The Importance of Considering Model Choices When Interpreting Results in Computational Neuroimaging

Model-based analyses open exciting opportunities for understanding neural information processing. In a commentary published in eNeuro, Gardner and Liu (2019) discuss the role of model specification in interpreting results derived from complex models of neural data. As a case study, they suggest that one such analysis, the inverted encoding model (IEM), should not be used to assay properties of "stimulus representations" because the ability to apply linear transformations at various stages of the analysis procedure renders results "arbitrary." Here, we argue that the specification of all models is arbitrary to the extent that an experimenter makes choices based on current knowledge of the model system. However, the results derived from any given model, such as the reconstructed channel response profiles obtained from an IEM analysis, are uniquely defined and are arbitrary only in the sense that changes in the model can predictably change results. IEM-based channel response profiles should therefore not be considered arbitrary when the model is clearly specified and guided by our best understanding of neural population representations in the brain regions being analyzed. Intuitions derived from this case study are important to consider when interpreting results from all model-based analyses, which are similarly contingent upon the specification of the models used.