Computational biology and bioinformatics for apoptosis have been gaining much momentum due to the advances in computational sciences. Both fields use extensive computational techniques and modeling to mimic real world behaviors. One problem of particular interest is on the study of reachability, in which the goal is to determine if a target state or protein concentration in the model is realizable for a signaling pathway. Another interesting problem is to examine faulty pathways and how a fault can make a previously unrealizable state possible, or vice versa. Such analysis can be extremely valuable to the understanding of apoptosis. However, these analyses can be costly or even impractical for some approaches, since they must simulate every aspect of the model. Our approach introduces an abstracted model to represent a portion of the apoptosis signaling pathways as a finite state machine. This abstraction allows us to apply hardware testing and verification techniques and also study the behaviors of the system without full simulation. We proposed a framework that is tailor-built to implement these verification techniques for the discrete model. Through solving Boolean constraint satisfaction problems (SAT-based) and with guided stimulation (Genetic Algorithm), we can further extract the properties and behaviors of the system. Furthermore, our model allows us to conduct cause-effect analysis of the apoptosis signaling pathways. By constructing single- and double-fault models, we are able to study what fault(s) can cause the model to malfunction and the reasons behind it. Unlike simulation, our abstraction approach allows us to study the system properties and system manipulations from a different perspective without fully relying on simulation. Using these observations as hypotheses, we aim to conduct laboratory experiments and further refine our model. / Master of Science

Clustering is the process in which data is differentiated, classified according to some criteria. As a result of partitioning process, data is grouped into clusters for specific purpose. In a social network, clustering of people is one of the most popular problems. Therefore, we mainly concentrated on finding an efficient algorithm for this problem. In our study, data is made up of two types of entities (e.g., people, groups vs. political issues, religious beliefs) and distinct from most previous works, signed weighted bipartite graphs are used to model relations among them. For the partitioning criterion, we use the strength of the opinions between the entities. Our main intention is to partition the data into k-clusters so that entities within clusters represent strong relationship. One such example from a political domain is the opinion of people on issues. Using the signed weights on the edges, these bipartite graphs can be partitioned into two or more clusters. In political domain, a cluster represents strong relationship among a group of people and a group of issues. After partitioning, each cluster in the result set contains like-minded people and advocated issues. Our work introduces a general mechanism for k-way partitioning of signed bipartite graphs. One of the great advantages of our thesis is that it does not require any preliminary information about the structure of the input dataset. The idea has been illustrated on real and randomly generated data and promising results have been shown.

Facing global and dynamic competition environment, companies have to collaborate with other companies instead of struggle alone to optimize performance of supply chain. In a distributed supply chain structure, it is an important issue for companies to coordinate seamlessly to effectively fulfill customer orders. In this thesis, we seek to propose a fast and flexible method to solve the order fulfillment scheduling conflicts among partners in a supply chain. Due to the risk of exposing trade secrets and the cost of gathering information, the centralized constraint satisfaction mechanism is infeasible to handle distributed scheduling problem in real world environment. Moreover, the distributed constraints satisfaction model just focuses on finding a globally executable order fulfillment schedule. Therefore, we propose an agent-based distributed coordination mechanism that integrates negotiation with generic algorithm. We chose the mold manufacturing industry as an example and conducted experiments to evaluate the performance of the proposed mechanism and to compare with other benchmark methods proposed by researchers prior to this study. The experimental results indicate that the distributed coordination mechanism we proposed is a feasible approach to solve the order fulfillment scheduling conflicts in outsourcing activities in a supply chain.

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This thesis focuses on the lower bounds for generic algorithms for discrete logarithms problem and Diffie-Hellman's problems. This thesis introduces two diffrent models of Black-Box for that purpose. On these models thesis approxi- mates and compares success probability of generic algorithms for given problems including Maurer's reduction. This reduction solves discrete logarithms problem using a appropriate elliptic curve and a Diffie-Hellman's oracle. This thesis also researches generic algorithm for identifiaction schemes, that are based on discrete logarithms problem. 1

Credit Decisions are extremely vital for any type of financial institution because it can stimulate huge financial losses generated from defaulters. A number of banks use judgmental decisions, means credit analysts go through every application separately and other banks use credit scoring system or combination of both. Credit scoring system uses many types of statistical models. But recently, professionals started looking for alternative algorithms that can provide better accuracy regarding classification. Neural network can be a suitable alternative. It is apparent from the classification outcomes of this study that neural network gives slightly better results than discriminant analysis and logistic regression. It should be noted that it is not possible to draw a general conclusion that neural network holds better predictive ability than logistic regression and discriminant analysis, because this study covers only one dataset. Moreover, it is comprehensible that a “Bad Accepted” generates much higher costs than a “Good Rejected” and neural network acquires less amount of “Bad Accepted” than discriminant analysis and logistic regression. So, neural network achieves less cost of misclassification for the dataset used in this study. Furthermore, in the final section of this study, an optimization algorithm (Genetic Algorithm) is proposed in order to obtain better classification accuracy through the configurations of the neural network architecture. On the contrary, it is vital to note that the success of any predictive model largely depends on the predictor variables that are selected to use as the model inputs. But it is important to consider some points regarding predictor variables selection, for example, some specific variables are prohibited in some countries, variables all together should provide the highest predictive strength and variables may be judged through statistical analysis etc. This study also covers those concepts about input variables selection standards.