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PubMed1998

Hybrid interior point training of modular neural networks.

Modular neural networks use a single gating neuron to select the outputs of a collection of agent neurons. Expectation-maximization (EM) algorithms provide one way of training modular neural networks to approximate non-linear functionals. This paper introduces a hybrid interior-point (HIP) algorithm for training modular networks. The HIP algorithm combines an interior-point linear programming (LP) algorithm with a Newton-Raphson iteration in such a way that the computational efficiency of the interior point LP methods is preserved. The algorithm is formally proven to converge asymptotically to locally optimal networks with a total computational cost that scales in a polynomial manner with problem size. Simulation experiments show that the HIP algorithm produces networks whose average approximation error is better than that of EM-trained networks. These results also demonstrate that the computational cost of the HIP algorithm scales at a slower rate than the EM-procedure and that, for small-size networks, the total computational costs of both methods are comparable.

Journal Article↗

PubMed1997

A Study of the Mean Field Approach to Knapsack Problems.

The mean field theory approach to knapsack problems is extended to multiple knapsacks and generalized assignment problems with Potts mean field equations governing the dynamics. Numerical tests against "state of the art" conventional algorithms shows good performance for the mean field approach. The inherently parallelism of the mean field equations makes them suitable for direct implementations in microchips. It is demonstrated numerically that the performance is essentially not affected when only a limited number of bits is used in the mean field equations. Also, a hybrid algorithm with linear programming and mean field components is showed to further improve the performance for the difficult homogeneous N x M knapsack problem. Copyright 1997 Elsevier Science Ltd. All Rights Reserved.

Journal Article↗

PubMed1999

Solving the N-bit parity problem using neural networks.

In this letter, a constructive solution to the N-bit parity problem is provided with a neural network that allows direct connections between the input layer and the output layer. The present approach requires no training and adaptation, and thus it warrants the use of the simple threshold activation function for the output and hidden layer neurons. It is previously shown that this choice of activation function and network structure leads to several solutions for the 3-bit parity problem obtained using linear programming. One of the solutions for the 3-bit parity problem is then generalized to obtain a solution for the N-bit parity problem using left floor N/2 right floor hidden layer neurons. It is shown that through the choice of a "staircase" type activation function, the left floor N/2 right floor hidden layer neurons can be further combined into a single hidden layer neuron.

Journal Article↗

PubMed1992

Computer-aided optimization of choice and positioning of bone plates and screws used for internal fixation of mandibular fractures.

The present study describes a biomechanical integrated model of the mandibular system in which the maxilla and mandible, the masticatory muscles, and the temporomandibular joints are regarded as one system. In this model, strains in plate-osteosynthesis devices for internal fixation of mandibular fractures can be minimized by optimizing their positions. The model evaluates maximal bite force strategies on all possible dental elements; it uses a linear programming technique and a muscle architecture model, resulting in muscle recruitment patterns. The shape of a "standard" lower jaw is digitized by means of a three-dimensional (3-D) coordinate retrieval device and drawn on a computer screen after its dimensions have been changed according to the clinical case at hand. The 3-D location of the fracture as well as the anatomic restrictions for screw placement can be indicated on the screen. Osteosynthesis devices can be indicated in terms of dimensions, number, and material properties.

Biomechanical Phenomena↗

PubMed2000

A probabilistic and decision-theoretic approach to the management of infectious disease at the ICU.

