A hybrid genetic algorithm for the optimal constrained web service selection problem in web service composition

Web service composition is an important problem in web service based systems. It is about how to build a new value-added web service using existing web services. A web service may have many implementations, all of which have the same functionality, but may have different QoS values. Thus, a significant research problem in web service composition is how to select a web service implementation for each of the web services such that the composite web service gives the best overall performance. This is so-called optimal web service selection problem. There may be mutual constraints between some web service implementations. Sometimes when an implementation is selected for one web service, a particular implementation for another web service must be selected. This is so called dependency constraint. Sometimes when an implementation for one web service is selected, a set of implementations for another web service must be excluded in the web service composition. This is so called conflict constraint. Thus, the optimal web service selection is a typical constrained ombinatorial optimization problem from the computational point of view. This paper proposes a new hybrid genetic algorithm for the optimal web service selection problem. The hybrid genetic algorithm has been implemented and evaluated. The evaluation results have shown that the hybrid genetic algorithm outperforms other two existing genetic algorithms when the number of web services and the number of constraints are large.

A grouping model for distributed pipeline assets maintenance decision

Distributed pipeline assets systems are crucial to society. The deterioration of these assets and the optimal allocation of limited budget for their maintenance correspond to crucial challenges for water utility managers. Decision makers should be assisted with optimal solutions to select the best maintenance plan concerning available resources and management strategies. Much research effort has been dedicated to the development of optimal strategies for maintenance of water pipes. Most of the maintenance strategies are intended for scheduling individual water pipe. Consideration of optimal group scheduling replacement jobs for groups of pipes or other linear assets has so far not received much attention in literature. It is a common practice that replacement planners select two or three pipes manually with ambiguous criteria to group into one replacement job. This is obviously not the best solution for job grouping and may not be cost effective, especially when total cost can be up to multiple million dollars. In this paper, an optimal group scheduling scheme with three decision criteria for distributed pipeline assets maintenance decision is proposed. A Maintenance Grouping Optimization (MGO) model with multiple criteria is developed. An immediate challenge of such modeling is to deal with scalability of vast combinatorial solution space. To address this issue, a modified genetic algorithm is developed together with a Judgment Matrix. This Judgment Matrix is corresponding to various combinations of pipe replacement schedules. An industrial case study based on a section of a real water distribution network was conducted to test the new model. The results of the case study show that new schedule generated a significant cost reduction compared with the schedule without grouping pipes.

Natural and engineered kallikrein inhibitors: an emerging pharmacopoeia

The kallikreins and kallikrein-related peptidases are serine proteases that control a plethora of developmental and homeostatic phenomena, ranging from semen liquefaction to skin desquamation and blood pressure. The diversity of roles played by kallikreins has stimulated considerable interest in these enzymes from the perspective of diagnostics and drug design. Kallikreins already have well-established credentials as targets for therapeutic intervention and there is increasing appreciation of their potential both as biomarkers and as targets for inhibitor design. Here, we explore the current status of naturally occurring kallikrein protease-inhibitor complexes and illustrate how this knowledge can interface with strategies for rational re-engineering of bioscaffolds and design of small-molecule inhibitors.

Shifting : one-inclusion mistake bounds and sample compression

We present new expected risk bounds for binary and multiclass prediction, and resolve several recent conjectures on sample compressibility due to Kuzmin and Warmuth. By exploiting the combinatorial structure of concept class F, Haussler et al. achieved a VC(F)/n bound for the natural one-inclusion prediction strategy. The key step in their proof is a d = VC(F) bound on the graph density of a subgraph of the hypercube—oneinclusion graph. The first main result of this paper is a density bound of n [n−1 <=d-1]/[n <=d] < d, which positively resolves a conjecture of Kuzmin and Warmuth relating to their unlabeled Peeling compression scheme and also leads to an improved one-inclusion mistake bound. The proof uses a new form of VC-invariant shifting and a group-theoretic symmetrization. Our second main result is an algebraic topological property of maximum classes of VC-dimension d as being d contractible simplicial complexes, extending the well-known characterization that d = 1 maximum classes are trees. We negatively resolve a minimum degree conjecture of Kuzmin and Warmuth—the second part to a conjectured proof of correctness for Peeling—that every class has one-inclusion minimum degree at most its VCdimension. Our final main result is a k-class analogue of the d/n mistake bound, replacing the VC-dimension by the Pollard pseudo-dimension and the one-inclusion strategy by its natural hypergraph generalization. This result improves on known PAC-based expected risk bounds by a factor of O(logn) and is shown to be optimal up to an O(logk) factor. The combinatorial technique of shifting takes a central role in understanding the one-inclusion (hyper)graph and is a running theme throughout.

