Modelling the MAPK signalling pathway using a two-stage identification algorithm

Signal transduction pathways describe the dynamics of cellular response to input signalling molecules at receptors on the cell membrane. The Mitogen-Activated Protein Kinase (MAPK) cascade is one of such pathways that are involved in many important cellular processes including cell growth and proliferation. This paper describes a black-box model of this pathway created using an advanced two-stage identification algorithm. Identification allows us to capture the unique features and dynamics of the pathway and also opens up the possibility of regulatory control design. In the approach described, an optimal model is obtained by performing model subset selection in two stages, where the terms are first determined by a forward selection method and then modified using a backward selection model refinement. The simulation results demonstrate that the model selected using the two-stage algorithm performs better than with the forward selection method alone.

Two-stage mixed discrete-continuous identification of radial basis function (RBF) neural models for nonlinear systems

The identification of nonlinear dynamic systems using radial basis function (RBF) neural models is studied in this paper. Given a model selection criterion, the main objective is to effectively and efficiently build a parsimonious compact neural model that generalizes well over unseen data. This is achieved by simultaneous model structure selection and optimization of the parameters over the continuous parameter space. It is a mixed-integer hard problem, and a unified analytic framework is proposed to enable an effective and efficient two-stage mixed discrete-continuous; identification procedure. This novel framework combines the advantages of an iterative discrete two-stage subset selection technique for model structure determination and the calculus-based continuous optimization of the model parameters. Computational complexity analysis and simulation studies confirm the efficacy of the proposed algorithm.

Locally regularised two-stage learning algorithm for RBF network centre selection

Nonlinear models constructed from radial basis function (RBF) networks can easily be over-fitted due to the noise on the data. While information criteria, such as the final prediction error (FPE), can provide a trade-off between training error and network complexity, the tunable parameters that penalise a large size of network model are hard to determine and are usually network dependent. This article introduces a new locally regularised, two-stage stepwise construction algorithm for RBF networks. The main objective is to produce a parsomous network that generalises well over unseen data. This is achieved by utilising Bayesian learning within a two-stage stepwise construction procedure to penalise centres that are mainly interpreted by the noise.

Two-stage RBF network construction based on particle swarm optimization

The conventional radial basis function (RBF) network optimization methods, such as orthogonal least squares or the two-stage selection, can produce a sparse network with satisfactory generalization capability. However, the RBF width, as a nonlinear parameter in the network, is not easy to determine. In the aforementioned methods, the width is always pre-determined, either by trial-and-error, or generated randomly. Furthermore, all hidden nodes share the same RBF width. This will inevitably reduce the network performance, and more RBF centres may then be needed to meet a desired modelling specification. In this paper we investigate a new two-stage construction algorithm for RBF networks. It utilizes the particle swarm optimization method to search for the optimal RBF centres and their associated widths. Although the new method needs more computation than conventional approaches, it can greatly reduce the model size and improve model generalization performance. The effectiveness of the proposed technique is confirmed by two numerical simulation examples.

Two-Stage Orthogonal Least Squares Methods for Neural Network Construction

A number of neural networks can be formulated as the linear-in-the-parameters models. Training such networks can be transformed to a model selection problem where a compact model is selected from all the candidates using subset selection algorithms. Forward selection methods are popular fast subset selection approaches. However, they may only produce suboptimal models and can be trapped into a local minimum. More recently, a two-stage fast recursive algorithm (TSFRA) combining forward selection and backward model refinement has been proposed to improve the compactness and generalization performance of the model. This paper proposes unified two-stage orthogonal least squares methods instead of the fast recursive-based methods. In contrast to the TSFRA, this paper derives a new simplified relationship between the forward and the backward stages to avoid repetitive computations using the inherent orthogonal properties of the least squares methods. Furthermore, a new term exchanging scheme for backward model refinement is introduced to reduce computational demand. Finally, given the error reduction ratio criterion, effective and efficient forward and backward subset selection procedures are proposed. Extensive examples are presented to demonstrate the improved model compactness constructed by the proposed technique in comparison with some popular methods.

A two-stage continuous culture system to study the effect of supplemental alpha-lactalbumin and glycomacropeptide on mixed cultures of human gut bacteria challenged with enteropathogenic Escherichia coli and Salmonella serotype Typhimurium

Aims: Certain milk factors may promote the growth of a gastrointestinal microflora predominated by bifidobacteria and may aid in overcoming enteric infections. This may explain why breast-fed infants experience fewer intestinal infections than their formula-fed counterparts. The effect of formula supplementation with two such factors was investigated in this study. Methods and Results: Infant faecal specimens were used to ferment formulae supplemented with glycomacropeptide (GMP) and alpha-lactalbumin (alpha-la) in a two-stage compound continuous culture model. At steady state, all fermenter vessels were inoculated with 5 ml of 0.1 M phosphate-buffered saline (pH 7.2) containing 10(8) CFU ml(-1) of either enteropathogenic Escherichia coli 2348/69 (O127:H6) or Salmonella serotype Typhimurium (DSMZ 5569). Bacteriology was determined by independent fluorescence in situ hybridization. Vessels that contained breast milk (BM), as well as alpha-la and GMP supplemented formula had stable total counts of bifidobacteria while lactobacilli increased significantly only in vessels with breast milk. Bacteroides, clostridia and E. coli decreased significantly in all three groups prior to pathogen addition. Escherichia coli counts decreased in vessels containing BM and alpha-la while Salmonella decreased significantly in all vessels containing BM, alpha-la and GMP. Acetate was the predominant acid. Significance and Impact of the Study: Supplementation of infant formulae with appropriate milk proteins may be useful in mimicking the beneficial bacteriological effects of breast milk.

