Knowledge discovery and data mining in biological databases

The new technologies for Knowledge Discovery from Databases (KDD) and data mining promise to bring new insights into a voluminous growing amount of biological data. KDD technology is complementary to laboratory experimentation and helps speed up biological research. This article contains an introduction to KDD, a review of data mining tools, and their biological applications. We discuss the domain concepts related to biological data and databases, as well as current KDD and data mining developments in biology.

Finite element modelling of dissipative structures for nonequilibrium chemical reactions in fluid-saturated porous media

We use the finite element method to model and predict the dissipative structures of chemical species for a nonequilibrium chemical reaction system in a fluid-saturated porous medium. In particular, we explore the conditions under which dissipative structures of the species may exist in the Brusselator type of nonequilibrium chemical reaction. Since this is the first time the finite element method and related strategies have been used to study the chemical instability problems in a fluid-saturated porous medium, it is essential to validate the method and strategies before they are put into application. For this purpose, we have rigorously derived the analytical solutions for dissipative structures of chemical species in a benchmark problem, which geometrically is a square. Comparison of the numerical solutions with the analytical ones demonstrates that the proposed numerical method and strategy are robust enough to solve chemical instability problems in a fluid-saturated porous medium. Finally, the related numerical results from two application examples indicate that both the regime and the magnitude of pore-fluid flow have significant effects on the nature of the dissipative structures that developed for a nonequilibrium chemical reaction system in a fluid-saturated porous medium. The motivation for this study is that self-organization under conditions of pore-fluid flow in a porous medium is a potential mechanism of the orebody formation and mineralization in the upper crust of the Earth. (C) 2000 Elsevier Science S.A. All rights reserved.

Finite element analysis of heat transfer and mineralization in layered hydrothermal systems with upward throughflow

We use the finite element method to solve the coupled problem between convective pore-fluid flow, heat transfer and mineralization in layered hydrothermal systems with upward throughflow. In particular, we present the improved rock alteration index (IRAI) concept for predicting the most probable precipitation and dissolution regions of gold (Au) minerals in the systems. To validate the numerical method used in the computation, analytical solutions to a benchmark problem have been derived. After the numerical method is validated, it is used to investigate the pattern of pore-fluid Aom, the distribution of temperature and the mineralization pattern of gold minerals in a layered hydrothermal system with upward throughflow. The related numerical results have demonstrated that the present concept of IRAI is useful and applicable for predicting the most probable precipitation and dissolution regions of gold (Au) minerals in hydrothermal systems. (C) 2000 Elsevier Science S.A. All rights reserved.

Finite element modeling of fluid-rock interaction problems in pore-fluid saturated hydrothermal/sedimentary basins

In order to use the finite element method for solving fluid-rock interaction problems in pore-fluid saturated hydrothermal/sedimentary basins effectively and efficiently, we have presented, in this paper, the new concept and numerical algorithms to deal with the fundamental issues associated with the fluid-rock interaction problems. These fundamental issues are often overlooked by some purely numerical modelers. (1) Since the fluid-rock interaction problem involves heterogeneous chemical reactions between reactive aqueous chemical species in the pore-fluid and solid minerals in the rock masses, it is necessary to develop the new concept of the generalized concentration of a solid mineral, so that two types of reactive mass transport equations, namely, the conventional mass transport equation for the aqueous chemical species in the pore-fluid and the degenerated mass transport equation for the solid minerals in the rock mass, can be solved simultaneously in computation. (2) Since the reaction area between the pore-fluid and mineral surfaces is basically a function of the generalized concentration of the solid mineral, there is a definite need to appropriately consider the dependence of the dissolution rate of a dissolving mineral on its generalized concentration in the numerical analysis. (3) Considering the direct consequence of the porosity evolution with time in the transient analysis of fluid-rock interaction problems; we have proposed the term splitting algorithm and the concept of the equivalent source/sink terms in mass transport equations so that the problem of variable mesh Peclet number and Courant number has been successfully converted into the problem of constant mesh Peclet and Courant numbers. The numerical results from an application example have demonstrated the usefulness of the proposed concepts and the robustness of the proposed numerical algorithms in dealing with fluid-rock interaction problems in pore-fluid saturated hydrothermal/sedimentary basins. (C) 2001 Elsevier Science B.V. All rights reserved.

