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PubMed2004

Mapping of microbial pathways through constrained mapping of orthologous genes.

We present a novel computer algorithm for mapping biological pathways from one prokaryotic genome to another. The algorithm maps genes in a known pathway to their homologous genes (if any) in a target genome that is most consistent with (a) predicted orthologous gene relationship, (b) predicted operon structures, and (c) predicted co-regulation relationship of operons. Mathematically, we have formulated this problem as a constrained minimum spanning tree problem (called a Steiner network problem), and demonstrated that this formulation has the desired property through applications. We have solved this mapping problem using a combinatorial optimization algorithm, with guaranteed global optimality. We have implemented this algorithm as a computer program, called PMAP. Our test results on pathway mapping are highly encouraging -- we have mapped a number of pathways of H. influenzae, B. subtilis, H. pylori, and M. tuberculosis to E. coli using P-MAP, whose homologous pathways in E coli. are known and hence the mapping accuracy could be checked. We have then mapped known E. coli pathways in the EcoCyc database to the newly sequenced organism Synechococcus sp WH8102, and predicted 158 Synechococcus pathways. Detailed analyses on the predicted pathways indicate that P-MAP's mapping results are consistent with our general knowledge about (local) pathways. We believe that P-MAP will be a useful tool for microbial genome annotation projects and inference of individual microbial pathways.

Algorithms↗

PubMed2003

State-estimation approach to the nonstationary optical tomography problem.

We propose a new numerical approach to the nonstationary optical (diffusion) tomography (OT) problem. The assumption in the method is that the absorption and/or diffusion coefficients are nonstationary in the sense that they may exhibit significant changes during the time that is needed to measure data for one traditional image frame. In the proposed method, the OT problem is formulated as a state-estimation problem. Within the state-estimation formulation, the absorption and/or diffusion coefficients are considered a stochastic process. The objective is to estimate a sequence of states for the process when the state evolution model for the process, the observation model for OT experiments, and data on the exterior boundary are given. In the proposed method, the state estimates are computed by using Kalman filtering techniques. The performance of the proposed method is evaluated on the basis of synthetic data. The simulations also illustrate that further improvements to the results in nonstationary applications can be obtained by adjustment of the measurement protocol.

Models, Theoretical↗

PubMed2006

Methods to detect objects in photon-limited images.

We investigate the problem of detecting and localizing a known signal in a photon-limited image, where Poisson noise is the dominant source of image degradation. For this purpose we developed and evaluated three new algorithms. The first two are based on the impulse restoration (IR) principle and the third is based on the generalized likelihood ratio test (GLRT). In the IR approach, the problem is formulated as one of restoring a delta function at the location of the desired object. In the GLRT approach, which is a well-known variation on the optimal likelihood ratio test, the problem is formulated as a hypothesis testing problem, in which the unknown background intensity of the image and the intensity scale of the object are obtained by maximum-likelihood estimation. We used Monte Carlo simulations and localization receiver operating characteristic (LROC) curves to evaluate the proposed algorithms quantitatively. LROC curves demonstrate the ability of an algorithm to detect and locate objects in a scene correctly. Our simulations demonstrate that the GLRT approach is superior to all other tested algorithms.

Algorithms↗

PubMed1995

Ultrasonic approach to obtaining partial thermodynamic characteristics of solutions.

We describe a method for evaluating the thermodynamic characteristics both of pure liquids and of solutes in solutions using data derived from ultrasonic velocity measurements. The principal possibility of using ultrasound velocity lies in the fact that the velocity of ultrasound is a simple function of the adiabatic compressibility. The problem is formulated as an initial value problem for the parabolic type differential equations in partial derivatives. The validity of the method is demonstrated by calculation of the thermodynamic parameters for water, glycine and alanine in aqueous solutions at infinite dilution.

Alanine↗

PubMed2004

A modeling framework for optimal long-term care insurance purchase decisions in retirement planning.

The level of need and costs of obtaining long-term care (LTC) during retired life require that planning for it is an integral part of retirement planning. In this paper, we divide retirement planning into two phases, pre-retirement and post-retirement. On the basis of four interrelated models for health evolution, wealth evolution, LTC insurance premium and coverage, and LTC cost structure, a framework for optimal LTC insurance purchase decisions in the pre-retirement phase is developed. Optimal decisions are obtained by developing a trade-off between post-retirement LTC costs and LTC insurance premiums and coverage. Two-way branching models are used to model stochastic health events and asset returns. The resulting optimization problem is formulated as a dynamic programming problem. We compare the optimal decision under two insurance purchase scenarios: one assumes that insurance is purchased for good and other assumes it may be purchased, relinquished and re-purchased. Sensitivity analysis is performed for the retirement age.

