Institut für biologische und chemische Informatik
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Advancements in hand-drawn chemical structure recognition through an enhanced DECIMER architecture
(2024)
Accurate recognition of hand-drawn chemical structures is crucial for digitising hand-written chemical information in traditional laboratory notebooks or facilitating stylus-based structure entry on tablets or smartphones. However, the inherent variability in hand-drawn structures poses challenges for existing Optical Chemical Structure Recognition (OCSR) software. To address this, we present an enhanced Deep lEarning for Chemical ImagE Recognition (DECIMER) architecture that leverages a combination of Convolutional Neural Networks (CNNs) and Transformers to improve the recognition of hand-drawn chemical structures. The model incorporates an EfficientNetV2 CNN encoder that extracts features from hand-drawn images, followed by a Transformer decoder that converts the extracted features into Simplified Molecular Input Line Entry System (SMILES) strings. Our models were trained using synthetic hand-drawn images generated by RanDepict, a tool for depicting chemical structures with different style elements. A benchmark was performed using a real-world dataset of hand-drawn chemical structures to evaluate the model's performance. The results indicate that our improved DECIMER architecture exhibits a significantly enhanced recognition accuracy compared to other approaches.
Advancements in Hand-Drawn Chemical Structure Recognition through an Enhanced DECIMER Architecture
(2024)
Accurate recognition of hand-drawn chemical structures is crucial for digitising hand-written chemical information found in traditional laboratory notebooks or for facilitating stylus-based structure entry on tablets or smartphones. However, the inherent variability in hand-drawn structures poses challenges for existing Optical Chemical Structure Recognition (OCSR) software. To address this, we present an enhanced Deep lEarning for Chemical ImagE Recognition (DECIMER) architecture that leverages a combination of Convolutional Neural Networks (CNNs) and Transformers to improve the recognition of hand-drawn chemical structures. The model incorporates an EfficientNetV2 CNN encoder that extracts features from hand-drawn images, followed by a Transformer decoder that converts the extracted features into Simplified Molecular Input Line Entry System (SMILES) strings. Our models were trained using synthetic hand-drawn images generated by RanDepict, a tool for depicting chemical structures with different style elements. To evaluate the model's performance, a benchmark was performed using a real-world dataset of hand-drawn chemical structures. The results indicate that our improved DECIMER architecture exhibits a significantly enhanced recognition accuracy compared to other approaches.
An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer-monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory-Huggins parameters and isotropic particle-particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLS-AA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach.
The translation of images of chemical structures into machine-readable representations of the depicted molecules is known as optical chemical structure recognition (OCSR). There has been a lot of progress over the last three decades in this field, but the development of systems for the recognition of complex hand-drawn structure depictions is still at the beginning. Currently, there is no data for the systematic evaluation of OCSR methods on hand-drawn structures available. Here we present DECIMER - Hand-drawn molecule images, a standardised, openly available benchmark dataset of 5088 hand-drawn depictions of diversely picked chemical structures. Every structure depiction in the dataset is mapped to a machine-readable representation of the underlying molecule. The dataset is openly available and published under the CC-BY 4.0 licence which applies very few limitations. We hope that it will contribute to the further development of the field.
The number of publications describing chemical structures has increased steadily over the last decades. However, the majority of published chemical information is currently not available in machine-readable form in public databases. It remains a challenge to automate the process of information extraction in a way that requires less manual intervention - especially the mining of chemical structure depictions. As an open-source platform that leverages recent advancements in deep learning, computer vision, and natural language processing, DECIMER.ai (Deep lEarning for Chemical IMagE Recognition) strives to automatically segment, classify, and translate chemical structure depictions from the printed literature. The segmentation and classification tools are the only openly available packages of their kind, and the optical chemical structure recognition (OCSR) core application yields outstanding performance on all benchmark datasets. The source code, the trained models and the datasets developed in this work have been published under permissive licences. An instance of the DECIMER web application is available at https://decimer.ai.
The translation of images of chemical structures into machine-readable representations of the depicted molecules is known as optical chemical structure recognition (OCSR). There has been a lot of progress over the last three decades in this field, but the development of systems for the recognition of complex hand-drawn structure depictions is still at the beginning. Currently, there is no data for the systematic evaluation of OCSR methods on hand-drawn structures available. Here we present DECIMER — Hand-drawn molecule images, a standardised, openly available benchmark dataset of 5088 hand-drawn depictions of diversely picked chemical structures. Every structure depiction in the dataset is mapped to a machine-readable representation of the underlying molecule. The dataset is openly available and published under the CC-BY 4.0 licence which applies very few limitations. We hope that it will contribute to the further development of the field.
Description and Analysis of Glycosidic Residues in the Largest Open Natural Products Database
(2021)
Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics (DPD)
Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics (DPD) with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated “all-in-one” simulation systems like MFsim.
Since Jdpd version 1.6.1.0 Jdpd is available in a (basic) double-precision version and a (derived) single-precision version (= JdpdSP) for all numerical calculations, where the single precision version needs about half the memory of the double precision version.
Jdpd uses the Apache Commons Math and Apache Commons RNG libraries and is published as open source under the GNU General Public License version 3. This repository comprises the Java bytecode libraries (including the Apache Commons Math and RNG libraries), the Javadoc HTML documentation and the Netbeans source code packages including Unit tests.
Jdpd has been described in the scientific literature (the final manuscript 2018 - van den Broek - Jdpd - Final Manucsript.pdf is added to the repository) and used for DPD studies (see references below).
See text file JdpdVersionHistory.txt for a version history with more detailed information.
From https://github.com/zielesny/Jdpd:
Jdpd - An open Java Simulation Kernel for Molecular Fragment Dissipative Particle Dynamics (DPD)
Jdpd is an open Java simulation kernel for Molecular Fragment Dissipative Particle Dynamics (DPD) with parallelizable force calculation, efficient caching options and fast property calculations. It is characterized by an interface and factory-pattern driven design for simple code changes and may help to avoid problems of polyglot programming. Detailed input/output communication, parallelization and process control as well as internal logging capabilities for debugging purposes are supported. The kernel may be utilized in different simulation environments ranging from flexible scripting solutions up to fully integrated “all-in-one” simulation systems like MFsim.
Since Jdpd version 1.6.1.0 Jdpd is available in a (basic) double-precision version and a (derived) single-precision version (= JdpdSP) for all numerical calculations, where the single precision version needs about half the memory of the double precision version.
Jdpd uses the Apache Commons Math and Apache Commons RNG libraries and is published as open source under the GNU General Public License version 3. This repository comprises the Java bytecode libraries (including the Apache Commons Math and RNG libraries), the Javadoc HTML documentation and the Netbeans source code packages including Unit tests.
Jdpd has been described in the scientific literature (the final manuscript 2018 - van den Broek - Jdpd - Final Manucsript.pdf is added to the repository) and used for DPD studies (see references below).
See text file JdpdVersionHistory.txt for a version history with more detailed information.