Computer Science
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Alshafah, Samira (Beograd , 2018)[more][less]
Abstract: Proteins with intrinsically disordered regions are involved in large number of key cell processes including signaling, transcription, and chromatin remodeling functions . On the other side, such proteins have been observed in people suffering from neurological and cardiovascular diseases, as well as various malignancies. Process of experimentally determining disordered regions in proteins is a very expensive and long  term process. As a consequence, a various computer programs for predicting position of disordered regions in proteins have been developed and constantly improved. In this thesis a new method for determining Amino acid sequences that characterize ordered/disordered regions is presented. Material used in research includes 4076 viruses wit h more than 190000 proteins. Proposed method is based on defining correspondence between n grams (including both repeats and palindromic sequence s) characteristics and their belonging to ordered/disordered protein regions. Positions of ordered/disordered regions are predicted using three different predictors. The features of the repetitive strings used in the research include mol e fractions, fract ional differences, and z values. Also, data mining techniques association rules and classification were applied on both repeats and palindromes. The results obtained by all techniques show a high level of agreement for a short length of less than 6, while the level of agreement grows up to the maximum with increasing the length of the sequences. The high reliability of the results obtained by the data mining techniques shows that there are n grams, both repeating sequences and palindromes, which uniquely ch aracterize the disordered/ ordered regions of the proteins . The obtained results were verified by comparing with the results based on n grams from the DisProt database which contain s the positions of experimentally verified disordered regions of the protein. Results can be used both for the fast localization of disordered/ordered regions in proteins as well as for further improving existing programs for their prediction. URI: http://hdl.handle.net/123456789/4746 Files in this item: 1
ThesisSamira_Alshafah.pdf ( 3.106Mb ) 
Đenić, Aleksandar (Beograd , 2018)[more][less]
Abstract: This pap er considers two discrete lo cation problems: Bus Terminal Lo cation Problem (BTLP) and Longterm Care Facility Lo cation Problem (LTCFLP). Vari able Neighb orho o d Search (VNS) metho d for solving BTLP and LTCFLP is pre sented in this pap er. VNS is a singlesolution based metaheuristic based on system atic change of neighb orho o ds while searching for optimal solution of the problem. It consists two main phases: shake phase and lo cal search phase. BTLP is a discrete lo cation problem which considers lo cating bus terminals in order to provide the highest p ossible quality of public service to the clients. Clients are presented as public transp ortation stations, such as bus or metro stations. VNS algorithm is used for solving BTLP. This algorithm uses improved lo cal search based on e cient neighb orho o d interchange. VNS is parallelized (PVNS) which leads to signi cant time improvement in function of the pro cessor core count. Computa tional results show that prop osed PVNS metho d improves existing results from the literature in terms of quality. Larger instances, based on instances from the Trav eling Salesman Problem library, are presented and computational results for those instances are rep orted. LTCFLP is created as a part of health care infrastructure planning in South Korea. Clients are considered as groups of patients with a need of longterm health care, while established facilities present lo cations where the centers that provide health care services should b e built. Prede ned are n lo cations where centers are to b e established. This problem seeks at most K lo cations to establish health centers so they are to b e equally loaded with clients demand. For solving LTCFLP, by using VNS algorithm, data structure based on fast interchange is presented. It reduces the time complexity of one iteration of lo cal search algorithm to O ( n · max( n,K 2 )) comparing to the known time complexity from the literature O ( K 2 · n 2 ) . Reduced time complexity of the presented VNS leads to b etter quality solutions, due to larger numb er of VNS iterations that can b e p erformed in less computational time. This pap er presents computational results that outp erform the b est known results from the literature. URI: http://hdl.handle.net/123456789/4744 Files in this item: 1
Aleksandar_Djenic_phd.pdf ( 2.183Mb ) 
Čukić, Ivan (Beograd , 2018)[more][less]
Abstract: There is a big class of problems that require software systems with asynchronously executed components. For example, distributed computations have the distributed nodes that process the data asynchronously to one anot her, serviceoriented architectures need to process separate requests asynchrono usly, and multicore and heterogeneous systems need to have multiple separa te tasks running concurrently to best utilize the hardware. Even ordinary GUI applications need asynchronous components – the user interface needs to be re sponsive at all times which means that no matter in what state the program is in, it needs to process and react to the input events coming from the user. The necessity of concurrency and asynchronous execution brings in the added com plexity of the Inversion of Control (IoC) into the system, either through mes sage passing or through event processing. IoC makes code difficult to develop and reason about, it increases component coupling and inhibits clean functional or objectoriented software design. In this dissertation, a method for solving the problems that IoC introduces is presented. It presents a way to model both synchronous and different types of asynchronous tasks with the continuation monad. The continuation monad serves as a primitive