A Factor Graph Approach to Scalable Multi-Output Gaussian Process Regression

Multi-output Gaussian process regression scales cubically in the number of observations times outputs, and dense kernel-matrix methods need bespoke handling whenever different outputs are observed at different inputs. We express multi-output Gaussian process regression as a Forney-style factor graph in which a nearest-neighbor chain orders a fixed candidate set of $C$ inputs into a one-dimensional sequence. Along this chain, latent Matérn processes evolve through linear-Gaussian transition factors, while the linear model of coregionalization mixes $L$ latent processes into $D$ outputs through a deterministic mixing factor and per-output scalar observation factors. Posterior computation reduces to exact Gaussian message passing on the chain at cost $\mathcal{O}(C(DL^2 + L^3))$ after chain construction, and missing observations omit their local factor without any covariance-matrix restructuring. The formulation therefore scales in the number of data samples and in the rate of missing observations, while remaining best suited to candidate sets in low input dimension.We compare the factor-graph formulation against an exact kernel-matrix baseline, a sparse-variational inducing-point baseline, and a nearest-neighbor baseline on a synthetic input-dimension sweep and on electricity time series forecasting. At low input dimension the factor-graph posterior tracks the exact kernel-matrix posterior closely, and the gap grows gradually as input dimension increases while staying competitive with both approximate baselines. On the electricity time series our factor-graph formulation matches all three baselines in forecast accuracy while scaling linearly in the number of data points, where the exact kernel-matrix method becomes infeasible and the inducing-point baseline remains substantially slower.

Thermalizing Stochastic Programs

We present a set of tools for mapping general stochastic programs to thermodynamic hardware designed for energy-efficient stochastic sampling. Given a target stochastic program expressed as a Directed Factor Graph (DFG) of stochastic channels, or equivalently as a Parametrized Stochastic Circuit (PSC), we first introduce a method to approximately compile each factor in the DFG to an Energy-Based Model (EBM) that is native to the hardware. We then analyze how the error of the compiled DFG accumulates from the per-factor errors, and introduce two training refinements, context matching and trajectory-level REINFORCE post-training, which can reduce the residual error left by training each factor in isolation. The \texttt{thermalizers} framework takes a stochastic program expressed in the \texttt{torx} library and replaces its factors with thermodynamic kernels implemented and sampled using the \texttt{thrml} library. We demonstrate it on several example applications, including a market simulator that learns the joint day-to-day dynamics of a panel of financial time series from recorded market history alone, a probabilistic model from mathematical ecology, Gibbs sampling of an EBM the hardware cannot natively express, and a sequential Bayesian design loop over a Gaussian stochastic circuit.

When Do Learned Diffusion Proposals Help Constraint Solving? A Controlled Study on Continuous Algebraic Systems

Solving a continuous algebraic constraint system requires two decisions: which values satisfy the constraints, and which structural augmentation renders an unsolvable system solvable. Classical solvers answer the first well and the second only by enumeration. On that discrete decision, a candidate-conditioned repair ranker choosing among K augmentations reaches the exhaustive-search ceiling at a fraction of the calls, outperforming random (0.997 vs 0.236 balanced nonlinear menu accuracy; p < 10^-70; 0.982 +/- 0.006 across seeds) and beating a budget-matched per-candidate probe on accuracy and cost. MARC turns such a system into a factor graph, over which a graph-neural diffusion denoiser proposes assignments, descent on an exact computer-algebra energy polishes them, and an exact symbolic checker certifies solutions. Evaluations of diffusion-based proposals rarely include one control: random multi-start under the same refinement budget. Applied to our system, it sharply curtails what the learned proposal contributes on the value decision. Does it beat random multi-start at choosing satisfying assignments? Only narrowly, in a predictable regime. Across trapped low-dimensional families it ties with random restart, but dominates in high dimension, where random search fails. Once variables couple, the advantage is gone. Since all methods share one polish and one checker, best-of-K random multi-start succeeds with probability exactly 1 - (1 - q(n))^K, where q(n) is single-start reachability; one measured constant, with no free parameters, reproduces the entire curve (mean absolute error 0.012). The favorable regime is not specific to our synthetic families: across eight real-world systems in robotics, positioning, optimization, and algebra, classical multi-start solved all eight, none in the learning-favorable regime. We map the regimes in which learned proposals improve solvers.

