Document Processing
GutenOCR Mascot

GutenOCR: A Grounded Vision-Language Front-End for Documents

GutenOCR is a family of vision-language models designed to serve as a ‘grounded OCR front-end’, providing high-quality text transcription and explicit geometric grounding.

Computational Chemistry
Dual-encoder architecture diagram for MarkushGrapher-2 showing vision and VTL encoding pipelines

MarkushGrapher-2: End-to-End Markush Recognition

An 831M-parameter encoder-decoder model that jointly encodes image, OCR text, and layout information through a two-stage training strategy, achieving state-of-the-art multimodal Markush structure recognition while remaining competitive on standard molecular structure recognition.

Machine Learning
Diagram showing NaViT packing variable-resolution image patches into a single sequence

NaViT: Native Resolution Vision Transformer

NaViT applies sequence packing (Patch n’ Pack) to Vision Transformers, enabling training on images of arbitrary resolution and aspect ratio while improving training efficiency by up to 4x over standard ViT.

Computational Chemistry
Bar chart showing vision language model performance across chemistry tasks including equipment identification, molecule matching, spectroscopy, and laboratory safety

MaCBench: Multimodal Chemistry and Materials Benchmark

MaCBench evaluates frontier vision language models across 1,153 chemistry and materials science tasks spanning data extraction, experimental execution, and data interpretation, uncovering fundamental limitations in spatial reasoning and cross-modal integration.

Computational Biology
Three-panel diagram showing input point sets, SVD factorization of the cross-covariance matrix, and the aligned result

Arun et al.: SVD-Based Least-Squares Fitting of 3D Points

Presents a concise SVD-based algorithm for finding the optimal rotation and translation between two 3D point sets, with analysis of the degenerate reflection case that Umeyama later corrected.

Computational Biology
Diagram showing the polar decomposition of the cross-covariance matrix M into orthonormal factor U and positive semidefinite square root

Horn et al.: Absolute Orientation Using Orthonormal Matrices

The matrix-based companion to Horn’s 1987 quaternion method, deriving the optimal rotation as the orthonormal factor in the polar decomposition of the cross-covariance matrix via eigendecomposition of a 3x3 symmetric matrix.

Computational Biology
Side-by-side comparison showing naive SVD producing a reflected alignment versus Umeyama's corrected proper rotation

Umeyama's Method: Corrected SVD for Point Alignment

Corrects a flaw in prior SVD-based alignment methods (Arun et al., Horn et al.) that could produce reflections instead of rotations under noisy data, and provides a complete closed-form solution for similarity transformations in arbitrary dimensions.

Computational Chemistry
AdaptMol domain adaptation pipeline showing encoder-decoder with MMD alignment between labeled source and unlabeled target domain images

AdaptMol: Domain Adaptation for Molecular OCSR (2026)

AdaptMol combines an end-to-end graph reconstruction model with unsupervised domain adaptation via class-conditional MMD on bond features and SMILES-validated self-training. Achieves 82.6% accuracy on hand-drawn molecules (10.7 points above prior best) while maintaining state-of-the-art results on four literature benchmarks, using only 4,080 real hand-drawn images for adaptation.

Computational Chemistry
GraphReco system architecture showing component extraction, atom and bond ambiguity resolution, and graph reconstruction stages

GraphReco: Probabilistic Structure Recognition (2026)

GraphReco presents a rule-based OCSR system with two key innovations: a Fragment Merging line detection algorithm for precise bond identification and a Markov network for probabilistic resolution of atom/bond ambiguity during graph assembly. Achieves 94.2% accuracy on USPTO-10K, outperforming both traditional rule-based and some ML-based methods.

Computational Chemistry
GraSP feed-forward architecture showing GNN, FiLM-conditioned CNN, and MLP classification head

GraSP: Graph Recognition via Subgraph Prediction (2026)

GraSP introduces a general framework for recognizing graphs in images by framing it as sequential subgraph prediction with a binary classifier. A GNN conditions a CNN via FiLM layers to predict whether a candidate graph is a subgraph of the target. Applied to OCSR on QM9, GraSP achieves 67.5% accuracy with no domain-specific modifications.

Computational Biology
3D scatter plot showing left and right point sets with rotation axis and quaternion rotation arc

Horn's Method: Absolute Orientation via Unit Quaternions

Derives the optimal rotation between two 3D point sets as the eigenvector of a 4x4 symmetric matrix built from cross-covariance sums, using unit quaternions to enforce the orthogonality constraint.

Computational Chemistry
Uni-Parser pipeline diagram showing document pre-processing, layout detection, semantic parsing, content gathering, and format conversion stages

Uni-Parser: Industrial-Grade Multi-Modal PDF Parsing (2025)

Technical report on Uni-Parser, an industrial-grade document parsing engine that uses a modular multi-expert architecture to parse scientific PDFs into structured representations. Integrates MolParser 1.5 for OCSR, achieving 88.6% accuracy on chemical structures while processing up to 20 pages per second.