Clinical guidelines are developed to assist healthcare practitioners to make decisions on a patient&#039 / s medical problems and as such they communicate with external applications to retrieve patient data, to initiate medical actions through clinical workflows and to transmit information to alert/reminder systems. The interoperability problems in the healthcare IT domain for interacting with heterogeneous clinical workflow systems and Electronic Healthcare Record (EHR) Systems prevent wider deployment of clinical guidelines because each deployment requires a tedious custom adaptation phase. In this thesis, we provide machine processable mechanisms that express the semantics of clinical guideline interfaces so that automated processes can be used to access the clinical resources for guideline deployment and execution. For this purpose, we propose a semantically enriched clinical guideline representation formalism by extending one of the computer interpretable guideline representation languages, GuideLine Interchange Format (GLIF). To be able to deploy the semantically extended guidelines to healthcare settings semi-automatically, the underlying application&#039 / s semantics must also be available. We describe how this can be achieved based on two prominent implementation technologies in use in the eHealth domain: Integrating Healthcare Enterprise (IHE) Cross Enterprise Document Sharing Integration Profile (XDS) for discovering and exchanging EHRs and Web service technology for interacting with the clinical workflows and wireless medical sensor devices. Since the deployment and execution architecture should be dynamic, and address the heterogeneity of underlying clinical environment, the deployment and execution is coordinated by a multi-agent system. The system described in this thesis is realized within the scope of the SAPHIRE Project.

In this study, we developed an animation tool to animate 3D virtual characters. The tool offers facilities to integrate motion capture data with a 3D character mesh and animate the mesh by using Skeleton Subsurface Deformation and Dual Quaternion Skinning Methods. It is a compact tool, so it is possible to distribute, install and use the tool with ease. This tool can be used to illustrate medical kinematic gait data for educational purposes. For validation, we obtained medical motion capture data from two separate sources and animated a 3D mesh model by using this data. The animations are presented to physicians for evaluation. The results show that the tool is sufficient in displaying obvious gait patterns of the patients. The tool provides interactivity for inspecting the movements of patient from different angles and distances. We animate anonymous virtual characters which provide anonymity of the patient.

With the advances in sequencing technologies, the number of protein sequences with unknown function increases rapidly. Hence, computational methods for functional annotation of these protein sequences become of the upmost importance. In this thesis, we first defined a feature space mapping of protein primary sequences to fixed dimensional numerical vectors. This mapping, which is called the Subsequence Profile Map (SPMap), takes into account the models of the subsequences of protein sequences. The resulting vectors were used as an input to support vector machines (SVM) for functional classification of proteins. Second, we defined the protein functional annotation problem as a classification problem and construct a classification framework defined on Gene Ontology (GO) terms. Dierent classification methods as well as their combinations are assessed on this framework which is based on 300 GO molecular function terms. The reiv sults showed that combination enhances the classification accuracy. The resultant system is made publicly available as an online function annotation tool.

Pathfinding algorithms used in today&rsquo / s computer games consider path length or a similar criterion as the only measure of optimality. However, these games usually involve opposing parties, whose agents can inflict damage on those of the others&rsquo / . Therefore, the shortest path in such games may not always be the safest one. Consequently, a new suboptimal offline path search algorithm that takes the threat sources into consideration was developed, based on the A* algorithm. Given an upper bound value as the tolerable amount of damage for an agent, this algorithm searches for the shortest path from a starting location to a destination that would cause the agent suffer no more damage than the specified maximum. Due to its mentioned behavior, the algorithm is called Limited-Damage A* (LDA*). Performance of LDA* was tested in randomly-generated and hand-crafted fully-observable maze-like square environments with 8-way grid-abstractions against Multiobjective A* (MOA*), which is a complete and optimal algorithm. It was found to perform much faster than MOA* with allowable sub-optimality in path length.

In this research, component oriented development is supported with design guidance by extending the Axiomatic Design Theory for component orientation, and utilizing domain engineering and ontology mechanisms. Guidance is offered in the form of suggesting missing components and discovering incompatibilities among the candidate elements of software development, corresponding to different phases such as requirement analysis, design, and implementation. A mature domain concept is developed suggesting the availability of reference models for customer needs, software system requirements, software design, and also a rich set of implemented components. As the system is being defined starting with the customer needs and progressing towards components, at every step the developer is presented what is available in the domain and what becomes unavailable. This guidance is based on the selections made so far, utilizing ontology based constraint checking. Feature Models are incorporated for modeling customer needs. Case studies are presented for demonstration purposes.

