Computational cognitive models, which formalize theories of cognition, enable researchers to quantify cognitive processes and arbitrate between competing theories by fitting models to behavioral data. Traditionally, these models are handcrafted, which requires significant domain knowledge, coding expertise, and time investment.

Neural population activity exhibits complex, nonlinear dynamics, varying in time, over trials, and across experimental conditions. Here, we develop Conditionally Linear Dynamical System (CLDS) models as a general-purpose method to characterize these dynamics. These models use Gaussian Process (GP) priors to capture the nonlinear dependence of circuit dynamics on task and behavioral variables. Conditioned on these covariates, the data is modeled with linear dynamics. This allows for transparent interpretation and tractable Bayesian inference. We find that CLDS models can perform well even in severely data-limited regimes (e.g. one trial per condition) due to their Bayesian formulation and ability to share statistical power across nearby task conditions. In example applications, we apply CLDS to model thalamic neurons that nonlinearly encode heading direction and to model motor cortical neurons during a cued reaching task.

We study the problem of likelihood maximization when the likelihood function is intractable but model simulations are readily available. We propose a sequential, gradient-based optimization method that directly models the Fisher score based on a local score matching technique which uses simulations from a localized region around each parameter iterate. By employing a linear parameterization for the surrogate score model, our technique admits a closed-form, least-squares solution. This approach yields a fast, flexible, and efficient approximation to the Fisher score, effectively smoothing the likelihood objective and mitigating the challenges posed by complex likelihood landscapes. We provide theoretical guarantees for our score estimator, including bounds on the bias introduced by the smoothing. Empirical results on a range of synthetic and real-world problems demonstrate the superior performance of our method compared to existing benchmarks.

There is growing interest in using machine learning (ML) to support clinical diagnosis, but most approaches rely on static, fully observed datasets and fail to reflect the sequential, resource-aware reasoning clinicians use in practice. Diagnosis remains complex and error prone, especially in high-pressure or resource-limited settings, underscoring the need for frameworks that help clinicians make timely and cost-effective decisions. We propose ACTMED(Adaptive Clinical Test selection via Model-based Experimental Design), a diagnostic framework that integrates Bayesian Experimental Design (BED) with large language models (LLMs) to better emulate real-world diagnostic reasoning. At each step, ACTMED selects the test expected to yield the greatest reduction in diagnostic uncertainty for a given patient. LLMs act as flexible simulators, generating plausible patient state distributions and supporting belief updates without requiring structured, task-specific training data. Clinicians can remain in the loop; reviewing test suggestions, interpreting intermediate outputs, and applying clinical judgment throughout. We evaluate ACTMEDon real-world datasets and show it can optimize test selection to improve diagnostic accuracy, interpretability, and resource use. This represents a step toward transparent, adaptive, and clinician-aligned diagnostic systems that generalize across settings with reduced reliance on domain-specific data.

Deep ensembles deliver state-of-the-art, reliable uncertainty quantification, but their heavy computational and memory requirements hinder their practical deployments to real applications such as on-device AI. Knowledge distillation compresses an ensemble into small student models, but existing techniques struggle to preserve uncertainty partly because reducing the size of DNNs typically results in variation reduction. To resolve this limitation, we introduce a new method of distribution distillation (i.e.

Inverse folding models have proven to be highly effective zero-shot predictors of protein stability. Despite this success, the link between the amino acid preferences of an inverse folding model and the free-energy considerations underlying thermodynamic stability remains incompletely understood. A better understanding would be of interest not only from a theoretical perspective, but also potentially provide the basis for stronger zero-shot stability prediction. In this paper, we take steps to clarify the free-energy foundations of inverse folding models. Our derivation reveals the standard practice of likelihood ratios as a simplistic approximation and suggests several paths towards better estimates of the relative stability. We empirically assess these approaches and demonstrate that considerable gains in zero-shot performance can be achieved with fairly simple means.