The medical community is presently in a state of transition from a situation dominated by the paper medical record to a future situation where all patient data will be available on-line by an electronic clinical information system. In data-intensive clinical environments, such as intensive care units (ICUs), clinical patient data are already fully managed by such systems in a number of hospitals. However, providing facilities for storing and retrieving patient data to clinicians is not enough; clinical information systems should also offer facilities to assist clinicians in dealing with hard clinical problems. Extending an information system's capabilities by integrating it with a decision-support system may be a solution. In this paper, we describe the development of a probabilistic and decision-theoretic system that aims to assist clinicians in diagnosing and treating patients with pneumonia in the intensive-care unit. Its underlying probabilistic-network model includes temporal knowledge to diagnose pneumonia on the basis of the likelihood of laryngotracheobronchial-tree colonisation by pathogens, and symptoms and signs actually present in the patient. Optimal antimicrobial therapy is selected by balancing the expected efficacy of treatment, which is related to the likelihood of particular pathogens causing the infection, against the spectrum of antimicrobial treatment. The models were built on the basis of expert knowledge. The patient data that were available were of limited value in the initial construction of the models because of problems of incompleteness. In particular, detailed temporal information was missing. By means of a number of different techniques, among others from the theory of linear programming, these data have been used to check the probabilistic information elicited from infectious-disease experts. The results of an evaluation of a number of slightly different models using retrospective patient data are discussed as well.

Anti-Bacterial Agents↗

PubMed2000

Hybrid optimization techniques for the workshift and rest assignment of nursing personnel.

In this paper, a detailed model and an efficient solution methodology for the monthly workshift and rest assignment of hospital nursing personnel is presented. A model that satisfies the rules of a typical hospital environment based both on published research data and on local hospital requirements is designed. A hybrid methodology that utilizes the strengths of operations research and artificial intelligence was used for the solution of the problem. In particular, an approximate integer linear programming (ILP) model is firstly solved and its solution is further improved using local search techniques. Finally, a tabu search strategy that uses as its neighborhood the solution space that the local heuristics define is presented. The use of heuristics is required because one of the main user requirements involving the user preference for specific workstretch patterns is not, for efficiency reasons, explicitly modeled in the ILP. In addition, for comparison and evaluation purposes the CLP based ILOG solver is also used to solve the same problem. The inferior computational results obtained with the ILOG solver do verify the speed and efficiency of the hybrid solution approach suggested in this paper. Extensive computational results are presented together with a detailed discussion on the quality, the computational efficiency and the operational acceptability of the solutions.

Artificial Intelligence↗

PubMed1999

Brachytherapy optimal planning with application to intravascular radiation therapy.

We have been studying brachytherapy planning with the objective of minimizing the maximum deviation of the delivered dose from prescribed dose bounds for treatment volumes. A general framework for optimal treatment planning is presented and the minmax optimization is formulated as a linear program. Dose rate calculations are based on the dosimetry formulation of the American Association of Physicists in Medicine, Task Group 43. We apply the technique to optimal planning for intravascular brachytherapy of intimal hyperplasia using ultrasound data and 192Ir seeds. The planning includes determination of an optimal dwell-time sequence for a train of seeds that deliver radiation while stepping through the vessel lesion. The results illustrate the advantage of this strategy over the common approach of delivering radiation by positioning a single train of seeds along the whole lesion.

Algorithms↗

PubMed2000

What is the cost of a healthy diet in terms of achieving RDAs?

OBJECTIVE: Assessing how the Italian average food pattern would be affected in terms of consumption structure and expenditure by the adoption of nutritional prescriptions. DESIGN: A linear programming model with nutritional and food habits constraints was employed to generate a pattern following recommended daily allowances (RDAs) and nutritional guidelines provided for the Italian population. SETTING: Food consumption data from ISTAT Household Budget Survey of Italian population. SUBJECTS: Italian families investigated by the Family Budget Survey of the National Institute of Statistics. RESULTS: Compared to actual behaviour, the pattern generated by the model implies an increased consumption of vegetables, pasta, rice and fresh fish, and a decreased consumption of meats, bread, sugars and cakes, and especially fats and oils. At given prices, total expenditure is lower than actual expenditure. CONCLUSIONS: Differences between actual behaviour and the generated pattern are consistent with long-term trends in food consumption. The adoption of RDAs is unlikely to result in an increased food expenditure.

Budgets↗

PubMedDate not supplied

13C NMR evidence for pyruvate kinase flux attenuation underlying suppressed acid formation in Bacillus subtilis.