Today, the application of information and communication technologies to healthcare is on the agenda of many countries. The main aim is to make Electronic Healthcare Records (EHR) of a patient accessible anywhere at any time to all authorized users. This is even valid in the cross-border case / the European Commission has published eHealth interoperability recommendations to the EU Member States, in which the RIDE Project contributed, for the purpose of an interoperable European Health Network. Interoperable cross-border clinical data exchange is an ambitious goal with some challenges, the most obvious one being the variety of standards. This issue gets more complicated with the locally developed standards and coding systems. Each country has its own set of standards and it is not reasonable to make all possible combinations of mappings among them during multi-party EHR exchange. Instead, what needs to be done is keeping the legacy infrastructures of the participants and agreeing on a set of common EHR standards and coding systems. Then, each country shall develop &quot / Adapters&quot / transforming local EHR instances to the commonly agreed formats which will most probably be based on widely accepted standards such as HL7 CDA. This approach enables the structure level interoperability. As the second step, in order to achieve semantic interoperability, coded terms from locally defined coding systems shall be translated to international counterparts. In this thesis, our methodology is confirmed on Turkey&#039 / s National Health Information System. &quot / Transmission Schemas&quot / are automatically transformed to HL7 v3 CDA R2 and CEN EN 13606 standard formats. The local coded terms are translated by developing a mapping platform based on Unified Medical Language System (UMLS).

In this study, a 3D face representation and recognition method based on spherical harmonics expansion is proposed. The input data to the method is range image of the face. This data is called 2.5 dimensional. Input faces are manually marked on the two eyes, nose and chin points. In two dimensions, using the marker points, the human face is modeled as two concentric half ellipses for the selection of region of interest. These marker points are also used in three dimensions to register the faces so that the nose point tip is at the origin and the line across the two eyes lies parallel to the horizontal plane. A PCA based component analysis is done to further align the faces vertically. The aligned face is stitched and mapped to an ellipsoid and transformed using real spherical harmonics expansion. The real harmonics expansion coefficients are labeled and stored into a gallery. Using these coefficients as input, several classification algorithms are applied and the results are reported.

In the 1990s, software projects became larger in size and more complicated in structure. The traditional development processes were not able to answer the needs of these growing projects. Comprehensive documentation in traditional methodologies made processes slow and discouraged the developers. Testing, after all code is written, was time consuming, too costly and made error correction and debugging much harder. Fixing the code at the end of the project also affects the internal quality of the software. Agile software development processes evolved to bring quick solutions to these existing problems of the projects. Test Driven Development (TDD) is a technique, used in many agile methodologies, that suggests minimizing documentation, writing automated tests before implementing the code and frequently run tests to get immediate feedback. The aim is to increase software productivity by shortening error correction duration and increase software quality by providing rapid feedback to the developer. In this thesis work, a software project is developed with TDD and compared with a control project developed using traditional development techniques in terms of software productivity and software quality. In addition, TDD project is compared with an early work in terms of product quality. The benefits and the challenges of TDD are also investigated during the whole process.

In this thesis, we defined a new assignment problem and named it as the artillery target assignment problem(ATAP). The artillery target assignment problem is about assigning artillery weapons to targets at different time instances while optimizing some objectives. Since decisions at a time instance may affect decisions at other time instances, solving this assignment problem is harder than the classical assignment problem. For constructing a solution approach, we defined a base case and some variations of the problem which reflects subproblems of the main problem. These sub-problems are investigated for possible solutions. For two of these sub-problems, genetic algorithm solutions with customized representations and genetic operators are developed. Experiments of these solutions and related results are presented in this thesis.

In this thesis, we present a simple and efficient automated analysis tool called DoSSO that detects shared objects in multithreaded Java programs. DoSSO reports only the shared objects that are modified by at least one thread. Based on this tool, we propose a new approach in developing concurrent software where programmers implement the system without considering synchronization issues first and then use appropriate locking mechanism only for the objects reported by DoSSO. To evaluate the applicability of DoSSO, we have conducted a case study on a distributed and concurrent system with graphical user interfaces. Case study results showed that DoSSO is able to identify objects that become shared among explicitly defined threads and event threads, and objects that become shared through RMI.