Shifting : one-inclusion mistake bounds and sample compression

We present new expected risk bounds for binary and multiclass prediction, and resolve several recent conjectures on sample compressibility due to Kuzmin and Warmuth. By exploiting the combinatorial structure of concept class F, Haussler et al. achieved a VC(F)/n bound for the natural one-inclusion prediction strategy. The key step in their proof is a d=VC(F) bound on the graph density of a subgraph of the hypercube—one-inclusion graph. The first main result of this report is a density bound of n∙choose(n-1,≤d-1)/choose(n,≤d) < d, which positively resolves a conjecture of Kuzmin and Warmuth relating to their unlabeled Peeling compression scheme and also leads to an improved one-inclusion mistake bound. The proof uses a new form of VC-invariant shifting and a group-theoretic symmetrization. Our second main result is an algebraic topological property of maximum classes of VC-dimension d as being d-contractible simplicial complexes, extending the well-known characterization that d=1 maximum classes are trees. We negatively resolve a minimum degree conjecture of Kuzmin and Warmuth—the second part to a conjectured proof of correctness for Peeling—that every class has one-inclusion minimum degree at most its VC-dimension. Our final main result is a k-class analogue of the d/n mistake bound, replacing the VC-dimension by the Pollard pseudo-dimension and the one-inclusion strategy by its natural hypergraph generalization. This result improves on known PAC-based expected risk bounds by a factor of O(log n) and is shown to be optimal up to a O(log k) factor. The combinatorial technique of shifting takes a central role in understanding the one-inclusion (hyper)graph and is a running theme throughout

Classification of packet contents for malware detection

Many existing schemes for malware detection are signature-based. Although they can effectively detect known malwares, they cannot detect variants of known malwares or new ones. Most network servers do not expect executable code in their in-bound network traffic, such as on-line shopping malls, Picasa, Youtube, Blogger, etc. Therefore, such network applications can be protected from malware infection by monitoring their ports to see if incoming packets contain any executable contents. This paper proposes a content-classification scheme that identifies executable content in incoming packets. The proposed scheme analyzes the packet payload in two steps. It first analyzes the packet payload to see if it contains multimedia-type data (such as . If not, then it classifies the payload either as text-type (such as or executable. Although in our experiments the proposed scheme shows a low rate of false negatives and positives (4.69% and 2.53%, respectively), the presence of inaccuracies still requires further inspection to efficiently detect the occurrence of malware. In this paper, we also propose simple statistical and combinatorial analysis to deal with false positives and negatives.

Comparative Studies Simplified in GPFlow

We present a novel, web-accessible scientific workflow system which makes large-scale comparative studies accessible without programming or excessive configuration requirements. GPFlow allows a workflow defined on single input values to be automatically lifted to operate over collections of input values and supports the formation and processing of collections of values without the need for explicit iteration constructs. We introduce a new model for collection processing based on key aggregation and slicing which guarantees processing integrity and facilitates automatic association of inputs, allowing scientific users to manage the combinatorial explosion of data values inherent in large scale comparative studies. The approach is demonstrated using a core task from comparative genomics, and builds upon our previous work in supporting combined interactive and batch operation, through a lightweight web-based user interface.

