Mini-batch optimization enables training of ODE models on large-scale datasets
Published 2022 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Mini-batch optimization enables training of ODE models on large-scale datasets
Authors
Keywords
-
Journal
Nature Communications
Volume 13, Issue 1, Pages -
Publisher
Springer Science and Business Media LLC
Online
2022-01-10
DOI
10.1038/s41467-021-27374-6
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- PEtab—Interoperable specification of parameter estimation problems in systems biology
- (2021) Leonard Schmiester et al. PLoS Computational Biology
- On Nonconvex Optimization for Machine Learning
- (2021) Chi Jin et al. JOURNAL OF THE ACM
- AMICI: high-performance sensitivity analysis for large ordinary differential equation models
- (2021) Fabian Fröhlich et al. BIOINFORMATICS
- K-FIT: An accelerated kinetic parameterization algorithm using steady-state fluxomic data
- (2020) Saratram Gopalakrishnan et al. METABOLIC ENGINEERING
- CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy
- (2020) Bo Yuan et al. Cell Systems
- Benchmark Problems for Dynamic Modeling of Intracellular Processes
- (2019) Helge Hass et al. BIOINFORMATICS
- A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae
- (2019) Ulrike Münzner et al. Nature Communications
- Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens
- (2019) Fiona M. Behan et al. NATURE
- Hierarchical optimization for the efficient parametrization of ODE models
- (2018) Carolin Loos et al. BIOINFORMATICS
- A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens
- (2018) Mehdi Bouhaddou et al. PLoS Computational Biology
- Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression
- (2018) Philippe Lucarelli et al. Cell Systems
- Benchmarking optimization methods for parameter estimation in large kinetic models
- (2018) Alejandro F Villaverde et al. BIOINFORMATICS
- Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
- (2017) David Henriques et al. PLoS Computational Biology
- Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
- (2017) Fabian Fröhlich et al. PLoS Computational Biology
- Identification of Nascent Memory CD8 T Cells and Modeling of Their Ontogeny
- (2017) Fabien Crauste et al. Cell Systems
- Minimizing finite sums with the stochastic average gradient
- (2016) Mark Schmidt et al. MATHEMATICAL PROGRAMMING
- Suppression of IGF-I signals in neural stem cells enhances neurogenesis and olfactory function during aging
- (2015) Zayna Chaker et al. AGING CELL
- Perturbation biology nominates upstream–downstream drug combinations in RAF inhibitor resistant melanoma cells
- (2015) Anil Korkut et al. eLife
- A community effort to assess and improve drug sensitivity prediction algorithms
- (2014) James C Costello et al. NATURE BIOTECHNOLOGY
- Efficient gradient computation for dynamical models
- (2014) B. Sengupta et al. NEUROIMAGE
- Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model
- (2013) Cihan Oguz et al. BMC Systems Biology
- The Regulation of Cell Size
- (2013) Alison C. Lloyd CELL
- Lessons Learned from Quantitative Dynamical Modeling in Systems Biology
- (2013) Andreas Raue et al. PLoS One
- The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
- (2012) Jordi Barretina et al. NATURE
- Comprehensive molecular portraits of human breast tumours
- (2012) Daniel C. Koboldt et al. NATURE
- Total kinetic analysis reveals how combinatorial methylation patterns are established on lysines 27 and 36 of histone H3
- (2012) Y. Zheng et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Measuring and Modeling Apoptosis in Single Cells
- (2011) Sabrina L. Spencer et al. CELL
- Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range
- (2011) J. Bachmann et al. Molecular Systems Biology
- Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics
- (2010) K. A. Fujita et al. Science Signaling
- Input–output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data
- (2009) William W Chen et al. Molecular Systems Biology
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExplorePublish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn More