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Volume 4 Issue 8, August 2022

Uncovering cellular metabolism with generative learning

Complex metabolic behaviour in cells can be captured with dynamic kinetic models. Such models are challenging to develop owing to the lack of knowledge about the characteristic kinetic parameter values that govern the cellular physiology of organisms. A new generative deep learning framework called REKINDLE has been developed by Subham Choudhury et al. to efficiently parameterize large-scale kinetic models, which helps to navigate the complex physiologies of various types of cellular organisms. Transfer learning in the low data regime allows REKINDLE to significantly expand the potential applications of kinetic modelling.

See Subham Choudhury et al.

Image: Subham Choudhury, EPFL. Cover design: Thomas Phillips

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Reviews

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Research

  • Targeted drug delivery is an exciting application of nanorobotics, but directing particles in the blood stream to the right location and in sufficient number is challenging. Gu and colleagues have developed a microtubule scaffold with embedded micromagnets that allows cargo, such as drug particles, to be transported in microvascular networks with precision and speed.

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    • Shadi Albarqouni
    Article
  • Kinetic models of metabolism capture time-dependent behaviour of cellular states and provide valuable insights into cellular physiology, but, due to the lack of experimental data, traditional kinetic modelling can be unreliable and computationally inefficient. A generative framework based on deep learning called REKINDLE can efficiently parameterize large-scale kinetic models, enabling new opportunities to study cellular metabolic behaviour.

    • Subham Choudhury
    • Michael Moret
    • Ljubisa Miskovic
    Article Open Access
  • Finding stable radical compounds for redox flow batteries is a challenging molecular design task. Sowndarya et al. combine an AlphaZero-based framework with a surrogate objective function trained on quantum chemistry simulations to generate suitable radical candidates that are stable. The approach promises to contribute to the development of low-cost, reliable energy storage technologies.

    • Shree Sowndarya S. V.
    • Jeffrey N. Law
    • Peter C. St. John
    Article Open Access
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