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PubMed2005

Infant speech perception bootstraps word learning.

By their first birthday, infants can understand many spoken words. Research in cognitive development has long focused on the conceptual changes that accompany word learning, but learning new words also entails perceptual sophistication. Several developmental steps are required as infants learn to segment, identify and represent the phonetic forms of spoken words, and map those word forms to different concepts. We review recent research on how infants' perceptual systems unfold in the service of word learning, from initial sensitivity for speech to the learning of language-specific sound patterns. Building on a recent theoretical framework and emerging new methodologies, we show how speech perception is crucial for word learning, and suggest that it bootstraps the development of a separate but parallel phonological system that links sound to meaning.

Humans↗

PubMed2006

Exploiting the bootstrap method for quantifying parameter confidence intervals in dynamical systems.

A quantitative description of dynamical systems requires the estimation of uncertain kinetic parameters and an analysis of their precision. A method frequently used to describe the confidence intervals of estimated parameters is based on the Fisher-Information-Matrix. The application of this traditional method has two important shortcomings: (i) it gives only lower bounds for the variance of a parameter if the solution of the underlying model equations is non-linear in parameters. (ii) The resulting confidence interval is symmetric with respect to the estimated parameter. Here, we show that by applying the bootstrap method a better approximation of (possibly) asymmetric confidence intervals for parameters could be obtained. In contrast to previous applications devoted to non-parametric problems, a dynamical model describing a bio-chemical network is used to evaluate the method.

Algorithms↗

PubMed2003

Estimation of demographic toxicity through the double bootstrap.

Toxicity to organisms is usually expressed in terms of an observable effect on individuals from which a summary endpoint (such as the NOEC or ECx) is derived for risk assessment and environmental quality standards. However, toxicity evaluated in terms of a demographic endpoint may be more relevant to such regulatory applications. In this paper the effect of toxicity on population growth rate r is explored in tandem with a 'double bootstrap' to incorporate uncertainty. Exemplifying the approach with a set of individualized life table response data obtained for Daphnia magna exposed to zinc sulphate solution, the influence of increasing concentrations is assessed. A demographic-based metric for r, the ErCx (effect on r concentration percentage), is defined to permit alternative population level estimation of a 'safe effect' concentration.

Animals↗

PubMed1997

A bootstrap approach to medical decision analysis.

In economic evaluations of health treatments, the sensitivity of a cost-benefit (CB), cost-effectiveness (CE) or cost-utility (CU) analysis to changes in modeling assumptions, variation in data, and sampling error is important. The typical approach to this problem is ad hoc experimentation; namely, a few parameters of particular interest are changed, either separately or in combination, over plausible ranges. The impact of random variation in the data is seldom explored beyond parametric tests of the statistical significance of estimated coefficients. This note suggests a systematic approach to sensitivity analysis. Bootstrap sampling is used to determine to what extent the patients' response to treatment and economic consequences might vary due to many replications of a clinical trial.

Clinical Medicine↗

PubMed2004

A semiparametric bootstrap approach to correlated data analysis problems.

In this note, we outline a simple to use yet powerful bootstrap algorithm for handling correlated outcome variables in terms of either hypothesis testing or confidence intervals using only the marginal models. This new method can handle combinations of continuous and discrete data and can be used in conjunction with other covariates in a model. The procedure is based upon estimating the family-wise error (FWE) rate and then making a Bonferroni-type correction. A simulation study illustrates the accuracy of the algorithm over a variety of correlation structures.

Algorithms↗

PubMed1999

Differences in human visual evoked potentials during the perception of colour as revealed by a bootstrap method to compare cortical activity. A prospective study.

The aim of this prospective study was to investigate the colour related information in cortical activity as it is recorded from the scalp, by comparing the shape of the potential fields. Six healthy volunteers and two volunteers with known protanopsia were used to record multichannel visual evoked potentials after stimulation with chromatic stimuli of equally perceived brightness. The scalp fields resulting from each of the four chromatic stimuli were compared in pairs, in every possible combination and for each time point, using Efron's bootstrap method. It was found that, in comparison to other stimuli responses, the long dominant wavelength stimulus results in significant differences of cortical activity. These are mainly identified in two time periods: (a) at mid-latency responses, usually during the onset and development of P100 component, and (b) after the peak (on the decline) of P100 component. Similar but less evident behaviour was identified when the responses from the short dominant wavelength stimulus were compared with those from the other stimuli. Colour effects were not significant in protanops. The proposed method can be used to locate in time and quantify the differences in cortical activity during colour perception.

