Sharif Digital Repository

Multiple sequence alignment (MSA) is one of the basic and important problems in molecular biology. MSA can be used for different purposes including finding the conserved motifs and structurally important regions in protein sequences and determine evolutionary distance between sequences. Aligning several sequences cannot be done in polynomial time and therefore heuristic methods such as genetic algorithms can be used to find approximate solutions of MSA problems. Several algorithms based on genetic algorithms have been developed for this problem in recent years. Most of these algorithms use very complicated, problem specific and time consuming mutation operators. In this paper, we propose a... 

Repetitive decomposing of the objective concept hierarchically, developed for design involves a human intentional activity, ranging from management to physical works. This model proved the empirical rules in Industrial Engineering. In addition to these "design" process characteristics, the "test" process is found to be a defect attenuating process with the attenuation rate of its error rate of the second kind. As these are applicable to any software process, they are very useful  

"Product" and "process" are two mutually orthogonal and important aspects of software. As Part 1 discusses "product", Part 2 discusses "process". "Process" is independent of "product" and is used commonly by various "producers". This paper first explains the structure of "process" and then introduces important technique by "divide and conquer". Various important management issues are discussed  

The QoS attributes of Grid services play important roles in several tasks in Grid computing such as QoS-aware service composition, service negotiation, resource management, service discovery and scheduling. By considering the dynamic aspects of the Grid environments and also the uncertainty related to Grid services, in this paper, we present BNQM, a Bayesian network based probabilistic QoS Model for Grid service composition. Application of Bayesian network in QoS management makes it possible to indicate the conditional independence relationships among QoS attributes and to provide an effective probabilistic approach to predict new values for some QoS attributes while others are changed.... 

Web services foster functionality of current web to service oriented architecture. Nascent semantic web is capable of automating activities by annotating shared ontological semantics to documents and services. Although, a zillion web services with diversity have been made since the inception of its diffusion, it is not a panacea for software development and it is still in its infancy. A middle agent (broker) simplifies the interaction of service providers and service requester, especially in the case that an atomic web service cannot fulfill user's need. The broker composes a desired value-added service and orchestrates the execution of bundled sub-processes. It is inevitable that several... 

In many cases, atomic Semantic Web services are not able to provide requested functionalities. Therefore, in order to satisfy users' requests, the composition task is required on available atomic services. In addition, Context awareness in Web services is gaining momentum as the opportunity to benefit the interactions between human, applications and the environment. So it seems reasonable to use available context information in composition procedure to provide a composite Semantic Web service which is adapted to the context of participant Web services and the requester. In this paper, we introduce a novel approach for semi-automatic context-aware graph-based composition of Semantic Web... 

One of the most important services in the Semantic Web is the Reasoning Service. According to the Semantic Web requirements, reasoning under time pressure or other restrictions is needed; and, reasoning which is not 'perfect' but instead 'good enough' for given tasks is acceptable. One of the approaches for the improvement of reasoning performance is approximation; of course, there is an effort for raising more precise approximations. One of the fields in which approximation seems to be useful is query. So far, all of the approximation strategies introduced for conjunctive queries just consider the query's structure. In this paper, a semantic approach for conjunctive query approximation... 

Many complex networks such as social networks and computer show modular structures, where edges between nodes are much denser within modules than between modules. It is strongly believed that cellular networks are also modular, reflecting the relative independence and coherence of different functional units in a cell. In this paper we used a human curated dataset. In this paper we consider each module in the PPI network as ontology. Using techniques in ontology alignment, we compare each pair of modules in the network. We want to see that is there a correlation between the structure of each module or they have totally different structures. Our results show that there is no correlation... 

Clustering search results helps the user to overview returned results and to focus on the desired clusters. Most of search result clustering methods use title, URL and snippets returned by a search engine as the source of information for creating the clusters. In this paper we propose a new method for search results clustering (SRC) which uses social annotations as the main source of information about web pages. Social annotations are high-level descriptions for web pages and as the experiments show, clustering based on social annotations yields good clusters with informative labels. © 2008 Springer-Verlag  

In this paper, we propose a new method for automatic news event detection. An event is a specific happening in a particular time and place. We propose a new model in this paper to detect news events using a label based clustering approach. The model takes advantage of the fact that news events are news clusters with high internal similarity whose articles are about an event in a specific time and place. Since news articles about a particular event may appear in several consecutive days, we developed this model to be able to distinguish such events and merge the corresponding news articles. Although event detection is propounded as a stand alone news mining task, it has also applications in... 