Rational design of serine protease inhibitors

Proteases regulate a spectrum of diverse physiological processes, and dysregulation of proteolytic activity drives a plethora of pathological conditions. Understanding protease function is essential to appreciating many aspects of normal physiology and progression of disease. Consequently, development of potent and specific inhibitors of proteolytic enzymes is vital to provide tools for the dissection of protease function in biological systems and for the treatment of diseases linked to aberrant proteolytic activity. The studies in this thesis describe the rational design of potent inhibitors of three proteases that are implicated in disease development. Additionally, key features of the interaction of proteases and their cognate inhibitors or substrates are analysed and a series of rational inhibitor design principles are expounded and tested. Rational design of protease inhibitors relies on a comprehensive understanding of protease structure and biochemistry. Analysis of known protease cleavage sites in proteins and peptides is a commonly used source of such information. However, model peptide substrate and protein sequences have widely differing levels of backbone constraint and hence can adopt highly divergent structures when binding to a protease’s active site. This may result in identical sequences in peptides and proteins having different conformations and diverse spatial distribution of amino acid functionalities. Regardless of this, protein and peptide cleavage sites are often regarded as being equivalent. One of the key findings in the following studies is a definitive demonstration of the lack of equivalence between these two classes of substrate and invalidation of the common practice of using the sequences of model peptide substrates to predict cleavage of proteins in vivo. Another important feature for protease substrate recognition is subsite cooperativity. This type of cooperativity is commonly referred to as protease or substrate binding subsite cooperativity and is distinct from allosteric cooperativity, where binding of a molecule distant from the protease active site affects the binding affinity of a substrate. Subsite cooperativity may be intramolecular where neighbouring residues in substrates are interacting, affecting the scissile bond’s susceptibility to protease cleavage. Subsite cooperativity can also be intermolecular where a particular residue’s contribution to binding affinity changes depending on the identity of neighbouring amino acids. Although numerous studies have identified subsite cooperativity effects, these findings are frequently ignored in investigations probing subsite selectivity by screening against diverse combinatorial libraries of peptides (positional scanning synthetic combinatorial library; PS-SCL). This strategy for determining cleavage specificity relies on the averaged rates of hydrolysis for an uncharacterised ensemble of peptide sequences, as opposed to the defined rate of hydrolysis of a known specific substrate. Further, since PS-SCL screens probe the preference of the various protease subsites independently, this method is inherently unable to detect subsite cooperativity. However, mean hydrolysis rates from PS-SCL screens are often interpreted as being comparable to those produced by single peptide cleavages. Before this study no large systematic evaluation had been made to determine the level of correlation between protease selectivity as predicted by screening against a library of combinatorial peptides and cleavage of individual peptides. This subject is specifically explored in the studies described here. In order to establish whether PS-SCL screens could accurately determine the substrate preferences of proteases, a systematic comparison of data from PS-SCLs with libraries containing individually synthesised peptides (sparse matrix library; SML) was carried out. These SML libraries were designed to include all possible sequence combinations of the residues that were suggested to be preferred by a protease using the PS-SCL method. SML screening against the three serine proteases kallikrein 4 (KLK4), kallikrein 14 (KLK14) and plasmin revealed highly preferred peptide substrates that could not have been deduced by PS-SCL screening alone. Comparing protease subsite preference profiles from screens of the two types of peptide libraries showed that the most preferred substrates were not detected by PS SCL screening as a consequence of intermolecular cooperativity being negated by the very nature of PS SCL screening. Sequences that are highly favoured as result of intermolecular cooperativity achieve optimal protease subsite occupancy, and thereby interact with very specific determinants of the protease. Identifying these substrate sequences is important since they may be used to produce potent and selective inhibitors of protolytic enzymes. This study found that highly favoured substrate sequences that relied on intermolecular cooperativity allowed for the production of potent inhibitors of KLK4, KLK14 and plasmin. Peptide aldehydes based on preferred plasmin sequences produced high affinity transition state analogue inhibitors for this protease. The most potent of these maintained specificity over plasma kallikrein (known to have a very similar substrate preference to plasmin). Furthermore, the efficiency of this inhibitor in blocking fibrinolysis in vitro was comparable to aprotinin, which previously saw clinical use to reduce perioperative bleeding. One substrate sequence particularly favoured by KLK4 was substituted into the 14 amino acid, circular sunflower trypsin inhibitor (SFTI). This resulted in a highly potent and selective inhibitor (SFTI-FCQR) which attenuated protease activated receptor signalling by KLK4 in vitro. Moreover, SFTI-FCQR and paclitaxel synergistically reduced growth of ovarian cancer cells in vitro, making this inhibitor a lead compound for further therapeutic development. Similar incorporation of a preferred KLK14 amino acid sequence into the SFTI scaffold produced a potent inhibitor for this protease. However, the conformationally constrained SFTI backbone enforced a different intramolecular cooperativity, which masked a KLK14 specific determinant. As a consequence, the level of selectivity achievable was lower than that found for the KLK4 inhibitor. Standard mechanism inhibitors such as SFTI rely on a stable acyl-enzyme intermediate for high affinity binding. This is achieved by a conformationally constrained canonical binding loop that allows for reformation of the scissile peptide bond after cleavage. Amino acid substitutions within the inhibitor to target a particular protease may compromise structural determinants that support the rigidity of the binding loop and thereby prevent the engineered inhibitor reaching its full potential. An in silico analysis was carried out to examine the potential for further improvements to the potency and selectivity of the SFTI-based KLK4 and KLK14 inhibitors. Molecular dynamics simulations suggested that the substitutions within SFTI required to target KLK4 and KLK14 had compromised the intramolecular hydrogen bond network of the inhibitor and caused a concomitant loss of binding loop stability. Furthermore in silico amino acid substitution revealed a consistent correlation between a higher frequency of formation and the number of internal hydrogen bonds of SFTI-variants and lower inhibition constants. These predictions allowed for the production of second generation inhibitors with enhanced binding affinity toward both targets and highlight the importance of considering intramolecular cooperativity effects when engineering proteins or circular peptides to target proteases. The findings from this study show that although PS-SCLs are a useful tool for high throughput screening of approximate protease preference, later refinement by SML screening is needed to reveal optimal subsite occupancy due to cooperativity in substrate recognition. This investigation has also demonstrated the importance of maintaining structural determinants of backbone constraint and conformation when engineering standard mechanism inhibitors for new targets. Combined these results show that backbone conformation and amino acid cooperativity have more prominent roles than previously appreciated in determining substrate/inhibitor specificity and binding affinity. The three key inhibitors designed during this investigation are now being developed as lead compounds for cancer chemotherapy, control of fibrinolysis and cosmeceutical applications. These compounds form the basis of a portfolio of intellectual property which will be further developed in the coming years.

