From Uniform to Learned Graph Priors: Diffusion for Structure Discovery

Warm-started diffusion samplers accelerate iterative inference, but it is rarely clear which part of the pipeline carries the gain. We study \textbf{retrieval-warmed energy-based reasoning (RW-EBR)} -- an IRED energy-based diffusion model \cite{du2024ired} augmented with a Modern Hopfield trajectory memory -- and contribute a \textbf{five-arm ablation methodology} (oracle, best-constant, per-query-random, shuffled, aligned) that separates three confounded effects: class-prior bias shift, stochastic warm-starting, and graph-aligned value reuse. The diagnostic decomposition is adapted from LLM-RAG evaluation \cite{ru2024ragchecker}. On \textbf{connectivity-2} (Erdős--Rényi all-pairs reachability), the aligned-vs-shuffled-oracle swing reaches \textbf{$+35$,pp} balanced accuracy on a fixed 1{,}000-graph validation-set diagnostic, with value distribution and retrieval mechanics fixed, only per-graph alignment destroyed, while per-query random initialisation falls below cold -- per-graph alignment, not bias shift or stochasticity, dominates. Yet the \emph{deployable} cold-prediction pipeline misses the acceptance gate at stored-value quality. The same diagnostic logic, stopped at the key-quality screen, applied to \textbf{Sudoku} with a task-specific key encoder produces a clean negative at a \emph{different} component -- key quality, under the current setup. The decomposition names the first blocking component on each task. The setting -- graph reachability refined by an iterative diffusion sampler, with explainability of failure modes as the lens -- places the work within structured and spatio-temporal reasoning.

Graph inference over relational data can expose sensitive edge information, and this risk becomes more severe in dynamic graphs, where repeated model updates cause privacy loss to accumulate. We formulate Edge-level Differentially Private Dynamic Graph Inference (EDG) and propose PriDyG, a private inference framework that combines GNN-based structural learning with LLM-based semantic reasoning. PriDyG introduces incremental private multi-hop aggregation, which buffers newly arrived edges and processes each edge exactly once. By parallel composition, the total privacy cost equals that of a single static release, independent of the number or schedule of model updates. Compared with geometrically decaying budget allocation, incremental aggregation avoids exponentially increasing noise while preserving exact one-hop signals and at least half of two-hop information transfers. PriDyG further complements privatized GNN outputs with LLM predictions derived solely from node text, incurring no additional edge-level privacy cost. Experiments on four benchmarks for node classification and link prediction show that PriDyG consistently outperforms geometrically decaying baselines under the same privacy budget and matches the utility of naive per-update retraining while reducing cumulative privacy cost by up to three orders of magnitude.

Bayesian causal discovery seeks to determine the posterior distribution of causal theories, which are interpreted as directed acyclic graphs (DAGs) that explain the observed data. The resulting posterior allows systematic reasoning regarding epistemic uncertainty within these theories. Nonetheless, finding such graphs is difficult due to identifiability problems and limited observational data. Furthermore, precisely approximating posterior over graphs is challenging given vast range of potential DAGs. Recent Bayesian approaches have addressed some of these challenges, yet they remain limited as they fail to encode dependencies between edges, and lack principled ways to incorporate domain knowledge as inductive biases during the search process. To overcome these limitations, we propose SVI-DAG, 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. To mitigate mode seeking behaviour in evidence lower bound optimization and promote mode coverage, we use stein variational gradient descent to update the node potentials using a kernel in acyclicity space. We evaluate SVI-DAG against 5 state-of-the-art Bayesian DAG learning methods and demonstrate superior performance in uncertainty quantification while remaining competitive in terms of structural accuracy.