Adult↗

PubMed1997

Statistical evaluation of the role of Helicobacter pylori in stress gastritis: applications of splines and bootstrapping to the logistic model.

Stress gastritis is a serious problem in the intensive care unit population. The recent discovery of the causal nature of Helicobacter pylori (H. pylori) in the development of gastric ulcers led us to examine its relationship with stress gastritis. We investigated this relationship in 874 veterans admitted to intensive care units who were tested for the presence of H. pylori and followed for 6 weeks for the development of stress gastritis. We fit spline models to assess functional relationships and used the logistic model to determine the association between H. pylori and stress gastritis. The predictive ability of the model was assessed with receiver operating characteristic (ROC) curve analysis and validated with the bootstrapping technique. Increased anti-H. pylori immunoglobulin A concentrations were found to be an important predictor of stress gastritis independent of other known risk factors.

Aged↗

PubMed1998

An approximate bootstrap technique for variance estimation in parametric images.

Parametric imaging procedures offer the possibility of comprehensive assessment of tissue metabolic activity. Estimating variances of these images is important for the development of inference tools in a diagnostic setting. However, these are not readily obtained because the complexity of the radio-tracer models used in the generation of a parametric image makes analytic variance expressions intractable. On the other hand, a natural extension of the usual bootstrap resampling approach is infeasible because of the expanded computational effort. This paper suggests a computationally practical, approximate simulation strategy to variance estimation. Results of experiments done to evaluate the approach in a simplified model one-dimensional problem are very encouraging. Diagnostic checks performed on a single real-life positron emission tomography (PET) image to test for the feasibility of applying the procedure in a real-world PET setting also show some promise. The suggested methodology is evaluated here in the context of parametric images extracted by mixture analysis; however, the approach is general enough to extend to other parametric imaging methods.

Algorithms↗

PubMed1992

Estimating effective population size from samples of sequences: a bootstrap Monte Carlo integration method.

We would like to use maximum likelihood to estimate parameters such as the effective population size N(e) or, if we do not know mutation rates, the product 4N(e) mu of mutation rate per site and effective population size. To compute the likelihood for a sample of unrecombined nucleotide sequences taken from a random-mating population it is necessary to sum over all genealogies that could have led to the sequences, computing for each one the probability that it would have yielded the sequences, and weighting each one by its prior probability. The genealogies vary in tree topology and in branch lengths. Although the likelihood and the prior are straightforward to compute, the summation over all genealogies seems at first sight hopelessly difficult. This paper reports that it is possible to carry out a Monte Carlo integration to evaluate the likelihoods approximately. The method uses bootstrap sampling of sites to create data sets for each of which a maximum likelihood tree is estimated. The resulting trees are assumed to be sampled from a distribution whose height is proportional to the likelihood surface for the full data. That it will be so is dependent on a theorem which is not proven, but seems likely to be true if the sequences are not short. One can use the resulting estimated likelihood curve to make a maximum likelihood estimate of the parameter of interest, N(e) or of 4N(e) mu. The method requires at least 100 times the computational effort required for estimation of a phylogeny by maximum likelihood, but is practical on today's work stations. The method does not at present have any way of dealing with recombination.

Base Sequence↗

PubMed1990

Input evidence regarding the semantic bootstrapping hypothesis.

The input language addressed to 18 language-learning children (MLU 1.00-3.00) was analysed so as to assess the quality of the semantic-syntactic correspondence posited by the semantic bootstrapping hypothesis. The correspondence appears to be quite satisfactory with little variation from the lower to the higher MLUs. All the persons and things referred to in the corpora were labelled by the mothers using nouns. All the actions referred to were labelled using verbs. Most of the attributive information was conveyed by adjectives. Spatial information was expressed through the use of spatial prepositions. As to the functional categories, all agents of actions and causes of events were encoded as subjects of sentences. All patients, themes, sources, goals, locations, and instruments were encoded as objects of sentences (either direct or oblique). This good semantic-syntactic correspondence may make the child's construction of grammatical categories easier.