Use of batch culture and a two-stage continuous culture system to study the effect of supplemental a-lactalbumin and glycomacropeptide on mixed populations of human gut bacteria

Certain milk factors can promote the growth of a host-friendly gastrointestinal microflora. This may explain why breast-fed infants experience fewer intestinal infections than their formula-fed counterparts. The effect of formula supplementation with two such factors was investigated in this study. Infant faecal specimens were used to ferment formulas supplemented with glycomacropeptide and α-lactalbumin in a two-stage compound continuous culture model. Bacteriology was determined by fluorescence in situ hybridisation. Vessels that contained breast milk as well as α-lactalbumin and glycomacropeptide had stable counts of bifidobacteria while lactobacilli increased significantly only in vessels with breast milk. Bacteroides, clostridia and Escherichia coli decreased significantly in all runs. Acetate was the principal acid found along with high amounts of propionate and lactate. Supplementation of infant formulas with appropriate milk proteins may be useful in simulating the beneficial bacteriological effects of breast milk.

An Information Theory framework for two-stage binary image operator design

The design of translation invariant and locally defined binary image operators over large windows is made difficult by decreased statistical precision and increased training time. We present a complete framework for the application of stacked design, a recently proposed technique to create two-stage operators that circumvents that difficulty. We propose a novel algorithm, based on Information Theory, to find groups of pixels that should be used together to predict the Output Value. We employ this algorithm to automate the process of creating a set of first-level operators that are later combined in a global operator. We also propose a principled way to guide this combination, by using feature selection and model comparison. Experimental results Show that the proposed framework leads to better results than single stage design. (C) 2009 Elsevier B.V. All rights reserved.

Performance of balanced two-stage empirical predictors of realized cluster latent values from finite populations: A simulation study

Predictors of random effects are usually based on the popular mixed effects (ME) model developed under the assumption that the sample is obtained from a conceptual infinite population; such predictors are employed even when the actual population is finite. Two alternatives that incorporate the finite nature of the population are obtained from the superpopulation model proposed by Scott and Smith (1969. Estimation in multi-stage surveys. J. Amer. Statist. Assoc. 64, 830-840) or from the finite population mixed model recently proposed by Stanek and Singer (2004. Predicting random effects from finite population clustered samples with response error. J. Amer. Statist. Assoc. 99, 1119-1130). Predictors derived under the latter model with the additional assumptions that all variance components are known and that within-cluster variances are equal have smaller mean squared error (MSE) than the competitors based on either the ME or Scott and Smith`s models. As population variances are rarely known, we propose method of moment estimators to obtain empirical predictors and conduct a simulation study to evaluate their performance. The results suggest that the finite population mixed model empirical predictor is more stable than its competitors since, in terms of MSE, it is either the best or the second best and when second best, its performance lies within acceptable limits. When both cluster and unit intra-class correlation coefficients are very high (e.g., 0.95 or more), the performance of the empirical predictors derived under the three models is similar. (c) 2007 Elsevier B.V. All rights reserved.

The kinetics of two-stage formation of TiAl3 in multilayered Ti/Al foils prepared by accumulative roll bonding

The solid-state reactions of Ti/Al multilayered samples produced by Accumulative Roll Bonding (ARB) have been investigated using differential scanning calorimetry, X-ray diffraction and scanning electron microscopy. The kinetics of the formation of the intermetallic compound TiAl3 was highlighted. Experimental evidence and analysis of the data shows that, there was a two-stage process in the formation of TiAl₃ in the ARB Ti/Al reactive multilayered samples. Calorimetric and microstructural analyses also suggest that the interdiffusion of Al and Ti which led to solid solutions preceded the formation of intermetallic compounds. Despite the apparent chaos in the thickness of the ARB multilayered samples, the distribution of layer spacing did not become broad enough to lose the main features of the double exothermal behaviour. Isothermal DSC shows a larger Avarami constant in ARB Ti/Al multilayered structures than was found in Ti/Al thin films. A modified model based on thin films was set up to describe the kinetic characteristics of the formation of the intermetallic compound TiAl₃ in ARB samples.

