RetroGEF: Dynamic Graph Edit Flow for Single-Step Retrosynthesis

Retrosynthesis prediction aims to identify reactants that can synthesize a given product molecule. Although molecular large language models (LLMs) have recently shown promising results, most existing methods either generate reactants directly or provide only generic product-level analysis, without explicitly reasoning about bond-disconnection strategies that justify specific reactant choices. This paper proposes RetroReasoner, a retrosynthetic reasoning model that captures chemists' strategic disconnection-based thinking. RetroReasoner is trained with supervised fine-tuning and reinforcement learning. For supervised fine-tuning, SyntheticRetro generates structured disconnection rationales paired with reactant predictions. For reinforcement learning, a round-trip reward evaluates predicted reactants by passing them through a forward synthesis model and rewarding predictions that reconstruct the original product. RetroReasoner can also be applied to multi-step retrosynthetic planning by incorporating it into a parallelized Monte Carlo tree search framework, reducing search time while increasing the number and diversity of valid synthetic pathways. Experimental results show that RetroReasoner outperforms prior baselines, including not only molecular LLMs but also retrosynthesis-specific expert models, and generates a broader range of feasible reactant proposals, especially for challenging reaction instances. The code is available at https://github.com/KU-AGI/RetroReasoner.

Stochastic process-based molecular graph generators have become the state of the art for template-free single-step retrosynthesis. However, these models are typically trained only on product-reactant pairs, thereby acquiring chemistry-relevant representations in an indirect and implicit manner. Meanwhile, recent advances in computer vision demonstrate that offering representation guidance to a generator can effectively distill semantics from pretrained encoders into DiTs, substantially improving both convergence and generation quality. Whether similar gains extend to the retrosynthesis task, and what graph-specific design choices can make them work, remains an open question. To address these questions, we conduct a systematic empirical study over a unified design space spanning teacher molecular representations, endpoint and granularity choices, injection depths in the denoiser, correspondence strategies and guidance scheme. Guided by these considerations, we develop Graph-oriented Representation Guidance (GRG), which achieves 58.6 / 77.2 / 83.4 / 87.1 top-1 / 3 / 5 / 10 accuracy on USPTO-50k, while increasing diversity to 15.5, both substantially outperforming the adopted base generator. Notably, GRG consistently improves all top-k metrics in out-of-distribution settings, suggesting that representation guidance facilitates the acquisition of intrinsic chemical semantics. Meanwhile, the introduced representation guidance reduces the number of epochs by 35% and the wall-clock time by 30% to reach comparable performance. In addition, we introduce a simple yet effective representation-similarity-based reranking mechanism, which further improves the top of the ranked list without training an additional verifier.

Retrosynthetic planning seeks to connect a target molecule to commercially available starting materials through a multistep route. Classical planners construct such routes by iteratively applying single-step reaction models within a search procedure; constrained variants often require specialized algorithms or architectural changes. Direct route generation reframes retrosynthesis as sequence generation, but existing direct-generation methods still train separate models for different planning specifications. We introduce Ariadne, a decoder-only route generator that represents the target, optional constraints, and route in one prompt-completion sequence. On the RetroCast/PaRoutes mkt-cnv-160 benchmark family, one 24-layer checkpoint follows route-depth and required-starting-material prompts: adding the corresponding prompt fields raises Solv-0 by 13.7 points for depth constraints and 31.2 points for required-leaf constraints. Ariadne also improves over DESP, a bidirectional search planner, on required-leaf Top-10 and Solv-0 in 24 GPU-minutes versus 6.8 GPU-hours. On standard reconstruction, Ariadne is comparable to DMS Explorer XL at about half the reported inference time. Across additional target-only benchmarks, Ariadne's clearest gains are on route-holdout reconstruction, whereas AiZynthFinder MCTS remains stronger on several Solv-0 comparisons. These results extend sequence generation from specialist retrosynthesis models to prompt-conditioned structural route generation. We release the codebase and training scripts to support further work, but do not introduce Tier-1--3 route checkers; those remain the main bottleneck before models of this kind can become useful to experimental chemists.