Uncertainpy: A Python Toolbox for Uncertainty Quantification and Sensitivity Analysis in Computational Neuroscience

Frontiers in Neuroinformatics
Simen TennøeGaute T Einevoll

Abstract

Computational models in neuroscience typically contain many parameters that are poorly constrained by experimental data. Uncertainty quantification and sensitivity analysis provide rigorous procedures to quantify how the model output depends on this parameter uncertainty. Unfortunately, the application of such methods is not yet standard within the field of neuroscience. Here we present Uncertainpy, an open-source Python toolbox, tailored to perform uncertainty quantification and sensitivity analysis of neuroscience models. Uncertainpy aims to make it quick and easy to get started with uncertainty analysis, without any need for detailed prior knowledge. The toolbox allows uncertainty quantification and sensitivity analysis to be performed on already existing models without needing to modify the model equations or model implementation. Uncertainpy bases its analysis on polynomial chaos expansions, which are more efficient than the more standard Monte-Carlo based approaches. Uncertainpy is tailored for neuroscience applications by its built-in capability for calculating characteristic features in the model output. The toolbox does not merely perform a point-to-point comparison of the "raw" model output (e.g., membrane voltage tra...Continue Reading

References

Jan 1, 1994·Journal of Neurophysiology·E De Schutter, J M Bower
Aug 15, 1997·Neural Computation·M L Hines, N T Carnevale
Jul 3, 1999·Neuroscience·J J ZhuW W Lytton
Oct 9, 1999·Journal of Computational Neuroscience·R D BeerJ C Gallagher
May 16, 2000·Journal of Computational Neuroscience·N Brunel
Nov 8, 2001·Proceedings of the National Academy of Sciences of the United States of America·G M Edelman, J A Gally
Feb 5, 2002·Journal of Neurophysiology·Jorge GolowaschEve Marder
Jun 29, 2002·Risk Analysis : an Official Publication of the Society for Risk Analysis·Andrea Saltelli
Nov 24, 2004·Nature Neuroscience·Astrid A PrinzEve Marder
Jun 9, 2006·Journal of Neurophysiology·Anne-Elise Tobin, Ronald L Calabrese
Jun 23, 2006·Nature Reviews. Neuroscience·Eve Marder, Jean-Marc Goaillard
Jul 20, 2006·PLoS Computational Biology·Pablo Achard, Erik De Schutter
Feb 8, 2007·Bio Systems·Geir HalnesPeter Arhem
Jul 27, 2007·Proceedings of the National Academy of Sciences of the United States of America·David J SchulzEve E Marder
Oct 10, 2007·PLoS Computational Biology·Ryan N GutenkunstJames P Sethna
Feb 5, 2008·IEEE Transactions on Neural Networks·E M Izhikevich
Feb 23, 2008·Proceedings of the National Academy of Sciences of the United States of America·Eugene M Izhikevich, Gerald M Edelman
Jun 24, 2008·Journal of Theoretical Biology·Simeone MarinoDenise E Kirschner
Nov 18, 2008·Biological cybernetics·W Van GeitP Achard
May 1, 2009·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Adam L TaylorEve Marder
Jan 1, 2009·Frontiers in Neuroscience·Gaute T Einevoll
Jan 29, 2011·Nature Neuroscience·Eve Marder, Adam L Taylor
Oct 8, 2011·PLoS Computational Biology·Geir HalnesMichele Migliore
Apr 25, 2012·Journal of Neuroscience Methods·Armin BahlArnd Roth
Mar 29, 2013·Journal of Neurophysiology·Etay HayIdan Segev
Sep 1, 1994·Environmental Monitoring and Assessment·D M Hamby
Jan 15, 2014·Nature Neuroscience·Antonin Blot, Boris Barbour
Mar 7, 2014·Frontiers in Neuroinformatics·Samuel GarciaAndrew P Davison
May 1, 2015·Frontiers in Neuroinformatics·Eilif MullerAndrew P Davison
Jul 15, 2015·Seminars in Cell & Developmental Biology·G Wayne Brodland
Oct 10, 2015·Cell·Henry MarkramFelix Schürmann
Oct 16, 2015·Journal of Mathematical Neuroscience·Aldemar Torres ValderramaJoke Blom
Oct 18, 2015·International Journal for Numerical Methods in Biomedical Engineering·V G EckWouter Huberts
Nov 1, 2016·Nature Neuroscience·Kishore V KuchibhotlaRobert C Froemke
Jun 29, 2017·Bulletin of Mathematical Biology·Thomas J SnowdenMarcus J Tindall
Aug 5, 2017·Journal of the Royal Society, Interface·Ann C Babtie, Michael P H Stumpf
May 1, 2018·Frontiers in Neuroinformatics·Svenn-Arne DraglyAnders Malthe-Sørenssen

❮ Previous
Next ❯

Citations

May 17, 2019·PLoS Computational Biology·Elisabetta IavaroneSean L Hill
Aug 23, 2019·PLoS Computational Biology·Geir HalnesKjetil Hodne
May 26, 2020·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Shulin CaoAndrew D McCulloch
May 26, 2020·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Ariel WangDaniela Valdez-Jasso
Aug 2, 2020·Scientific Reports·Marilisa CortesiEmanuele Giordano
Sep 5, 2019·Frontiers in Synaptic Neuroscience·Ola BykowskaRui Ponte Costa
Oct 22, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Julius ZimmermannUrsula van Rienen
Mar 30, 2021·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·D GroenP V Coveney
Jul 17, 2021·ELife·Cornelius SchröderTom Baden
Nov 4, 2021·Journal of Mathematical Biology·Jason G Miles, Nicholas A Battista

❮ Previous
Next ❯

Methods Mentioned

BETA
Feature Extraction

Software Mentioned

SpikingFeatures
NeuronModel
Chaospy
Elephant Python
Github
NeuralEnsemble
method
Jupyter
Data
pc

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

© 2022 Meta ULC. All rights reserved