A structured variational approximation is offered that retains graph dependencies, preserves compositional uncertainty, and captures the explaining-away behaviour of colliders, attaining state-of-the-art performance while recovering low-fidelity contributions and yielding interpretability of the simulator hierarchy.
Abstract
Many real-world processes can be represented as compositions of functions along a directed acyclic graph (DAG). In causal modelling, these correspond to the underlying mechanisms; in engineering, to multiple fidelity levels; and in gene-regulatory networks, to transcription factors. These functions are partially observed across the DAG, with noisy and heterogeneously sampled measurements, posing significant challenges for reconstruction, uncertainty propagation, and inference. To tackle these challenges, we place priors over functions and naturally arrive at Deep Gaussian Processes over DAGs. We theoretically study their prior-collapse behaviour, and the effect of graph topology and intermediate observations on the preservation of information. We obtain almost-sure lower bounds on the asymptotic frequency of depths at which the distinction between inputs is preserved, identify broad kernel classes for which these hold, and prove an observation by \cite{dunlop2018} on the role of input connections. We offer a structured variational approximation that retains graph dependencies, preserves compositional uncertainty, and captures the explaining-away behaviour of colliders. Finally, we empirically validate our theoretical results and our methodology, and model a latent-collider DAG, a protein signalling network, and a multi-fidelity heavy-ion collision emulation task, attaining state-of-the-art performance while recovering low-fidelity contributions and yielding interpretability of the simulator hierarchy.
A Laplace-approximated Bayesian scoring function for the non-conjugate Normal--Gamma prior is developed and, through the DAG-probit extension, predicts malignancy from nuclear morphometry with a cross-validated ROC-AUC of $0.94$ using a sparse, interpretable set of direct predictors.
Samaneh Nazari, Mohammad Arashi, Abdolnasser Sadeghkhani· 0 citations
A new approach is introduced that estimates a global structure while accounting for local cluster-level effects, and presents a differentiable graph coupling mechanism that guarantees the union of the fixed- and random-effects graphs remains acyclic.
Ryan Thompson, Matt P. Wand, V. Baladandayuthapani· 0 citations
We introduce a framework for graph signal processing (GSP) in which signals are represented as graph distribution-valued signals (GDSs), i.e., probability measures in a Wasserstein space. This perspective addresses fundamental limitations of classical vector-based GSP, including the requirement for complete synchronous observations across vertices and the need for strict temporal correspondence in observed filter input--output pairs. Furthermore, by modeling the graph structure as a distribution conditioned on signal realizations, we provide a principled approach to signal-dependent graph structures, which are common in real-world applications, while explicitly encoding uncertainty in graph topology. Our framework inherently captures uncertainty and stochasticity while strictly generalizing traditional graph signals, which can be interpreted as Dirac delta measures. We develop a systematic correspondence between foundational GSP concepts and their GDS analogs, showing that classical formulations emerge as special cases of our framework. We establish theoretical continuity results for GDS transforms, providing stability guarantees for input perturbations and distribution approximations. We demonstrate the utility of this approach through example applications, including graph filter learning and anomaly detection, and validate its effectiveness through empirical studies.
Yanan Zhao, Feng Ji, Xingchao Jian et al.· 0 citations
SVI-DAG is proposed, a structured variational inference approach to Bayesian causal discovery using observational data and prior beliefs that uses normalizing flows to model dependencies between edges, supporting expressive and multimodal posterior learning over DAGs.
Generating signals on graphs requires permutation-equivariant models that exhibit stability with respect to relative structural perturbations. While favorable stability properties of Graph Neural Networks (GNNs) have been well documented, it is unclear how structural errors propagate through the dynamics of continuous generative flow models that are gaining traction for graph signal generation. In this paper, we analyze continuous normalized flow models parameterized by GNNs and show that permutation equivariance is preserved for both the resulting continuous-time ordinary differential equations and their discrete numerical approximations used as graph signal samplers. Our primary contribution is to derive explicit stability bounds on the generated probability distributions, which quantify how relative graph perturbations affect the final sampled signals. Motivated by these theoretical bounds, we introduce a stability-promoting regularized flow matching strategy that actively penalizes the spatial Lipschitz constant of the vector field during model training. Experiments using synthetic smooth signals on stochastic block model graphs and real-world fMRI signals on brain connectomes demonstrate that this bound-oriented approach yields generative models that are more robust to structural noise, without sacrificing output quality.
Oversmoothing is a fundamental limitation of deep graph neural networks (GNNs), where repeated message passing causes node representations to become increasingly similar, eventually collapsing toward a low-dimensional subspace. This phenomenon limits the effective depth of message-passing architectures and motivates the search for mechanisms that preserve representation diversity. In this paper, we study a recurrent graph neural network in which independent Gaussian noise is injected after every propagation step and analyze the resulting architecture as a stochastic dynamical system. Under a standard global contraction assumption on the deterministic update, we prove that the hidden representations form a geometrically ergodic Markov chain admitting a unique invariant probability measure. Our main theoretical result establishes an explicit positive lower bound on the expected stationary Dirichlet energy, proportional to both the noise variance and the spectral gap of the underlying graph. Consequently, the stationary representations cannot collapse onto the constant manifold, providing a rigorous guarantee that asymptotic oversmoothing is prevented in the sense of non-vanishing Dirichlet energy. Our analysis reveals persistent stochastic perturbations as a fundamentally different mechanism for combating oversmoothing, complementing existing deterministic approaches based on residual connections, normalization, and graph rewiring. Finally, numerical experiments on both linear and nonlinear recurrent graph neural networks closely match the theoretical predictions, illustrating the emergence of a stationary distribution and the predicted dependence of the limiting Dirichlet energy on the noise intensity.
M. H. Chehreghani· arXiv.org· 0 citations
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