Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Ensemble methods”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 361 records · Page 20Linked to original sources
PubMed2005

Transferable potentials for phase equilibria. 8. United-atom description for thiols, sulfides, disulfides, and thiophene.

An extension of the transferable potentials for phase equilibria united-atom (TraPPE-UA) force field to thiol, sulfide, and disulfide functionalities and thiophene is presented. In the TraPPE-UA force field, nonbonded interactions are governed by a Lennard-Jones plus fixed point charge functional form. Partial charges are determined through a CHELPG analysis of electrostatic potential energy surfaces derived from ab initio calculations at the HF/6-31g+(d,p) level. The Lennard-Jones well depth and size parameters for four new interaction sites, S (thiols), S(sulfides), S(disulfides), and S(thiophene), were determined by fitting simulation data to pure-component vapor-equilibrium data for methanethiol, dimethyl sulfide, dimethyl disulfide, and thiophene, respectively. Configurational-bias Monte Carlo simulations in the grand canonical ensemble combined with histogram-reweighting methods were used to calculate the vapor-liquid coexistence curves for methanethiol, ethanethiol, 2-methyl-1-propanethiol, 2-methyl-2-propanethiol, 2-butanethiol, pentanethiol, octanethiol, dimethyl sulfide, diethyl sulfide, ethylmethyl sulfide, dimethyl disulfide, diethyl disulfide, and thiophene. Excellent agreement with experiment is achieved, with unsigned errors of less than 1% for saturated liquid densities and less than 3% for critical temperatures. The normal boiling points were predicted to within 1% of experiment in most cases, although for certain molecules (pentanethiol) deviations as large as 5% were found. Additional calculations were performed to determine the pressure-composition behavior of ethanethiol+n-butane at 373.15 K and the temperature-composition behavior of 1-propanethiol+n-hexane at 1.01 bar. In each case, a good reproduction of experimental vapor-liquid equilibrium separation factors is achieved; both of the coexistence curves are somewhat shifted because of overprediction of the pure-component vapor pressures.

Journal Article↗
PubMed2006

Molecular simulations of the pressure, temperature, and chemical potential dependencies of clay swelling.

A new method for the determination of clay swelling thermodynamics from computer simulation is discussed and evaluated. This method allows for the determination of temperature, pressure, and water chemical potential dependence of clay swelling from simulations at a single thermodynamic state point. The temperature dependence and pressure dependence of clay swelling are shown to be directly related to the composite system entropy and volume change, respectively, that accompany swelling. Expressions for the chemical potential dependence of clay swelling are used to determine constant pressure layer spacing and adsorption isotherms, quantities that are well suited for comparison with experimental measurements. This method is evaluated through grand isoshear ensemble simulations of Na-montmorillonite, a prototypical swelling clay. Approximations associated with all expressions are discussed with explicit calculations used to demonstrate their regimes of validity.

Journal Article↗
PubMed2005

Neuronal synapse interaction reconstituted between live cells and supported lipid bilayers.

In the nervous system, homophilic and heterophilic adhesion molecules participate in the induction and differentiation of presynaptic transmitter release sites. We focus on the heterophilic interaction between postsynaptic neuroligin-1 (Nlg) and presynaptic beta-neurexin (Nrx). Nlg has previously been shown to trigger presynaptic differentiation in a Nrx-expressing axon even when presented on a non-neuronal cell or on beads coated with lipid bilayers. We have now developed a new method to measure single molecule and ensemble distribution of Nrx and Nlg at the contact site between a non-neuronal Nrx-expressing cell and a flat supported glycosylphosphoinositol-neuroligin-1 (GPI-Nlg) lipid bilayer and relate them to adhesion as measured by cell migration and gravity dissociation. We find that within minutes after cell-bilayer contact, Nrx accumulates at the contact site and the contact area is expanded. The strength of cell-bilayer adhesion depends on the morphology of Nrx accumulation, with the focal concentration strengthening adhesion. The results suggest that Nlg-Nrx interaction rapidly establishes a weak, but specific, adhesion between dynamic pre- and postsynaptic processes, which may ultimately require additional molecules for synapse stabilization.

