Fast and robust estimation of spectro-temporal receptive fields using stochastic approximations

Journal of Neuroscience Methods
Arne F MeyerJörn Anemüller

Abstract

The receptive field (RF) represents the signal preferences of sensory neurons and is the primary analysis method for understanding sensory coding. While it is essential to estimate a neuron's RF, finding numerical solutions to increasingly complex RF models can become computationally intensive, in particular for high-dimensional stimuli or when many neurons are involved. Here we propose an optimization scheme based on stochastic approximations that facilitate this task. The basic idea is to derive solutions on a random subset rather than computing the full solution on the available data set. To test this, we applied different optimization schemes based on stochastic gradient descent (SGD) to both the generalized linear model (GLM) and a recently developed classification-based RF estimation approach. Using simulated and recorded responses, we demonstrate that RF parameter optimization based on state-of-the-art SGD algorithms produces robust estimates of the spectro-temporal receptive field (STRF). Results on recordings from the auditory midbrain demonstrate that stochastic approximations preserve both predictive power and tuning properties of STRFs. A correlation of 0.93 with the STRF derived from the full solution may be obtain...Continue Reading

References

Jun 28, 1991·Science·W BialekD Warland
Jul 1, 1968·IEEE Transactions on Bio-medical Engineering·R de Boer, P Kuyper
Oct 24, 1997·Vision Research·D L RingachR Shapley
Apr 2, 1998·Proceedings. Biological Sciences·J H van Hateren, A van der Schaaf
Jun 20, 1998·Science·R C deCharmsM M Merzenich
Aug 8, 1994·Physical Review Letters·D L Ruderman, W Bialek
Jun 19, 2001·Network : Computation in Neural Systems·E J Chichilnisky
Aug 15, 2001·Current Opinion in Neurobiology·J Touryan, Y Dan
Aug 25, 2001·Annual Review of Neuroscience·E P Simoncelli, B A Olshausen
Oct 11, 2001·Proceedings of the National Academy of Sciences of the United States of America·E N BrownV Solo
Dec 19, 2002·Neural Computation·Garrett B Stanley
Mar 26, 2003·Nature Neuroscience·Nachum UlanovskyIsrael Nelken
Aug 27, 2003·Network : Computation in Neural Systems·Liam Paninski
Nov 19, 2003·The European Journal of Neuroscience·Bernhard H Gaese, Joachim Ostwald
Nov 19, 2003·Neuron·Thomas L AdelmanRobert M Olberg
Feb 6, 2004·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Christian K MachensAnthony M Zador
Mar 10, 2004·Neural Computation·Tatyana SharpeeWilliam Bialek
Apr 9, 2004·Neural Computation·Uri T EdenEmery N Brown
Aug 6, 2004·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Stephen V DavidJack L Gallant
Nov 2, 2004·Neural Computation·Liam PaninskiEero P Simoncelli
Dec 17, 2004·Network : Computation in Neural Systems·Liam Paninski
Feb 24, 2006·Nature·Tatyana O SharpeeKenneth D Miller
Mar 7, 2006·Journal of Computational Neuroscience·David J KleinShihab A Shamma
Jun 17, 2006·Annual Review of Neuroscience·Michael C-K WuJack L Gallant
Aug 8, 2006·Journal of Vision·Odelia SchwartzEero P Simoncelli
Aug 11, 2007·Current Opinion in Neurobiology·Jan BendaAndreas Vm Herz
Sep 14, 2007·Network : Computation in Neural Systems·Stephen V DavidShihab A Shamma
Jan 11, 2008·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·G Björn ChristiansonJennifer F Linden
May 23, 2008·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Nicholas A Lesica, Benedikt Grothe
Jul 5, 2008·The European Journal of Neuroscience·Sandra TolnaiRudolf Rübsamen
Oct 22, 2008·Neural Computation·Jeremy LewiLiam Paninski
Aug 20, 2010·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Max F K HappelFrank W Ohl
Jan 29, 2011·Nature Neuroscience·Ian H Stevenson, Konrad P Kording
Jun 22, 2011·Neuron·Neil C RabinowitzAndrew J King
Aug 19, 2011·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·David M Schneider, Sarah M N Woolley
Dec 14, 2011·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Shai NetserYoram Gutfreund
Feb 4, 2012·PLoS Biology·Brian N PasleyEdward F Chang
Nov 1, 2012·Proceedings of the National Academy of Sciences of the United States of America·Gal Chechik, Israel Nelken
May 21, 2013·Nature Neuroscience·Jeremy FreemanJ Anthony Movshon
Jul 9, 2013·Journal of Computational Neuroscience·Alexandro D Ramirez, Liam Paninski
Jul 12, 2013·Annual Review of Neuroscience·Tatyana O Sharpee
Mar 7, 2014·Frontiers in Neuroinformatics·Alexandre AbrahamGaël Varoquaux
Jan 8, 2015·Frontiers in Computational Neuroscience·Arne F MeyerJörn Anemüller

❮ Previous
Next ❯

Citations

Jul 31, 2016·Hearing Research·Johan Westö, Patrick J C May
May 3, 2018·Journal of Neurophysiology·Johan Westö, Patrick J C May
Feb 25, 2017·Frontiers in Systems Neuroscience·Jörg-Hendrik BachJörn Anemüller
Jul 18, 2017·Frontiers in Neuroscience·Mijail D Serruya
Jan 28, 2017·Frontiers in Systems Neuroscience·Arne F MeyerManeesh Sahani
Oct 14, 2021·PloS One·Mehrad SarmashghiUri Eden

❮ Previous
Next ❯

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.