Aged↗

PubMed1989

Allocating blood to hospitals.

A method is proposed for the allocation of units of blood from a regional blood transfusion centre to the hospitals of its area, taking into consideration the characteristics of the individual hospitals, such as the transfusion activity, the demand of each hospital and the regional blood transfusion service policy concerning the allocation of units of blood expressed through a utility function. The problem is formulated as a stochastic programming problem but reduces to a linear programming problem and therefore is easily applicable. The method is suitable for application in systems with a National Health Service system, such as the British. Finally the results are given of an application to the despatches of units of blood in the Regional Blood Transfusion Service of Glasgow and West of Scotland.

Blood Banks↗

PubMed2004

Excitable dynamics and threshold sets in nonlinear systems.

Following our previous work [J. Zagora et al., Faraday Discuss. 120, 313 (2001)], we present a quantitative definition of a threshold that separates large-amplitude excitatory responses and small-amplitude nonexcitatory responses to a perturbation of an excitable system with a single globally attracting steady state. For systems with two variables, finding the threshold set is formulated as a boundary value problem supplemented by a condition of a maximum separation rate. For this highly nonlinear problem we formulate a numerical method based on the use of multiple shooting and continuation methods. The threshold phenomena are examined by using an example dynamical system with chemical reaction--the bromate-sulfite-ferrocyanide system. In a model of this reaction we find the threshold set, construct a bifurcation diagram and discuss how excitability can vanish. These results are compared with recent experiments. We also discuss relevance of other definitions of the excitability threshold including the concept of nullclines.

Journal Article↗

PubMed2005

Dynamic motion planning for the design of robotic gait rehabilitation.

In this paper we examine a method to control the stepping motion of a paralyzed person suspended over a treadmill using a robot attached to the pelvis. A leg swing motion is created by moving the pelvis without contact with the legs. The problem is formulated as an optimal control problem for an underactuated articulated chain. The optimal control problem is converted into a discrete parameter optimization and an efficient gradient-based algorithm is used to solve it. Motion capture data from an unimpaired human subject is compared to the simulation results from the dynamic motion optimization. Our results suggest that it is feasible to drive repetitive stepping on a treadmill by a paralyzed person by assisting in torso movement alone. The optimized, pelvic motion strategies are comparable to "hip-hiking" gait strategies used by people with lower limb prostheses or hemiparesis. The resulting motions can be found at the web site http://ww.eng.uci.edu/-chwang/project/stepper/stepper.html.

Computer Simulation↗

PubMed2005

Fast and cheap genome wide haplotype construction via optical mapping.

We describe an efficient algorithm to construct genome wide haplotype restriction maps of an individual by aligning single molecule DNA fragments collected with Optical Mapping technology. Using this algorithm and small amount of genomic material, we can construct the parental haplotypes for each diploid chromosome for any individual. Since such haplotype maps reveal the polymorphisms due to single nucleotide differences (SNPs) and small insertions and deletions (RFLPs), they are useful in association studies, studies involving genomic instabilities in cancer, and genetics, and yet incur relatively low cost and provide high throughput. If the underlying problem is formulated as a combinatorial optimization problem, it can be shown to be NP-complete (a special case of K-population problem). But by effectively exploiting the structure of the underlying error processes and using a novel analog of the Baum-Welch algorithm for HMM models, we devise a probabilistic algorithm with a time complexity that is linear in the number of markers for an epsilon-approximate solution. The algorithms were tested by constructing the first genome wide haplotype restriction map of the microbe T. pseudoana, as well as constructing a haplotype restriction map of a 120 Mb region of Human chromosome 4. The frequency of false positives and false negatives was estimated using simulated data. The empirical results were found very promising.

Algorithms↗

PubMed2000

An optimization approach to design of generalized BSB neural associative memories.

