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  1. Article ; Online: Using machine learning as a surrogate model for agent-based simulations.

    Angione, Claudio / Silverman, Eric / Yaneske, Elisabeth

    PloS one

    2022  Volume 17, Issue 2, Page(s) e0263150

    Abstract: In this proof-of-concept work, we evaluate the performance of multiple machine-learning methods as surrogate models for use in the analysis of agent-based models (ABMs). Analysing agent-based modelling outputs can be challenging, as the relationships ... ...

    Abstract In this proof-of-concept work, we evaluate the performance of multiple machine-learning methods as surrogate models for use in the analysis of agent-based models (ABMs). Analysing agent-based modelling outputs can be challenging, as the relationships between input parameters can be non-linear or even chaotic even in relatively simple models, and each model run can require significant CPU time. Surrogate modelling, in which a statistical model of the ABM is constructed to facilitate detailed model analyses, has been proposed as an alternative to computationally costly Monte Carlo methods. Here we compare multiple machine-learning methods for ABM surrogate modelling in order to determine the approaches best suited as a surrogate for modelling the complex behaviour of ABMs. Our results suggest that, in most scenarios, artificial neural networks (ANNs) and gradient-boosted trees outperform Gaussian process surrogates, currently the most commonly used method for the surrogate modelling of complex computational models. ANNs produced the most accurate model replications in scenarios with high numbers of model runs, although training times were longer than the other methods. We propose that agent-based modelling would benefit from using machine-learning methods for surrogate modelling, as this can facilitate more robust sensitivity analyses for the models while also reducing CPU time consumption when calibrating and analysing the simulation.
    MeSH term(s) Neural Networks, Computer
    Language English
    Publishing date 2022-02-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0263150
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Using machine learning as a surrogate model for agent-based simulations.

    Claudio Angione / Eric Silverman / Elisabeth Yaneske

    PLoS ONE, Vol 17, Iss 2, p e

    2022  Volume 0263150

    Abstract: In this proof-of-concept work, we evaluate the performance of multiple machine-learning methods as surrogate models for use in the analysis of agent-based models (ABMs). Analysing agent-based modelling outputs can be challenging, as the relationships ... ...

    Abstract In this proof-of-concept work, we evaluate the performance of multiple machine-learning methods as surrogate models for use in the analysis of agent-based models (ABMs). Analysing agent-based modelling outputs can be challenging, as the relationships between input parameters can be non-linear or even chaotic even in relatively simple models, and each model run can require significant CPU time. Surrogate modelling, in which a statistical model of the ABM is constructed to facilitate detailed model analyses, has been proposed as an alternative to computationally costly Monte Carlo methods. Here we compare multiple machine-learning methods for ABM surrogate modelling in order to determine the approaches best suited as a surrogate for modelling the complex behaviour of ABMs. Our results suggest that, in most scenarios, artificial neural networks (ANNs) and gradient-boosted trees outperform Gaussian process surrogates, currently the most commonly used method for the surrogate modelling of complex computational models. ANNs produced the most accurate model replications in scenarios with high numbers of model runs, although training times were longer than the other methods. We propose that agent-based modelling would benefit from using machine-learning methods for surrogate modelling, as this can facilitate more robust sensitivity analyses for the models while also reducing CPU time consumption when calibrating and analysing the simulation.
    Keywords Medicine ; R ; Science ; Q
    Subject code 006
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: The poly-omics of ageing through individual-based metabolic modelling.

    Yaneske, Elisabeth / Angione, Claudio

    BMC bioinformatics

    2018  Volume 19, Issue Suppl 14, Page(s) 415

    Abstract: Background: Ageing can be classified in two different ways, chronological ageing and biological ageing. While chronological age is a measure of the time that has passed since birth, biological (also known as transcriptomic) ageing is defined by how time ...

