Johanna Schlimme | Searcharxiv

arXiv2026

Direct Message Approximation (DMA): A Consistency-Based Framework for Tractable Approximate Inference on Factor Graphs

Approximate message passing on factor graphs underlies two dominant families of probabilistic inference algorithms: expectation propagation (EP) and variational message passing (VMP). Both methods approximate the marginal at each factor edge, forcing an iterative round-robin schedule, risking negative-precision messages, and, for VMP, collapsing to point estimates at Dirac-delta factors. We introduce Direct Message Approximation (DMA), which approximates factor-to-variable messages directly rather than the marginal. For normalisable factors, we define a consistency condition (requiring exactness when all other incoming messages are Dirac deltas) to guide message construction. We prove a master theorem (proper messages, any graph) bounding marginal KL from message KL, with three structural corollaries: Dirac-input consistency, no EP-style inner-loop iteration, and no negative-precision messages. Further, we prove a complementary $O(1/r^2)$ guarantee for the inherently improper backward message of the product factor, whose closed-form treatment has resisted prior work. As a concrete instantiation, we derive explicit DMA messages for the product and leaky-ReLU factors and assemble a Bayesian neural network (BNN) inference algorithm with one forward/backward sweep per training example and no gradient learning-rate hyperparameter, validating that the structural guarantees translate to predictive uncertainty that widens in data-sparse regions, including under model mismatch.

cs.LG↗

arXiv2025

BaGGLS: A Bayesian Shrinkage Framework for Interpretable Modeling of Interactions in High-Dimensional Biological Data

Biological data sets are often high-dimensional, noisy, and governed by complex interactions among sparse signals. This poses major challenges for interpretability and reliable feature selection. Tasks such as identifying motif interactions in genomics exemplify these difficulties, as only a small subset of biologically relevant features (e.g., motifs) are typically active, and their effects are often non-linear and context-dependent. While statistical approaches often result in more interpretable models, deep learning models have proven effective in modeling complex interactions and prediction accuracy, yet their black-box nature limits interpretability. We introduce BaGGLS, a flexible and interpretable probabilistic binary regression model designed for high-dimensional biological inference involving feature interactions. BaGGLS incorporates a Bayesian group global-local shrinkage prior, aligned with the group structure introduced by interaction terms. This prior encourages sparsity while retaining interpretability, helping to isolate meaningful signals and suppress noise. To enable scalable inference, we employ a partially factorized variational approximation that captures posterior skewness and supports efficient learning even in large feature spaces. In extensive simulations, we can show that BaGGLS outperforms the other methods with regard to interaction detection and is many times faster than MCMC sampling under the horseshoe prior. We also demonstrate the usefulness of BaGGLS in the context of interaction discovery from motif scanner outputs and noisy attribution scores from deep learning models. This shows that BaGGLS is a promising approach for uncovering biologically relevant interaction patterns, with potential applicability across a range of high-dimensional tasks in computational biology.

stat.ME↗