Effects of hot intrusions on pore-fluid flow and heat transfer in fluid-saturated rocks

We use the finite element method to solve coupled problems between pore-fluid flow and heat transfer in fluid-saturated porous rocks. In particular, we investigate the effects of both the hot pluton intrusion and topographically driven horizontal flow on the distributions of the pore-flow velocity and temperature in large-scale hydrothermal systems. Since general mineralization patterns are strongly dependent on distributions of both the pore-fluid velocity and temperature fields, the modern mineralization theory has been used to predict the general mineralization patterns in several realistic hydrothermal systems. The related numerical results have demonstrated that: (1) The existence of a hot intrusion can cause an increase in the maximum value of the pore-fluid velocity in the hydrothermal system. (2) The permeability of an intruded pluton is one of the sensitive parameters to control the pore-fluid flow, heat transfer and ore body formation in hydrothermal systems. (3) The maximum value of the pore-fluid velocity increases when the bottom temperature of the hydrothermal system is increased. (4) The topographically driven flow has significant effects on the pore-fluid flow, temperature distribution and precipitation pattern of minerals in hydrothermal systems. (5) The size of the computational domain may have some effects on the pore-fluid flow and heat transfer, indicating that the size of a hydrothermal system may affect the pore-fluid flow and heat transfer within the system. (C) 2003 Elsevier Science B.V. All rights reserved.

An equivalent algorithm for simulating thermal effects of magma intrusion problems in porous rocks

An equivalent algorithm is proposed to simulate thermal effects of the magma intrusion in geological systems, which are composed of porous rocks. Based on the physical and mathematical equivalence, the original magma solidification problem with a moving boundary between the rock and intruded magma is transformed into a new problem without the moving boundary but with a physically equivalent heat source. From the analysis of an ideal solidification model, the physically equivalent heat source has been determined in this paper. The major advantage in using the proposed equivalent algorithm is that the fixed finite element mesh with a variable integration time step can be employed to simulate the thermal effect of the intruded magma solidification using the conventional finite element method. The related numerical results have demonstrated the correctness and usefulness of the proposed equivalent algorithm for simulating the thermal effect of the intruded magma solidification in geological systems. (C) 2003 Elsevier B.V. All rights reserved.

A note on the multiple partners assignment game

In the assignment game of Shapley and Shubik [Shapley, L.S., Shubik, M., 1972. The assignment game. I. The core, International journal of Game Theory 1, 11-130] agents are allowed to form one partnership at most. That paper proves that, in the context of firms and workers, given two stable payoffs for the firms there is a stable payoff which gives each firm the larger of the two amounts and also one which gives each of them the smaller amount. Analogous result applies to the workers. Sotomayor [Sotomayor, M., 1992. The multiple partners game. In: Majumdar, M. (Ed.), Dynamics and Equilibrium: Essays in Honor to D. Gale. Mcmillian, pp. 322-336] extends this analysis to the case where both types of agents may form more than one partnership and an agent`s payoff is multi-dimensional. Instead, this note concentrates in the total payoff of the agents. It is then proved the rather unexpected result that again the maximum of any pair of stable payoffs for the firms is stable but the minimum need not be, even if we restrict the multiplicity of partnerships to one of the sides. (C) 2009 Elsevier B.V. All rights reserved.

Bayesian analysis of the error correction model

This paper presents a method for estimating the posterior probability density of the cointegrating rank of a multivariate error correction model. A second contribution is the careful elicitation of the prior for the cointegrating vectors derived from a prior on the cointegrating space. This prior obtains naturally from treating the cointegrating space as the parameter of interest in inference and overcomes problems previously encountered in Bayesian cointegration analysis. Using this new prior and Laplace approximation, an estimator for the posterior probability of the rank is given. The approach performs well compared with information criteria in Monte Carlo experiments. (C) 2003 Elsevier B.V. All rights reserved.

Controllability of Volterra-Fredholm type systems in Banach spaces

We show the results in Chalishajar [Controllability of mixed Volterra-Fredholm-type integro-differential systems in Banach space, J. Franklin Inst. 344(1) (2007) 12-21] and Chang and Chalishajar [Controllability of mixed Volterra-Fredholm type integro-differential systems in Banach space, J. Franklin Inst., doi:10.1016/j. jfranklin.2008.02.002] are only valid for ordinary differential control systems. As a result the examples provided cannot be recovered as applications of the abstract results. (C) 2008 The Franklin Institute. Published by Elsevier Ltd. All rights reserved.