When batch and continuous Bacillus subtilis cultures are provided with a small amount of citrate, acid production ceases, carbon yield increases by more than 2-fold, and the productivity of recombinant protein increases. It has been hypothesized that pyruvate kinase activity is attenuated, which in turn lowers glucose flux and minimizes the acid overflow prompted by low Krebs cycle capacity. To complement existing enzyme activity, linear programming, and metabolite pool studies, (13)C NMR studies were performed. Atom mapping and isotopomer mapping matrix methods were used to select the best glucose label. "Best" was defined such that the NMR spectra of glutamate associated with metabolizing labeled glucose via the different candidate metabolic trafficking scenarios would differ considerably in fine structure (e.g., relative singlet intensities). When experiments were performed with 1-(13)C glucose, the observed NMR spectra corresponded well to the one predicted to arise when the metabolic trafficking occurs according to a pyruvate kinase attenuation scenario. This evidence further fortifies the prospects for successfully basing a metabolic engineering strategy on reducing pyruvate kinase activity to better match glycolytic and Krebs cycle capacities.

Bacillus subtilis↗

PubMedDate not supplied

Flux balance analysis of photoautotrophic metabolism.

Photosynthesis is the principal process responsible for fixation of inorganic carbon dioxide into organic molecules with sunlight as the energy source. Potentially, many chemicals could be inexpensively produced by photosynthetic organisms. Mathematical modeling of photoautotrophic metabolism is therefore important to evaluate maximum theoretical product yields and to deeply understand the interactions between biochemical energy, carbon fixation, and assimilation pathways. Flux balance analysis based on linear programming is applied to photoautotrophic metabolism. The stoichiometric network of a model photosynthetic prokaryote, Synechocystis sp. PCC 6803, has been reconstructed from genomic data and biochemical literature and coupled with a model of the photophosphorylation processes. Flux map topologies for the hetero-, auto-, and mixotrophic modes of metabolism under conditions of optimal growth were determined and compared. The roles of important metabolic reactions such as the glyoxylate shunt and the transhydrogenase reaction were analyzed. We also theoretically evaluated the effect of gene deletions or additions on biomass yield and metabolic flux distributions.

Biomass↗

PubMedDate not supplied

A computational procedure for optimal engineering interventions using kinetic models of metabolism.

The identification of optimal intervention strategies is a key step in designing microbial strains with enhanced capabilities. In this paper, we propose a general computational procedure to determine which genes/enzymes should be eliminated, repressed or overexpressed to maximize the flux through a product of interest for general kinetic models. The procedure relies on the generalized linearization of a kinetic description of the investigated metabolic system and the iterative application of mixed-integer linear programming (MILP) optimization to hierarchically identify all engineering interventions allowing for reaction eliminations and/or enzyme level modulations. The effect of the magnitude of the allowed changes in concentrations and enzyme levels is investigated, and a variant of the method to explore high-fold changes in enzyme levels is also analyzed. The proposed framework is demonstrated using a kinetic model modeling part of the central carbon metabolism of E. coli for serine overproduction. The proposed computational procedure is a general approach that can be applied to any metabolic system for which a kinetic description is provided.

Computer Simulation↗

PubMedDate not supplied

Medium term planning of biopharmaceutical manufacture with uncertain fermentation titers.

The growing trend of employing multiproduct manufacturing facilities along with the randomness inherent in the biopharmaceutical manufacturing environment is creating significant scheduling and planning challenges for the biopharmaceutical industry. This work focuses on capturing the effect of uncertainty in fermentation titers when optimizing the planning of biopharmaceutical manufacturing campaigns. A mixed integer linear programming (MILP) model based on previous work is derived via chance constrained programming (CCP). The methodology is applied to two illustrative examples, and the results are compared with those from the deterministic model and a multiscenario model accompanied by an iterative construction algorithm. The computational results indicate that the proposed methodology offers significant improvements in solution quality over the compared approaches and presents an opportunity for biopharmaceutical manufacturers to make better medium term planning decisions, particularly under uncertain manufacturing conditions.