Reduction of Probabilistic Chemical Reaction Networks

Programming adaptive behaviors at the cellular level is a long-standing goal that raises the question of how probabilistic computation can be implemented in biochemical systems. Chemical reaction networks (CRNs) provide such a substrate and have been shown to realize probabilistic models, including hidden Markov models and factor graphs, with dynamics reproducing Bayesian inference and belief propagation. However, encoding these algorithms typically requires prohibitively large reaction networks, and classical CRN reduction techniques do not directly apply. By recovering the factor graph structure encoded in Napp--Adams-compiled CRNs, we transport recent factor-graph reduction results to their chemical implementations, obtaining significantly smaller CRNs while preserving the belief-propagation fixed points on surviving variables.

Inducing Comparability of Factorised Probability Distributions

To allow for principled comparison between two probabilistic graphical models defined over non-identical variable sets, they have to be lifted to a common measurable space. To this end, we propose an extension scheme for any two given models and establish the formal foundation: Unmatched components are completed using conditionally uniform (Laplace) extensions such that the resulting joint distributions differ from the original ones only by multiplicative constants and coincide under projection. This preserves the probabilistic semantics while enabling the application of well-defined distributional discrepancy measures. We establish the invariance of the induced joint under projection and use the extensions to provide a minimal structural extension of two factor graphs to the smalles common measurable space as well as to a common graphical structure by a deterministic algorithm. In addition, we discuss structural and measure-theoretic properties and identify promising criteria for comparison methodologies.

Information Lattice Learning as Probabilistic Graphical Model Structure Learning

Information lattice learning (ILL) learns interpretable rules of a signal by alternately projecting the signal onto a partition lattice that encodes a hierarchy of abstractions and lifting selected rules back to the signal domain. When the signal is a probability mass function, we show the probabilistic rules learned by ILL admit a natural probabilistic graphical model (PGM) interpretation and develop this interpretation in detail. A partition in ILL induces a deterministic quotient variable, and a rule is the marginal law of that quotient variable. A rule set is therefore a collection of marginal constraints over interpretable abstractions. General lifting is the feasible family of all joint distributions satisfying those constraints, while special lifting chooses a maximum-ignorance reconstruction, implemented in ILL by an L2 uniformity principle closely related to maximum entropy. Under a Shannon-entropy lifting, the same constraints yield a log-linear factor graph whose factors are indexed by learned abstractions. The information lattice itself, however, is not a Bayesian network: its edges encode refinement and coarsening of abstractions, not conditional dependence. Thus ILL is best viewed as structure learning for interpretable constraint-based factor graphs over quotient variables. This view clarifies how ILL relates to graphical models and maximum entropy models, while suggesting new directions for inference, identifiability, and hybrid symbolic-probabilistic learning.

Equivariant Neural Belief Propagation

Probabilistic inference over spatially embedded variables requires beliefs that respect $SE(3)$ symmetry, yet existing equivariant networks produce only scalars and vectors -- not the rank-2 precision tensors needed for anisotropic uncertainty, and single-component messages collapse multi-modal energy landscapes to physically meaningless averages. We introduce Equivariant Neural Belief Propagation (ENBP), a factor-graph framework whose messages are equivariant Gaussian mixture models with sufficient statistics that transform exactly under $SE(3)$. Rank-2 precision matrices are synthesised via equivariant outer products, ingested through differentiable spectral decomposition, and kept tractable by a greedy KL-based mixture reduction that provably commutes with $SE(3)$. On GEOM-QM9 and GEOM-Drugs, ENBP achieves 98.9% conformational coverage at 0.090 $\mathring{A}$ error with sub-second latency -- over $100\times$ faster than diffusion baselines at higher accuracy. On multi-body robotic inference, vanilla loopy BP diverges at 15+ agents while ENBP converges with near-zero collision rates and machine-precision equivariance error (${\sim}10^{-7}$ vs.\ $10^{-1}$ for augmented baselines).