Child Language↗

PubMedDate not supplied

Inferring lifetime distributions from kinetics by maximizing entropy using a bootstrapped model.

A bootstrapped model is used to improve the lifetime distribution recovered using the maximum entropy method from kinetics that involves overlapping exponential and distributed phases. The model defaulted to in the limit of low signal-to-noise is iteratively derived from the data to counter the tendency of regularization methods to over-smooth sharp features while under-smoothing broad ones. Upon each revision, some of the lifetime distribution is focused and the rest is blurred. This differential blurring can produce distributions that are virtually free of artifacts. The change in the result obtained upon a reasonable change in the default model provides a useful measure of the uncertainty in the lifetime distribution. In particular, the widths of peaks may not be well determined.

Journal Article↗

PubMed2004

Bootstrap investigation of the stability of disease mapping of Bayesian cancer relative risk estimations.

BACKGROUND: Bayesian approaches to disease mapping of relative risks are useful for rare disease when geographical units have very different population sizes. As Bayesian approaches may induce very different estimations, it is useful to consider the stability of the estimations as a criterion for evaluating the quality of the results. MATERIAL: Cancer incidence data, from the Isere cancer registry (France) over the 1985-1994 period, have been used to check the proposed method: the study is based on 22 cancer sites among males and 24 among females. METHOD: A bootstrap approach has been retained to evaluate the stability of the estimations. The coefficient of variation was chosen as an indicator of stability. Three Bayesian models corresponding to global, local and combined smoothing techniques, have been considered. The stability analysis has taken account of the results of spatial autocorrelation and heterogeneity tests. RESULTS: Bayesian approaches do not necessarily lead to stable estimations. The local smoothing approach induces estimations that are often unstable. The global smoothing approach is the most stable, but is conservative. Combined smoothing appears to be a good compromise if significant spatial variations and heterogeneity of relative risks exist. CONCLUSION: Bayesian estimations of relative risks may be very unstable. However, when results of spatial autocorrelation and heterogeneity tests are taken into account to choose between the different Bayesian approaches, instability becomes negligible.

Algorithms↗

PubMed2005

The input to verb learning in Mandarin Chinese: a role for syntactic bootstrapping.

The authors investigated the role of syntax in verb learning in Mandarin Chinese, which allows pervasive ellipsis of noun arguments. Two questions were investigated using the Beijing corpus on CHILDES: (a) Does the input to young children manifest syntactic-semantic correspondences as needed for acquiring verb meanings? (b) Are verbs presented in multiple frames? Over 6,000 child-directed utterances were parsed. Analyses revealed that transitive verbs, motion verbs, and internal/communication verbs were distinguished syntactically; moreover, the 60 target verbs were used in multiple sentence frames. These findings support a role for syntactic bootstrapping in Mandarin verb learning.

Child, Preschool↗

PubMed2000

A double bootstrap method to analyze linear models with autoregressive error terms.

A new method for the analysis of linear models that have autoregressive errors is proposed. The approach is not only relevant in the behavioral sciences for analyzing small-sample time-series intervention models, but it is also appropriate for a wide class of small-sample linear model problems in which there is interest in inferential statements regarding all regression parameters and autoregressive parameters in the model. The methodology includes a double application of bootstrap procedures. The 1st application is used to obtain bias-adjusted estimates of the autoregressive parameters. The 2nd application is used to estimate the standard errors of the parameter estimates. Theoretical and Monte Carlo results are presented to demonstrate asymptotic and small-sample properties of the method; examples that illustrate advantages of the new approach over established time-series methods are described.

Bias↗

PubMed2005

An application of bootstrap resampling method to obtain confidence interval for percentile fatness cutoff points in childhood and adolescence overweight diagnoses.

