Training Chemical Plausibility-Aware Large Language Models for Single-Step Retrosynthesis

Chem-R: Learning to Reason as a Chemist

The proposed Chem-R, a general Chemical Reasoning model designed to emulate the deliberative processes of chemists, achieves state-of-the-art performance on comprehensive benchmarks, surpassing leading LLMs, including Gemini-3-Pro and Kimi-k2.5.

Toward Synthesizability-Aware Multi-Step Retrosynthetic Planning

URSA: Chemistry-Aware Benchmark for Utilitarian Retrosynthesis Assessment

Synthesis planning aiming to find pathways of reactions for a target molecule is one of the most important and challenging tasks in drug discovery. Recent progress has produced both specialized deep-learning retrosynthesis systems and general-purpose large language models, but objective comparison remains difficult due to the lack of flexible, chemically interpretable benchmarking protocols. In the current study, we are introducing the URSA (Utilitarian RetroSynthesis Assessment) evaluation framework that provides the opportunity to benchmark the synthetic routes not only from a formal perspective, such as convergence to commercially available starting materials, but also from a chemical plausibility perspective, mimicking the way expert chemists evaluate the reactions and routes. The study covers a comprehensive evaluation of both conventional end-to-end retrosynthesis solutions and LLMs for the synthesis planning task on a set of novel, diverse target molecules with undisclosed synthetic routes, which represent realistic tasks in the daily drug design routine. We find that while LLMs can support high-level strategic planning, they currently underperform specialized retrosynthesis models in reliably solving synthesis planning tasks.

RetroMPA: A Molecular Property-Aware Auxiliary Framework for Enhancing Retrosynthesis Prediction.

Retrosynthesis is a cornerstone of drug discovery and organic synthesis. While data-driven deep learning models have shown remarkable progress, they are designed to autonomously learn reaction patterns from extensive retrosynthesis data sets with limited explicit integration of established chemical knowledge as priors. To address this limitation, we introduce RetroMPA, a molecular property-aware, posthoc enhancement module that injects chemical knowledge into the retrosynthesis pipeline. Rather than functioning as an independent, standalone SMILES sequence generator from scratch, RetroMPA is conceptualized as a broadly applicable, model-agnostic chemical filter designed to recalibrate and optimize the predictive pathways of various existing algorithms. This plug-and-play framework can be seamlessly integrated with a range of existing data-driven retrosynthesis methods, enhancing model outputs without necessitating any modifications to the original model architecture or requiring resource-intensive, model-specific retraining procedures. By operating at the molecular level and leveraging a property-aware latent embedding space, RetroMPA consistently improves top-1 accuracy across eight representative retrosynthesis models by an average of 5.50% on USPTO-50K. Furthermore, we demonstrate its scalability by validating its performance on the large-scale USPTO-Full data set, achieving an average improvement of about 2.03% across both template-based and template-free architectures. In addition, wet-lab experiments provide preliminary support for the practical utility of the framework. These syntheses confirmed viable, previously unreported substrate combinations for established, classic reaction paradigms─specifically, the Suzuki-Miyaura coupling, the Bucherer reaction, and the Friedel-Crafts acylation, thereby suggesting that RetroMPA can operate beyond mere data fitting. The code is open-sourced at https://github.com/MengzhouLu/RetroMPA.

Beyond Reaction Data: Learning Chemical Knowledge from Large-Scale Molecules for Retrosynthesis

Retrosynthesis, the process of predicting reactants from products, remains a critical challenge in computational chemistry and drug discovery. While recent deep learning methods have shown strong performance, they remain overly reliant on reaction datasets, which are limited in availability and quality. Large-scale unlabeled molecular data encode rich structural patterns that can be leveraged to learn transferable chemical knowledge, but remain largely unexplored. In this work, we propose KnowRetro (Knowledge-Guided Retrosynthesis Prediction), a chemically-aware framework that learns chemical knowledge from large-scale unlabeled molecules to enhance the accuracy and diversity of retrosynthesis prediction. Specifically, KnowRetro first builds a hierarchical knowledge graph from millions of unlabeled molecules, which captures transformation-relevant relationships among molecules, substructures, and functional groups. It then employs chemically guided pre-training based on substructure decomposition to encourage the model to capture fundamental reaction patterns, followed by fine-tuning with an adapter designed to inject task-relevant knowledge into reactant generation. Extensive experiments demonstrate that KnowRetro achieves high accuracy with improved robustness and diversity in reactant generation. Our code is available at https://github.com/chenyujie1127/KnowRetro.

Robust out-of-distribution prediction of Buchwald-Hartwig reactions.

A framework that systematically standardizes and integrates multiple reaction datasets into a high-quality, unique-structure-per-entity dataset, coupled with active learning to strategically expand chemical space is introduced, establishing a blueprint for robust machine learning in synthetic chemistry.