#01Oct 16, 2026
stat.ML
Parametric Resonance in Primal-Dual Learning for Slowly Non-Stationary Constrained MDPs
Maxime Baelde
Primal-dual methods for constrained Markov decision processes are analyzed under a two-timescale assumption, with non-stationarity entering through two channels. In the additive channel, where the constraint level oscillates, the dual oscillation saturates at a floor set by the moving optimum and is amplified linearly by the timescale ratio. In the parametric channel, where the constraint sensitivity oscillates, a coherent modulation carries no resonant forcing at any depth: the dual update's stiffness modulation cancels the primal update's damping modulation. Instability instead comes from a mismatch between the constraint estimate used by the primal update and the measurement used by the dual update, producing a parametric resonance at twice the pair's natural frequency. The tolerated mismatch grows with the square root of the forcing bandwidth and collapses with the square root of the dual-to-primal step-size ratio. These results hold on the tangent linear-quadratic reduction around an active saddle, for one constraint and for $K$ constraints under a common modulation and an isotropy condition. Driving both updates from the same estimate removes the resonant forcing but introduces a stationary offset equal to the estimator's bias. In a Lagrangian soft actor-critic agent, the multiplier locks onto the sub-harmonic at the timescale ratios its identified linear loop predicts and a coherent cost critic suppresses the lock-in, while a proportional (PID) term, predicted to leave the lock-in in place, suppresses most of it through the projection of the multiplier.
#02Oct 16, 2026
cs.LG
Logic-Guided Graph Denoising Diffusion Models
Samuel Cognolato, Luciano Serafini, Alessandro Sperduti and 1 more
Graph diffusion models are competitive approaches for generating complex graph-structured data. However, when such distributions have strict structural constraints, diffusion models may fail to capture them exactly, resulting in the generation of invalid graphs. In this paper, we propose a method for grounding graph diffusion models in domain-specific knowledge via First Order Logic (FOL), leveraging its expressive and interpretable formalism to impose structural constraints on the generative process. We incorporate domain knowledge using classifier guidance, a technique that conditions the diffusion model's distribution on external variables to exert control over the sampled data. During the generative process, classifier guidance steers the denoising trajectory to optimize an objective function, which we define as a fuzzy and differentiable relaxation of the logical rules. Our methodology requires only the specification of constraints in FOL, whose satisfaction is encouraged at inference time to guide a pre-trained generative model. We evaluate our approach by comparing the unconditional generation of knowledge graphs with our logic-guided framework, which incorporates domain ontologies as structural constraints during inference. This approach significantly increases the proportion of generated graphs that satisfy the ontological constraints.
#03Oct 16, 2026
cond-mat.dis-nn
Sampling the XY model with an attention-based neural network
Piotr Białas, Christian D. Morales, Tomasz Stebel and 1 more
We present a transformer-based variational autoregressive network for sampling lattice systems with continuous degrees of freedom and apply it to the two-dimensional XY model near the Berezinskii-Kosterlitz-Thouless transition. The architecture is combined with physics-informed ingredients: locality-informed attention and approximate probabilities. The resulting sampler significantly outperforms existing neural samplers. We train the model on lattices up to $96\times96$, verify with a mode-dropping estimator that no parts of the configuration space are missed, and reproduce the energy, magnetization and helicity modulus obtained with the traditional Markov Chain Monte Carlo algorithm.
#04Oct 16, 2026
stat.ML
ENFR: Evidence Networks with Flow-Matched References for Amortized Simulation-Based Model Inference
Kai Lehman, Jameson Dong, Carolina Cuesta-Lazaro and 5 more
The evidence, $\mathcal{Z} = p(x | \mathcal{M})$, of a data-generating model $\mathcal{M}$ is a powerful tool in Bayesian frameworks: it enables model inference, model misspecification tests, and goodness-of-fit assessment as an alternative to standard discrepancy statistics, e.g. $χ^2$. While versatile, the evidence is notoriously difficult to compute, even when the likelihood is available. In both likelihood-based and simulation-based inference, estimating $\mathcal{Z}$ provides an immediate solution to high-dimensional goodness-of-fit or model misspecification tests: using $\mathcal{Z}(x)$ as the test statistic induces a minimum-volume level-$α$ test. Such tests are essential to assess model fidelity, which is necessary to trust simulation-based parameter inference. Existing learned approaches largely target Bayes factors, which only measure evidence ratios. Instead, we provide accurate, fast, and amortized estimates of the absolute evidence. We present ENFR: Evidence Networks with Flow-matched References. Building on the Evidence Network framework of Jeffrey & Wandelt (2024), the proposed method first learns Bayes factors with respect to a flow-matched reference, from which the absolute evidence is recovered. We show improvement in estimation of $\mathcal{Z}$ over the flow-based baseline in all applications considered and the best performance of all density estimation methods considered in our benchmarks. We furthermore introduce and provide the proof for an architecture that jointly learns the individual evidences of a set of models $\{\mathcal{M}_i\}$. We demonstrate the performance and scaling behavior of these approaches on data from a variety of scientific applications.
#05Oct 16, 2026
cs.AI
DrugHarness: An Evolvable Agent Harness for Computational Drug Discovery
Yuxing Chen, Zhisheng Zhang, Cheng Tang and 20 more
Computational drug discovery requires agents to compose scientific operations and adapt to changing evidence and constraints. Here we introduce DrugHarness, an evolvable agent harness coupling composable scientific execution with conditional skill induction. Its environment integrates over 80 scientific operations, biomedical resources and task-specific code, preserving associations among candidates, results and artifacts. From execution trajectories and outcome feedback, DrugHarness induces action hypotheses with observable applicability conditions, recommended actions and supporting evidence. An independent review agent evaluates candidate skills derived from these hypotheses through source verification and, when needed, targeted execution trials. Admitted skills guide subsequent tasks and are revised through feedback. Evaluation on MolBench and SMDD-Bench demonstrates capabilities in molecular screening, optimization and constrained design. Without evolution, DrugHarness exceeds reported MolClaw-CC results by 10.8 percentage points in affinity-comparison accuracy and 55% in mean top-three active hits on MolBench. Retrospective evaluation on skill-development tasks shows that evolution increases Qwen's affinity-comparison accuracy from 62.2% to 81.1% and optimization success from 79.5% to 87.2%. In a prospective HPK1 study, DrugHarness achieves a more favorable median docking score than Biomni among system-specific candidates. A synthesized compound achieves a cellular IC50 of 14.19 nM, a 2.64-fold potency improvement over the best input reference, with activity competitive with two selected compounds designed by experienced medicinal chemists. These results support conditional skill evolution for scientific agents and demonstrate a workflow connecting computational drug design with experimental validation.