This article is concerned with the synthesis of the optimally performing GBSB (generalized brain-state-in-a-box) neural associative memory given a set of desired binary patterns to be stored as asymptotically stable equilibrium points. Based on some known qualitative properties and newly observed fundamental properties of the GBSB model, the synthesis problem is formulated as a constrained optimization problem. Next, we convert this problem into a quasi-convex optimization problem called GEVP (generalized eigenvalue problem). This conversion is particularly useful in practice, because GEVPs can be efficiently solved by recently developed interior point methods. Design examples are given to illustrate the proposed approach and to compare with existing synthesis methods.

Association Learning↗

PubMed2005

Online fault adaptive control for efficient resource management in Advanced Life Support Systems.

This article presents the design and implementation of a controller scheme for efficient resource management in Advanced Life Support Systems. In the proposed approach, a switching hybrid system model is used to represent the dynamics of the system components and their interactions. The operational specifications for the controller are represented by utility functions, and the corresponding resource management problem is formulated as a safety control problem. The controller is designed as a limited-horizon online supervisory controller that performs a limited forward search on the state-space of the system at each time step, and uses the utility functions to decide on the best action. The feasibility and accuracy of the online algorithm can be assessed at design time. We demonstrate the effectiveness of the scheme by running a set of experiments on the Reverse Osmosis (RO) subsystem of the Water Recovery System (WRS).

Algorithms↗

PubMed2003

Optimization of the treatment of piggery wastes in water hyacinth ponds.

This work investigates the optimal management of water hyacinth ponds for the improvement of piggery waste treatment. The optimal harvesting strategy for the water hyacinth was studied using a single mathematical model. The water hyacinth optimal harvesting problem was formulated as an optimal control problem that was solved by application of Pontryagin's Maximum Principle. The optimization of the water hyacinth control in the pond indicates that the plant density should be reduced whenever it reaches half of the maximum capacity for growth. Two experimental systems were used to validate the mathematical model, one in real scale and the other in pilot scale. The results demonstrated the feasibility of the proposed harvesting strategy. For example, a comparison of the total nitrogen removal in the different pilot ponds confirmed the modeling results, in that the performance of the pond maintained with 50% water hyacinth cover was better than the others.

Animals↗

PubMed2002

Asking for 'rules of thumb': a way to discover tacit knowledge in general practice.

BACKGROUND: Research in decision-making has identified heuristics (rules of thumb) as shortcuts to simplify search and choice. OBJECTIVE: To find out if GPs recognize the use of rules of thumb and if they could describe what they looked like. METHODS: An explorative and descriptive study was set up using focus group interviews. The interview guide contained the questions: Do you recognize the use of rules of thumb? Are you able to give some examples? What are the benefits and dangers in using rules of thumb? Where do they come from? The interviews were transcribed and analysed using the templates in the interview guide, and the examples of rules were classified by editing analysis. RESULTS: Four groups with 23 GPs were interviewed. GPs recognized using rules of thumb, producing examples covering different aspects of the consultation. The rules for somatic problems were formulated as axiomatic simplified medical knowledge and taken for granted, while rules for psychosocial problems were formulated as expressions of individual experience and were followed by an explanation. The rules seemed unaffected by the sparse objections given. A GP's clinical experience was judged a prerequisite for applying the rules. The origin of many rules was via word-of-mouth from a colleague. The GPs acknowledged the benefits of using the rules, thereby simplifying work. CONCLUSION: GPs recognize the use of rules of thumb as an immediate and semiconscious kind of knowledge that could be called tacit knowledge. Using rules of thumb might explain why practice remains unchanged although educational activities result in more elaborate knowledge.

Decision Making↗

PubMed1993

Working memory and the Self-Ordered Pointing Task: further evidence of early prefrontal decline in normal aging.

Two major lines of investigation are currently clarifying the nature of the impairment of working memory associated with normal aging. Cognitive psychology has formulated the problem in terms such as the balance of impairment of encoding, retrieval, storage and/or attention, whereas neuropsychology has formulated the problem in terms such as the balance of frontal (executive) versus temporal (mnemonic) degeneration. The findings of this study support the contention that the primary impairment of working memory in early normal aging is an active attentional executive processing deficit. Specifically, on the Self-Ordered Pointing Task, there is significantly ineffective exploitation of top-down clustering strategy as a function of aging. On this task, self-organization of encoding and retrieval must occur simultaneously with ongoing responding. The finding cannot be explained as an impairment of encoding, retrieval, storage, or build-up and/or release of proactive interference, since indexes of these did not discriminate young-adult from middle-aged samples.