Evolutionary placement of continuously operating reference stations of network Real-Time Kinematic

Network RTK (Real-Time Kinematic) is a technology that is based on GPS (Global Positioning System) or more generally on GNSS (Global Navigation Satellite System) observations to achieve centimeter-level accuracy positioning in real time. It is enabled by a network of Continuously Operating Reference Stations (CORS). CORS placement is an important problem in the design of network RTK as it directly affects not only the installation and running costs of the network RTK, but also the Quality of Service (QoS) provided by the network RTK. In our preliminary research on the CORS placement, we proposed a polynomial heuristic algorithm for a so-called location-based CORS placement problem. From a computational point of view, the location-based CORS placement is a largescale combinatorial optimization problem. Thus, although the heuristic algorithm is efficient in computation time it may not be able to find an optimal or near optimal solution. Aiming at improving the quality of solutions, this paper proposes a repairing genetic algorithm (RGA) for the location-based CORS placement problem. The RGA has been implemented and compared to the heuristic algorithm by experiments. Experimental results have shown that the RGA produces better quality of solutions than the heuristic algorithm.

A parallel cooperative co-evolutionary genetic algorithm for the composite SaaS placement problem in Cloud computing

A composite SaaS (Software as a Service) is a software that is comprised of several software components and data components. The composite SaaS placement problem is to determine where each of the components should be deployed in a cloud computing environment such that the performance of the composite SaaS is optimal. From the computational point of view, the composite SaaS placement problem is a large-scale combinatorial optimization problem. Thus, an Iterative Cooperative Co-evolutionary Genetic Algorithm (ICCGA) was proposed. The ICCGA can find reasonable quality of solutions. However, its computation time is noticeably slow. Aiming at improving the computation time, we propose an unsynchronized Parallel Cooperative Co-evolutionary Genetic Algorithm (PCCGA) in this paper. Experimental results have shown that the PCCGA not only has quicker computation time, but also generates better quality of solutions than the ICCGA.

