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Assessing and tuning brain decoders: Cross-validation, caveats, and guidelines
2017
NeuroImage
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Such evaluation is achieved via cross-validation, a method also used to tune decoders' hyper-parameters. This paper is a review on cross-validation procedures for decoding in neuroimaging. ...
Nested cross-validation can tune decoders' parameters while avoiding circularity bias. However we find that it can be more favorable to use sane defaults, in particular for non-sparse decoders. ...
Results: cross-validation to assess predictive power Reliability of the cross-validation measure. ...
doi:10.1016/j.neuroimage.2016.10.038
pmid:27989847
fatcat:ffbhhxp37vfhdohas3rd66ttom
Eye Movement-Related Confounds in Neural Decoding of Visual Working Memory Representations
2018
eNeuro
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However, with its promises also come potential caveats. ...
Significance Statement Neural decoding is an important and relatively novel technique that has opened up new avenues for cognitive neuroscience research. ...
To test whether we could decode stimulus identity from the MEG signal, we applied the classifier to the same (pooled) data using cross-validation and found successful decoding during a period of up to ...
doi:10.1523/eneuro.0401-17.2018
pmid:30310862
pmcid:PMC6179574
fatcat:23h73x3kqfag5pq7pi7vsrvtta
Using Coherence-based spectro-spatial filters for stimulus features prediction from electro-corticographic recordings
2020
Scientific Reports
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and brain responses manually. ...
In decoding tasks, on the contrary, brain responses are used to predict the stimuli, and traditionally, the signals are assumed stationary within trials, which is rarely the case for natural stimuli. ...
Acknowledgements This work was performed thanks for the Swiss National Funds project grant to ALG 320030_163040, and to the EU FET-BrainCom project and NINDS R3723115. The authors thanks Dr. ...
doi:10.1038/s41598-020-63303-1
pmid:32376909
pmcid:PMC7203138
fatcat:rajl3wh6vbbhrjz346rmcq6qpm
Thought-based interaction: Same data, same methods, different results?
2019
PLoS Biology
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What is the best practice to ensure that results are stringent and conclusive and analyses replicable? ...
However, the validity of the evidence has been questioned: independent reanalysis of the same data yielded significantly different results. ...
Exceeding chance level by chance: The caveat of theoretical chance levels in brain signal classification and statistical assessment of decoding accuracy. ...
doi:10.1371/journal.pbio.3000190
pmid:30958813
pmcid:PMC6453358
fatcat:qw6nun7w5zagxpylzbfdrqt5y4
Classification Accuracy of Neuroimaging Biomarkers in Attention-Deficit/Hyperactivity Disorder: Effects of Sample Size and Circular Analysis
2018
Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
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Motivated by an inconsistency between reports of high diagnosis-classification accuracies and known heterogeneity in attention-deficit/hyperactivity disorder (ADHD), this study assessed classification ...
Varoquaux G, Raamana PR, Engemann DA, Hoyos-Idrobo A, Schwartz Y, Thirion B (2017):
Assessing and tuning brain decoders: Cross-validation, caveats, and guidelines. Neuroimage.
145:166-179. ...
Combrisson E, Jerbi K (2015): Exceeding chance level by chance: The caveat of theoretical chance levels in brain signal classification and statistical assessment of decoding accuracy. ...
doi:10.1016/j.bpsc.2018.06.003
pmid:30064848
pmcid:PMC6310118
fatcat:thwebnsgkzfyhfpenk7ou7bsju
Population Coding in an Innately Relevant Olfactory Area
2017
Neuron
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tuning, reliability and correlation structure. ...
These results demonstrate that brain regions mediating odordriven innate behaviors can, like brain areas involved in odor learning, represent odor objects using distributive population codes; these findings ...
SRD is supported by fellowships from the Burroughs Wellcome Fund, the Vallee Foundation, the Khodadad Program, by grant RO11DC011558 from the National Institutes of Health, and by the Global Brain Initiative ...
doi:10.1016/j.neuron.2017.02.010
pmid:28238549
pmcid:PMC5370575
fatcat:jph7xswhrjejddgn2os22hklgq
MEG/EEG group study with MNE: recommendations, quality assessments and best practices
[article]
2017
bioRxiv
pre-print
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The analysis covers preprocessing steps, quality assurance steps, sensor space analysis of evoked responses, source localization, and statistics in both sensor and source space. ...
inverse versus LCMV beamformer, and the use of univariate or multivariate statistics. ...
Acknowledgement We would like to thank the many members of the MNE community who have contributed through code, comments, and even complaints, to the improvement and design of this software. ...
doi:10.1101/240044
fatcat:cgw6ubvyqrgxvnq2dmwechcx6m
A Reproducible MEG/EEG Group Study With the MNE Software: Recommendations, Quality Assessments, and Good Practices
2018
Frontiers in Neuroscience
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LCMV beamformer, and the use of univariate or multivariate statistics. ...
The analysis covers preprocessing steps, quality assurance steps, sensor space analysis of evoked responses, source localization, and statistics in both sensor and source space. ...