Animals↗
PubMed1999

Isopower maps of the electrogastrogram (EGG) after total gastrectomy or total colectomy.

Isopower or topographic electrogastrograms (EGG) correspond to topographic electroencephalograms. Both project the topographic localizations of the spectral frequencies on the abdominal surface or scalp. This paper compares the pre-operative control isopower EGG maps with those of total gastrectomy or total colectomy. EGGs were recorded simultaneously at 27 locations on the epigastro-abdominal surface. Spectral analysis by the maximal entropy method (MEM) was performed and the ensemble means of pre-prandial and post-prandial spectra were calculated. The spectral frequencies were arbitrarily classified into five groups, 1 cycle per minute (cpm) (0-2.4 cpm), 3 cpm (2.5-4.9 cpm), 6 cpm (5.0-7.4 cpm), 8 cpm (7.5-9.9 cpm) and 10 cpm (10.0-12.9 cpm). Maximal power peaks in each spectral group, and electrode locations which were expressed by x-y coordinates were the indicators for making the isopower EGG maps by using a contour map program. Thereafter, the maximal power spots or foci in each spectral group were determined. The pre-operative maximal power foci of the 1, 8 and 10 cpm groups were distributed rather evenly on the epigastro-abdominal surface. Those of the 3 and 6 cpm groups, mainly concentrated in the epigastric region, were absent in almost all patients who had undergone total gastrectomy. The infra-umbilical foci of the 3 and 6 cpm groups completely disappeared after total colectomy. The infra-umbilical foci of the 3 and 6 cpm groups (2.5-7.4) may reflect the colonic activities and the epigastric 3 cpm foci, the gastric activities. The pre-operative maximal power of the 3 cpm foci decreased significantly after total or sub-total gastrectomy.

Adult↗
PubMed2005

Scaling of non-Markovian Monte Carlo wave-function methods.

We demonstrate a scaling method for non-Markovian Monte Carlo wave-function simulations used to study open quantum systems weakly coupled to their environments. We derive a scaling equation, from which the result for the expectation values of arbitrary operators of interest can be calculated, all the quantities in the equation being easily obtainable from the scaled Monte Carlo wave-function simulations. In the optimal case, the scaling method can be used, within the weak coupling approximation, to reduce the size of the generated Monte Carlo ensemble by several orders of magnitude. Thus, the developed method allows faster simulations and makes it possible to solve the dynamics of the certain class of non-Markovian systems whose simulation would be otherwise too tedious because of the requirement for large computational resources.

Journal Article↗
PubMed2006

Phase diagram of Bose-Fermi mixtures in one-dimensional optical lattices.

The ground state phase diagram of the one-dimensional Bose-Fermi Hubbard model is studied in the canonical ensemble using a quantum Monte Carlo method. We focus on the case where both species have half filling in order to maximize the pairing correlations between the bosons and the fermions. In case of equal hopping we distinguish among phase separation, a Luttinger liquid phase, and a phase characterized by strong singlet pairing between the species. True long-range density waves exist with unequal hopping amplitudes.

Journal Article↗
PubMed1989

Single sodium channels from canine ventricular myocytes: voltage dependence and relative rates of activation and inactivation.

