# Molecular Identifier Visual Prompt and Verifiable Reinforcement Learning for Chemical Reaction Diagram Parsing

arXiv: https://arxiv.org/abs/2603.15011 · HTML: https://mlsanity.com/paper/2603.15011/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 38 of its 55 references that are in the map.
- First posted on arXiv 16 Mar 2026.

## Builds on (most cited first, 30 of 38)

- [DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models](https://mlsanity.com/paper/2402.03300/) (2024)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [Qwen2.5-VL Technical Report](https://mlsanity.com/paper/2502.13923/) (2025)
- [GPT-4o System Card](https://mlsanity.com/paper/2410.21276/) (2024)
- [Qwen2-VL: Enhancing Vision-Language Model's Perception of the World at Any Resolution](https://mlsanity.com/paper/2409.12191/) (2024)
- [Qwen Technical Report](https://mlsanity.com/paper/2309.16609/) (2023)
- [DAPO: An Open-Source LLM Reinforcement Learning System at Scale](https://mlsanity.com/paper/2503.14476/) (2025)
- [Understanding R1-Zero-Like Training: A Critical Perspective](https://mlsanity.com/paper/2503.20783/) (2025)
- [Tulu 3: Pushing Frontiers in Open Language Model Post-Training](https://mlsanity.com/paper/2411.15124/) (2024)
- [SFT Memorizes, RL Generalizes: A Comparative Study of Foundation Model Post-training](https://mlsanity.com/paper/2501.17161/) (2025)
- [Vision-R1: Incentivizing Reasoning Capability in Multimodal Large Language Models](https://mlsanity.com/paper/2503.06749/) (2025)
- [VLM-R1: A Stable and Generalizable R1-style Large Vision-Language Model](https://mlsanity.com/paper/2504.07615/) (2025)
- [Open-Reasoner-Zero: An Open Source Approach to Scaling Up Reinforcement Learning on the Base Model](https://mlsanity.com/paper/2503.24290/) (2025)
- [OCR-free Document Understanding Transformer](https://mlsanity.com/paper/2111.15664/) (2021)
- [Hallucination of Multimodal Large Language Models: A Survey](https://mlsanity.com/paper/2404.18930/) (2024)
- [OBELICS: An Open Web-Scale Filtered Dataset of Interleaved Image-Text Documents](https://mlsanity.com/paper/2306.16527/) (2023)
- [Reinforcement Learning with Verifiable Rewards Implicitly Incentivizes Correct Reasoning in Base LLMs](https://mlsanity.com/paper/2506.14245/) (2025)
- [MinerU: An Open-Source Solution for Precise Document Content Extraction](https://mlsanity.com/paper/2409.18839/) (2024)
- [Nougat: Neural Optical Understanding for Academic Documents](https://mlsanity.com/paper/2308.13418/) (2023)
- [Multimodal C4: An Open, Billion-scale Corpus of Images Interleaved with Text](https://mlsanity.com/paper/2304.06939/) (2023)
- [TextMonkey: An OCR-Free Large Multimodal Model for Understanding Document](https://mlsanity.com/paper/2403.04473/) (2024)
- [ViP-LLaVA: Making Large Multimodal Models Understand Arbitrary Visual Prompts](https://mlsanity.com/paper/2312.00784/) (2023)
- [Perception-R1: Pioneering Perception Policy with Reinforcement Learning](https://mlsanity.com/paper/2504.07954/) (2025)
- [On Designing Effective RL Reward at Training Time for LLM Reasoning](https://mlsanity.com/paper/2410.15115/) (2024)
- [MM-RLHF: The Next Step Forward in Multimodal LLM Alignment](https://mlsanity.com/paper/2502.10391/) (2025)
- [Image-of-Thought Prompting for Visual Reasoning Refinement in Multimodal Large Language Models](https://mlsanity.com/paper/2405.13872/) (2024)
- [OmniCorpus: A Unified Multimodal Corpus of 10 Billion-Level Images Interleaved with Text](https://mlsanity.com/paper/2406.08418/) (2024)
- [RLVER: Reinforcement Learning with Verifiable Emotion Rewards for Empathetic Agents](https://mlsanity.com/paper/2507.03112/) (2025)
- [RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing](https://mlsanity.com/paper/2305.11845/) (2023)
- [OpenChemIE: An Information Extraction Toolkit For Chemistry Literature](https://mlsanity.com/paper/2404.01462/) (2024)

## Built on by (most cited first, 2 of 2)

- [MinerU.Chem: A High-Precision System for Optical Chemical Structure and Reaction Recognition](https://mlsanity.com/paper/2608.03525/) (2026)
- [Comprehensive pKa Data Augmentation from Limited Real Data through an Engineered Models-Quantum Framework](https://mlsanity.com/paper/2606.17077/) (2026)

## Abstract (arXiv)

Reaction diagram parsing (RxnDP) is critical for extracting chemical synthesis information from literature. Although recent Vision-Language Models (VLMs) have emerged as a promising paradigm to automate this complex visual reasoning task, their application is fundamentally bottlenecked by the inability to align visual chemical entities with pre-trained knowledge, alongside the inherent discrepancy between token-level training and reaction-level evaluation. To address these dual challenges, this work enhances VLM-based RxnDP from two complementary perspectives: prompting representation and learning paradigms. First, we propose Identifier as Visual Prompting (IdtVP), which leverages naturally occurring molecule identifiers (e.g., bold numerals like 1a) to activate the chemical knowledge acquired during VLM pre-training. IdtVP enables powerful zero-shot and out-of-distribution capabilities, outperforming existing prompting strategies. Second, to further optimize performance within fine-tuning paradigms, we introduce Re3-DAPO, a reinforcement learning algorithm that leverages verifiable rewards to directly optimize reaction-level metrics, thereby achieving consistent gains over standard supervised fine-tuning. Additionally, we release the ScannedRxn benchmark, comprising scanned historical reaction diagrams with real-world artifacts, to rigorously assess model robustness and out-of-distribution ability. Our contributions advance the accuracy and generalization of VLM-based reaction diagram parsing. We will release data, models, and code on GitHub.