    Abstract Background: Ageing can be classified in two different ways, chronological ageing and biological ageing. While chronological age is a measure of the time that has passed since birth, biological (also known as transcriptomic) ageing is defined by how time and the environment affect an individual in comparison to other individuals of the same chronological age. Recent research studies have shown that transcriptomic age is associated with certain genes, and that each of those genes has an effect size. Using these effect sizes we can calculate the transcriptomic age of an individual from their age-associated gene expression levels. The limitation of this approach is that it does not consider how these changes in gene expression affect the metabolism of individuals and hence their observable cellular phenotype.
    Results: We propose a method based on poly-omic constraint-based models and machine learning in order to further the understanding of transcriptomic ageing. We use normalised CD4 T-cell gene expression data from peripheral blood mononuclear cells in 499 healthy individuals to create individual metabolic models. These models are then combined with a transcriptomic age predictor and chronological age to provide new insights into the differences between transcriptomic and chronological ageing. As a result, we propose a novel metabolic age predictor.
    Conclusions: We show that our poly-omic predictors provide a more detailed analysis of transcriptomic ageing compared to gene-based approaches, and represent a basis for furthering our knowledge of the ageing mechanisms in human cells.
    MeSH term(s) Adult ; Aging/genetics ; Aging/metabolism ; Cluster Analysis ; Female ; Genomics ; Humans ; Male ; Middle Aged ; Models, Biological ; Principal Component Analysis ; Regression Analysis ; T-Lymphocytes/metabolism ; Young Adult
    Language English
    Publishing date 2018-11-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-018-2383-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Genome-scale metabolic modelling of SARS-CoV-2 in cancer cells reveals an increased shift to glycolytic energy production.

    Yaneske, Elisabeth / Zampieri, Guido / Bertoldi, Loris / Benvenuto, Giuseppe / Angione, Claudio

    FEBS letters

    2021  Volume 595, Issue 18, Page(s) 2350–2365

    Abstract: Cancer is considered a high-risk condition for severe illness resulting from COVID-19. The interaction between severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and human metabolism is key to elucidating the risk posed by COVID-19 for cancer ... ...

    Abstract Cancer is considered a high-risk condition for severe illness resulting from COVID-19. The interaction between severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and human metabolism is key to elucidating the risk posed by COVID-19 for cancer patients and identifying effective treatments, yet it is largely uncharacterised on a mechanistic level. We present a genome-scale map of short-term metabolic alterations triggered by SARS-CoV-2 infection of cancer cells. Through transcriptomic- and proteomic-informed genome-scale metabolic modelling, we characterise the role of RNA and fatty acid biosynthesis in conjunction with a rewiring in energy production pathways and enhanced cytokine secretion. These findings link together complementary aspects of viral invasion of cancer cells, while providing mechanistic insights that can inform the development of treatment strategies.
    MeSH term(s) COVID-19/complications ; COVID-19/metabolism ; Cell Line, Tumor ; Genome, Human ; Glycolysis ; Humans ; Models, Biological ; Neoplasms/complications ; Neoplasms/metabolism ; Proteomics ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/metabolism
    Language English
    Publishing date 2021-09-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 212746-5
    ISSN 1873-3468 ; 0014-5793
    ISSN (online) 1873-3468
    ISSN 0014-5793
    DOI 10.1002/1873-3468.14180
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Machine and deep learning meet genome-scale metabolic modeling.

    Zampieri, Guido / Vijayakumar, Supreeta / Yaneske, Elisabeth / Angione, Claudio

    PLoS computational biology

    2019  Volume 15, Issue 7, Page(s) e1007084

    Abstract: Omic data analysis is steadily growing as a driver of basic and applied molecular biology research. Core to the interpretation of complex and heterogeneous biological phenotypes are computational approaches in the fields of statistics and machine ... ...

