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Volume 4 Issue 9, September 2022

Predicting chemical reactivity in a digital lab

The outcome of organic reactions can be hard to predict without comprehensive knowledge of organic chemistry and known reactions. To speed up the development of new synthesis pathways (cover image), Chen and Jung use graph neural networks to extract a low number of general templates that can describe a large number of known organic reactions.

See Shuan Chen & Yousung Jung

Image: Shuan Chen and Yousung Jung. Cover design: Thomas Phillips

Editorial

  • The public release of ‘Stable Diffusion’, a high-quality image generation tool, sets new standards in open-source AI development and raises new questions.

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Comment & Opinion

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News & Views

  • In animals, both body and neural control have co-evolved to be adaptable to the environment. While a newborn foal learns quickly how to use its legs, traditional robotic approaches require careful engineering and calibration for stable walking robots. Bio-inspired robotics aims to bridge this gap.

    • Francisco J. Valero-Cuevas
    • Andrew Erwin
    News & Views
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Research

  • PROTACs can directly and selectively degrade proteins, which opens promising applications in the design of novel drugs, but designing effective PROTACs is a hard challenge due to the complexity of pharmacokinetics. Zheng et al. use a deep generative model to create likely candidates and screen them further to identify a novel BRD4-degrading PROTAC.

    • Shuangjia Zheng
    • Youhai Tan
    • Yuedong Yang
    Article
  • To understand reactions in organic chemistry, ideally simple rules would help us predict the outcome of new reactions, but in reality such rules are not easily identified. Chen and Jung extract generalized reaction templates from data and show that they can be used in graph neural networks to predict the outcome of reactions and, despite simplification, still represent a high percentage of existing reactions.

    • Shuan Chen
    • Yousung Jung
    Article
  • Producing high-quality 3D refractive index maps from 2D intensity-only measurements is a long-standing objective in computational microscopy, with many applications involving the visualization of cellular and subcellular structures. A new method can reconstruct high-contrast and artefact-free images by employing the neural fields technique, which can learn a continuous 3D representation using a neural network that maps spatial coordinates to the refractive index values.

    • Renhao Liu
    • Yu Sun
    • Ulugbek S. Kamilov
    Article
  • The performance of machine learning models is usually compared via the mean value of a selected performance measure such as the area under the receiver operating characteristic curve on a specific benchmark data set. However, this measure, its mean value or even relative differences between models do not provide a good prediction of whether the results can translate to other data sets. Gosiewska and colleagues present here a comparison based on Elo ranking, which offers a probabilistic interpretation of how much better one model is than another.

    • Alicja Gosiewska
    • Katarzyna Woźnica
    • Przemysław Biecek
    Article
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