ST and MH interpreted the data, participated in the scientific discussions, and provided critical insights. All authors reviewed the manuscript and approved it for publication. ...
doi:10.3389/fnins.2018.00530
pmid:30127712
pmcid:PMC6088222
fatcat:22t3ir7eznbohknhi2tgo42ywm
Audiovisual Modulation in Mouse Primary Visual Cortex Depends on Cross-Modal Stimulus Configuration and Congruency
2017
Journal of Neuroscience
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Using two-photon imaging of large groups of neurons, we show that multisensory modulation of V1 populations is strongly determined by the individual and shared features of cross-modal stimulus constituents ...
stimuli, and their prevalence was balanced. ...
A leave-one-out cross-validation procedure was used in which the to-bedecoded trial was excluded from the training set when determining the likelihood functions. ...
doi:10.1523/jneurosci.0468-17.2017
pmid:28821672
fatcat:7wxkpnmnrrcw5ax3eoso52ukzy
Population coding in mouse visual cortex: response reliability and dissociability of stimulus tuning and noise correlation
2014
Frontiers in Computational Neuroscience
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We show that the variability of neuronal responses may hamper the decoding of population activity, and that a normalization to correct for this variability may be of critical importance for correct decoding ...
Second, by comparing noise correlations and stimulus tuning we find that these properties have dissociated anatomical correlates, even though noise correlations have been previously hypothesized to reflect ...
ACKNOWLEDGMENTS This work was supported by the Netherlands Organization for Scientific Research-Excellence grant for the Brain & Cognition project 433-09-208 and the EU FP7-ICT grant 270108. ...
doi:10.3389/fncom.2014.00058
pmid:24917812
pmcid:PMC4040453
fatcat:lkltcwch55akrjxhyexi5mfot4
Simple Acoustic Features Can Explain Phoneme-Based Predictions of Cortical Responses to Speech
2019
Current Biology
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We find that two recent results, the improved performance of an encoding model in which annotated linguistic and acoustic features were combined and the decoding of phoneme subgroups from phoneme-locked ...
By replicating our results in publicly available electroencephalography (EEG) data, we conclude that models of brain responses based on linguistic features can serve as excellent benchmarks. ...
Assessing and tuning brain decoders: cross-validation, caveats, and guidelines. Neuroimage 145 (Pt B), 166-179. 45. Acerbi, L., and Ma, W.J. (2017). ...
doi:10.1016/j.cub.2019.04.067
pmid:31130454
pmcid:PMC6584359
fatcat:ub46l7mij5civae2ugot6hxhzi
MVPA-Light: A Classification and Regression Toolbox for Multi-Dimensional Data
2020
Frontiers in Neuroscience
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., time x time) and searchlight analysis. The toolbox performs cross-validation, hyperparameter tuning, and nested preprocessing. ...
It computes various classification and regression metrics and establishes their statistical significance, is modular and easily extendable. ...
., and Thirion, B. (2017). Assessing and tuning brain decoders: cross-validation, caveats, and guidelines. ...
doi:10.3389/fnins.2020.00289
pmid:32581662
pmcid:PMC7287158
fatcat:7mxsgmesynayjk5q34jehmm5j4
Comparing Task-Relevant Information Across Different Methods of Extracting Functional Connectivity
[article]
2018
bioRxiv
pre-print
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between-subject cross-validation, which aims at extracting signatures that generalize across subjects. ...
The measures are evaluated in their ability to discriminate the five tasks with two types of crossvalidation: within-subject cross-validation, which reflects the stability of the signature over time; and ...
Acknowledgements This research was funded by the European Union's Horizon 2020 Research and Innovation Programme under Grant Agreements No. 7202070 (HBP SGA1) and 737691 (HBP SGA2). ...
doi:10.1101/509059
fatcat:cjlghfavyze4vdz5sfmcxxtljy
Classical Statistics and Statistical Learning in Imaging Neuroscience
2017
Frontiers in Neuroscience
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Throughout recent years, statistical learning methods enjoy increasing popularity especially for applications in rich and complex data, including cross-validated out-of-sample prediction using pattern ...
Brain-imaging research has predominantly generated insight by means of classical statistics, including regression-type analyses and null-hypothesis testing using t-test and ANOVA. ...
Assessing generalization performance of different sparse models using 5fold cross-validation yields the non-zero coefficients for few brain voxels whose volumetric information is most predictive of an ...
doi:10.3389/fnins.2017.00543
pmid:29056896
pmcid:PMC5635056
fatcat:ilwuesppwzelphg6rjrpj6b4ri
OUP accepted manuscript
2018
Cerebral Cortex
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These findings suggest that characteristic tuning of human auditory cortex to slow temporal modulations is unique and may have emerged as a critical step in the evolution of speech and language. ...
Conversely, we observed a striking interspecies difference in cortical sensitivity to temporal modulations: While decoding from macaque auditory cortex was most accurate at fast rates ( > 30 Hz), humans ...
Notes We thank Vittoria de Angelis, Giancarlo Valente and Michelle Moerel for useful discussions on data analysis. We thank three anonymous reviewers for their valuable comments. ...
doi:10.1093/cercor/bhy243
pmid:30395192
fatcat:eadsfyg4zba5zlm5ir3mgaejym
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