Statistical inference on representational geometries

Elife. 2023 Aug 23:12:e82566. doi: 10.7554/eLife.82566.


Neuroscience has recently made much progress, expanding the complexity of both neural activity measurements and brain-computational models. However, we lack robust methods for connecting theory and experiment by evaluating our new big models with our new big data. Here, we introduce new inference methods enabling researchers to evaluate and compare models based on the accuracy of their predictions of representational geometries: A good model should accurately predict the distances among the neural population representations (e.g. of a set of stimuli). Our inference methods combine novel 2-factor extensions of crossvalidation (to prevent overfitting to either subjects or conditions from inflating our estimates of model accuracy) and bootstrapping (to enable inferential model comparison with simultaneous generalization to both new subjects and new conditions). We validate the inference methods on data where the ground-truth model is known, by simulating data with deep neural networks and by resampling of calcium-imaging and functional MRI data. Results demonstrate that the methods are valid and conclusions generalize correctly. These data analysis methods are available in an open-source Python toolbox (

Keywords: human; mouse; neuroscience; representational similarity analysis; statistical inference; toolbox.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Big Data*
  • Calcium, Dietary
  • Generalization, Psychological
  • Humans
  • Neural Networks, Computer
  • Neurosciences*


  • Calcium, Dietary

Grants and funding

The funders had no role in study design, data collection, and interpretation, or the decision to submit the work for publication.