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A flexible framework for simulating and fitting generalized drift-diffusion models [article]

Maxwell Shinn, Norman H Lam, John D Murray
2020 bioRxiv   pre-print
This speed allows GDDMs to be fit to data using maximum likelihood on the full response time (RT) distribution.  ...  We show that a GDDM fit with our framework explains a classic open dataset with better accuracy and fewer parameters than several DDMs implemented using the latest methodology.  ...  model fit to the RT distribution.  ... 
doi:10.1101/2020.03.14.992065 fatcat:7zwpw4d3ovhxjaakavyulfy6wy

A flexible framework for simulating and fitting generalized drift-diffusion models

Maxwell Shinn, Norman H Lam, John D Murray
2020 eLife  
This speed allows GDDMs to be fit to data using maximum likelihood on the full response time (RT) distribution.  ...  Here, we introduce the generalized drift-diffusion model (GDDM) framework for building and fitting DDM extensions, and provide a software package which implements the framework.  ...  Example estimated RT distributions with different numerical parameters. 332 To evaluate the execution time vs error tradeoff, we perform a parameter sweep across values 333 of Δ and Δ for these three  ... 
doi:10.7554/elife.56938 pmid:32749218 pmcid:PMC7462609 fatcat:fmcjeuthy5bava7azfta7uayhi

Design of experiments for fitting subsystem metamodels

Russell R. Barton
1997 Proceedings of the 29th conference on Winter simulation - WSC '97  
The development of a metamodel-based integration strategy for system-level design depends on effective experiment design strategies for fitting and updating subsystem metamodels.  ...  A metamodel-based integration strategy allows simulation results from multiple submodels to be combined into a system-level simulation.  ...  ACKNOWLEDGMENTS This research was supported in part by NSF grant DMI-9700040 and by a Total Quality Management Grant from the IBM Corporation.  ... 
doi:10.1145/268437.268495 fatcat:7xz7vziymnaddmc6ly27rfpsce

Bloom Filters: One Size Fits All?

Paul Hurley, Marcel Waldvogel
2007 32nd IEEE Conference on Local Computer Networks (LCN 2007)  
We analyze, through modelling, how far Bloom filters are from the optimal and then examine application specific issues in a distributed web caching scenario.  ...  Bloom filters impress by their sheer elegance and have become a widely and indiscriminately used tool in network applications, although, as we show, their performance can often be far from optimal.  ...  We then look at how well we can apply our findings in practice by a performance evaluation in a distributed cache scenario.  ... 
doi:10.1109/lcn.2007.17 dblp:conf/lcn/HurleyW07 fatcat:zmee6ai3wjec7e7s75qy7kvjci

FIT: Tag based method for fusion proteins identification [article]

Kang Ning, Alexey I. Nesvizhskii
2014 arXiv   pre-print
In this work, we present a sequence tag based fusion protein identi-fication algorithm, FIT, that combines the virtue of both de novo sequence tag retrieval and peptide-spectrum matching for identifi-cation  ...  Results on simulated datasets show high sensitivity and low false positive rates for fusion protein identifica-tion by the FIT algorithm.  ...  As a tradeoff, we selected the protein coverage threshold of 0.5 (required for at least one of the two fusion partner candidates) as a filter.  ... 
arXiv:1408.4950v1 fatcat:bj6epthcpvff3feqpnus7nogne

No one (cluster) size fits all

Herodotos Herodotou, Fei Dong, Shivnath Babu
2011 Proceedings of the 2nd ACM Symposium on Cloud Computing - SOCC '11  
that involve finding the cluster size, the type of resources to use in the cluster from the large number of choices offered by current IaaS cloud platforms, and the job configurations that best meet the performance  ...  In this paper, we introduce the Elastisizer, a system to which users can express cluster sizing problems as queries in a declarative fashion.  ...  Relative (fitness) modeling is a black-box approach proposed recently for complex storage devices [21] .  ... 
doi:10.1145/2038916.2038934 dblp:conf/cloud/HerodotouDB11 fatcat:qvlugswksraqfdcmpqjh3kfstu

Human Digital Twin for Fitness Management

Barbara Rita Barricelli, Elena Casiraghi, Jessica Gliozzo, Alessandro Petrini, Stefano Valtolina
2020 IEEE Access  
The athlete's team is integrated into SmartFit, a software framework for supporting trainers and coaches in monitoring and manage athletes' fitness activity and results.  ...  Our research work describes a team of human Digital Twins (DTs), each tracking fitness-related measurements describing an athlete's behavior in consecutive days (e.g. food income, activity, sleep).  ...  This allows observing that each athlete has a quite variable fitness score distribution.  ... 
doi:10.1109/access.2020.2971576 fatcat:yshyipdjzjdnzbtiib72zgb6hi

A biophysical protein folding model accounts for most mutational fitness effects in viruses [article]

C Scott Wylie, Eugene I Shakhnovich
2011 arXiv   pre-print
The distribution of fitness effects (DFE) among random mutations is an essential component of every evolutionary model and a mathematical portrait of robustness.  ...  Fitness effects of mutations fall on a continuum ranging from lethal to deleterious to beneficial.  ...  Lorenz, and especially A. Serohijos and S. Bershtein for comments on the manuscript. This work was supported by the National Institute of Health.  ... 
arXiv:1105.0448v1 fatcat:jxitjuuu7rcsxnwddcrikchime

