UASN routing protocol designs reported in recent years. In this paper, all the routing protocols have been classified into different groups according to their characteristics and routing algorithms, such as the non-cross-layer design routing protocol, the traditional cross-layer design routing protocol, and the intelligent algorithm based routing protocol. This is also the first paper that introduces intelligent algorithm-based UASN routing protocols. In addition, in this paper, we investigate the development trends of UASN routing protocols, which can provide researchers with clear and direct insights for further research.

Location management and routing in urban vehicular ad hoc networks

In recent years, urban vehicular ad hoc networks (VANETs) are gaining importance for inter-vehicle communication, because they allow for the local communication between vehicles without any infrastructure, configuration effort, and without expensive cellular networks. But such architecture may increase the complexity of routing since there is no central control system in urban VANETs. Therefore, a challenging research task is to improve urban VANETs' routing efficiency. ^ Hence, in this dissertation we propose two location-based routing protocols and a location management protocol to facilitate location-based routing in urban VANETs. The Multi-hop Routing Protocol (MURU) is proposed to make use of predicted mobility and geometry map in urban VANETs to estimate a path's life time and set up robust end-to-end routing paths. The Light-weight Routing Protocol (LIRU) is proposed to take advantage of the node diversity under dynamic channel condition to exploit opportunistic forwarding to achieve efficient data delivery. A scalable location management protocol (MALM) is also proposed to support location-based routing protocols in urban VANETs. MALM uses high mobility in VANETs to help disseminate vehicles' historical location information, and a vehicle is able to implement Kalman-filter based predicted to predict another vehicle's current location based on its historical location information. ^

Impact of node mobility in user-centric routing

Recent paradigms in wireless communication architectures describe environments where nodes present a highly dynamic behavior (e.g., User Centric Networks). In such environments, routing is still performed based on the regular packet-switched behavior of store-and-forward. Albeit sufficient to compute at least an adequate path between a source and a destination, such routing behavior cannot adequately sustain the highly nomadic lifestyle that Internet users are today experiencing. This thesis aims to analyse the impact of the nodes’ mobility on routing scenarios. It also aims at the development of forwarding concepts that help in message forwarding across graphs where nodes exhibit human mobility patterns, as is the case of most of the user-centric wireless networks today. The first part of the work involved the analysis of the mobility impact on routing, and we found that node mobility significance can affect routing performance, and it depends on the link length, distance, and mobility patterns of nodes. The study of current mobility parameters showed that they capture mobility partially. The routing protocol robustness to node mobility depends on the routing metric sensitivity to node mobility. As such, mobility-aware routing metrics were devised to increase routing robustness to node mobility. Two categories of routing metrics proposed are the time-based and spatial correlation-based. For the validation of the metrics, several mobility models were used, which include the ones that mimic human mobility patterns. The metrics were implemented using the Network Simulator tool using two widely used multi-hop routing protocols of Optimized Link State Routing (OLSR) and Ad hoc On Demand Distance Vector (AODV). Using the proposed metrics, we reduced the path re-computation frequency compared to the benchmark metric. This means that more stable nodes were used to route data. The time-based routing metrics generally performed well across the different node mobility scenarios used. We also noted a variation on the performance of the metrics, including the benchmark metric, under different mobility models, due to the differences in the node mobility governing rules of the models.

Training control centers' operators in incident diagnosis and power restoration using intelligent tutoring systems

The activity of Control Center operators is important to guarantee the effective performance of Power Systems. Operators’ actions are crucial to deal with incidents, especially severe faults like blackouts. In this paper, we present an Intelligent Tutoring approach for training Portuguese Control Center operators in tasks like incident analysis and diagnosis, and service restoration of Power Systems. Intelligent Tutoring System (ITS) approach is used in the training of the operators, having into account context awareness and the unobtrusive integration in the working environment. Several Artificial Intelligence techniques were criteriously used and combined together to obtain an effective Intelligent Tutoring environment, namely Multiagent Systems, Neural Networks, Constraint-based Modeling, Intelligent Planning, Knowledge Representation, Expert Systems, User Modeling, and Intelligent User Interfaces.

Algorithms and tools for in silico design of cell factories

PhD thesis in Bioengineering

Algorithms and computational tools for metabolic flux analysis

PhD thesis in Biomedical Engineering

A critical evaluation of methods for the reconstruction of tissue-specific models

Under the framework of constraint based modeling, genome-scale metabolic models (GSMMs) have been used for several tasks, such as metabolic engineering and phenotype prediction. More recently, their application in health related research has spanned drug discovery, biomarker identification and host-pathogen interactions, targeting diseases such as cancer, Alzheimer, obesity or diabetes. In the last years, the development of novel techniques for genome sequencing and other high-throughput methods, together with advances in Bioinformatics, allowed the reconstruction of GSMMs for human cells. Considering the diversity of cell types and tissues present in the human body, it is imperative to develop tissue-specific metabolic models. Methods to automatically generate these models, based on generic human metabolic models and a plethora of omics data, have been proposed. However, their results have not yet been adequately and critically evaluated and compared. This work presents a survey of the most important tissue or cell type specific metabolic model reconstruction methods, which use literature, transcriptomics, proteomics and metabolomics data, together with a global template model. As a case study, we analyzed the consistency between several omics data sources and reconstructed distinct metabolic models of hepatocytes using different methods and data sources as inputs. The results show that omics data sources have a poor overlapping and, in some cases, are even contradictory. Additionally, the hepatocyte metabolic models generated are in many cases not able to perform metabolic functions known to be present in the liver tissue. We conclude that reliable methods for a priori omics data integration are required to support the reconstruction of complex models of human cells.