Cross-entropy optimization for scaling factors of a fuzzy controller : a see-and-avoid approach for unmanned aerial systems

The Cross-Entropy (CE) is an efficient method for the estimation of rare-event probabilities and combinatorial optimization. This work presents a novel approach of the CE for optimization of a Soft-Computing controller. A Fuzzy controller was designed to command an unmanned aerial system (UAS) for avoiding collision task. The only sensor used to accomplish this task was a forward camera. The CE is used to reach a near-optimal controller by modifying the scaling factors of the controller inputs. The optimization was realized using the ROS-Gazebo simulation system. In order to evaluate the optimization a big amount of tests were carried out with a real quadcopter.

Decentralized detector generation in cooperative intrusion detection system

We consider Cooperative Intrusion Detection System (CIDS) which is a distributed AIS-based (Artificial Immune System) IDS where nodes collaborate over a peer-to-peer overlay network. The AIS uses the negative selection algorithm for the selection of detectors (e.g., vectors of features such as CPU utilization, memory usage and network activity). For better detection performance, selection of all possible detectors for a node is desirable but it may not be feasible due to storage and computational overheads. Limiting the number of detectors on the other hand comes with the danger of missing attacks. We present a scheme for the controlled and decentralized division of detector sets where each IDS is assigned to a region of the feature space. We investigate the trade-off between scalability and robustness of detector sets. We address the problem of self-organization in CIDS so that each node generates a distinct set of the detectors to maximize the coverage of the feature space while pairs of nodes exchange their detector sets to provide a controlled level of redundancy. Our contribution is twofold. First, we use Symmetric Balanced Incomplete Block Design, Generalized Quadrangles and Ramanujan Expander Graph based deterministic techniques from combinatorial design theory and graph theory to decide how many and which detectors are exchanged between which pair of IDS nodes. Second, we use a classical epidemic model (SIR model) to show how properties from deterministic techniques can help us to reduce the attack spread rate.

Design and analysis of key management schemes for distributed wireless sensor networks

Secure communications in distributed Wireless Sensor Networks (WSN) operating under adversarial conditions necessitate efficient key management schemes. In the absence of a priori knowledge of post-deployment network configuration and due to limited resources at sensor nodes, key management schemes cannot be based on post-deployment computations. Instead, a list of keys, called a key-chain, is distributed to each sensor node before the deployment. For secure communication, either two nodes should have a key in common in their key-chains, or they should establish a key through a secure-path on which every link is secured with a key. We first provide a comparative survey of well known key management solutions for WSN. Probabilistic, deterministic and hybrid key management solutions are presented, and they are compared based on their security properties and re-source usage. We provide a taxonomy of solutions, and identify trade-offs in them to conclude that there is no one size-fits-all solution. Second, we design and analyze deterministic and hybrid techniques to distribute pair-wise keys to sensor nodes before the deployment. We present novel deterministic and hybrid approaches based on combinatorial design theory and graph theory for deciding how many and which keys to assign to each key-chain before the sensor network deployment. Performance and security of the proposed schemes are studied both analytically and computationally. Third, we address the key establishment problem in WSN which requires key agreement algorithms without authentication are executed over a secure-path. The length of the secure-path impacts the power consumption and the initialization delay for a WSN before it becomes operational. We formulate the key establishment problem as a constrained bi-objective optimization problem, break it into two sub-problems, and show that they are both NP-Hard and MAX-SNP-Hard. Having established inapproximability results, we focus on addressing the authentication problem that prevents key agreement algorithms to be used directly over a wireless link. We present a fully distributed algorithm where each pair of nodes can establish a key with authentication by using their neighbors as the witnesses.