Bayesian adaptive stimulus selection for dissociating models of psychophysical data

Cooke, J. R. H.; Selen, L. P. J.; van Beers, R. J.; Medendorp, W. P.

doi:10.1101/220590

Home/Archive/bioRxiv

bioRxiv · 10.1101/220590

Bayesian adaptive stimulus selection for dissociating models of psychophysical data

Cooke, J. R. H.·Selen, L. P. J.·van Beers, R. J.·Medendorp, W. P.

View original source ↗Export metadata ↓

Abstract

Comparing models facilitates testing different hypotheses regarding the computational basis of perception and action. Effective model comparison requires stimuli for which models make different predictions. Typically, experiments use a predetermined set of stimuli or sample stimuli randomly. Both methods have limitations; a predetermined set may not contain stimuli that dissociate the models whereas random sampling may be inefficient. To overcome these limitations, we expanded the psi-algorithm (Kontsevich & Tyler, 1999) from estimating the parameters of a psychometric curve to distinguishing models. To test our algorithm, we applied it to two distinct problems. First, we investigated dissociating sensory noise models. We simulated ideal observers with different noise models performing a 2-afc task. Stimuli were selected randomly or using our algorithm. We found using our algorithm improved the accuracy of model comparison. We also validated the algorithm in subjects by inferring which noise model underlies speed perception. Our algorithm converged quickly to the model previously proposed (Stocker & Simoncelli, 2006), whereas if stimuli were selected randomly model probabilities separated slower and sometimes supported alternative models. Second, we applied our algorithm to a different problem; comparing models of target selection under body acceleration. Previous work found target choice preference is modulated by whole body acceleration (Rincon-Gonzalez et al., 2016). However, the effect is subtle making model comparison difficult. We show that selecting stimuli adaptively could have led to stronger conclusions in model comparison. We conclude that our technique is more efficient and more reliable than current methods of stimulus selection for dissociating models.\n\nData AvailabilityAll data and code will be posted on our institutional repository system following acceptance. In the meantime feel free to contact the authors if you would like any of the code.

Source connections

Published article ↗

Explore related subjects

neuroscience Preprint

Keep this discovery

BibTeX RIS

Cooke, J. R. H., Selen, L. P. J., van Beers, R. J., Medendorp, W. P.. 2017-11-17. Bayesian adaptive stimulus selection for dissociating models of psychophysical data. https://doi.org/10.1101/220590

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

The Unreasonable Effectiveness of Cell Types in Describing Neuronal Physiological Features

Single-cell RNA sequencing (scRNA-seq) captures detailed gene expression profiles at scale, while patch-clamp recordings measure intrinsic neuronal electrophysiological properties. Modeling the relations between these two modalities remains a challenge. Here, we compare how well electrophysiological features can be predicted by traditional transcriptomic cell type classification, representations derived from a foundational model (scGPT) pretrained on large-scale scRNA-seq datasets, ion channel-coding genes, and highly variable genes. Using paired transcriptomic and electrophysiological patch-sequencing data from 495 human neurons from neurosurgical tissue, we find that cluster-level cell type representations consistently outperform highly variable gene selection, ion channel gene selection, and context-enriched scGPT embeddings. Notably, performance varies across model architectures and initializations, and the best results are obtained by combining the outputs of separate cell type and scGPT-based models. Together, these findings suggest that traditional discrete cellular classification is highly effective in predicting physiological features. For maximum performance it can be complemented by pretrained transformer models.

neuroscience↗

bioRxiv2026

A nonlinear inhibition pathway underlying cortical responses to tuned holographic optogenetic perturbations

Optogenetics enables causal manipulation of cortical activity. Perturbation responses can be counterintuitive due to network interactions, making theory essential for predicting them. Existing approaches often rely on linear approximations, which fail for many biologically relevant perturbations. Here we develop a nonlinear theory of responses to holographic perturbations in cell-type-specific recurrent networks with structured connectivity. We fit a nonlinear model to mouse V1 data, which shows cotuned-ensemble suppression: perturbing spatially clustered neurons with similar preferred orientations yields markedly stronger short-range suppression than perturbing untuned ensembles. We show that cotuned-ensemble suppression arises from a feature-tuned, nonlinear inhibition pathway implicating somatostatin-positive (SST) interneurons. The theory predicts that cotuned ensembles suppress parvalbumin-positive (PV) neurons but facilitate SST neurons, and links the degree of cotuned-ensemble suppression or facilitation to the variance of the SST response. This framework identifies mechanisms by which nonlinear inhibition sculpts cortical dynamics and establishes a predictive basis for targeted optogenetic interventions.

neuroscience↗

bioRxiv2026

Proteomic signatures of APOE ε4 across human tissues and cell types in Alzheimers disease

The apolipoprotein E {varepsilon}4 (APOE {varepsilon}4) allele is the strongest genetic risk factor for late-onset Alzheimers disease (AD). However, the underlying molecular mechanisms remain unclear. This study included 1691 participants from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP), 1226 participants from the Accelerating Medicines Partnership - Alzheimers Disease (AMP-AD) Diverse Cohorts Study, and 735 participants from the Alzheimers Disease Neuroimaging Initiative (ADNI). To characterise APOE {varepsilon}4 molecular effects, we analysed proteomic data from plasma, cerebrospinal fluid (CSF), and induced pluripotent stem cell (iPSC)-derived astrocytes and neurons, as well as transcriptomic and proteomic data from multiple brain regions. The association of APOE {varepsilon}4 with AD neuropathology was also examined. APOE {varepsilon}4 carriers shared a plasma proteomic signature enriched for immune processes, irrespective of AD diagnosis. A machine learning classifier trained on this signature discriminated APOE {varepsilon}4 carriers from non-carriers in an independent cohort using CSF proteomics. APOE {varepsilon}4 carriage was associated with higher Braak stages and Consortium to Establish a Registry for Alzheimers Disease (CERAD) score. However, only limited APOE {varepsilon}4-associated transcriptomic and proteomic changes were observed in bulk brain tissue, with poor cross-layer concordance. Proteomic analyses of iPSC-derived astrocytes and neurons further revealed cell-type-specific APOE {varepsilon}4-associated changes. APOE {varepsilon}4 is associated with a consistent proteomic signature across plasma and CSF. Its molecular effects in the brain differ across cell types, brain regions and molecular layers. These findings support the need for cell-type-resolved multi-omic studies to elucidate how APOE {varepsilon}4 confers AD risk.

neuroscience↗