People use trust to cope with uncertainty which is a result of the free will of others. Previous approaches for inferring trust have focused on homogeneous relationships and attempted to infer missing information based on existing information in a single relationship. In this paper we propose using methods of social network analysis to infer trust in a heterogeneous social network. We have extended the problem of relation extraction and allowed using any type of binary operator on matrixes, whereas previous work have focused on linear combination of base matrixes (the only allowed operator was summation of two matrixes). We present two genetic algorithms which use ordinary numerical and... 

Nowadays, there are plenty of online websites related to news. Hence, new technologies, tools and special search engines are created for having access to the news on these websites. Online news is a special type of public information which has exclusive characteristics. These characteristics contribute news engines tasks such as discovering, collecting and searching to be different with similar tasks in traditional web search engines. Clustering plays conspicuous role in news engines tasks. In this paper we study various tasks in news engines and also focusing on clustering applications in them. © 2007 Springer  

Recent years have witnessed an explosion in the availability of news articles on the World Wide Web. In addition, organizing the results of a news search facilitates the user(s) in overviewing the returned news. In this work, we have focused on the label-based clustering approaches for news meta-search engines, and which clusters news articles based on their topics. Furthermore, our engine for NEws meta-Search REsult Clustering (NeSReC) is implemented along. NeSReC takes queries from the users and collect the snippets of news which are retrieved by The Altavista News Search Engine for the queries. Afterwards, it performs the hierarchical clustering and labeling based on news snippets in a... 

Recent evaluations of mapping systems show that lack of background knowledge, most often domain specific knowledge, is one of the key problems of mapping systems these days. In fact, at present, most state of the art systems, for the tasks of mapping large ontologies, perform not with such high values of recall (~ 30%), because they mainly rely on label and structure based similarity measures. Disregarding context knowledge in ontology mapping is another drawback that almost all current approaches suffer from. In this paper we use the semantic web as background knowledge and introduce a novel approach for capturing context knowledge from the ontology for improving mapping results. We have... 

A huge amount of web services are deployed on the Web, nowadays. These services can be used to fulfill online requests. Requests are getting more and more complicated over time. So, there exists a lot of frequent request that cannot be fulfilled using just one web service. For using web services, composing individual services to create the added-value composite web service to fulfill the user request is necessary in most cases. Web services can be composed manually but it is a too tedious and time consuming task. The ability of automatic web service composition to create a new composite web service is one of the key enabling features for the future for the semantic web. There are some... 

The rapid growth of the world-wide web poses unprecedented scaling challenges for general-purpose crawlers and search engines. A focused crawler aims at selectively seek out pages that are relevant to a pre-defined set of topics. Besides specifying topics by some keywords, it is customary also to use some exemplary documents to compute the similarity of a given web document to the topic. In this paper we Introduce a new hybride focused crawler, which uses link structure of documents as well as similarity of pages to the topic to crawl the web © 2006 HEE  

The distributed nature and complexity of computer networks and various services provided via them, makes the networks vulnerable to numerous attacks. The TCP/IP presumptions which are based on using this protocol to provide a simple, open communication infrastructure in an academic and collaborative environment, causes this protocol lack of built-in mechanisms for authentication, integrity and privacy. Even though in the last few years a more systematic approach to TCP/IP network security problem has been followed, a formal approach to this problem is lacking. In this paper, we propose using Description Logics as a formal model which could be used to analyze TCP/IP networks against attacks.... 

We study the problem of optimizing the symbol error probability (SEP) performance of cluster-based cooperative wireless sensor networks (WSNs). It is shown in the literature that an efficient relay selection protocol based on simple geographical information of the nodes to execute the cooperative diversity transmission, can significantly improve the SEP performance at the destination of such networks. Also, a similar analysis on the optimal power allocation for the source and the relay exists in the literature. However, we propose that to achieve the minimum SEP at the destination, a joint optimization of power allocation and relay selection should be accomplished. To this aim, we... 

The spin configuration, equilibrium crystal structure, and electronic structure of BaFe2−xNixAs2 (x = 0, 1, 2) have been investigated by using ab initio pseudopotential Quantum Espresso code in the generalized gradient approximation. The total energy of different Fe(Ni) spin configurations has been calculated to determine the ground state in each doping. The results show an antiferromagnetic order in x = 0.0 and a nonmagnetic state for x = 2.0. Equilibrium lattice and internal parameters for this system have been calculated and compared with the literature data. This study shows that the lattice parameters in the magnetic calculations have been... 

Progressive use of Web based information retrieval systems such as general purpose search engines and dynamic nature of the Web make it necessary to continually maintain Web based information retrieval systems. Crawlers facilitate this process by following hyperlinks in Web pages to automatically download new and updated Web pages. Freshness (recency) is one of the important maintaining factors of Web search engine crawlers that takes weeks to months. Many large Web crawlers start from seed pages, fetch every links from them, and continually repeat this process without any policies that help them to better crawling and improving performance of those. We believe that data mining techniques...