1. Single sodium channel currents were recorded from canine ventricular myocytes in cell-attached patches. The relative rates of single-channel activation vs. inactivation as well as the voltage dependence of the rate of open-channel inactivation were studied. 2. Ensemble-averaged sodium currents showed relatively normal activation and inactivation kinetics, although the mid-point of the steady-state inactivation (h infinity) curve was shifted by 20-30 mV in the hyperpolarizing direction. This shift was due to the bath solution, which contained isotonic KCl to depolarize the cell to 0 mV. 3. Steady-state activation showed less of a voltage shift. The threshold for eliciting channel opening was around -70 mV and the mid-point of activation occurred near -50 mV. 4. The decline of the ensemble-averaged sodium current during a maintained depolarization was fitted by a single exponential function characterizing the apparent time constant of inactivation (tau h). The apparent rate of inactivation was voltage dependent, with tau h decreasing e-fold for a 15.4 mV depolarization. 5. The relative contributions of the rates of single-channel activation and inactivation in determining the time course of current decay (tau h) were examined using the approach of Aldrich, Corey & Stevens (1983). Mean channel open time (tau o) showed significant voltage dependence, increasing from 0.5 ms at -70 mV to around 0.8 ms at -40 mV. At -70 mV tau h was much greater than tau o, while at -40 mV the two time constants were similar. 6. The degree to which the kinetics of single-channel activation contribute to tau h was studied using the first latency distribution. The first latency function was fitted by two exponentials. The slow component was voltage dependent, decreasing from 19 ms at -70 mV to 0.5 ms at -40 mV. The fast component (0.1-0.5 ms) was not well resolved. 7. Comparing the first latency distribution with the time course of the ensemble-averaged sodium current at -40 mV showed that activation is nearly complete by the time of peak inward sodium current. However, at -70 mV, activation overlaps significantly with the apparent time course of inactivation of the ensemble-averaged current. 8. Using the methods of Aldrich et al. (1983) we also measured the apparent rate of open-channel closing (a) and open-channel inactivation (b). Both rates were voltage dependent, with a showing an e-fold decrease for an 11 mV depolarization and b showing an e-fold increase for a 30 mV depolarization.(ABSTRACT TRUNCATED AT 400 WORDS)

Action Potentials↗
PubMed1995

Squatting revisited: comparison of haemodynamic responses in normal individuals and heart transplantation recipients.

BACKGROUND: Squatting produces a prompt increase in cardiac output and arterial blood pressure which is accompanied by an immediate decrease in heart rate and forearm vascular resistance. The rise in cardiac output and blood pressure has been attributed to augmented venous return from compression of leg veins, while the decreases in heart rate and forearm vascular resistance are probably due to activation of cardiopulmonary and arterial baroreflexes. Haemodynamic patterns in nine normal men and six heart transplant recipients during 2 min of squatting were examined to determine the role of cardiac innervation in the mediation of these responses. METHODS: Stroke volume was monitored by ensemble averaged thoracic impedance cardiography and blood pressure was determined with an Ohmeda fingertip plethysmograph. These techniques provided continuous measurements which were capable of detecting transient and non-steady state changes. Forearm blood flow was measured with venous occlusion plethysmography. Measurements were obtained after 3 min of quiet standing, immediately after squatting, and at 20, 60, and 120 s of sustained squatting. RESULTS: Both groups exhibited similar increases in stroke volume index (normal individuals 10.5 ml/m2; heart transplant recipients 10.3 ml/m2) and mean arterial pressure (normal individuals 8.5 mm Hg; heart transplant recipients 5.0 mm Hg) which were sustained throughout squatting. Each group also showed an initial decrease in peripheral resistance (normal individuals 3.6 units; heart transplant recipients 7.7 units) followed by a return to baseline values after 20 s. Heart rate decreased in normal individuals (10 beats/min) but was unchanged or minimally increased (2 beats/min) in heart transplant recipients. Forearm vascular resistance was conspicuously decreased in normal individuals (47.8 units) but only minimally (20.9 units) and not significantly in heart transplant recipients. CONCLUSIONS: The major haemodynamic responses to squatting (increased cardiac output and blood pressure) are similar in normal individuals and heart transplant recipients. These responses are primarily due to augmented venous return and are not altered by cardiac denervation. Both groups also exhibited a transient decline in peripheral vascular resistance which is most likely mediated by arterial baroreflexes activated by the acute rise in arterial blood pressure. The absence of a significant decrease in forearm vascular resistance in heart transplant recipients suggests that this response is partially mediated by cardiopulmonary or ventricular baroreflexes or that local forearm flow mediated vasodilatation remains impaired after heart transplantation.