to build more complex control flow structures that mimic the control flow structures of the host programming language. It also allows for building more complex control structures specialized for parallelism, transactional execution, and for simulating functional programming idioms with asynchronous tasks through a generalization of the continuation monad that allows the asynchronous tasks to generate results one at a time. This allows for writing programming systems with asynchronously executed components by writing seemingly synchronous imperati ve or functional code while leaving it up to the compiler to do all the heavy lifting and convert the written code to asynchronously executed set of tasks. Another benefit of the presented method is that it allows for easier automatic handling of the data lifetime without the need for garbage collection. This method has been successfully applied and tested in several Free/Libre Open Source Software and proprietary realworld software projects used by hun dreds of millions of people around the world. In this dissertation, an example of a secure project management system is described which is based on a similar system implemented as a part of the KDE Plasma project. This dissertation also contains the important parts of the implementation of the AsynQt library which extends the Qt library, and its concurrency primitive – QFuture class – with functional reactive programming patterns based on the method proposed in this dissertation. URI: http://hdl.handle.net/123456789/4738 Files in this item: 1
ivan_cukic_phd.pdf ( 1.328Mb ) 
Radojčić, Nina (Beograd , 2018)[more][less]
Abstract: In this dissertation, three NPhard optimization problems are studied and va rious computational intelligence methods are considered for solving them, with a special emphasis on the possibilities of applying fuzzy logic in order to improve the performances of proposed methods. In addition, it is shown how fuzzy logic can be incorporated into a model to make it more adequate to real world applications. The first problem considered is the RiskConstrained CashinTransit Vehicle Routing Problem (RCTVRP) that represents a special case of the vehicle routing problem (VRP). Similar to the classical VRP, the aim is to determine the collection routes from one depot to a number of customers in order to minimize the overall travel distance (or cost). Additionally, the safety aspect of the routed risk constraints are introduced in the case of RCTVRP. The RCTVRP concerns the issue of secu rity during the transportation of cash or valuable goods (e.g. in the cashintransit industry). The other two problems studied in this dissertation belong to the class of loca tion problems: the Load Balancing Problem (LOBA) and the MaxMin Diversity Problem (MMDP). The goal of the LOBA problem is to locate a fixed number of facilities, such that the difference between the maximum and minimum number of customers served by each facility is balanced. The LOBA model is useful in cases where customers naturally choose the closest facility. The MMDP consists of se lecting a subset of a fixed number of elements from a given set in such a way that the diversity among the selected elements is maximized. This problem also arises in real world situations encompassing a variety of fields, particularly the social and biological sciences. In order to solve the RCTVRP, a fuzzy GRASP (Greedy Randomized Adaptive Search Procedure) is hybridized with Path Reliking (PR) methodology. Carefully adjusted fuzzy modification incorporated into the proposed GRASP for the RC TVRP improved its performance. Moreover, in this dissertation a new PR structure is implemented and can be used for other vehicle routing problems. To improve the algorithm’s time complexity, a new data structure for the RCTVRP is incor porated. The proposed fuzzy GRASP with PR hybrid shows better computational performance compared to its nonfuzzy version. Furthermore, computational results on publicly available data sets indicate that the proposed algorithm outperforms all existing methods from the literature for solving the RCTVRP. For solving the LOBA problem two efficient hybrid metaheuristic methods are proposed: a combination of reduced and standard variable neighborhood search met hods (RVNSVNS) and hybridization of evolutionary algorithm and VNS approach (EAVNS). The proposed hybrid methods are first benchmarked and compared to all the other methods on existing test instances for the LOBA problem with up to 100 customers and potential suppliers. In order to test the effectiveness of the pro posed methods, we modify several largescale instances from the literature with up to 402 customers and potential suppliers. Exhaustive computational experiments show that the proposed hybrid methods quickly reach all known optimal solutions while providing solutions on largescale problem instances in short CPU times. Re garding solution quality and running times, we conclude that the proposed EAVNS approach outperforms other considered methods for solving the LOBA problem. EA approach is also proposed for solving the MMDP. Computational experi ments on a smaller benchmark data set showed that the classic EA quickly reached all optimal solutions obtained previously by an exact solver. However, some of the larger instances of MMDP were challenging for classic EA. Although researchers have established the most commonly used parameter setting for EA that has good performance for most of the problems, it is still challenging to choose the adequate values for the parameters of the algorithm. One approach to overcome this is chan ging parameter values during the algorithm run. As part of this dissertation this problem was addressed by extending the evolutionary algorithm by adding a fuzzy rule formulated from EA experts’ knowledge and experience. The implemented fuzzy rule changes the mutation parameter during the algorithm run. The results on tested instances indicate that the proposed fuzzy approach is more suitable for solving the MMDP than classic EA. For