Prediction of gene essentiality using machine learning and genome-scale metabolic models

IFAC-PapersOnLine 55:23 (2022)

Authors:

Lilli J Freischem, Mauricio Barahona, Diego A Oyarzún

Abstract:

The identification of essential genes, i.e. those that impair cell survival when deleted, requires large growth assays of knock-out strains. The complexity and cost of such experiments has triggered a growing interest in computational methods for prediction of gene essentiality. In the case of metabolic genes, Flux Balance Analysis (FBA) is widely employed to predict essentiality under the assumption that cells maximize their growth rate. However, this approach assumes that knock-out strains optimize the same objectives as the wild-type, which excludes cases in which deletions cause large physiological changes to meet other objectives for survival. Here, we resolve this limitation with a novel machine learning approach that predicts essentiality directly from wild-type flux distributions. We first project the wild-type FBA solution onto a mass flow graph, a digraph with reactions as nodes and edge weights proportional to the mass transfer between reactions, and then train binary classifiers on the connectivity of graph nodes. We demonstrate the efficacy of this approach using the most complete metabolic model of Escherichia coli, achieving near state-of-the art prediction accuracy for essential genes. Our approach suggests that wild-type FBA solutions contain enough information to predict essentiality, without the need to assume optimality of deletion strains.

The fractal nature of clouds in global storm-resolving models

Geophysical Research Letters American Geophysical Union 48:23 (2021) e2021GL095746

Authors:

Hannah M Christensen, Oliver GA Driver

Abstract:

Clouds in observations are fractals: they show self-similarity across scales ranging from one to 1000 km. This includes individual storms and large-scale cloud structures typical of organised convection. It is not known whether global storm-resolving models reproduce the observed fractal scaling laws for clouds and organised convection. We compute the fractal dimension of clouds using Himawari satellite data and compare this to global storm-resolving model simulations completed as part of the DYAMOND intercomparison project. We find cloud fields in these simulations are indeed fractal, and reproduce the observed fractal dimension to within 10%. We find the fractal dimension is sensitive to the choice of boundary layer parametrisation scheme used in each model simulation, and not to the convection parametrisation as might have been expected.

Opportunities and challenges for machine learning in weather and climate modelling: hard, medium and soft AI.

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences 379:2194 (2021) ARTN 20200083

Authors:

Matthew Chantry, Hannah Christensen, Peter Dueben, Tim Palmer

Abstract:

In September 2019, a workshop was held to highlight the growing area of applying machine learning techniques to improve weather and climate prediction. In this introductory piece, we outline the motivations, opportunities and challenges ahead in this exciting avenue of research. This article is part of the theme issue 'Machine learning for weather and climate modelling'.

Scale‐aware space‐time stochastic parameterization of subgrid‐scale velocity enhancement of sea surface fluxes

Journal of Advances in Modeling Earth Systems American Geophysical Union (AGU) (2021)

Authors:

Julie Bessac, Hannah M Christensen, Kota Endo, Adam H Monahan, Nils Weitzel

Impact of stochastic physics and model resolution on the simulation of tropical cyclones in climate GCMs

Journal of Climate American Meteorological Society 34:11 (2021) 4315-4341

Authors:

Pl Vidale, K Hodges, B Vanniere, P Davini, M Roberts, Kristian Strommen, A Weisheimer, E Plesca, S Corti

Abstract:

The role of model resolution in simulating geophysical vortices with the characteristics of realistic Tropical Cyclones (TCs) is well established. The push for increasing resolution continues, with General Circulation Models (GCMs) starting to use sub-10km grid spacing. In the same context it has been suggested that the use of Stochastic Physics (SP) may act as a surrogate for high resolution, providing some of the benefits at a fraction of the cost. Either technique can reduce model uncertainty, and enhance reliability, by providing a more dynamic environment for initial synoptic disturbances to be spawned and to grow into TCs. We present results from a systematic comparison of the role of model resolution and SP in the simulation of TCs, using EC-Earth simulations from project Climate-SPHINX, in large ensemble mode, spanning five different resolutions. All tropical cyclonic systems, including TCs, were tracked explicitly. As in previous studies, the number of simulated TCs increases with the use of higher resolution, but SP further enhances TC frequencies by ≈ 30%, in a strikingly similar way. The use of SP is beneficial for removing systematic climate biases, albeit not consistently so for interannual variability; conversely, the use of SP improves the simulation of the seasonal cycle of TC frequency. An investigation of the mechanisms behind this response indicates that SP generates both higher TC (and TC seed) genesis rates, and more suitable environmental conditions, enabling a more efficient transition of TC seeds into TCs. These results were confirmed by the use of equivalent simulations with the HadGEM3-GC31 GCM.