The ability of machine learning to generate structured objects has progressed dramatically in the lastfewyears.

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However,mostofthem are cumbersome and lack interpretability about their predictions.

Retrosynthesis is the process of identifying a set of reactants to synthesize a target molecule. It is of vital importance to material design and drug discovery. Existing machine learning approaches based on language models and graph neural networks have achieved encouraging results. However, the inner connections of these models are rarely discussed, and rigorous evaluations of these models are largely in need. In this paper, we propose a framework that unifies sequence-and graph-based methods as energy-based models (EBMs) with different energy functions. This unified view establishes connections and reveals the differences between models, thereby enhancing our understanding of model design. We also provide a comprehensive assessment of performance to the community. Moreover, we present a novel dual variant within the framework that performs consistent training to induce the agreement between forward-and backward-prediction. This model improves the state-of-the-art of template-free methods with or without reaction types.

Progress in computer-aided synthesis planning (CASP) is obscured by the lack of standardized evaluation infrastructure and the reliance on metrics that prioritize topological completion over chemical validity. We introduce RetroCast, a unified evaluation suite that standardizes heterogeneous model outputs into a common schema to enable statistically rigorous, apples-to-apples comparison. The framework includes a reproducible benchmarking pipeline with stratified sampling and bootstrapped confidence intervals, accompanied by SynthArena, an interactive platform for qualitative route inspection. We utilize this infrastructure to evaluate leading search-based and sequence-based algorithms on a new suite of standardized benchmarks. Our analysis reveals a divergence between "solvability" (stock-termination rate) and route quality; high solvability scores often mask chemical invalidity or fail to correlate with the reproduction of experimental ground truths. Furthermore, we identify a "complexity cliff" in which search-based methods, despite high solvability rates, exhibit a sharp performance decay in reconstructing long-range synthetic plans compared to sequence-based approaches. We release the full framework, benchmark definitions, and a standardized database of model predictions to support transparent and reproducible development in the field.

The disconnect between AI-generated molecules with desirable properties and their synthetic feasibility remains a critical bottleneck in computational discovery of drugs and materials. While generative AI has accelerated the proposal of candidate molecules, many of these structures prove challenging or impossible to synthesize using established chemical reactions. Here, we introduce SynTwins, a novel retrosynthesis-guided molecule design framework that finds synthetically accessible molecular analogs by emulating expert chemists' strategies in three steps: retrosynthesis, searching similar building blocks, and virtual synthesis. Using a search algorithm instead of a stochastic data-driven generator, SynTwins outperforms state-of-the-art machine learning models at exploring synthetically accessible analogs while maintaining high structural similarity to original target molecules. Furthermore, when integrated into existing molecular property-optimization frameworks, our hybrid approach produces synthetically feasible analogs with minimal loss in property scores. Our comprehensive benchmarking across diverse molecular datasets demonstrates that SynTwins effectively bridges the gap between computational design and experimental synthesis, providing a practical solution for accelerating the discovery of synthesizable molecules with desired properties for a wide range of applications.

Retrosynthesis planning aims to decompose target molecules into available building blocks, forming a synthetic tree where each internal node represents an intermediate compound and each leaf ideally corresponds to a purchasable reactant. However, this tree becomes invalid if any leaf node is not a valid building block, making the planning process vulnerable to the "weakest link" in the synthetic route. Existing methods often optimise for average performance across branches, failing to account for this worst-case sensitivity. In this paper, we reframe retrosynthesis as a worst-path optimisation problem within tree-structured Markov Decision Processes (MDPs). We prove that this formulation admits a unique optimal solution and provides monotonic improvement guarantees. Building on this insight, we introduce Interactive Retrosynthesis Planning (InterRetro), a method that interacts with the tree MDP, learns a value function for worst-path outcomes, and improves its policy through self-imitation, preferentially reinforcing past decisions with high estimated advantage. Empirically, InterRetro achieves state-of-the-art results - solving 100% of targets on the Retro*-190 benchmark, shortening synthetic routes by 4.9%, and achieving promising performance using only 10% of the training data.

Applications of machine learning in chemistry are often limited by the scarcity and expense of labeled data, restricting traditional supervised methods. In this work, we introduce a framework for molecular reasoning using general-purpose Large Language Models (LLMs) that operates without requiring labeled training data. Our method anchors chain-of-thought reasoning to the molecular structure by using unique atomic identifiers. First, the LLM performs a one-shot task to identify relevant fragments and their associated chemical labels or transformation classes. In an optional second step, this position-aware information is used in a few-shot task with provided class examples to predict the chemical transformation. We apply our framework to single-step retrosynthesis, a task where LLMs have previously underperformed. Across academic benchmarks and expert-validated drug discovery molecules, our work enables LLMs to achieve high success rates in identifying chemically plausible reaction sites ($\geq90\%$), named reaction classes ($\geq40\%$), and final reactants ($\geq74\%$). Beyond solving complex chemical tasks, our work also provides a method to generate theoretically grounded synthetic datasets by mapping chemical knowledge onto the molecular structure and thereby addressing data scarcity.