Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 2610.08750

Neural Petri flows for chemical reactions

Jose Eduardo Escrig Molina·Daniel Probst
View original source ↗Read source document ↗Export metadata ↓

Abstract

Petri nets have been used to describe chemical processes such as reactions.They map well to chemistry: Places are the bonds between atoms and the free valence of each atom, a token is a unit of bond order, a transition forms or breaks a bond, the conserved quantities are the valence budgets of the atoms, and the enabling rule is the valence rule. These semantics are not guaranteed by learned models of reactions or neural networks that are built on Petri nets that use the net as a scaffold for message passing. Here, we ask what architecture remains a Petri net for every value of its weights. We find the answer in the theory, where all semantics of a net share the firing form $m^\prime=m+Cσ$, locality, as enabling reads only the inputs of a transition, and the enabling rule, and we prove that conservation forces the firing form and that non-negativity forces the enabling rule on local rate laws. This leaves free the rate law, which is the propensity of each transition to fire. We introduce Neural Petri Flow, which learns this rate law, or a readout for classification, and hard-wires the rest as parameter-free layers. On what we denote a valence net, atom mapping, reaction classification, and forward prediction become three tasks on one firing vector. Without training, the minimum firing vector maps 88.8% of the curated Golden set against 85.6% for RXNMapper, and 88.7 against 77.9% of the enzymatic reactions of EnzymeMap. On USPTO-480K, NPF trained on these firing vectors predicts 87.7% of the products and 67.4% when trained on a 1% subset of the training reactions. EC numbers of ECREACT are predicted at the third level for 90.2% of reactions, 5.6 points ahead of the best published method. With electrons as tokens, the same token game predicts 90.5% of the elementary steps of FlowER first, ahead of the published baseline, and every top-1 prediction is a valid molecule without a filter.

Explore related subjects

cs.LGphysics.chem-phq-bio.QM

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Jose Eduardo Escrig Molina, Daniel Probst. 2026-10-06. Neural Petri flows for chemical reactions. https://arxiv.org/abs/2610.08750

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Probabilistic Truly Unordered Rule Sets

Rule set learning has recently been frequently revisited because of its interpretability. Existing methods have several shortcomings though. First, most existing methods impose orders among rules, either explicitly or implicitly, which makes the models less comprehensible. Second, due to the difficulty of handling conflicts caused by overlaps (i.e., instances covered by multiple rules), existing methods often do not consider probabilistic rules. Third, learning classification rules for multi-class target is understudied, as most existing methods focus on binary classification or multi-class classification via the ``one-versus-rest" approach. To address these shortcomings, we propose TURS, for Truly Unordered Rule Sets. To resolve conflicts caused by overlapping rules, we propose a novel model that exploits the probabilistic properties of our rule sets, with the intuition of only allowing rules to overlap if they have similar probabilistic outputs. We next formalize the problem of learning a TURS model based on the MDL principle and develop a carefully designed heuristic algorithm. We benchmark against a wide range of rule-based methods and demonstrate that our method learns rule sets that have lower model complexity and highly competitive predictive performance. In addition, we empirically show that rules in our model are empirically ``independent" and hence truly unordered.

cs.LG↗
arXiv2026

FreDF: Learning to Forecast in the Frequency Domain

Time series modeling presents unique challenges due to autocorrelation in both historical data and future sequences. While current research predominantly addresses autocorrelation within historical data, the correlations among future labels are often overlooked. Specifically, modern forecasting models primarily adhere to the Direct Forecast (DF) paradigm, generating multi-step forecasts independently and disregarding label autocorrelation over time. In this work, we demonstrate that the learning objective of DF is biased in the presence of label autocorrelation. To address this issue, we propose the Frequency-enhanced Direct Forecast (FreDF), which mitigates label autocorrelation by learning to forecast in the frequency domain, thereby reducing estimation bias. Our experiments show that FreDF significantly outperforms existing state-of-the-art methods and is compatible with a variety of forecast models. Code is available at https://github.com/Master-PLC/FreDF.

cs.LG↗
arXiv2026

Convergence of Sharpness-Aware Minimization Algorithms using Increasing Batch Size and Decaying Learning Rate

The sharpness-aware minimization (SAM) algorithm and its variants, including gap guided SAM (GSAM), have been successful at improving the generalization capability of deep neural network models by finding flat local minima of the empirical loss in training. Meanwhile, it has been shown theoretically and practically that increasing the batch size or decaying the learning rate avoids sharp local minima of the empirical loss. In this paper, we consider the GSAM algorithm with increasing batch sizes or decaying learning rates, such as cosine annealing or linear learning rate, and theoretically show its convergence. Moreover, we numerically compare SAM (GSAM) with and without an increasing batch size and conclude that using an increasing batch size { achieves a lower worst-case $\ell_\infty$ adaptive sharpness} than compared with using a constant batch size and learning rate.

cs.LG↗