Adult↗
PubMed2004

Detection of non-Brownian diffusion in the cell membrane in single molecule tracking.

Molecules undergo non-Brownian diffusion in the plasma membrane, but the mechanism behind this anomalous diffusion is controversial. To characterize the anomalous diffusion in the complex system of the plasma membrane and to understand its underlying mechanism, single-molecule/particle methods that allow researchers to avoid ensemble averaging have turned out to be highly effective. However, the intrinsic problems of time-averaging (resolution) and the frequency of the observations have not been explored. These would not matter for the observations of simple Brownian particles, but they do strongly affect the observation of molecules undergoing anomalous diffusion. We examined these effects on the apparent motion of molecules undergoing simple, totally confined, or hop diffusion, using Monte Carlo simulations of particles undergoing short-term confined diffusion within a compartment and long-term hop diffusion between these compartments, explicitly including the effects of time-averaging during a single frame of the camera (exposure time) and the frequency of observations (frame rate). The intricate relationships of these time-related experimental parameters with the intrinsic diffusion parameters have been clarified, which indicated that by systematically varying the frame time and rate, the anomalous diffusion can be clearly detected and characterized. Based on these results, single-particle tracking of transferrin receptor in the plasma membrane of live PtK2 cells were carried out, varying the frame time between 0.025 and 33 ms (0.03-40 kHz), which revealed the hop diffusion of the receptor between 47-nm (average) compartments with an average residency time of 1.7 ms, with the aid of single fluorescent-molecule video imaging.

Animals↗
PubMed1992

Computer algorithms to characterize individual subject EMG profiles during gait.

Three methods of precisely determining onset and cessation times of gait EMG were investigated. Subjects were 24 normal adults and 32 individuals with gait pathologies. Soleus muscle EMG during free speed level walking was obtained with fine wires, and was normalized by manual muscle test (%MMT). Linear envelopes were generated from the rectified, integrated EMG at each percent gait cycle (%GC) of each stride in individual gait trials. Three methods were used to generate EMG profiles for each tested subject. The ensemble average (EAV) was determined for each subject from the mean relative intensity of the linear envelopes. Low relative intensity or short duration EMG was removed from the ensemble average to create the intensity filtered average (IFA). The packet analysis method (PAC) created an EMG profile from the linear envelopes in successive strides whose respective centroid %GC locations were within +/- 15%GC of each other. Control values for onset and cessation times of individual gait trials were calculated after spurious outliers were removed. Mean onset and cessation times across subjects for control values and the experimental methods (EAV, IFA, and PAC) were calculated. Dunnett's test (p less than .05) was performed to compare control and experimental groups in patient and normal trials. EAV differed from control values for onsets (p less than .01), cessations (p less than .01), and durations (p less than .01) in both normal and patient trials. IFA and PAC had no significant differences from control value means. IFA was selected for clinical use as automatic analysis could be performed on all trials and a minimum number of decision rules were needed.

Adult↗
PubMedDate not supplied

Boosting: an ensemble learning tool for compound classification and QSAR modeling.

