Model synthesis and identifiability analysis of stiff chemical reaction systems with inVAErt networks

From neural ODEs to continuous-time machine learning, differentiable solvers allow physics, optimization, and simulation to become trainable components within deep learning systems. This has opened the path to a new generation of deep learning frameworks for scientific computing, with many promising applications still emerging. In this paper, we integrate a differentiable chemistry solver into a modified physics-informed neural network to solve parameterized reaction systems that are inherently stiff. The proposed framework introduces several key components required to overcome limitations of standard physics-informed neural networks. These include a differentiable chemistry solver, a network architecture for parameterized solutions, and residual weighting tailored to stiff reactions. We evaluate the framework on a set of differential equations related to hydrogen combustion, which include initial/boundary value problems, inverse parameter identification, and a parameterized partial differential equation. Our results highlight the ability of the proposed approach to extend physics-informed neural networks to stiff chemical systems that were previously inaccessible.

Neural surrogates for stiff differential-algebraic equations (DAEs) face two barriers: soft-constraint methods leave algebraic residuals that stiffness amplifies into errors, and hard-constraint methods require trajectory data from stiff integrators. We introduce an extended Newton implicit layer that enforces algebraic constraints exactly and reduces fast dynamics to their quasi-steady-state values in a single differentiable solve. Embedded in a physics-informed DeepONet, the layer recovers all fast and algebraic states exactly from slow-state predictions, removes the per-window stiffness-amplification pathway, and yields a stiffness-scaled Implicit Function Theorem gradient absent from penalty methods. Cascaded implicit layers extend this to multi-component systems with provable convergence. On a grid-forming inverter (stiffness ratio of about 4712), extended Newton attains 1.42% error versus 39.3% (penalty) and 57.0% (standard Newton); augmented Lagrangian and feedback linearization diverged. Two independently trained models compose without retraining (0.72% to 1.16% error, exact constraint satisfaction). Cross-domain validation on the Robertson stiff DAE (stiffness ratio up to $10^5$) confirms generalization. Conformal prediction provides 90% coverage with automatic out-of-distribution detection.

Mapping a chemical reaction network, the graph of minima and transition states (TS) and the elementary reactions connecting them, is the natural language of chemistry, from catalysis to combustion to the origin of life. Constructing such a reaction network for a given chemistry has been impractical: it requires finding and characterizing tens of thousands of TS, a task for which traditional methods such as density functional theory (DFT) are typically prohibitively slow and require reactant and product as input. We introduce ReactionAtlas, which builds a reaction network $\textit{ab origine}$ from a handful of seed molecules and without hand-crafted rules. Specifically, our machine-learned generative model proposes reactions from kinetically sampled candidate compounds and a DFT-trained machine learned force field (MLFF) filters them to valid TS, the resulting products of which enter the search as new seeds. Starting from eight pre-biotic seeds (CH$_2$O, H$_2$O, OH$^-$, H$_3$O$^+$, CO$_2$, H$_2$CO$_3$, HCO$_3^-$, H), ReactionAtlas discovers $\sim$47,000 reactions among $\sim$12,000 compounds. The MLFF TSs match the PBE0 references within 0.5 Å RMSD in 85% of the cases and can be easily brought to the PBE0 level. Thus, ReactionAtlas maps small carbohydrate chemistry up to C$_4$H$_8$O$_4$ at unprecedented scale and accuracy, including charge and stereo information. It enables novel insights into many well-studied reaction paths, including the formose cycle, which we highlight for its centrality to the chemical origins of life. Notably, our framework also allows establishing alternative reaction pathways for formose chemistry.