Tim Strohmeyer

Tim Strohmeyer, Lucas Morin, Gerhard Ingmar Meijer et al.

Automatically extracting chemical structures from documents is essential for the large-scale analysis of the literature in chemistry. Automatic pipelines have been developed to recognize molecules represented either in figures or in text independently. However, methods for recognizing chemical structures from multimodal descriptions (Markush structures) lag behind in precision and cannot be used for automatic large-scale processing. In this work, we present MarkushGrapher-2, an end-to-end approach for the multimodal recognition of chemical structures in documents. First, our method employs a dedicated OCR model to extract text from chemical images. Second, the text, image, and layout information are jointly encoded through a Vision-Text-Layout encoder and an Optical Chemical Structure Recognition vision encoder. Finally, the resulting encodings are effectively fused through a two-stage training strategy and used to auto-regressively generate a representation of the Markush structure. To address the lack of training data, we introduce an automatic pipeline for constructing a large-scale dataset of real-world Markush structures. In addition, we present IP5-M, a large manually-annotated benchmark of real-world Markush structures, designed to advance research on this challenging task. Extensive experiments show that our approach substantially outperforms state-of-the-art models in multimodal Markush structure recognition, while maintaining strong performance in molecule structure recognition. Code, models, and datasets are released publicly.

Nikolaos Livathinos, Christoph Auer, Ahmed Nassar et al.

This technical report documents the development of novel Layout Analysis models integrated into the Docling document-conversion pipeline. We trained several state-of-the-art object detectors based on the RT-DETR, RT-DETRv2 and DFINE architectures on a heterogeneous corpus of 150,000 documents (both openly available and proprietary). Post-processing steps were applied to the raw detections to make them more applicable to the document conversion task. We evaluated the effectiveness of the layout analysis on various document benchmarks using different methodologies while also measuring the runtime performance across different environments (CPU, Nvidia and Apple GPUs). We introduce five new document layout models achieving 20.6% - 23.9% mAP improvement over Docling's previous baseline, with comparable or better runtime. Our best model, "heron-101", attains 78% mAP with 28 ms/image inference time on a single NVIDIA A100 GPU. Extensive quantitative and qualitative experiments establish best practices for training, evaluating, and deploying document-layout detectors, providing actionable guidance for the document conversion community. All trained checkpoints, code, and documentation are released under a permissive license on HuggingFace.