A classification and regression tool, J. H. Friedman's Stochastic Gradient Boosting (SGB), is applied to predicting a compound's quantitative or categorical biological activity based on a quantitative description of the compound's molecular structure. Stochastic Gradient Boosting is a procedure for building a sequence of models, for instance regression trees (as in this paper), whose outputs are combined to form a predicted quantity, either an estimate of the biological activity, or a class label to which a molecule belongs. In particular, the SGB procedure builds a model in a stage-wise manner by fitting each tree to the gradient of a loss function: e.g., squared error for regression and binomial log-likelihood for classification. The values of the gradient are computed for each sample in the training set, but only a random sample of these gradients is used at each stage. (Friedman showed that the well-known boosting algorithm, AdaBoost of Freund and Schapire, could be considered as a particular case of SGB.) The SGB method is used to analyze 10 cheminformatics data sets, most of which are publicly available. The results show that SGB's performance is comparable to that of Random Forest, another ensemble learning method, and are generally competitive with or superior to those of other QSAR methods. The use of SGB's variable importance with partial dependence plots for model interpretation is also illustrated.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2004

Free energy, energy, and entropy of swelling in Cs-, Na-, and Sr-montmorillonite clays.

A Monte Carlo method for grand canonical and grand isoshear ensemble simulations has been used to characterize the free energy, energy, and entropy of clay mineral swelling. The Monte Carlo approach was found to be more efficient at simulating water content fluctuations in the highly constrained clay environment than a previously developed molecular dynamics method. Swelling thermodynamics calculated for Cs-, Na-, and Sr-montmorillonite clays indicate a strong dependence of swelling on the interlayer ion identity, in agreement with various experimental measurements. The Sr clay swells most readily, and both the Na and Sr clays prefer expanded states (two-layer hydrate or greater) when in contact with bulk water. In contrast, swelling is inhibited in the Cs clay. Differences in swelling behavior are traced directly to the tendency of the different ions to hydrate. The swelling free energies are decomposed into their energetic and entropic components, revealing an overall energetic driving force for the swelling phenomena. Entropic effects provide a smaller, mediating role in the swelling processes. The results provide a unique molecular perspective on experimentally well-characterized swelling phenomena.

Journal Article↗
PubMed2005

Target flexibility in molecular recognition.

Induced-fit effects are well known in the binding of small molecules to proteins and other macromolecular targets. Among other targets, protein kinases are particularly flexible proteins, so that such effects should be considered in attempts at structure-based inhibitor design for kinase targets. This paper outlines some recent progress in methods for including target flexibility in computational studies of molecular recognition. A focus is the "relaxed complex method," in which ligands are docked to an ensemble of conformations of the target, and the best complexes are re-scored to provide predictions of optimal binding geometries. Early applications of this method have suggested a new approach to the development of inhibitors of HIV-1 Integrase.

Computer Simulation↗
PubMed2007

A comparison of decision tree ensemble creation techniques.

We experimentally evaluate bagging and seven other randomization-based approaches to creating an ensemble of decision tree classifiers. Statistical tests were performed on experimental results from 57 publicly available data sets. When cross-validation comparisons were tested for statistical significance, the best method was statistically more accurate than bagging on only eight of the 57 data sets. Alternatively, examining the average ranks of the algorithms across the group of data sets, we find that boosting, random forests, and randomized trees are statistically significantly better than bagging. Because our results suggest that using an appropriate ensemble size is important, we introduce an algorithm that decides when a sufficient number of classifiers has been created for an ensemble. Our algorithm uses the out-of-bag error estimate, and is shown to result in an accurate ensemble for those methods that incorporate bagging into the construction of the ensemble.

Algorithms↗
PubMedDate not supplied

Time-frequency distribution technique in biological signal processing.

Time-frequency distribution (TFD) has gained wide acceptance for deterministic non-stationary signal processing, particularly for biological signals, in both basic research and commercial production. This paper presents the results of a comparison of the TFD technique with other methods for determining physiologic parameters, particularly the ventricular ejection time (VET) and (dZ/dtmax), the differentiation of the thoracic-fluid signal Z0 from non-stationary impedence cardiography dZ/dt. The TFD technique was found to be more accurate--in terms of both time and signal magnitude--than traditional methods such as the baseline and ensemble-averaging techniques when compared with phonocardiograms and hand calculations by experts in the field. It is shown that TFD can also reduce ventilatory/respiratory noise, electrical and muscle noise, and patient-motion artifacts. Correlation analysis and regression analysis as well as Bland-Altman studies showed stronger correlational methods tested.