OBJECTIVE: To present a resampling approach to obtain confidence intervals (CIs) and the empirical distributions for the studentized regression residuals percentiles when used as cutoff points for overweight and obesity diagnosis in children and adolescents. METHOD: A tutorial for the nonparametric bootstrap with bias accelerating correction is presented. A classical method, the Binomial interpretation, is used as comparing criterion. SUBJECTS: A case study comprising 418 randomly selected subjects from a private secondary school (age: 10-17 y, boys: 52%). MEASUREMENTS: Body fat percentage (by), age (y) and Tanner criteria. RESULTS: The empirical distributions presented skewness suggesting that the CIs should not be symmetric. CIs obtained by the proposed approach were more realistic than the classical ones. CONCLUSIONS: We propose a simple and efficient way to obtain the interval estimates and the distribution properties of cutoff points for overweight and obese classification using a sample-based method that allows the comparison of cutoffs among many subpopulations.

Adipose Tissue↗

PubMed2004

Army ants algorithm for rare event sampling of delocalized nonadiabatic transitions by trajectory surface hopping and the estimation of sampling errors by the bootstrap method.

The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory surface hopping (TSH) calculations is the so-called anteater algorithm, which is inefficient for sampling low-probability nonadiabatic events. We present a new sampling scheme (called the army ants algorithm) for carrying out TSH calculations that is applicable to systems with any strength of coupling. The army ants algorithm is a form of rare event sampling whose efficiency is controlled by an input parameter. By choosing a suitable value of the input parameter the army ants algorithm can be reduced to the anteater algorithm (which is efficient for strongly coupled cases), and by optimizing the parameter the army ants algorithm may be efficiently applied to systems with low-probability events. To demonstrate the efficiency of the army ants algorithm, we performed atom-diatom scattering calculations on a model system involving weakly coupled electronic states. Fully converged quantum mechanical calculations were performed, and the probabilities for nonadiabatic reaction and nonreactive deexcitation (quenching) were found to be on the order of 10(-8). For such low-probability events the anteater sampling scheme requires a large number of trajectories ( approximately 10(10)) to obtain good statistics and converged semiclassical results. In contrast by using the new army ants algorithm converged results were obtained by running 10(5) trajectories. Furthermore, the results were found to be in excellent agreement with the quantum mechanical results. Sampling errors were estimated using the bootstrap method, which is validated for use with the army ants algorithm.

Journal Article↗

PubMed2005

Exact solution of a jamming transition: closed equations for a bootstrap percolation problem.

Jamming, or dynamical arrest, is a transition at which many particles stop moving in a collective manner. In nature it is brought about by, for example, increasing the packing density, changing the interactions between particles, or otherwise restricting the local motion of the elements of the system. The onset of collectivity occurs because, when one particle is blocked, it may lead to the blocking of a neighbor. That particle may then block one of its neighbors, these effects propagating across some typical domain of size named the dynamical correlation length. When this length diverges, the system becomes immobile. Even where it is finite but large the dynamics is dramatically slowed. Such phenomena lead to glasses, gels, and other very long-lived nonequilibrium solids. The bootstrap percolation models are the simplest examples describing these spatio-temporal correlations. We have been able to solve one such model in two dimensions exactly, exhibiting the precise evolution of the jamming correlations on approach to arrest. We believe that the nature of these correlations and the method we devise to solve the problem are quite general. Both should be of considerable help in further developing this field.

Journal Article↗

PubMed2000

Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap.

Quantitative analyses of biological sequences generally proceed under the assumption that individual DNA or protein sequence elements vary independently. However, this assumption is not biologically realistic because sequence elements often vary in a concerted manner resulting from common ancestry and structural or functional constraints. We calculated intersite associations among aligned protein sequences by using mutual information. To discriminate associations resulting from common ancestry from those resulting from structural or functional constraints, we used a parametric bootstrap algorithm to construct replicate data sets. These data are expected to have intersite associations resulting solely from phylogeny. By comparing the distribution of our association statistic for the replicate data against that calculated for empirical data, we were able to assign a probability that two sites covaried resulting from structural or functional constraint rather than phylogeny. We tested our method by using an alignment of 237 basic helix-loop-helix (bHLH) protein domains. Comparison of our results against a solved three-dimensional structure confirmed the identification of several sites important to function and structure of the bHLH domain. This analytical procedure has broad utility as a first step in the identification of sites that are important to biological macromolecular structure and function when a solved structure is unavailable.

Models, Genetic↗