Cost-effectiveness analysis of a two-stage screening intervention for hepatocellular carcinoma in Taiwan

Background/Purpose

Hepatocellular carcinoma (HCC) has been the leading cause of cancer death in Taiwan since the 1980s. A two-stage screening intervention was introduced in 1996 and has been implemented in a limited number of hospitals. The present study assessed the costs and health outcomes associated with the introduction of screening intervention, from the perspective of the Taiwanese government. The cost-effectiveness analysis aimed to assist informed decision making by the health authority in Taiwan.
Methods

A two-phase economic model, 1-year decision analysis and a 60-year Markov simulation, was developed to conceptualize the screening intervention within current practice, and was compared with opportunistic screening alone. Incremental analyses were conducted to compare the incremental costs and outcomes associated with the introduction of the intervention. Sensitivity analyses were performed to investigate the uncertainties that surrounded the model.
Results

The Markov model simulation demonstrated an incremental cost-effectiveness ratio (ICER) of NT$498,000 (US$15,600) per life-year saved, with a 5% discount rate. An ICER of NT$402,000 (US$12,600) per quality-adjusted life-year was achieved by applying utility weights. Sensitivity analysis showed that excess mortality reduction of HCC by screening and HCC incidence rates were the most influential factors on the ICERs. Scenario analysis also indicated that expansion of the HCC screening intervention by focusing on regular monitoring of the high-risk individuals could achieve a more favorable result.
Conclusion

Screening the population of high-risk individuals for HCC with the two-stage screening intervention in Taiwan is considered potentially cost-effective compared with opportunistic screening in the target population of an HCC endemic area.

A two-stage dynamic group decision making method for processing ordinal information

In group decision making (GDM) problems, ordinal data provide a convenient way of articulating preferences from decision makers (DMs). A number of GDM models have been proposed to aggregate such kind of preferences in the literature. However, most of the GDM models that handle ordinal preferences suffer from two drawbacks: (1) it is difficult for the GDM models to manage conflicting opinions, especially with a large number of DMs; and (2) the relationships between the preferences provided by the DMs are neglected, and all DMs are assumed to be of equal importance, therefore causing the aggregated collective preference not an ideal representative of the group's decision. In order to overcome these problems, a two-stage dynamic group decision making method for aggregating ordinal preferences is proposed in this paper. The method consists of two main processes: (i) a data cleansing process, which aims to reduce the influence of conflicting opinions pertaining to the collective decision prior to the aggregation process; as such an effective solution for undertaking large-scale GDM problems is formulated; and (ii) a support degree oriented consensus-reaching process, where the collective preference is aggregated by using the Power Average (PA) operator; as such, the relationships of the arguments being aggregated are taken into consideration (i.e., allowing the values being aggregated to support each other). A new support function for the PA operator to deal with ordinal information is defined based on the dominance-based rough set approach. The proposed GDM model is compared with the models presented by Herrera-Viedma et al. An application related to controlling the degradation of the hydrographic basin of a river in Brazil is evaluated. The results demonstrate the usefulness of the proposed method in handling GDM problems with ordinal information.

A new two-stage fuzzy inference system-based approach to prioritize failures in failure mode and effect analysis

This paper presents a new Fuzzy Inference System (FIS)-based Risk Priority Number (RPN) model for the prioritization of failures in Failure Mode and Effect Analysis (FMEA). In FMEA, the monotonicity property of the RPN scores is important. To maintain the monotonicity property of an FIS-based RPN model, a complete and monotonically-ordered fuzzy rule base is necessary. However, it is impractical to gather all (potentially a large number of) fuzzy rules from FMEA users. In this paper, we introduce a new two-stage approach to reduce the number of fuzzy rules that needs to be gathered, and to satisfy the monotonicity property. In stage-1, a Genetic Algorithm (GA) is used to search for a small set of fuzzy rules to be gathered from FMEA users. In stage-2, the remaining fuzzy rules are deduced approximately by a monotonicity-preserving similarity reasoning scheme. The monotonicity property is exploited as additional qualitative information for constructing the FIS-based RPN model. To assess the effectiveness of the proposed approach, a real case study with information collected from a semiconductor manufacturing plant is conducted. The outcomes indicate that the proposed approach is effective in developing an FIS-based RPN model with only a small set of fuzzy rules, which is able to satisfy the monotonicity property for prioritization of failures in FMEA.

Evaluation of Diuron (3-[3,4-dichlorophenyl]-1,1-dimethyl urea) in a Two-stage Mouse Skin Carcinogenesis Assay

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Economic design of two-stage (X)over-bar charts: the Markov chain approach

When the (X) over bar chart is in use, samples are regularly taken from the process, and their means are plotted on the chart. In some cases, it is too expensive to obtain the X values, but not the values of a correlated variable Y. This paper presents a model for the economic design of a two-stage control chart, that is. a control chart based on both performance (X) and surrogate (Y) variables. The process is monitored by the surrogate variable until it signals an out-of-control behavior, and then a switch is made to the (X) over bar chart. The (X) over bar chart is built with central, warning. and action regions. If an X sample mean falls in the central region, the process surveillance returns to the (Y) over bar chart. Otherwise. The process remains under the (X) over bar chart's surveillance until an (X) over bar sample mean falls outside the control limits. The search for an assignable cause is undertaken when the performance variable signals an out-of-control behavior. In this way, the two variables, are used in an alternating fashion. The assumption of an exponential distribution to describe the length of time the process remains in control allows the application of the Markov chain approach for developing the cost function. A study is performed to examine the economic advantages of using performance and surrogate variables. (C) 2003 Elsevier B.V. All rights reserved.