Evidence map›Paper›PMID 35668480›Full record

ArticleJournal of cheminformatics2022

RanDepict: Random chemical structure depiction generator.

Henning Otto Brinkhaus, Kohulan Rajan, Achim Zielesny, Christoph Steinbeck

Abstract read
In one paragraph

Article in Journal of cheminformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Review
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4 · The record

Corrections and comments

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5 · Who and what money

Authors and funding

4 authors.

Henning Otto BrinkhausInstitute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany.
Kohulan RajanInstitute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany.
Achim ZielesnyInstitute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, D-45665, Recklinghausen, Germany.
Christoph SteinbeckInstitute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Lessingstr. 8, 07743, Jena, Germany. christoph.steinbeck@uni-jena.de.

Funding

ChemBioSys CRC1127
6 · The paper itself

Abstract

The development of deep learning-based optical chemical structure recognition (OCSR) systems has led to a need for datasets of chemical structure depictions. The diversity of the features in the training data is an important factor for the generation of deep learning systems that generalise well and are not overfit to a specific type of input. In the case of chemical structure depictions, these features are defined by the depiction parameters such as bond length, line thickness, label font style and many others. Here we present RanDepict, a toolkit for the creation of diverse sets of chemical structure depictions. The diversity of the image features is generated by making use of all available depiction parameters in the depiction functionalities of the CDK, RDKit, and Indigo. Furthermore, there is the option to enhance and augment the image with features such as curved arrows, chemical labels around the structure, or other kinds of distortions. Using depiction feature fingerprints, RanDepict ensures diversely picked image features. Here, the depiction and augmentation features are summarised in binary vectors and the MaxMin algorithm is used to pick diverse samples out of all valid options. By making all resources described herein publicly available, we hope to contribute to the development of deep learning-based OCSR systems.

Indexed as

CDKChemical image depictionDepiction generator image augmentationIndigoOCSRRDKit

Identifiers

PMID35668480
PMCPMC9169273

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.