Algorithms↗

PubMedDate not supplied

Optimal design of protein production plants with time and size factor process models.

In this work we propose an optimization model for the design of a biotechnological multiproduct batch plant. A first level of detail posynomial model is constructed for each unit, as well as decisions regarding the structural optimization of the plant. A particular feature of this model is that it contains composite units in which semicontinuous items operate on the material contained by batch items. This occurs in the purification steps, in particular with the microfilters operating between retentate and permeate vessels, and with the homogenizer and ultrafilters operating on the material contained in a batch holding vessel. Also, the unit models rely on batch operating time expressions that depend on both the batch size and the size of semicontinuous items. The model takes into account all of the available options to increase the efficiency of the batch plant design: unit duplication in-phase and out-of-phase and intermediate storage tanks. The resulting mathematical model for the minimization of the plant capital cost is a mixed integer non-linear program (MINLP), which is solved to global optimality with an implementation of the outer approximation/ equality relaxation/ augmented penalty (OA/ER/AP) method. A plant that produces four recombinant proteins in eight processing stages is used to illustrate the proposed approach. An interesting feature of this example is that it represents an attempt to standardize a plant for the production of both therapeutic and nontherapeutic proteins; the model applied is generic and can thus be applied to any such modular plant. Results indicate that the best solution in terms of minimal capital cost contains no units in parallel and with intermediate storage tank allocation.

Algorithms↗

PubMed2001

Cell surface electrochemical heterogeneity of the Fe(III)-reducing bacteria Shewanella putrefaciens.

Acid-base titration experiments and electrostatic force microscopy (EFM) were used to investigate the cell surface electrochemical heterogeneity of the Fe(III)-reducing bacteria, Shewanella putrefaciens. The acid-base titrations extended from pH 4 to 10, and the titration data were fit using a linear programming pKa spectrum approach. Overall, a five-site model accounted for the observed titration behavior with the most acidic sites corresponding to carboxylic groups and phosphodiester groups, intermediate sites phosphoryl groups, and two basic sites equivalent to amine or hydroxyl groups. The pH for the point of zero charge on the bacteria was 5.4. In EFM images of cells rinsed in solutions at pH 4.0, 7.0, and 8.0, a pronounced increase in small (< or = 100 nm diameter) high contrast patches was observed on the cells with increasing pH. The pH dependence of EFM image contrast paralleled the pattern of cell surface charge development inferred from the titration experiments; however, quantitative analysis of high contrast regions in the EFM images yielded lower surface charge values than those anticipated from the titration data. For example at pH 7, the calculated surface charge of high contrast regions in EFM images of the bacterial cells was -0.23 microC/cm2 versus -20.0 microC/cm2 based on the titration curve. The differences in surface charge estimates between the EFM images and titration data are consistent not only with charge development throughout the entire volume of the bacterial cell wall (i.e., in association with functional groups that are not directly exposed at the cell surface) but also with the presence of a thin structural layer of water containing charge-compensating counterions. In combination, the pKa spectra and EFM data demonstrate that a particularly high degree of electrochemical heterogeneity exists within the cell wall and at the cell surface of S. putrefaciens.

Cell Membrane↗

PubMed2004

Co-control of urban air pollutants and greenhouse gases in Mexico City.

This study addresses the synergies of mitigation measures to control urban air pollutant and greenhouse gas (GHG) emissions, in developing integrated "co-control" strategies for Mexico City. First, existing studies of emissions reduction measures--PROAIRE (the air quality plan for Mexico City) and separate GHG studies--are used to construct a harmonized database of options. Second, linear programming (LP) is developed and applied as a decision-support tool to analyze least-cost strategies for meeting co-control targets for multiple pollutants. We estimate that implementing PROAIRE measures as planned will reduce 3.1% of the 2010 metropolitan CO2 emissions, in addition to substantial local air pollutant reductions. Applying the LP, PROAIRE emissions reductions can be met at a 20% lower cost, using only the PROAIRE measures, by adjusting investments toward the more cost-effective measures; lower net costs are possible by including cost-saving GHG mitigation measures, but with increased investment. When CO2 emission reduction targets are added to PROAIRE targets, the most cost-effective solutions use PROAIRE measures for the majority of local pollutant reductions, and GHG measures for additional CO2 control. Because of synergies, the integrated planning of urban-global co-control can be beneficial, but we estimate that for Mexico City these benefits are often small.