While deep neural networks possess the capability to perform semantic segmentation, producing a single deterministic output limits reliability in safety-critical applications caused by uncertainty and annotation variability. To address this, stochastic segmentation models using Conditional Variational Autoencoders (CVAE), Bayesian networks, and diffusion have been explored. However, existing approaches suffer from limited latent expressiveness and interpretability. Furthermore, our experiments showed that models like Probabilistic U-Net rely excessively on high latent variance, leading to posterior collapse. This work propose a novel framework by integrating Gaussian Mixture Model (GMM) with Normalizing Flow (NF) in CVAE for stochastic segmentation. GMM structures the latent space into meaningful semantic clusters, while NF captures feature deformations with quantified uncertainty. Our method stabilizes latent distributions through constrained variance and mean ranges. Experiments on LIDC, Crack500, and Cityscapes datasets show that our approach outperformed state-of-the-art in curvilinear structure and medical image segmentation.

Simulation-based inference (SBI) offers a flexible and general approach to performing Bayesian inference: In SBI, a neural network is trained on synthetic data simulated from a model and used to rapidly infer posterior distributions for observed data. A key goal for SBI is to achieve accurate inference with as few simulations as possible, especially for expensive simulators. In this work, we address this challenge by repurposing recent probabilistic foundation models for tabular data: We show how tabular foundation models--specifically TabPFN--can be used as pre-trained autoregressive conditional density estimators for SBI. We propose Neural Posterior Estimation with Prior-data Fitted Networks (NPE-PFN) and show that it is competitive with current SBI approaches in terms of accuracy for both benchmark tasks and two complex scientific inverse problems. Crucially, it often substantially outperforms them in terms of simulation efficiency, sometimes requiring orders of magnitude fewer simulations. NPE-PFN eliminates the need for selecting and training an inference network and tuning its hyperparameters. We also show that it exhibits superior robustness to model misspecification and can be scaled to simulation budgets that exceed the context size limit of TabPFN. NPE-PFN provides a new direction for SBI, where training-free, general-purpose inference models offer efficient, easy-to-use, and flexible solutions for a wide range of stochastic inverse problems.

Modern reinforcement learning (RL) algorithms have found success by using probabilistic models, such as transformers, energy-based models, and diffusion/flowbased models. To this end, researchers often choose to pay the price of accommodating these models into their algorithms - diffusion models are expressive, but are computationally intensive due to their reliance on solving differential equations, while autoregressive transformer models are scalable but typically require learning discrete representations. Normalizing flows (NFs), by contrast, seem to provide an appealing alternative, as they enable likelihoods and sampling without solving differential equations or autoregressive architectures. However, their potential in RL has received limited attention, partly due to the prevailing belief that normalizing flows lack sufficient expressivity. We show that this is not the case. Building on recent work in NFs, we propose a single NF architecture which integrates seamlessly into RL algorithms, serving as a policy, Q-function, and occupancy measure. Our approach leads to much simpler algorithms, and achieves higher performance in imitation learning, offline, goal conditioned RL and unsupervised RL.1

Recent advancements in diffusion policies have demonstrated promising performance in decision-making tasks. To align these policies with human preferences, a common approach is incorporating Preference-based Reinforcement Learning (PbRL) into policy tuning. However, since preference data is practically collected from populations with different backgrounds, a key challenge lies in handling the inherent uncertainties in people's preferences during policy updates. To address this challenge, we propose the Diff-UAPA algorithm, designed for uncertainty-aware preference alignment in diffusion policies. Specifically, Diff-UAPA introduces a novel iterative preference alignment framework in which the diffusion policy adapts incrementally to preferences from different user groups. To accommodate this online learning paradigm, Diff-UAPA employs a maximum posterior objective, which aligns the diffusion policy with regret-based preferences under the guidance of an informative Beta prior. This approach enables direct optimization of the diffusion policy without specifying any reward functions, while effectively mitigating the influence of inconsistent preferences across different user groups. We conduct extensive experiments across both simulated and real-world robotics tasks, and diverse human preference configurations, demonstrating the robustness and reliability of Diff-UAPA in achieving effective preference alignment.