# COMO: Closed-Loop Optical Molecule Recognition with Minimum Risk Training

arXiv: https://arxiv.org/abs/2604.23546 · HTML: https://mlsanity.com/paper/2604.23546/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 23 references that are in the map.
- First posted on arXiv 26 Apr 2026.

## Builds on (most cited first, 12 of 12)

- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [EfficientNetV2: Smaller Models and Faster Training](https://mlsanity.com/paper/2104.00298/) (2021)
- [Scheduled Sampling for Sequence Prediction with Recurrent Neural Networks](https://mlsanity.com/paper/1506.03099/) (2015)
- [Sequence Level Training with Recurrent Neural Networks](https://mlsanity.com/paper/1511.06732/) (2015)
- [Self-critical Sequence Training for Image Captioning](https://mlsanity.com/paper/1612.00563/) (2016)
- [Minimum Risk Training for Neural Machine Translation](https://mlsanity.com/paper/1512.02433/) (2015)
- [MolScribe: Robust Molecular Structure Recognition with Image-To-Graph Generation](https://mlsanity.com/paper/2205.14311/) (2022)
- [Molecular Structure Extraction From Documents Using Deep Learning](https://mlsanity.com/paper/1802.04903/) (2018)
- [MolGrapher: Graph-based Visual Recognition of Chemical Structures](https://mlsanity.com/paper/2308.12234/) (2023)
- [MolParser: End-to-end Visual Recognition of Molecule Structures in the Wild](https://mlsanity.com/paper/2411.11098/) (2024)
- [OCSU: Optical Chemical Structure Understanding for Molecule-centric Scientific Discovery](https://mlsanity.com/paper/2501.15415/) (2025)

## Abstract (arXiv)

Optical chemical structure recognition (OCSR) translates molecular images into machine-readable representations like SMILES strings or molecular graphs, but remains challenging in real-world documents due to inexhaustible variations in chemical structures, shorthand conventions, and visual noise. Most existing deep-learning-based approaches rely on teacher forcing with token-level Maximum Likelihood Estimation (MLE). This training paradigm suffers from exposure bias, as models are trained under ground-truth prefixes but must condition on their own previous predictions during inference. Moreover, token-level MLE objectives hinder the optimization towards molecular-level evaluation criteria such as chemical validity and structural similarity. Here we introduce Minimum Risk Training (MRT) to OCSR and propose COMO (Closed-loop Optical Molecule recOgnition), a closed-loop framework that mitigates exposure bias by directly optimizing over molecule-level, non-differentiable objectives, by iteratively sampling and evaluating the model's own predictions. Experiments on ten benchmarks including synthetic and real-world chemical diagrams from patent and scientific literature demonstrate that COMO substantially outperforms existing rule-based and learning-based methods with less training data. Ablation studies further show that MRT is architecture-agnostic, demonstrating its potential for broad application to end-to-end OCSR systems.