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1. GPIRT: A Gaussian Process Model for Item Response Theory

   Duck-Mayr, JBrandon; Garnett, Roman; Montgomery, Jacob (April 2020, Proceedings of Machine Learning Research)

   null (Ed.)

   The goal of item response theoretic (IRT) models is to provide estimates of latent traits from binary observed indicators and at the same time to learn the item response funcitons (IRFs) that map from latent trait to observed response. However, in many cases observed behavior can deviate significantly from the parametric assumptions of traditional IRT models. Nonparametric IRT (NIRT) models overcome these challenges by relaxing assumptions about the form of the IRFs, but standard tools are unable to simultaneously estimate flexible IRFs and recover ability estimates for respondents. We propose a Bayesian nonparametric model that solves this problem by placing Gaussian process priors on the latent functions defining the IRFs. This allows us to simultaneously relax assumptions about the shape of the IRFs while preserving the ability to estimate latent traits. This in turn allows us to easily extend the model to further tasks such as active learning. GPIRT therefore provides a simple and intuitive solution to several longstanding problems in the IRT literature. 

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2. Environmental dynamics shape perceptual decision bias

   https://doi.org/10.1371/journal.pcbi.1011104  

   Charlton, Julie A; Młynarski, Wiktor F; Bai, Yoon H; Hermundstad, Ann M; Goris, Robbe_L T (June 2023, PLOS Computational Biology)

   Soltani, Alireza (Ed.)

   To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals. 

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3. The tilt illusion arises from an efficient reallocation of neural coding resources at the contextual boundary

   https://doi.org/10.1073/pnas.2421565122  

   Zhang, Ling-Qi; Mao, Jiang; Aguirre, Geoffrey_K; Stocker, Alan_A (April 2025, Proceedings of the National Academy of Sciences)

   The tilt illusion—a bias in the perceived orientation of a center stimulus induced by an oriented surround—illustrates how context shapes visual perception. Although extensively studied for decades, we still lack a comprehensive account of the illusion that connects its behavioral and neural characteristics. Here, we demonstrate that the tilt illusion originates from dynamic changes in neural coding precision induced by the surround context. We simultaneously obtained psychophysical and functional MRI responses from human subjects while they viewed gratings in the absence and presence of an oriented surround and independently extracted sensory encoding precision from their behavioral and neural data. Both measures show that in the absence of an oriented surround, encoding reflects the natural scene statistics of orientation. However, with an oriented surround, encoding precision is significantly increased for stimuli similar to the surround orientation. This local change in encoding is sufficient to predict the behavioral characteristics of the tilt illusion using a Bayesian observer model. The effect of surround modulation increases along the ventral stream and is localized to the portion of the visual cortex with receptive fields at the center-surround boundary. The pattern of change in coding accuracy reflects the surround-conditioned orientation statistics in natural scenes, but cannot be explained by local stimulus configuration. Our results suggest that the tilt illusion naturally emerges from an adaptive coding strategy that efficiently reallocates neural coding resources based on the current stimulus context. 

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4. Choosing priors in Bayesian ecological models by simulating from the prior predictive distribution

   https://doi.org/10.1002/ecs2.3739  

   Wesner, Jeff S.; Pomeranz, Justin P. F. (September 2021, Ecosphere)

   Abstract Bayesian data analysis is increasingly used in ecology, but prior specification remains focused on choosing non‐informative priors (e.g., flat or vague priors). One barrier to choosing more informative priors is that priors must be specified on model parameters (e.g., intercepts, slopes, and sigmas), but prior knowledge often exists on the level of the response variable. This is particularly true for common models in ecology, like generalized linear mixed models that have a link function and potentially dozens of parameters, each of which needs a prior distribution. We suggest that this difficulty can be overcome by simulating from the prior predictive distribution and visualizing the results on the scale of the response variable. In doing so, some common choices for non‐informative priors on parameters can easily be seen to produce biologically impossible values of response variables. Such implications of prior choices are difficult to foresee without visualization. We demonstrate a workflow for prior selection using simulation and visualization with two ecological examples (predator–prey body sizes and spider responses to food competition). This approach is not new, but its adoption by ecologists will help to better incorporate prior information in ecological models, thereby maximizing one of the benefits of Bayesian data analysis. 

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5. Graph-based prior and forward models for inverse problems on manifolds with boundaries

   https://doi.org/10.1088/1361-6420/ac3994  

   Harlim, John; Jiang, Shixiao W; Kim, Hwanwoo; Sanz-Alonso, Daniel (January 2022, Inverse Problems)

   Abstract This paper develops manifold learning techniques for the numerical solution of PDE-constrained Bayesian inverse problems on manifolds with boundaries. We introduce graphical Matérn-type Gaussian field priors that enable flexible modeling near the boundaries, representing boundary values by superposition of harmonic functions with appropriate Dirichlet boundary conditions. We also investigate the graph-based approximation of forward models from PDE parameters to observed quantities. In the construction of graph-based prior and forward models, we leverage the ghost point diffusion map algorithm to approximate second-order elliptic operators with classical boundary conditions. Numerical results validate our graph-based approach and demonstrate the need to design prior covariance models that account for boundary conditions. 

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