New algorithms for automated phylogenetic reconstruction using artificial intelligence and data mining techniques

Academic and industrial research in the late 90s have brought about an exponential explosion of DNA sequence data. Automated expert systems are being created to help biologists to extract patterns, trends and links from this ever-deepening ocean of information. Two such systems aimed on retrieving and subsequently utilizing phylogenetically relevant information have been developed in this dissertation, the major objective of which was to automate the often difficult and confusing phylogenetic reconstruction process. ^ Popular phylogenetic reconstruction methods, such as distance-based methods, attempt to find an optimal tree topology (that reflects the relationships among related sequences and their evolutionary history) by searching through the topology space. Various compromises between the fast (but incomplete) and exhaustive (but computationally prohibitive) search heuristics have been suggested. An intelligent compromise algorithm that relies on a flexible “beam” search principle from the Artificial Intelligence domain and uses the pre-computed local topology reliability information to adjust the beam search space continuously is described in the second chapter of this dissertation. ^ However, sometimes even a (virtually) complete distance-based method is inferior to the significantly more elaborate (and computationally expensive) maximum likelihood (ML) method. In fact, depending on the nature of the sequence data in question either method might prove to be superior. Therefore, it is difficult (even for an expert) to tell a priori which phylogenetic reconstruction method—distance-based, ML or maybe maximum parsimony (MP)—should be chosen for any particular data set. ^ A number of factors, often hidden, influence the performance of a method. For example, it is generally understood that for a phylogenetically “difficult” data set more sophisticated methods (e.g., ML) tend to be more effective and thus should be chosen. However, it is the interplay of many factors that one needs to consider in order to avoid choosing an inferior method (potentially a costly mistake, both in terms of computational expenses and in terms of reconstruction accuracy.) ^ Chapter III of this dissertation details a phylogenetic reconstruction expert system that selects a superior proper method automatically. It uses a classifier (a Decision Tree-inducing algorithm) to map a new data set to the proper phylogenetic reconstruction method. ^

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Modelling and improving maintenance decisions:Having foresight with simulation and artificial intelligence

Machine breakdowns are one of the main sources of disruption and throughput fluctuation in highly automated production facilities. One element in reducing this disruption is ensuring that the maintenance team responds correctly to machine failures. It is, however, difficult to determine the current practice employed by the maintenance team, let alone suggest improvements to it. 'Knowledge based improvement' is a methodology that aims to address this issue, by (a) eliciting knowledge on current practice, (b) evaluating that practice and (c) looking for improvements. The methodology, based on visual interactive simulation and artificial intelligence methods, and its application to a Ford engine assembly facility are described. Copyright © 2002 Society of Automotive Engineers, Inc.

Knowledge based improvement:simulation and artificial intelligence for identifying and improving human decision-making in an operations systems

The performance of most operations systems is significantly affected by the interaction of human decision-makers. A methodology, based on the use of visual interactive simulation (VIS) and artificial intelligence (AI), is described that aims to identify and improve human decision-making in operations systems. The methodology, known as 'knowledge-based improvement' (KBI), elicits knowledge from a decision-maker via a VIS and then uses AI methods to represent decision-making. By linking the VIS and AI representation, it is possible to predict the performance of the operations system under different decision-making strategies and to search for improved strategies. The KBI methodology is applied to the decision-making surrounding unplanned maintenance operations at a Ford Motor Company engine assembly plant.

Evaluating the performance of a EuroDivisia index using artificial intelligence techniques

We compare two methods in order to predict inflation rates in Europe. One method uses a standard back propagation neural network and the other uses an evolutionary approach, where the network weights and the network architecture is evolved. Results indicate that back propagation produces superior results. However, the evolving network still produces reasonable results with the advantage that the experimental set-up is minimal. Also of interest is the fact that the Divisia measure of money is superior as a predictive tool over simple sum.

Evaluating the performance of a EuroDivisia index using artificial intelligence techniques

This paper compares two methods to predict in°ation rates in Europe. One method uses a standard back propagation neural network and the other uses an evolutionary approach, where the network weights and the network architecture are evolved. Results indicate that back propagation produces superior results. However, the evolving network still produces reasonable results with the advantage that the experimental set-up is minimal. Also of interest is the fact that the Divisia measure of money is superior as a predictive tool over simple sum.

Application of the Artificial Intelligence Algorithms for System Analysis of Multi Dimension Physiological Data for Developing Polyparametric Information System of Public Health Diagnostics

The polyparametric intelligence information system for diagnostics human functional state in medicine and public health is developed. The essence of the system consists in polyparametric describing of human functional state with the unified set of physiological parameters and using the polyparametric cognitive model developed as the tool for a system analysis of multitude data and diagnostics of a human functional state. The model is developed on the basis of general principles geometry and symmetry by algorithms of artificial intelligence systems. The architecture of the system is represented. The model allows analyzing traditional signs - absolute values of electrophysiological parameters and new signs generated by the model – relationships of ones. The classification of physiological multidimensional data is made with a transformer of the model. The results are presented to a physician in a form of visual graph – a pattern individual functional state. This graph allows performing clinical syndrome analysis. A level of human functional state is defined in the case of the developed standard (“ideal”) functional state. The complete formalization of results makes it possible to accumulate physiological data and to analyze them by mathematics methods.

Application of Artificial Intelligence Methods to Computer Design of Inorganic Compounds

In this paper the main problems for computer design of materials, which would have predefined properties, with the use of artificial intelligence methods are presented. The DB on inorganic compound properties and the system of DBs on materials for electronics with completely assessed information: phase diagram DB of material systems with semiconducting phases and DB on acousto-optical, electro-optical, and nonlinear optical properties are considered. These DBs are a source of information for data analysis. Using the DBs and artificial intelligence methods we have predicted thousands of new compounds in ternary, quaternary and more complicated chemical systems and estimated some of their properties (crystal structure type, melting point, homogeneity region etc.). The comparison of our predictions with experimental data, obtained later, showed that the average reliability of predicted inorganic compounds exceeds 80%. The perspectives of computational material design with the use of artificial intelligence methods are considered.

Formal Definition of Artificial Intelligence

* This publication is partially supported by the KT-DigiCult-Bg project.

About the Journal of RAAI ”News of Artificial Intelligence”

Beginning from 1991, Russian (initially Soviet) Association for Artificial Intelligence (RAAI) publishes the own journal ‘News of Artificial Intelligence’. The journal is founded on the initiative of the famous specialist in the field of Artificial Intelligence (AI), the first president of Soviet Association for Artificial Intelligence, the academician of Russian Academy of Natural Science (RANS), doctor of technical sciences (d.t.s.), professor D.A. Pospelov, which from 1991 up to 2001 was its main editor.