# Representation Alignment as a Bottleneck in LLM-Based Retrosynthesis Planning

arXiv: https://arxiv.org/abs/2609.35571 · HTML: https://mlsanity.com/paper/2609.35571/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Reasoning for agents, planning and code, one of 17 directions in LLM reasoning.
- Builds on 21 of its 35 references that are in the map.
- First posted on arXiv 28 Sep 2026.

## Placed in

- LLM reasoning / [Reasoning for agents, planning and code](https://mlsanity.com/lr/reasoning-for-agents-planning-and-code/)

## Builds on (most cited first, 21 of 21)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [Sparks of Artificial General Intelligence: Early experiments with GPT-4](https://mlsanity.com/paper/2303.12712/) (2023)
- [Do As I Can, Not As I Say: Grounding Language in Robotic Affordances](https://mlsanity.com/paper/2204.01691/) (2022)
- [Least-to-Most Prompting Enables Complex Reasoning in Large Language Models](https://mlsanity.com/paper/2205.10625/) (2022)
- [Code as Policies: Language Model Programs for Embodied Control](https://mlsanity.com/paper/2209.07753/) (2022)
- [Inner Monologue: Embodied Reasoning through Planning with Language Models](https://mlsanity.com/paper/2207.05608/) (2022)
- [Program of Thoughts Prompting: Disentangling Computation from Reasoning for Numerical Reasoning Tasks](https://mlsanity.com/paper/2211.12588/) (2022)
- [PAL: Program-aided Language Models](https://mlsanity.com/paper/2211.10435/) (2022)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [LLM+P: Empowering Large Language Models with Optimal Planning Proficiency](https://mlsanity.com/paper/2304.11477/) (2023)
- [PlanBench: An Extensible Benchmark for Evaluating Large Language Models on Planning and Reasoning about Change](https://mlsanity.com/paper/2206.10498/) (2022)
- [On the Planning Abilities of Large Language Models : A Critical Investigation](https://mlsanity.com/paper/2305.15771/) (2023)
- [Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction](https://mlsanity.com/paper/1811.02633/) (2018)
- [PDDLStream: Integrating Symbolic Planners and Blackbox Samplers via Optimistic Adaptive Planning](https://mlsanity.com/paper/1802.08705/) (2018)
- [Learning Symbolic Operators for Task and Motion Planning](https://mlsanity.com/paper/2103.00589/) (2021)
- [BioPlanner: Automatic Evaluation of LLMs on Protocol Planning in Biology](https://mlsanity.com/paper/2310.10632/) (2023)
- [On Grounded Planning for Embodied Tasks with Language Models](https://mlsanity.com/paper/2209.00465/) (2022)
- [Process-Level Representation of Scientific Protocols with Interactive Annotation](https://mlsanity.com/paper/2101.10244/) (2021)

## Abstract (arXiv)

While LLMs show promise in general reasoning, symbolic planning in chemistry remains a bottleneck. Direct ''SMILES-to-PDDL'' attempts fail because they force models to juggle chemical analysis and planning-language structuring simultaneously. We hypothesize that this failure stems from a lack of intermediate abstractions rather than insufficient model capacity. By decomposing retrosynthesis into molecule mapping, reaction mapping, and PDDL generation, we achieve high success rates where end-to-end approaches fail. This provides evidence that a primary bottleneck lies in representation alignment rather than raw model capacity. Our structural analysis demonstrates that intermediate representations are essential in retrosynthesis planning, highlighting the importance of representation-centric design in future systems.