Adult↗

PubMed1980

[The problem-oriented case report--a method for the improvement of clinical training].

Abroad in the clinical education of the students the problem-oriented case report after Weed stood the test as a new training principle. In contrast to the classical case report the complaints and findings are formulated as problems and summarized in a list of problems. As problem is regarded what needs a diagnostic or therapeutic solution or a change of the patient's behaviour. For solution of the problem in a second step, the plan, the establishment of the ways of solution for every problem is done. In the notices of the course, the third part, the newly got findings are distributed to the adequate problems and their valency for the solution of the problem is tested. As advantages for the training are regarded: the establishment of the problems is more complete, the classification of psychic, social and health-educational problems is simpler. The physician is compelled to go over from the fixation on an individual problem to the valuation of all problems and to the correlations of several problems. Thus in the increasing specialisation an integrating role belongs to the problem-orientated case report. Independent formulation of the problems, development of the diagnostic and therapeutic steps, classification and valuation of their results in the notices of the course further the own responsibility of the student and renders possible a better control for the clinical instructor. The problem-oriented case report also forms the prerequisites for a problem-related letter of the physician.

Education, Medical↗

PubMed1998

An optimal and efficient new gridding algorithm using singular value decomposition.

The problem of handling data that falls on a nonequally spaced grid occurs in numerous fields of science, ranging from radio-astronomy to medical imaging. In MRI, this condition arises when sampling under time-varying gradients in sequences such as echo-planar imaging (EPI), spiral scans, or radial scans. The technique currently being used to interpolate the nonuniform samples onto a Cartesian grid is called the gridding algorithm. In this paper, a new method for uniform resampling is presented that is both optimal and efficient. It is first shown that the resampling problem can be formulated as a problem of solving a set of linear equations Ax = b, where x and b are vectors of the uniform and nonuniform samples, respectively, and A is a matrix of the sinc interpolation coefficients. In a procedure called Uniform Re-Sampling (URS), this set of equations is given an optimal solution using the pseudoinverse matrix which is computed using singular value decomposition (SVD). In large problems, this solution is neither practical nor computationally efficient. Another method is presented, called the Block Uniform Re-Sampling (BURS) algorithm, which decomposes the problem into solving a small set of linear equations for each uniform grid point. These equations are a subset of the original equations Ax = b and are once again solved using SVD. The final result is both optimal and computationally efficient. The results of the new method are compared with those obtained using the conventional gridding algorithm via simulations.

Algorithms↗

PubMed2005

An alternative approach for neural network evolution with a genetic algorithm: crossover by combinatorial optimization.

In this work we present a new approach to crossover operator in the genetic evolution of neural networks. The most widely used evolutionary computation paradigm for neural network evolution is evolutionary programming. This paradigm is usually preferred due to the problems caused by the application of crossover to neural network evolution. However, crossover is the most innovative operator within the field of evolutionary computation. One of the most notorious problems with the application of crossover to neural networks is known as the permutation problem. This problem occurs due to the fact that the same network can be represented in a genetic coding by many different codifications. Our approach modifies the standard crossover operator taking into account the special features of the individuals to be mated. We present a new model for mating individuals that considers the structure of the hidden layer and redefines the crossover operator. As each hidden node represents a non-linear projection of the input variables, we approach the crossover as a problem on combinatorial optimization. We can formulate the problem as the extraction of a subset of near-optimal projections to create the hidden layer of the new network. This new approach is compared to a classical crossover in 25 real-world problems with an excellent performance. Moreover, the networks obtained are much smaller than those obtained with classical crossover operator.

Algorithms↗

PubMed2004

Stable real-time 3D tracking using online and offline information.

We propose an efficient real-time solution for tracking rigid objects in 3D using a single camera that can handle large camera displacements, drastic aspect changes, and partial occlusions. While commercial products are already available for offline camera registration, robust online tracking remains an open issue because many real-time algorithms described in the literature still lack robustness and are prone to drift and jitter. To address these problems, we have formulated the tracking problem in terms of local bundle adjustment and have developed a method for establishing image correspondences that can equally well handle short and wide-baseline matching. We then can merge the information from preceding frames with that provided by a very limited number of keyframes created during a training stage, which results in a real-time tracker that does not jitter or drift and can deal with significant aspect changes.

Algorithms↗