Transferring Information Across Interventions in Causal Bayesian Optimization
Authors: Mohammad Ali Javidian
Organizations: Computer Science Department Appalachian State University Boone, USA
Abstract
Bayesian optimization is a popular way to optimize expensive systems, where every experiment, simulation, or intervention costs time or money. In its standard form, it treats the variables we control as plain inputs to a black box and cannot tell apart mere correlation from a real cause and effect. Causal Bayesian optimization closes part of this gap by using a known causal graph together with observational data to decide which variables are worth intervening on. Existing methods, however, learn the effect of each possible intervention almost in isolation, even though in a causal system these effects usually share the same underlying mechanisms. We propose graph-coupled causal Bayesian optimization, which ties the different intervention effects together through the uncertainty we have about a small set of shared causal parameters. The result is a causal kernel that lets evidence collected from one intervention improve our estimate of related interventions. For identifiable linear Gaussian causal models, we show that this kernel has low rank, bounded by the number of shared parameters rather than by the size of the intervention menu. This in turn yields an information-gain bound that grows only logarithmically in the optimization horizon, and a regret bound that cleanly separates three sources of error: optimization, causal estimation, and the choice of which intervention sets to consider. We also describe nonlinear and adaptive extensions. Across theory-aligned Gaussian systems, shared-mechanism stress tests, and standard causal optimization benchmarks, the method keeps the benefits of causal Bayesian optimization while transferring information across related interventions, with the clearest gains when direct interventions on the target's parents are unavailable and sparse interventional data must be reused across a large family of candidate interventions.
Uncovering the causal mechanisms of complex real-world systems remains a significant challenge, as these systems often entail high data collection costs and involve unknown interventions. We introduce MetaCaDI, the first framework to cast the identification of unknown interventions as a meta-learning problem, explicitly leveraging a jointly learned causal graph. MetaCaDI is a Bayesian framework that learns a shared causal structure across multiple environments and is optimized to rapidly adapt to new, few-shot intervention target identification tasks. A key innovation is our model's analytical adaptation, which uses a closed-form solution to bypass expensive and potentially unstable gradient-based bilevel optimization. Extensive experiments on synthetic and complex gene expression data demonstrate that MetaCaDI significantly outperforms state-of-the-art methods. It excels at identifying intervention targets from as few as 3 samples - where existing methods collapse to random chance - while robustly recovering the shared causal graph, proving its effectiveness in data-scarce scenarios.
Learning causal graphs from interventional data is a challenging problem with broad applications. In molecular biology, for example, a central goal is to uncover gene regulatory networks from large-scale perturbation data. An ideal algorithm for this task should scale to thousands of nodes, incorporate interventions even when their targets are unknown, quantify uncertainty, and provide identifiability guarantees. However, existing approaches---e.g. approaches using score-based optimization or approximate Bayesian inference---often fail to meet all of these criteria. To address these limitations, we develop Amortized Bayesian Causal Discovery of Extended Factor Graphs (ABCDEFG). Our method guarantees exact acyclicity, scales to graphs with thousands of nodes, and naturally handles interventions even when their targets are unknown. Additionally, ABCDEFG estimates a posterior distribution whose maximum a posteriori estimate provably identifies the true causal graph up to an equivalence class. On simulated datasets, ABCDEFG achieves state-of-the-art accuracy, producing a well-calibrated posterior distribution while outperforming previous score-based and approximate Bayesian methods. Applied to large-scale single-cell perturbation data, ABCDEFG identifies both established and novel gene targets of growth factors.
Causal bandits exploit structural relationships among variables to share information across interventions and accelerate the identification of high-reward decisions. In many applications, however, some variables cannot be directly manipulated, even though they influence the reward and provide useful information about the underlying causal system. We study contextual causal bandits with non-manipulable variables, where context variables are observed before action selection and additional variables are observed after each intervention. Assuming a known causal graph without latent confounding, we adopt a Bayesian formulation in which the conditional probability tables of the observational distribution constitute the unknown parameter. This representation allows observations collected under one intervention to update reward estimates for other interventions through their shared causal mechanisms. We develop causal variants of Thompson Sampling and Information-Directed Sampling (IDS) for this setting. For Thompson Sampling, we establish an entropy-dependent sublinear Bayesian regret bound. For IDS, we derive an entropy-dependent regret bound that explicitly quantifies the additional error introduced by Monte Carlo approximation of the expected regret and information gain; when these quantities are available exactly, the bound recovers the standard sublinear IDS rate. We further provide high-probability confidence bounds for the Monte Carlo estimates used by the algorithm. Experiments on several synthetic causal bandit tasks show that the proposed methods outperform causal and non-causal baselines by more effectively exploiting information shared across interventions.
Muhammad Qasim Elahi, Murat Kocaoglu, Mahsa Ghasemi