Algorithms↗
PubMed2005

Analyzing functional connectivity using a network likelihood model of ensemble neural spiking activity.

Analyzing the dependencies between spike trains is an important step in understanding how neurons work in concert to represent biological signals. Usually this is done for pairs of neurons at a time using correlation-based techniques. Chornoboy, Schramm, and Karr (1988) proposed maximum likelihood methods for the simultaneous analysis of multiple pair-wise interactions among an ensemble of neurons. One of these methods is an iterative, continuous-time estimation algorithm for a network likelihood model formulated in terms of multiplicative conditional intensity functions. We devised a discrete-time version of this algorithm that includes a new, efficient computational strategy, a principled method to compute starting values, and a principled stopping criterion. In an analysis of simulated neural spike trains from ensembles of interacting neurons, the algorithm recovered the correct connectivity matrices and interaction parameters. In the analysis of spike trains from an ensemble of rat hippocampal place cells, the algorithm identified a connectivity matrix and interaction parameters consistent with the pattern of conjoined firing predicted by the overlap of the neurons' spatial receptive fields. These results suggest that the network likelihood model can be an efficient tool for the analysis of ensemble spiking activity.

Action Potentials↗
PubMedDate not supplied

[Spike transmission in statistical neuronal ensembles. IVa. Stating the problem in a diffusion approximation].

An area of tissue in the field CA3 of the Hippocampus has been selected controled by a basket cell. The functioning of the basket cell has been described by a point approximation method forthe transport equation, and that of the ensemble of pyramidal cells by a diffusion approximation one. Furthermore, the area of tissue is broken up into N2 of "cells" wherein a transition is effected from the diffusion equation of the N2 of the point equations involved. If the sizes of "cells" are commeasurable to the diffusional length of the pyramidal cell collaterals each "cells" being relatively independent generator of activity. In the latter case the fundamental interaction type is the mutual negative influence of the "cells" through the basket cell. Should the area be broken up into further, the mutual influence of the "cells" becomes noticeable and cannot be neglected. The behaviour of spatially homogenous diffusion approximation model is equivalent of the point approximation model.

Action Potentials↗
PubMed2026

LinearCapR: linear-time computation of per-nucleotide structural-context probabilities of RNA without base-pair span limits.

MOTIVATION: RNA molecules adopt dynamic ensembles of secondary structures, where the local structural context of each nucleotide-such as whether it resides in a stem or a specific type of loop-strongly shapes molecular interactions and regulatory function. Structural-context probabilities therefore provide a more functionally informative view of RNA folding than the minimum free energy structures or base-pairing probabilities. However, existing tools either require O(N3) time or employ span-restricted approximations that omit long-range base-pairs, limiting their applicability to large and biologically important RNAs. RESULTS: We introduce LinearCapR, enabling linear-time, span-unrestricted computation of structural-context marginalized probabilities, using beam-pruned Stochastic Context Free Grammar-based computation. LinearCapR retains global ensemble features lost by span-limited methods and yields superior predictive power on bpRNA-1m(90) dataset, especially for multiloops and exterior regions, as well as long-distance stems. LinearCapR supports analysis of long RNAs, demonstrated on the full genome of SARS-CoV-2. LinearCapR provides the first base-pair-span-unrestricted, linear-time framework for RNA structural-context analysis, retaining key thermodynamic ensemble features essential for functional interpretation. It enables large-scale studies of viral genomes, long non-coding RNAs, and downstream analyses such as RNA-binding protein site prediction. AVAILABILITY AND IMPLEMENTATION: The source code of LinearCapR is available at https://github.com/hoget157/LinearCapR. The archived software release used in this work is available at Zenodo: https://doi.org/10.5281/zenodo.19450645.

Nucleic Acid Conformation↗