MAELLE is a mechanistic reaction prediction framework that models chemical reactions as discrete flow matching over graph-structured electron occupation vectors. It formulates the reactant-to-product mapping as a Continuous-time Markov Chain on electron sites and uses Optimal Transport to generate mechanistically interpretable edit trajectories without elementary step annotations. The method achieves competitive accuracy on the USPTO-480K benchmark, remains robust in out-of-distribution scenarios, and can recover mechanistic pathways that align with known chemistry and predict side products.
arXiv:2608. 14076v1 Announce Type: cross Abstract: Transition-state (TS) structures define the energetic barriers and mechanistic pathways of elementary chemical reactions, yet their identification remains computationally demanding because conventional saddle-point searches require expensive quantum-mechanical calculations.
ReCurveflow is a flow‑matching framework that learns to predict transition state geometries by training on continuously curved reference paths derived from full NEB bands, rather than straight linear paths. It introduces an off‑path correction mechanism that generates corrective velocity fields when the model encounters geometries off the training path, improving resistance to exposure bias and TS prediction accuracy. Across multiple data splits and evaluation metrics, ReCurveflow outperforms seven baselines and produces reaction trajectories whose energy profiles closely follow the reference NEB path, aiding NEB optimization and demonstrating effective corrective behavior.
arXiv:2602. 13136v2 Announce Type: replace Abstract: Template-free retrosynthesis methods treat the task as black-box sequence generation, limiting learning efficiency, while semi-template approaches rely on rigid reaction libraries that constrain generalization.
arXiv:2608. 06259v1 Announce Type: new Abstract: Reaction yield prediction remains challenging because labeled data are scarce and reaction space is both combinatorially large and sparsely populated, limiting the generalization of existing reaction representations.
arXiv:2609.17736v1 Announce Type: cross Abstract: Most molecular transitions occur on timescales far beyond direct molecular dynamics simulations. The committor, the probability that a configuration...
arXiv:2605. 15354v2 Announce Type: replace Abstract: Despite the success of foundation models in language and vision, molecular graph generation still lacks a unified framework for heterogeneous design tasks with reliable controllability.
arXiv:2604.07669v3 Announce Type: replace-cross Abstract: Synthesizable molecular optimization seeks to improve target properties while ensuring that molecular modifications follow feasible synthetic...
PGFS++ is a synthesis‑aware reinforcement learning framework that improves molecular properties while ensuring the resulting molecules can be synthesized and remain structurally similar to the input. It builds on PGFS+ by using trainable embedding lookup tables for reaction templates and second reactants, a more effective scoring function, and a refined RL algorithm. Experiments demonstrate that PGFS++ enhances target properties and preserves high output diversity, overcoming the reward‑hacking failure mode seen in earlier versions.
The paper introduces Round-Trip Reinforcement Learning (RTRL), a framework that trains chemical language models to improve round‑trip consistency by rewarding successful forward and reverse transformations. By iteratively training forward and reverse mappings, RTRL leverages abundant unlabeled chemical data to enhance both consistency and overall performance across supervised, self‑supervised, and synthetic data regimes. Experiments show that RTRL outperforms strong baselines, demonstrating that round‑trip consistency can be treated as a trainable objective for more robust foundation models.
arXiv:2607. 08003v1 Announce Type: cross Abstract: Catalysts are essential for sustainable chemical manufacturing, yet discovering novel architectures remains a bottleneck dominated by trial-and-error experimentation and computationally intensive screening.
The paper introduces Equivariant-Free Transformer-Autoencoded Latent Flow Matching (EF‑TALFM), a two‑stage generative framework that uses a single fixed‑dimensional latent vector to produce variable‑size 3D molecules. The first stage samples the latent vector via flow matching, and the second stage employs an autoregressive Transformer decoder that determines molecule size while generating atom types, coordinates, and chemical states. EF‑TALFM outperforms prior methods on the PCQM4Mv2 benchmark, achieving higher uniqueness, novelty, and computational throughput, and its internal ranking improves the hit rate for target HOMO–LUMO gaps while maintaining novelty.
arXiv:2507. 03853v2 Announce Type: replace Abstract: We introduce OrbitAll, a geometry- and physics-informed deep learning framework that encodes any molecular system with arbitrary charges, spins, and environmental effects using electronic structure information.