The Use of Artificial Intelligence Techniques for Protein Structure Prediction

The conventional technique for computerized protein structure prediction uses several programming languages such as Fortran, C, Pascal etc. With recent advances in programming languages and the development of rule-based systems, the computerized part of the problem is undergoing major change. This thesis sets out the idea of extending the properties of an intelligent rule-based system and recognising incomplete nature of knowledge for this problem. It reviews the existing architectures and characteristics that embody an intelligent system. As the outcome of the idea, a new system called PREDMOLL, written in Prolog, is developed. PREDMOLL is based on the blackboard architecture with several other extra features. This thesis also reviews some current uncertainty techniques and developes a formula based on a modifications of the Bayes theorem, to deal with multiple hypotheses. The problem of conditional independence assumption is reduced to the minimum. The formula is used as a decision-making criterion to determine secondary structure boundaries. For tertiary structure prediction, this thesis suggests a similarity value for primary sequence homology to overcome the problem of arbitrary uncertainty values in rules. PREDMOLL and the uncertainty techniques incorporated with it are used to test the hypothesis that the performance of protein structure prediction is improved by combining several methods. The test is carried out by a series of experimental predictions with user-defined rules and predefined constraints. The behaviour of PREDMOLL during the problemsolving process of the experiments is shown. The results obtained yield improvements in precision for secondary structure prediction and further improvements are expected. For tertiary structure prediction, some preliminary progress is shown and, due to lack of genuine rules, ad-hoc rules are generated from the protein data base. The status of PREDMOLL and its advantages over other systems is discussed. Several suggestions are made to improve current facilities in PREDMOLL and problems in a wider domain. Suggestions are also made for further improvements in tertiary structure prediction

Expertise effects in memory recall: A reply to Vicente and Wang

This article may not exactly replicate the final version published in the APA journal. It is not the copy of record.In the January 1998 Psychological Review, Vicente and Wang propose a "constraint attunement hypothesis" to explain the large effects of domain expertise upon memory recall observed in a number of task domains. They claim to find serious defects in alternative explanations of these effects which their theory overcomes. Re-examination of the evidence shows that their theory is not novel, but has been anticipated by those they criticize, and that other current published theories of the phenomena do not have the defects Vicente and Wang attribute to them. Vicente and Wang's views reflect underlying differences (a) about emphasis upon performance versus process in psychology, and (b) about how theories and empirical knowledge interact and progress with the development of a science

An Approach for Supporting Ad-hoc Modifications in Distributed Workflow Management Systems

Supporting enterprise-wide or even cross-organizational business processes is a characteristic challenge for any workflow management system (WfMS). Scalability at the presence of high loads as well as the capability to dynamically modify running workflow (WF) instances (e.g., to cope with exceptional situations) are essential requirements in this context. Should the latter one, in particular, not be met, the WfMS will not have the necessary flexibility to cover the wide range of process-oriented applications deployed in many organizations. Scalability and flexibility have, for the most part, been treated separately in the relevant literature thus far. Even though they are basic needs for a WfMS, the requirements related with them are totally different. To achieve satisfactory scalability, on the one hand, the system needs to be designed such that a workflow instance can be controlled by several WF servers that are as independent from each other as possible. Yet dynamic WF modifications, on the other hand, necessitate a (logical) central control instance which knows the current and global state of a WF instance. For the first time, this paper presents methods which allow ad-hoc modifications (e.g., to insert, delete, or shift steps) to be performed in a distributed WfMS; i.e., in a WfMS with partitioned WF execution graphs and distributed WF control. It is especially noteworthy that the system succeeds in realizing the full functionality as given in the central case while, at the same time, achieving extremely favorable behavior with respect to communication costs

Routing efficiency in wireless sensor-actor networks considering semi-automated architecture

Wireless networks have become increasingly popular and advances in wireless communications and electronics have enabled the development of different kind of networks such as Mobile Ad-hoc Networks (MANETs), Wireless Sensor Networks (WSNs) and Wireless Sensor-Actor Networks (WSANs). These networks have different kind of characteristics, therefore new protocols that fit their features should be developed. We have developed a simulation system to test MANETs, WSNs and WSANs. In this paper, we consider the performance behavior of two protocols: AODV and DSR using TwoRayGround model and Shadowing model for lattice and random topologies. We study the routing efficiency and compare the performance of two protocols for different scenarios. By computer simulations, we found that for large number of nodes when we used TwoRayGround model and random topology, the DSR protocol has a better performance. However, when the transmission rate is higher, the routing efficiency parameter is unstable.Peer ReviewedPostprint (published version

Using Ontologies for the Design of Data Warehouses

Obtaining an implementation of a data warehouse is a complex task that forces designers to acquire wide knowledge of the domain, thus requiring a high level of expertise and becoming it a prone-to-fail task. Based on our experience, we have detected a set of situations we have faced up with in real-world projects in which we believe that the use of ontologies will improve several aspects of the design of data warehouses. The aim of this article is to describe several shortcomings of current data warehouse design approaches and discuss the benefit of using ontologies to overcome them. This work is a starting point for discussing the convenience of using ontologies in data warehouse design.Comment: 15 pages, 2 figure

Robust nonlinear control of vectored thrust aircraft

An interdisciplinary program in robust control for nonlinear systems with applications to a variety of engineering problems is outlined. Major emphasis will be placed on flight control, with both experimental and analytical studies. This program builds on recent new results in control theory for stability, stabilization, robust stability, robust performance, synthesis, and model reduction in a unified framework using Linear Fractional Transformations (LFT's), Linear Matrix Inequalities (LMI's), and the structured singular value micron. Most of these new advances have been accomplished by the Caltech controls group independently or in collaboration with researchers in other institutions. These recent results offer a new and remarkably unified framework for all aspects of robust control, but what is particularly important for this program is that they also have important implications for system identification and control of nonlinear systems. This combines well with Caltech's expertise in nonlinear control theory, both in geometric methods and methods for systems with constraints and saturations