Post-transcriptional regulation of Leishmania fitness gain [article]

Laura Piel, K. Shanmugha Rajan, Giovanni Bussotti, Hugo Varet, Rachel Legendre, Caroline Proux, Thibaut Douche, Quentin Giai Gianetto, Thibaut Chaze, Barbora Vojtkova, Nadav Gordon-Bar, Tirza Doniger (+12 others)
2021 bioRxiv   pre-print
Phenotypic analyses of parasites from early and late stages of culture adaptation revealed an important fitness tradeoff, with selection for accelerated growth (fitness gain) impairing infectivity (fitness  ...  Genome instability has been recognized as a driver in Leishmania fitness gain in response to environmental change or chemotherapy.  ...  informs on mechanisms underlying fitness tradeoff. We performed RNAseq analyses using poly(A+)-enriched mRNA obtained from three replicates of EP.1 and LP.1 log, stat, and EP.1 meta parasites.  ... 
doi:10.1101/2021.03.22.436378 fatcat:j3fajqygr5etdgf36htal2cu3u

Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

Ke Chen, Amitesh Anand, Connor Olson, Troy E. Sandberg, Ye Gao, Nathan Mih, Bernhard O. Palsson, Costas D. Maranas
2021 PLoS Computational Biology  
We found that the measured phenotypes distribute non-uniformly to form a highly stratified fitness landscape.  ...  The fitness landscape is a concept commonly used to describe evolution towards optimal phenotypes. It can be reduced to mechanistic detail using genome-scale models (GEMs) from systems biology.  ...  database GEO.  ... 
doi:10.1371/journal.pcbi.1008596 pmid:33465077 fatcat:r2sp7ecxjrbf3jbgb3ghpsrspa

Biotic interactions affect fitness across latitudes, but only drive local adaptation in the tropics [article]

Anna Hargreaves, Rachel Germain, Megan Bontrager, Joshua Persi, Amy Angert
2019 bioRxiv   pre-print
We tested this hypothesis using a meta-analysis of common-garden experiments from 138 studies (149 taxa). Across studies, local adaptation was common and biotic interactions affected fitness.  ...  Local adaptation to broad-scale environmental heterogeneity can increase species distributions and diversification, but which environmental components commonly drive local adaptation-particularly the importance  ...  Effect sizes were analyzed using a Gaussian error 277 distribution.  ... 
doi:10.1101/575498 fatcat:hq2xavlavvekto2y4327pis73i

Tradeoffs in the Design of Health Plan Payment Systems: Fit, Power and Balance

Michael Geruso, Thomas G. McGuire
2015 Social Science Research Network  
We find that a simple reinsurance system scores better on fit, power and balance than the risk adjustment formula in use in the Exchanges.  ...  We implement these metrics in a study of Exchange payment systems with data similar to that used to develop the Exchange risk adjustment scheme and describe the tradeoffs among the metrics.  ...  Note that the terms of the tradeoff in a mixed system are the same for any distribution of cost (the x i ); in other words, independent of the population under study.  ... 
doi:10.2139/ssrn.2567957 fatcat:tegaeulg2zcp7m7wjuz3zl2fni

ASP fits to multi-way layouts

Rodolf Beran
2005 Annals of the Institute of Statistical Mathematics  
ASP estimators weigh a large class of competing fits, including smooth fits for ordinal factors, to reduce risk through bias-variance tradeoff.  ...  ASP algorithms weigh competing biased fits in order to reduce risk through variance-bias tradeoff. The acronym ASP stands for Adaptive Shrinkage on Penalty bases.  ...  Performance of semiautomatic ASP fits on this data thus provides an extreme test case.  ... 
doi:10.1007/bf02507022 fatcat:q2rajx3xsfft3au5x5uydcl7fu

Relationship between fitness and heterogeneity in exponentially growing microbial populations [article]

Anna Paola Muntoni, Alfredo Braunstein, Andrea Pagnani, Daniele De Martino, Andrea De Martino
2022 arXiv   pre-print
To shed light on these issues, we develop an inverse modeling framework that connects the fitness of a population of cells (represented by the mean single-cell growth rate) to the underlying metabolic  ...  variability through the Maximum-Entropy inference of the distribution of metabolic phenotypes from data.  ...  The distribution inferred for each experiment yields a point in the (fitness, information) plane.  ... 
arXiv:2104.02594v2 fatcat:wrt2pcynonbfdoajnwxynhflaa

Active Contours Driven by Multi-Feature Gaussian Distribution Fitting Energy with Application to Vessel Segmentation

Lei Wang, Huimao Zhang, Kan He, Yan Chang, Xiaodong Yang, Paul J Atzberger
2015 PLoS ONE  
multi-feature Gaussian distribution fitting energy in this paper.  ...  This energy is then incorporated into a level set formulation with a regularization term for accurate segmentations.  ...  random variables with different means and variances, and then uses the two variables to construct a multi-feature Gaussian distribution fitting energy so as to improve the segmentation performances of  ... 
doi:10.1371/journal.pone.0143105 pmid:26571031 pmcid:PMC4646657 fatcat:kqfn4zhgc5flbftjiscvalu6eq
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