    Abstract Omic data analysis is steadily growing as a driver of basic and applied molecular biology research. Core to the interpretation of complex and heterogeneous biological phenotypes are computational approaches in the fields of statistics and machine learning. In parallel, constraint-based metabolic modeling has established itself as the main tool to investigate large-scale relationships between genotype, phenotype, and environment. The development and application of these methodological frameworks have occurred independently for the most part, whereas the potential of their integration for biological, biomedical, and biotechnological research is less known. Here, we describe how machine learning and constraint-based modeling can be combined, reviewing recent works at the intersection of both domains and discussing the mathematical and practical aspects involved. We overlap systematic classifications from both frameworks, making them accessible to nonexperts. Finally, we delineate potential future scenarios, propose new joint theoretical frameworks, and suggest concrete points of investigation for this joint subfield. A multiview approach merging experimental and knowledge-driven omic data through machine learning methods can incorporate key mechanistic information in an otherwise biologically-agnostic learning process.
    MeSH term(s) Computational Biology/methods ; Deep Learning ; Genome ; Genotype ; Machine Learning ; Metabolic Networks and Pathways ; Phenotype
    Language English
    Publishing date 2019-07-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1007084
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Genome‐scale metabolic modelling of SARS‐CoV‐2 in cancer cells reveals an increased shift to glycolytic energy production

    Yaneske, Elisabeth / Zampieri, Guido / Bertoldi, Loris / Benvenuto, Giuseppe / Angione, Claudio

    FEBS letters. 2021 Sept., v. 595, no. 18

    2021  

    Abstract: Cancer is considered a high‐risk condition for severe illness resulting from COVID‐19. The interaction between severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) and human metabolism is key to elucidating the risk posed by COVID‐19 for cancer ... ...

    Abstract Cancer is considered a high‐risk condition for severe illness resulting from COVID‐19. The interaction between severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) and human metabolism is key to elucidating the risk posed by COVID‐19 for cancer patients and identifying effective treatments, yet it is largely uncharacterised on a mechanistic level. We present a genome‐scale map of short‐term metabolic alterations triggered by SARS‐CoV‐2 infection of cancer cells. Through transcriptomic‐ and proteomic‐informed genome‐scale metabolic modelling, we characterise the role of RNA and fatty acid biosynthesis in conjunction with a rewiring in energy production pathways and enhanced cytokine secretion. These findings link together complementary aspects of viral invasion of cancer cells, while providing mechanistic insights that can inform the development of treatment strategies.
    Keywords COVID-19 infection ; RNA ; Severe acute respiratory syndrome coronavirus 2 ; biosynthesis ; cytokines ; disease severity ; energy ; fatty acids ; glycolysis ; humans ; risk ; secretion
    Language English
    Dates of publication 2021-09
    Size p. 2350-2365.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ZDB-ID 212746-5
    ISSN 1873-3468 ; 0014-5793
    ISSN (online) 1873-3468
    ISSN 0014-5793
    DOI 10.1002/1873-3468.14180
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: The poly-omics of ageing through individual-based metabolic modelling

    Elisabeth Yaneske / Claudio Angione

    BMC Bioinformatics, Vol 19, Iss S14, Pp 83-

    2018  Volume 96

    Abstract: Abstract Background Ageing can be classified in two different ways, chronological ageing and biological ageing. While chronological age is a measure of the time that has passed since birth, biological (also known as transcriptomic) ageing is defined by ... ...