all three problems addressed whereas the smaller instances that CPLEX was able to solve, obtained optimal solutions were used for comparison with proposed methods and all of the proposed methods obtained these optimal solutions. Moreover, in this dissertation it has been shown that fuzzy logic is a successful tool in modeling the RCTVRP. In this problem the risk constraints are set by using a risk threshold T on each route and thus, the routes with risk larger than T are forbidden. However, in this dissertation the aim is to take into account the probability of being robbed along each route instead of just allowing solutions with routes that satisfy the risk constraints. A new fuzzy model for the RCTVRP is developed which takes into account the value of the risk index of each route and the solutions with lower values of risk indexes on their routes are considered superior. In order to achieve that fuzzy numbers are used in the improved model. Moreover, two mixed integer program formulations of new fuzzy model are developed and presented in this dissertation. The introduced fuzzy model is compared with the model from the literature using an adequate example and the advantages of the newly proposed fuzzy RCTVRP is demonstrated. Computational experiments are performed and the comparison of the two models given in the paper show that the newly presented approach leads to safer routes. URI: http://hdl.handle.net/123456789/4737 Files in this item: 1
tezaNinaRadojicic.pdf ( 1.665Mb ) 
Vučković, Bojan (Beograd , 2017)[more][less]
Abstract: We present original results from the following fields of discrete mathematics: chromatic graph theory, extremal set theory and Boolean matrix theory. From the chromatic graph theory we investigate edge and total colorings satisfying the condition that neighboring vertices of a graph possess different values of multiset, set or sum, induced by the giving coloring. Multiset neighbordistinguishing edge coloring of a graph is an assignment of colors to edges such that, for every edge uv of a graph, multiset of the edges incident with the vertex u differs from the multiset of the edges incident with the vertex v. The previous best result concerning the minimum number of colors required for such a coloring of an arbitrary graph states that four colors are sufficient. The author’s contribution is a proof that such a coloring is always possible with only three colors, which is in general case the optimal number of colors. We construct a graph for which we subsequently prove that a different number of colors is required to obtain a multiset neighbordistinguishing coloring and neighbordistinguishing coloring by sum. As far as we know, this is the first example of such a graph. A few results concerning the neighbor expended sum distinguishing coloring are given. The main contribution is a proof that for an arbitrary graph there exists a total coloring from the set f1; 2; 3g, such that every two adjacent vertices have different sums of its adjacent vertices and incident edges. Also, for certain classes of graphs is proved that there exists such a coloring using only the colors from the set f1; 2g. Neighbordistinguishing edge coloring of a graph G requires that every two adjacent edges receive different colors, while the sets of the edges incident with the vertices u and v differ for every edge uv of G. The author presents a procedure of edge coloring for an arbitrary graph without isolated edges, where we a smaller number of colors is used compared to all known results. For the adjacent vertex distinguishing total coloring of a graph G the condition is that every two adjacent and incident elements of V (G) [ E(G) receive different colors, while for every edge uv of G the set composed from the colors assigned to the edges incident with u together with the color of u, differs from such a set for v. The author improves the upper bound of the minimum number of colors needed for such a coloring, relative to the maximal degree of a graph. Frankl’s conjecture from the extremal set theory states that for every family closed under union there exists an element contained in at least half of the sets of the family. We give a proof that Frankl’s conjecture holds for every family contained from 12 elements, while it is known that this is true for families contained from 11 or less elements. Our proof is based on the efficient algorithm that exhausts all the possibilities, while using the results for subfamilies that eventual counterexample cannot contain, which we obtained in a number of consecutive steps. Family of sets G is an FCfamily if for every family F containing G there exists an element from S G that appears in at least half of the sets of F. NonFCfamily is every family that is not FC. The author’s contribution is the complete classification of all families consisting of 6 or less elements into FC and NonFCfamilies. From the Boolean matrices theory we present our results concerning the row space cardinality. Boolean matrices are the matrices whose all components are from the set f0; 1g, while the row space of a Boolean matrix is the set of vectors that can be obtained by disjunction from the rows of a matrix. We present the set consisted of all values a from the interval [2n2 + 2n3; 2n2] such that there exists a matrix of dimension n n having the row space cardinality equal to a. For the least positive integer an for which there exists no matrix of dimension n n having the row space cardinality equal to an, the author gives a lower bound that is an improvement over the previously known results. All proofs for the main results in the dissertation are constructive. Proofs of some of them require the use of computers where there is a calculation of a great number of possibilities. For other proofs this was not necessity, though algorithms following the steps of the proofs can be implemented to obtain a graph coloring or a matrix with the desired properties. URI: http://hdl.handle.net/123456789/4661 Files in this item: 1
Disertacija__Bojan_Vuckovic.pdf ( 1.143Mb )