scholarly journals Voxelwise encoding models with non-spherical multivariate normal priors

2018 ◽  
Author(s):  
Anwar O. Nunez-Elizalde ◽  
Alexander G. Huth ◽  
Jack L. Gallant
Keyword(s):  
Efficient Method ◽  
Predictive Models ◽  
Ridge Regression ◽  
Theoretical Basis ◽  
Expert Knowledge ◽  
Fmri Data ◽  
Model Parameters ◽  
Multivariate Normal ◽  
Computationally Efficient ◽  
Regression Methods

AbstractPredictive models for neural or fMRI data are often fit using regression methods that employ priors on the model parameters. One widely used method is ridge regression, which employs a spherical Gaussian prior that assumes equal and independent variance for all parameters. However, a spherical prior is not always optimal or appropriate. There are many cases where expert knowledge or hypotheses about the structure of the model parameters could be used to construct a better prior. In these cases, non-spherical Gaussian priors can be employed using a generalized form of ridge known as Tikhonov regression. Yet Tikhonov regression is only rarely used in neuroscience. In this paper we discuss the theoretical basis for Tikhonov regression, demonstrate a computationally efficient method for its application, and show several examples of how Tikhonov regression can improve predictive models for fMRI data. We also show that many earlier studies have implicitly used Tikhonov regression by linearly transforming the regressors before performing ridge regression.

scholarly journals Application of a computationally efficient method to approximate gap model results with a probabilistic approach

2014 ◽  
Vol 7 (1) ◽  
pp. 1535-1600
Author(s):  
M. Scherstjanoi ◽  
J. O. Kaplan ◽  
H. Lischke
Keyword(s):  
Climate Change ◽  
Efficient Method ◽  
Tree Species ◽  
Forest Dynamics ◽  
Probabilistic Approach ◽  
Age Distribution ◽  
Change Scenario ◽  
Model Parameters ◽  
Computationally Efficient ◽  
Tree Species Composition

Abstract. To be able to simulate climate change effects on forest dynamics over the whole of Switzerland, we adapted the second generation DGVM LPJ-GUESS to the Alpine environment. We modified model functions, tuned model parameters, and implemented new tree species to represent the potential natural vegetation of Alpine landscapes. Furthermore, we increased the computational efficiency of the model to enable area-covering simulations in a fine resolution (1 km) sufficient for the complex topography of the Alps, which resulted in more than 32 000 simulation grid cells. To this aim, we applied the recently developed method GAPPARD (Scherstjanoi et al., 2013) to LPJ-GUESS. GAPPARD derives mean output values from a combination of simulation runs without disturbances and a patch age distribution defined by the disturbance frequency. With this computationally efficient method, that increased the model's speed by approximately the factor 8, we were able to faster detect shortcomings of LPJ-GUESS functions and parameters. We used the adapted LPJ-GUESS together with GAPPARD to assess the influence of one climate change scenario on dynamics of tree species composition and biomass throughout the 21st century in Switzerland. To allow for comparison with the original model, we additionally simulated forest dynamics along a north-south-transect through Switzerland. The results from this transect confirmed the high value of the GAPPARD method despite some limitations towards extreme climatic events. It allowed for the first time to obtain area-wide, detailed high resolution LPJ-GUESS simulation results for a large part of the Alpine region.

scholarly journals Application of a computationally efficient method to approximate gap model results with a probabilistic approach

2014 ◽  
Vol 7 (4) ◽  
pp. 1543-1571 ◽  
Author(s):  
M. Scherstjanoi ◽  
J. O. Kaplan ◽  
H. Lischke
Keyword(s):  
Climate Change ◽  
Efficient Method ◽  
Tree Species ◽  
Forest Dynamics ◽  
Probabilistic Approach ◽  
Age Distribution ◽  
Model Parameters ◽  
Gap Model ◽  
Computationally Efficient ◽  
Dynamic Global Vegetation Model

Abstract. To be able to simulate climate change effects on forest dynamics over the whole of Switzerland, we adapted the second-generation DGVM (dynamic global vegetation model) LPJ-GUESS (Lund–Potsdam–Jena General Ecosystem Simulator) to the Alpine environment. We modified model functions, tuned model parameters, and implemented new tree species to represent the potential natural vegetation of Alpine landscapes. Furthermore, we increased the computational efficiency of the model to enable area-covering simulations in a fine resolution (1 km) sufficient for the complex topography of the Alps, which resulted in more than 32 000 simulation grid cells. To this aim, we applied the recently developed method GAPPARD (approximating GAP model results with a Probabilistic Approach to account for stand Replacing Disturbances) (Scherstjanoi et al., 2013) to LPJ-GUESS. GAPPARD derives mean output values from a combination of simulation runs without disturbances and a patch age distribution defined by the disturbance frequency. With this computationally efficient method, which increased the model's speed by approximately the factor 8, we were able to faster detect the shortcomings of LPJ-GUESS functions and parameters. We used the adapted LPJ-GUESS together with GAPPARD to assess the influence of one climate change scenario on dynamics of tree species composition and biomass throughout the 21st century in Switzerland. To allow for comparison with the original model, we additionally simulated forest dynamics along a north–south transect through Switzerland. The results from this transect confirmed the high value of the GAPPARD method despite some limitations towards extreme climatic events. It allowed for the first time to obtain area-wide, detailed high-resolution LPJ-GUESS simulation results for a large part of the Alpine region.

