DECIMER 1.0 introduces a Transformer-based architecture coupled with EfficientNet-B3 to solve Optical Chemical Structure Recognition. By using the SELFIES representation (which guarantees 100% valid output strings) and scaling training to over 35 million molecules, it achieves 96.47% exact match accuracy on synthetic benchmarks, offering an open-source solution for mining chemical data from legacy literature.
This paper introduces a convolution-free, end-to-end transformer model for molecular image translation. By replacing CNN encoders with Vision Transformers, it achieves a Levenshtein distance of 6.95 on noisy datasets, compared to 7.49 for ResNet50-LSTM baselines.
Proposes a Random Conditional Guided Decoder (RCGD) and a Structure-Specific Markup Language (SSML) to handle the ambiguity and complexity of handwritten chemical structure recognition, validated on a new benchmark dataset (EDU-CHEMC) with 50,000 handwritten images.
This paper introduces ICMDT, a Transformer-based architecture for molecular translation (image-to-InChI). By enhancing the TNT block to fuse pixel, small patch, and large patch embeddings, the model achieves superior accuracy on the Bristol-Myers Squibb dataset compared to CNN-RNN and standard Transformer baselines.
This paper proposes an end-to-end deep learning architecture that translates chemical images directly into molecular graphs using a ResNet-Transformer encoder and a graph-aware decoder. It addresses the limitations of SMILES-based approaches by effectively handling non-atomic symbols (abbreviations) and varying drawing styles found in scientific literature.
A Transformer-based system for optical chemical structure recognition introducing a comprehensive data generation pipeline (FG-SMILES, Markush structures, visual contamination) achieving 79% accuracy on real-world images, outperforming rule-based systems like OSRA.
MICER treats optical chemical structure recognition as an image captioning task, using transfer learning with a fine-tuned ResNet encoder and attention-based LSTM decoder to convert molecular images into SMILES strings, reaching 97.54% sequence accuracy on synthetic data and 82.33% on real-world images.
MolMiner replaces traditional rule-based vectorization with a deep learning object detection pipeline (YOLOv5) to extract chemical structures from PDFs. It outperforms open-source baselines on four benchmarks and introduces a new real-world dataset of 3,040 images.
Proposes a patch-based image processing pipeline using Inception V3 to filter Markush structures from chemical documents, outperforming traditional fixed-feature (ORB) methods on low-SNR images.
This systematization paper traces the history of OCSR, comparing early rule-based systems like OSRA with modern deep learning approaches like DECIMER. It highlights the shift from image classification to image captioning and identifies critical gaps in dataset standardization and evaluation metrics.
This empirical study isolates the impact of chemical string representations on image-to-text translation models. It finds that while SMILES offers the highest overall accuracy, SELFIES provides a guarantee of structural validity, offering a trade-off for OCSR tasks.
Proposes an end-to-end architecture replacing standard CNN backbones with Swin Transformer to capture global image context. Introduces Multi-label Focal Loss to handle severe token imbalance in chemical datasets.