Generalization Analysis for Bayesian Optimal Experiment Design under Model Misspecification

In many settings in science and industry, such as drug discovery and clinical trials, a central challenge is designing experiments under time and budget constraints. Bayesian Optimal Experimental Design (BOED) is a paradigm to pick maximally informative designs that has been increasingly applied to such problems. During training, BOED selects inputs according to a pre-determined acquisition criterion. During testing, the model learned during training encounters a naturally occurring distribution of test samples. This leads to an instance of covariate shift, where the train and test samples are drawn from different distributions. Prior work has shown that in the presence of model misspecification, covariate shift amplifies generalization error. Our first contribution is to provide a mathematical decomposition of generalization error that reveals key contributors to generalization error in the presence of model misspecification. We show that generalization error under misspecification is the result of, in addition to covariate shift, a phenomenon we term error (de-)amplification which has not been identified or studied in prior work. Our second contribution is to provide a detailed empirical analysis to show that methods that result in representative and de-amplifying training data increase generalization performance. Our third contribution is to develop a novel acquisition function that mitigates the effects of model misspecification by including a term for representativeness and implicitly inducing de-amplification. Our experimental results demonstrate that our method outperforms traditional BOED in the presence of misspecification.

ALINE: Joint Amortization for Bayesian Inference and Active Data Acquisition

Many critical applications, from autonomous scientific discovery to personalized medicine, demand systems that can both strategically acquire the most informative data and instantaneously perform inference based upon it. While amortized methods for Bayesian inference and experimental design offer part of the solution, neither approach is optimal in the most general and challenging task, where new data needs to be collected for instant inference. To tackle this issue, we introduce the Amortized Active Learning and Inference Engine (ALINE), a unified framework for amortized Bayesian inference and active data acquisition. ALINE leverages a transformer architecture trained via reinforcement learning with a reward based on self-estimated information gain provided by its own integrated inference component. This allows it to strategically query informative data points while simultaneously refining its predictions. Moreover, ALINE can selectively direct its querying strategy towards specific subsets of model parameters or designated predictive tasks, optimizing for posterior estimation, data prediction, or a mixture thereof. Empirical results on regression-based active learning, classical Bayesian experimental design benchmarks, and a psychometric model with selectively targeted parameters demonstrate that ALINE delivers both instant and accurate inference along with efficient selection of informative points.

Epistemic Errors of Imperfect Multitask Learners When Distributions Shift

When data are noisy, a statistical learner's goal is to resolve epistemic uncertainty about the data it will encounter at test-time, i.e., to identify the distribution of test (target) data. Many real-world learning settings introduce sources of epistemic uncertainty that can not be resolved on the basis of training (source) data alone: The source data may arise from multiple tasks (multitask learning), the target data may differ systematically from the source data tasks (distribution shift), and/or the learner may not arrive at an accurate characterization of the source data (imperfect learning). We introduce a principled definition of epistemic error, and provide a generic, decompositional epistemic error bound. Our error bound is the first to (i) consider epistemic error specifically, (ii) accommodate all the sources of epistemic uncertainty above, and (iii) separately attribute the error to each of multiple aspects of the learning procedure and environment. As corollaries of the generic result, we provide (i) epistemic error bounds specialized to the settings of Bayesian transfer learning and distribution shift within $\epsilon$-neighborhoods, and (ii) a set of corresponding generalization bounds. Finally, we provide a novel definition of negative transfer, and validate its insights in a synthetic experimental setting.

Robust and Computation-Aware Gaussian Processes

Gaussian processes (GPs) are widely used for regression and optimization tasks such as Bayesian optimization (BO) due to their expressiveness and principled uncertainty estimates. However, in settings with large datasets corrupted by outliers, standard GPs and their sparse approximations struggle with computational tractability and robustness. We introduce Robust Computation-aware Gaussian Process (RCaGP), a novel GP model that jointly addresses these challenges by combining a principled treatment of approximation-induced uncertainty with robust generalized Bayesian updating. The key insight is that robustness and approximation-awareness are not orthogonal but intertwined: approximations can exacerbate the impact of outliers, and mitigating one without the other is insufficient. Unlike previous work that focuses narrowly on either robustness or approximation quality, RCaGP combines both in a principled and scalable framework, thus effectively managing both outliers and computational uncertainties introduced by approximations such as low-rank matrix multiplications. Our model ensures more conservative and reliable uncertainty estimates, a property we rigorously demonstrate. Additionally, we establish a robustness property and show that the mean function is key to preserving it, motivating a tailored model selection scheme for robust mean functions. Empirical results confirm that solving these challenges jointly leads to superior performance across both clean and outlier-contaminated settings, both on regression and high-throughput Bayesian optimization benchmarks.

PABBO: Preferential Amortized Black-Box Optimization

Preferential Bayesian Optimization (PBO) is a sample-efficient method to learn latent user utilities from preferential feedback over a pair of designs. It relies on a statistical surrogate model for the latent function, usually a Gaussian process, and an acquisition strategy to select the next candidate pair to get user feedback on. Due to the non-conjugacy of the associated likelihood, every PBO step requires a significant amount of computations with various approximate inference techniques. This computational overhead is incompatible with the way humans interact with computers, hindering the use of PBO in real-world cases. Building on the recent advances of amortized BO, we propose to circumvent this issue by fully amortizing PBO, meta-learning both the surrogate and the acquisition function. Our method comprises a novel transformer neural process architecture, trained using reinforcement learning and tailored auxiliary losses. On a benchmark composed of synthetic and real-world datasets, our method is several orders of magnitude faster than the usual Gaussian process-based strategies and often outperforms them in accuracy.