    Abstract Abstract Background Ageing can be classified in two different ways, chronological ageing and biological ageing. While chronological age is a measure of the time that has passed since birth, biological (also known as transcriptomic) ageing is defined by how time and the environment affect an individual in comparison to other individuals of the same chronological age. Recent research studies have shown that transcriptomic age is associated with certain genes, and that each of those genes has an effect size. Using these effect sizes we can calculate the transcriptomic age of an individual from their age-associated gene expression levels. The limitation of this approach is that it does not consider how these changes in gene expression affect the metabolism of individuals and hence their observable cellular phenotype. Results We propose a method based on poly-omic constraint-based models and machine learning in order to further the understanding of transcriptomic ageing. We use normalised CD4 T-cell gene expression data from peripheral blood mononuclear cells in 499 healthy individuals to create individual metabolic models. These models are then combined with a transcriptomic age predictor and chronological age to provide new insights into the differences between transcriptomic and chronological ageing. As a result, we propose a novel metabolic age predictor. Conclusions We show that our poly-omic predictors provide a more detailed analysis of transcriptomic ageing compared to gene-based approaches, and represent a basis for furthering our knowledge of the ageing mechanisms in human cells.
    Keywords Ageing ; Biological age ; Metabolic age ; Metabolic modelling ; Flux balance analysis ; Poly-omics ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2018-11-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Book ; Online: Using Machine Learning to Emulate Agent-Based Simulations

    Angione, Claudio / Silverman, Eric / Yaneske, Elisabeth

    2020  

    Abstract: In this proof-of-concept work, we evaluate the performance of multiple machine-learning methods as statistical emulators for use in the analysis of agent-based models (ABMs). Analysing ABM outputs can be challenging, as the relationships between input ... ...

    Abstract In this proof-of-concept work, we evaluate the performance of multiple machine-learning methods as statistical emulators for use in the analysis of agent-based models (ABMs). Analysing ABM outputs can be challenging, as the relationships between input parameters can be non-linear or even chaotic even in relatively simple models, and each model run can require significant CPU time. Statistical emulation, in which a statistical model of the ABM is constructed to facilitate detailed model analyses, has been proposed as an alternative to computationally costly Monte Carlo methods. Here we compare multiple machine-learning methods for ABM emulation in order to determine the approaches best suited to emulating the complex behaviour of ABMs. Our results suggest that, in most scenarios, artificial neural networks (ANNs) and gradient-boosted trees outperform Gaussian process emulators, currently the most commonly used method for the emulation of complex computational models. ANNs produced the most accurate model replications in scenarios with high numbers of model runs, although training times were longer than the other methods. We propose that agent-based modelling would benefit from using machine-learning methods for emulation, as this can facilitate more robust sensitivity analyses for the models while also reducing CPU time consumption when calibrating and analysing the simulation.
    Keywords Computer Science - Multiagent Systems ; Computer Science - Machine Learning ; 68U20 ; I.6.4 ; I.2.6
    Subject code 006
    Publishing date 2020-05-05
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Machine and deep learning meet genome-scale metabolic modeling.

    Guido Zampieri / Supreeta Vijayakumar / Elisabeth Yaneske / Claudio Angione

    PLoS Computational Biology, Vol 15, Iss 7, p e

    2019  Volume 1007084

    Abstract: Omic data analysis is steadily growing as a driver of basic and applied molecular biology research. Core to the interpretation of complex and heterogeneous biological phenotypes are computational approaches in the fields of statistics and machine ... ...

    Abstract Omic data analysis is steadily growing as a driver of basic and applied molecular biology research. Core to the interpretation of complex and heterogeneous biological phenotypes are computational approaches in the fields of statistics and machine learning. In parallel, constraint-based metabolic modeling has established itself as the main tool to investigate large-scale relationships between genotype, phenotype, and environment. The development and application of these methodological frameworks have occurred independently for the most part, whereas the potential of their integration for biological, biomedical, and biotechnological research is less known. Here, we describe how machine learning and constraint-based modeling can be combined, reviewing recent works at the intersection of both domains and discussing the mathematical and practical aspects involved. We overlap systematic classifications from both frameworks, making them accessible to nonexperts. Finally, we delineate potential future scenarios, propose new joint theoretical frameworks, and suggest concrete points of investigation for this joint subfield. A multiview approach merging experimental and knowledge-driven omic data through machine learning methods can incorporate key mechanistic information in an otherwise biologically-agnostic learning process.
    Keywords Biology (General) ; QH301-705.5
    Subject code 006
    Language English
    Publishing date 2019-07-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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