Speed vs. comfort: Testing the efficacy of a single question for predicting transit users’ route choices

2019 ◽  
Author(s):  
Joseph John Pyne Simons ◽  
Ilya Farber
Keyword(s):  
Data Collection ◽  
Efficient Method ◽  
Choice Task ◽  
The Self ◽  
Self Report ◽  
Model Parameters ◽  
Single Item ◽  
Alternative Approach ◽  
Single Question ◽  
Insight Into

Not all transit users have the same preferences when making route decisions. Understanding the factors driving this heterogeneity enables better tailoring of policies, interventions, and messaging. However, existing methods for assessing these factors require extensive data collection. Here we present an alternative approach - an easily-administered single item measure of overall preference for speed versus comfort. Scores on the self-report item predict decisions in a choice task and account for a proportion of the differences in model parameters between people (n=298). This single item can easily be included on existing travel surveys, and provides an efficient method to both anticipate the choices of users and gain more general insight into their preferences.

Nearly Exact Bayesian Estimation of Non-linear No-Arbitrage Term-Structure Models*

2021 ◽  
Author(s):  
Marcello Pericoli ◽  
Marco Taboga
Keyword(s):  
Bayesian Estimation ◽  
Term Structure ◽  
Broad Class ◽  
Model Parameters ◽  
State Variables ◽  
Computationally Efficient ◽  
Macroeconomic Factors ◽  
No Arbitrage ◽  
Term Structure Models ◽  
Non Linear

Abstract We propose a general method for the Bayesian estimation of a very broad class of non-linear no-arbitrage term-structure models. The main innovation we introduce is a computationally efficient method, based on deep learning techniques, for approximating no-arbitrage model-implied bond yields to any desired degree of accuracy. Once the pricing function is approximated, the posterior distribution of model parameters and unobservable state variables can be estimated by standard Markov Chain Monte Carlo methods. As an illustrative example, we apply the proposed techniques to the estimation of a shadow-rate model with a time-varying lower bound and unspanned macroeconomic factors.

scholarly journals An Effective Potential for Frenkel Excitons

2020 ◽  
Author(s):  
Bartosz Błasiak ◽  
Wojciech Bartkowiak ◽  
Robert Władysław Góra
Keyword(s):  
Energy Transfer ◽  
Excitation Energy ◽  
Efficient Method ◽  
Effective Potential ◽  
Excitation Energy Transfer ◽  
Computationally Efficient ◽  
Frenkel Excitons

Excitation energy transfer (EET) is a ubiquitous process in life and materials sciences. Here, a new and computationally efficient method of evaluating the electronic EET couplings between interacting chromophores is...

scholarly journals Bayesian Inference of Species Trees using Diffusion Models

2020 ◽  
Vol 70 (1) ◽  
pp. 145-161 ◽  
Author(s):  
Marnus Stoltz ◽  
Boris Baeumer ◽  
Remco Bouckaert ◽  
Colin Fox ◽  
Gordon Hiscott ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Numerical Algorithms ◽  
Diffusion Models ◽  
Model Parameters ◽  
Data Sets ◽  
Species Trees ◽  
Computationally Efficient ◽  
Data Set ◽  
Snp Data ◽  
Binary Markers

Abstract We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics combined with novel numerical algorithms. The diffusion approach allows for analysis of data sets containing hundreds or thousands of individuals. The method, which we call Snapper, has been implemented as part of the BEAST2 package. We conducted simulation experiments to assess numerical error, computational requirements, and accuracy recovering known model parameters. A reanalysis of soybean SNP data demonstrates that the models implemented in Snapp and Snapper can be difficult to distinguish in practice, a characteristic which we tested with further simulations. We demonstrate the scale of analysis possible using a SNP data set sampled from 399 fresh water turtles in 41 populations. [Bayesian inference; diffusion models; multi-species coalescent; SNP data; species trees; spectral methods.]

Nanoparticle Mass Transfer From Lung Airways to Systemic Regions—Part II: Multi-Compartmental Modeling

2013 ◽  
Vol 135 (12) ◽  
Author(s):  
Arun V. Kolanjiyil ◽  
Clement Kleinstreuer
Keyword(s):  
Mass Transfer ◽  
Model Parameters ◽  
Computationally Efficient ◽  
Nanoparticle Deposition ◽  
Aerosol Dynamics ◽  
Multicompartmental Model ◽  
Quantitative Results ◽  
Species Extrapolation ◽  
Critical Insight ◽  
Lung Airways

This is the second article of a two-part paper, combining high-resolution computer simulation results of inhaled nanoparticle deposition in a human airway model (Kolanjiyil and Kleinstreuer, 2013, “Nanoparticle Mass Transfer From Lung Airways to Systemic Regions—Part I: Whole-Lung Aerosol Dynamics,” ASME J. Biomech. Eng., 135(12), p. 121003) with a new multicompartmental model for insoluble nanoparticle barrier mass transfer into systemic regions. Specifically, it allows for the prediction of temporal nanoparticle accumulation in the blood and lymphatic systems and in organs. The multicompartmental model parameters were determined from experimental retention and clearance data in rat lungs and then the validated model was applied to humans based on pharmacokinetic cross-species extrapolation. This hybrid simulator is a computationally efficient tool to predict the nanoparticle kinetics in the human body. The study provides critical insight into nanomaterial deposition and distribution from the lungs to systemic regions. The quantitative results are useful in diverse fields such as toxicology for exposure-risk analysis of ubiquitous nanomaterial and pharmacology for nanodrug development and targeting.

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