Numerical simulation of double-diffusion driven convective flow and rock alteration in three-dimensional fluid-saturated geological fault zones

Numerical methods are used to simulate the double-diffusion driven convective pore-fluid flow and rock alteration in three-dimensional fluid-saturated geological fault zones. The double diffusion is caused by a combination of both the positive upward temperature gradient and the positive downward salinity concentration gradient within a three-dimensional fluid-saturated geological fault zone, which is assumed to be more permeable than its surrounding rocks. In order to ensure the physical meaningfulness of the obtained numerical solutions, the numerical method used in this study is validated by a benchmark problem, for which the analytical solution to the critical Rayleigh number of the system is available. The theoretical value of the critical Rayleigh number of a three-dimensional fluid-saturated geological fault zone system can be used to judge whether or not the double-diffusion driven convective pore-fluid flow can take place within the system. After the possibility of triggering the double-diffusion driven convective pore-fluid flow is theoretically validated for the numerical model of a three-dimensional fluid-saturated geological fault zone system, the corresponding numerical solutions for the convective flow and temperature are directly coupled with a geochemical system. Through the numerical simulation of the coupled system between the convective fluid flow, heat transfer, mass transport and chemical reactions, we have investigated the effect of the double-diffusion driven convective pore-fluid flow on the rock alteration, which is the direct consequence of mineral redistribution due to its dissolution, transportation and precipitation, within the three-dimensional fluid-saturated geological fault zone system. (c) 2005 Elsevier B.V. All rights reserved.

Supporting content-based image retrieval and computer-aided diagnosis systems with association rule-based techniques

In this work, we take advantage of association rule mining to support two types of medical systems: the Content-based Image Retrieval (CBIR) systems and the Computer-Aided Diagnosis (CAD) systems. For content-based retrieval, association rules are employed to reduce the dimensionality of the feature vectors that represent the images and to improve the precision of the similarity queries. We refer to the association rule-based method to improve CBIR systems proposed here as Feature selection through Association Rules (FAR). To improve CAD systems, we propose the Image Diagnosis Enhancement through Association rules (IDEA) method. Association rules are employed to suggest a second opinion to the radiologist or a preliminary diagnosis of a new image. A second opinion automatically obtained can either accelerate the process of diagnosing or to strengthen a hypothesis, increasing the probability of a prescribed treatment be successful. Two new algorithms are proposed to support the IDEA method: to pre-process low-level features and to propose a preliminary diagnosis based on association rules. We performed several experiments to validate the proposed methods. The results indicate that association rules can be successfully applied to improve CBIR and CAD systems, empowering the arsenal of techniques to support medical image analysis in medical systems. (C) 2009 Elsevier B.V. All rights reserved.

Analysis of flexural waves excited by rectangular contact type transducers

In this paper, an attempt was made to investigate a fundamental problem related to the flexural waves excited by rectangular transducers. Due to the disadvantages of the Green's function approach for solving this problem, a direct and effective method is proposed using a multiple integral transform method and contour integration technique. The explicit frequency domain solutions obtained from this newly developed method are convenient for understanding transducer behavior and theoretical optimization and experimental calibration of rectangular transducers. The time domain solutions can then be easily obtained by using the fast Fourier transform technique. (C) 2001 Elsevier Science B.V. All rights reserved.

Multi-threading and message communication in Qu-Prolog

This paper presents the multi-threading and internet message communication capabilities of Qu-Prolog. Message addresses are symbolic and the communications package provides high-level support that completely hides details of IP addresses and port numbers as well as the underlying TCP/IP transport layer. The combination of the multi-threads and the high level inter-thread message communications provide simple, powerful support for implementing internet distributed intelligent applications.

Economic and environmental impacts of pollution control in a system of environment and economic interdependence

The importance of the rate of change of the pollution stock in determining the damage to the environment has been an issue of increasing concern in the literature. This paper uses a three-sector (economy, population and environment), non-linear, discrete time, calibrated model to examine pollution control. The model explicitly links economic growth to the health of the environment. The stock of natural resources is affected by the rate of pollution flows, through their impact on the regenerative capacity of the natural resource stock. This can shed useful insights into pollution control strategies, particularly in developing countries where environmental resources are crucial for production in many sectors of the economy. Simulation exercises suggested that, under plausible assumptions, it is possible to reverse undesirable transient dynamics through pollution control expenditure, but this is dependent upon the strategies used for control. The best strategy is to spend money fostering the development of production technologies that reduce pollution rather than spending money dealing with the effects of the pollution flow into the environment. (C) 2001 Elsevier Science Ltd. All rights reserved.

Existence of a semicontinuous or continuous utility function: a unified approach and an elementary proof

In this paper, we present a new unified approach and an elementary proof of a very general theorem on the existence of a semicontinuous or continuous utility function representing a preference relation. A simple and interesting new proof of the famous Debreu Gap Lemma is given. In addition, we prove a new Gap Lemma for the rational numbers and derive some consequences. We also prove a theorem which characterizes the existence of upper semicontinuous utility functions on a preordered topological space which need not be second countable. This is a generalization of the classical theorem of Rader which only gives sufficient conditions for the existence of an upper semicontinuous utility function for second countable topological spaces. (C) 2002 Elsevier Science B.V. All rights reserved.