Memento No More: Coaching AI Agents to Master Multiple Tasks via Hints Internalization

As the general capabilities of artificial intelligence (AI) agents continue to evolve, their ability to learn to master multiple complex tasks through experience remains a key challenge. Current LLM agents, particularly those based on proprietary language models, typically rely on prompts to incorporate knowledge about the target tasks. This approach does not allow the agent to internalize this information and instead relies on ever-expanding prompts to sustain its functionality in diverse scenarios. This resembles a system of notes used by a person affected by anterograde amnesia, the inability to form new memories. In this paper, we propose a novel method to train AI agents to incorporate knowledge and skills for multiple tasks without the need for either cumbersome note systems or prior high-quality demonstration data. Our approach employs an iterative process where the agent collects new experiences, receives corrective feedback from humans in the form of hints, and integrates this feedback into its weights via a context distillation training procedure. We demonstrate the efficacy of our approach by implementing it in a Llama-3-based agent which, after only a few rounds of feedback, outperforms advanced models GPT-4o and DeepSeek-V3 in a taskset requiring correct sequencing of information retrieval, tool use, and question answering.

Towards modeling evolving longitudinal health trajectories with a transformer-based deep learning model

Health registers contain rich information about individuals' health histories. Here our interest lies in understanding how individuals' health trajectories evolve in a nationwide longitudinal dataset with coded features, such as clinical codes, procedures, and drug purchases. We introduce a straightforward approach for training a Transformer-based deep learning model in a way that lets us analyze how individuals' trajectories change over time. This is achieved by modifying the training objective and by applying a causal attention mask. We focus here on a general task of predicting the onset of a range of common diseases in a given future forecast interval. However, instead of providing a single prediction about diagnoses that could occur in this forecast interval, our approach enable the model to provide continuous predictions at every time point up until, and conditioned on, the time of the forecast period. We find that this model performs comparably to other models, including a bi-directional transformer model, in terms of basic prediction performance while at the same time offering promising trajectory modeling properties. We explore a couple of ways to use this model for analyzing health trajectories and aiding in early detection of events that forecast possible later disease onsets. We hypothesize that this method may be helpful in continuous monitoring of peoples' health trajectories and enabling interventions in ongoing health trajectories, as well as being useful in retrospective analyses.

Proxy-informed Bayesian transfer learning with unknown sources

Generalization outside the scope of one's training data requires leveraging prior knowledge about the effects that transfer, and the effects that don't, between different data sources. Bayesian transfer learning is a principled paradigm for specifying this knowledge, and refining it on the basis of data from the source (training) and target (prediction) tasks. We address the challenging transfer learning setting where the learner (i) cannot fine-tune in the target task, and (ii) does not know which source data points correspond to the same task (i.e., the data sources are unknown). We propose a proxy-informed robust method for probabilistic transfer learning (PROMPT), which provides a posterior predictive estimate tailored to the structure of the target task, without requiring the learner have access to any outcome information from the target task. Instead, PROMPT relies on the availability of proxy information. PROMPT uses the same proxy information for two purposes: (i) estimation of effects specific to the target task, and (ii) construction of a robust reweighting of the source data for estimation of effects that transfer between tasks. We provide theoretical results on the effect of this reweighting on the risk of negative transfer, and demonstrate application of PROMPT in two synthetic settings.

Amortized Bayesian Experimental Design for Decision-Making

Many critical decisions, such as personalized medical diagnoses and product pricing, are made based on insights gained from designing, observing, and analyzing a series of experiments. This highlights the crucial role of experimental design, which goes beyond merely collecting information on system parameters as in traditional Bayesian experimental design (BED), but also plays a key part in facilitating downstream decision-making. Most recent BED methods use an amortized policy network to rapidly design experiments. However, the information gathered through these methods is suboptimal for down-the-line decision-making, as the experiments are not inherently designed with downstream objectives in mind. In this paper, we present an amortized decision-aware BED framework that prioritizes maximizing downstream decision utility. We introduce a novel architecture, the Transformer Neural Decision Process (TNDP), capable of instantly proposing the next experimental design, whilst inferring the downstream decision, thus effectively amortizing both tasks within a unified workflow. We demonstrate the performance of our method across several tasks, showing that it can deliver informative designs and facilitate accurate decision-making.

Amortized Probabilistic Conditioning for Optimization, Simulation and Inference

Amortized meta-learning methods based on pre-training have propelled fields like natural language processing and vision. Transformer-based neural processes and their variants are leading models for probabilistic meta-learning with a tractable objective. Often trained on synthetic data, these models implicitly capture essential latent information in the data-generation process. However, existing methods do not allow users to flexibly inject (condition on) and extract (predict) this probabilistic latent information at runtime, which is key to many tasks. We introduce the Amortized Conditioning Engine (ACE), a new transformer-based meta-learning model that explicitly represents latent variables of interest. ACE affords conditioning on both observed data and interpretable latent variables, the inclusion of priors at runtime, and outputs predictive distributions for discrete and continuous data and latents. We show ACE's modeling flexibility and performance in diverse tasks such as image completion and classification, Bayesian optimization, and simulation-based inference.