Air Pollutants↗

PubMed2005

Inter-zonal tradable discharge permit system to control water pollution in Tianjin, China.

In recent years, Chinese environmental authorities have expressed interest in the use of Tradable Discharge Permits (TDP) as a regulatory instrument to control pollutant emissions. Environmental professionals still have not had enough experience, however, in designing and managing TDP systems, especially for non-uniformly dispersed pollutants. As an empirical study, this paper proposes an interzonal TDP system and analyzes its effectiveness in cost savings and environmental protection for reducing water pollutant COD (chemical oxygen demand) in Tianjin, China. Zonal permit system (ZPS) and emission permit system (EPS) are discussed for comparison. The inter-zonal TDP system is demonstrated to improve cost efficiency by allowing permit trades between zones, as long as water quality constraints are satisfied. The transactions are assumed to proceed in a multilateral sequential way and are simulated with a circularly running linear programming (LP) model. The simulation of permit transactions among 20 firms shows that to reach the same COD removal target, ZPS, interzonal TDP system, and EPS lowered the total reduction cost by 12.8%, 14.6%, and 15.8%, respectively. EPS, however, brought about "hot spots" problem. Finally, the transaction costs and the sensitivity of the three TDP systems to changes in both COD reduction rate and the initial permit allocation are discussed, and policy implications are addressed.

China↗

PubMed2005

Use of differential scanning calorimetry to study lipid oxidation. 1. Oxidative stability of lecithin and linolenic acid.

The oxidation of linolenic acid (LNA) and soy lecithin was studied by differential scanning calorimetry (DSC) with linear programmed heating rates (non-isothermal mode). The interpretation of the shape of DSC curves is discussed, and it has been concluded that temperatures of the extrapolated start of heat release are the most reliable data for the rapid estimation of the oxidative stability of lipid materials. The Ozawa-Flynn-Wall method was used to calculate the kinetic parameters of the process: for LNA autoxidation the activation energy, Ea, and pre-exponential factor, Z, are 66 +/- 4 kJ/mol and 1.5 x 10(7) s(-1), respectively, and the autoxidation of lecithin is described by Ea = 98 +/- 6 kJ/mol and Z = 9.1 x 10(10) s(-1). Values of Ea and Z can be applied for calculation of the overall first-order rate constant of autoxidation at various temperatures, k(T). For the two studied lipids the comparison of k(T) values shows the inversion of their oxidative stabilities; that is, below 167 degrees C lecithin is more stable than LNA, k(T)lecithin < k(T)LNA, and above that temperature (termed the isokinetic temperature) k(T)lecithin > k(T)LNA. The calculated inversion of oxidative stabilities can be an explanation of similar observations for other pairs of lipids if the results of accelerated tests measured at temperatures above 100 degrees C are compared with the results obtained at temperatures below 100 degrees C.

Calorimetry, Differential Scanning↗

PubMed1999

QALYs and the integration of claims in health-care rationing.

The paper argues against the polarization of the health economics literature into pro- and anti-QALY camps. In particular, we suggest that a crucial distinction should be made between the QALY measure as a metric of health, and QALY maximization as an applied social choice rule. We argue against the rule but for the measure and that the appropriate conceptualization of health-care rationing decisions should see the main task as the integration of competing and possibly incommensurable normative claim types. We identify the main types as consequences, rights, social contracts, individual votes and community values and note situations in which the contribution of each claim type is limited. We go on to show that the integration of (at least some of) these claim types can be formalized within the mathematical framework provided by non-linear programming.

Attitude to Health↗