Andreas Hellander
Senior Lecturer/Associate Professor at Department of Information Technology; Division of Scientific Computing
- Telephone:
- +46 18 471 29 72
- Mobile phone:
- +46 70 395 04 47, +46 73 469 70 10
- E-mail:
- andreas.hellander@it.uu.se
- Visiting address:
- Hus 10, Regementsvägen 10
- Postal address:
- Box 337
751 05 UPPSALA
- Academic merits:
- Docent
Short presentation
Hellander lab on Computational Science and Engineering: http://hellanderlab.research.it.uu.se
Keywords
- computational systems biology
- applied cloud computing
- escience
- computational science and engineering
Biography
Andreas Hellander is Associate Professor of Scientific Computing at Uppsala University where he leads a research group on computational science and engineering at the Division of Scientific Computing, Department of Information Technology.
His research centers around efficient and flexible computational methods and scientific software for computational experimentation in particular in the life sciences. Focus areas are computational systems biology, distributed (cloud) and data-intensive computing and multiscale modelling of stochastic reaction diffusion kinetics.
Research
Andreas Hellander is Associate Professor of Scientific Computing at Uppsala University where he leads a research group on computational science and engineering at the Division of Scientific Computing, Department of Information Technology.
His research centers around efficient and flexible computational methods and scientific software for computational experimentation in particular in the life sciences. Focus areas are computational systems biology, distributed (cloud) and data-intensive computing and multiscale modelling of stochastic reaction diffusion kinetics.

Publications
Recent publications
Part of Expert systems with applications, p. 121443-121443, 2024
Accelerating Fair Federated Learning: Adaptive Federated Adam
Part of IEEE Transactions on Machine Learning in Communications and Networking, p. 1017-1032, 2024
- DOI for Accelerating Fair Federated Learning: Adaptive Federated Adam
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Part of Artificial Intelligence in the Life Sciences, 2024
- DOI for Federated learning for predicting compound mechanism of action based on image-data from cell painting
- Download full text (pdf) of Federated learning for predicting compound mechanism of action based on image-data from cell painting
Part of Expert systems with applications, 2024
- DOI for Data management of scientific applications in a reinforcement learning-based hierarchical storage system
- Download full text (pdf) of Data management of scientific applications in a reinforcement learning-based hierarchical storage system
Toward efficient resource utilization at edge nodes in federated learning
Part of Progress in Artificial Intelligence, p. 101-117, 2024
- DOI for Toward efficient resource utilization at edge nodes in federated learning
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All publications
Articles in journal
Part of Expert systems with applications, p. 121443-121443, 2024
Accelerating Fair Federated Learning: Adaptive Federated Adam
Part of IEEE Transactions on Machine Learning in Communications and Networking, p. 1017-1032, 2024
- DOI for Accelerating Fair Federated Learning: Adaptive Federated Adam
- Download full text (pdf) of Accelerating Fair Federated Learning: Adaptive Federated Adam
Part of Artificial Intelligence in the Life Sciences, 2024
- DOI for Federated learning for predicting compound mechanism of action based on image-data from cell painting
- Download full text (pdf) of Federated learning for predicting compound mechanism of action based on image-data from cell painting
Part of Expert systems with applications, 2024
- DOI for Data management of scientific applications in a reinforcement learning-based hierarchical storage system
- Download full text (pdf) of Data management of scientific applications in a reinforcement learning-based hierarchical storage system
Toward efficient resource utilization at edge nodes in federated learning
Part of Progress in Artificial Intelligence, p. 101-117, 2024
- DOI for Toward efficient resource utilization at edge nodes in federated learning
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Efficient Hierarchical Storage Management Empowered by Reinforcement Learning
Part of IEEE Transactions on Knowledge and Data Engineering, p. 5780-5793, 2023
Contributions of cell behavior to geometric order in embryonic cartilage
Part of PloS Computational Biology, 2023
- DOI for Contributions of cell behavior to geometric order in embryonic cartilage
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CBMOS: a GPU-enabled Python framework for the numerical study of center-based models
Part of BMC Bioinformatics, 2022
- DOI for CBMOS: a GPU-enabled Python framework for the numerical study of center-based models
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FedQAS: Privacy-Aware Machine Reading Comprehension with Federated Learning
Part of Applied Sciences, 2022
- DOI for FedQAS: Privacy-Aware Machine Reading Comprehension with Federated Learning
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Living in darkness: Exploring adaptation of Proteus anguinus in 3 dimensions by X-ray imaging
Part of GigaScience, 2022
- DOI for Living in darkness: Exploring adaptation of Proteus anguinus in 3 dimensions by X-ray imaging
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Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods
Part of PloS Computational Biology, 2022
- DOI for Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods
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Convolutional Neural Networks as Summary Statistics for Approximate Bayesian Computation
Part of IEEE/ACM Transactions on Computational Biology & Bioinformatics, p. 3353-3365, 2022
Part of Nature Communications, 2022
- DOI for Altered developmental programs and oriented cell divisions lead to bulky bones during salamander limb regeneration
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Part of PloS Computational Biology, 2022
- DOI for Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation
- Download full text (pdf) of Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation
Surface flow for colonial integration in reef-building corals
Part of Current Biology, p. 2596-2609, 2022
- DOI for Surface flow for colonial integration in reef-building corals
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Part of F1000 Research, p. 513-513, 2021
Part of Journal of Chemical Physics, 2021
- DOI for A multiscale compartment-based model of stochastic gene regulatory networks using hitting-time analysis
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Part of BMC Bioinformatics, 2021
- DOI for Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators
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Epidemiological modeling in StochSS Live!
Part of Bioinformatics, p. 2787-2788, 2021
Scalable machine learning-assisted model exploration and inference using Sciope
Part of Bioinformatics, p. 279-281, 2021
- DOI for Scalable machine learning-assisted model exploration and inference using Sciope
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The machine learning life cycle and the cloud: implications for drug discovery.
Part of Expert Opinion on Drug Discovery, p. 1071-1079, 2021
Deep-learning models for lipid nanoparticle-based drug delivery
Part of Nanomedicine, p. 1097-1110, 2021
Part of GigaScience, p. 1-14, 2021
- DOI for Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit
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Impact of Force Function Formulations on the Numerical Simulation of Centre-Based Models.
Part of Bulletin of Mathematical Biology, 2020
- DOI for Impact of Force Function Formulations on the Numerical Simulation of Centre-Based Models.
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Hierarchical algorithm for the reaction–diffusion master equation
Part of Journal of Chemical Physics, 2020
Part of Mathematical Biosciences, 2020
Part of Bioinformatics, p. 5199-5206, 2019
A 3D multiscale model to explore the role of EGFR overexpression in tumourigenesis
Part of Bulletin of Mathematical Biology, p. 2323-2344, 2019
BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data
Part of BMC Bioinformatics, 2018
Robustness analysis of spatiotemporal models in the presence of extrinsic fluctuations
Part of SIAM Journal on Applied Mathematics, p. 1157-1183, 2017
Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning
Part of Journal of Chemical Physics, 2017
- DOI for Mesoscopic-microscopic spatial stochastic simulation with automatic system partitioning
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Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage
Part of eLIFE, 2017
GillesPy: A Python package for stochastic model building and simulation
Part of IEEE Life Sciences Letters, p. 35-38, 2016
Stochastic Simulation Service: Bridging the gap between the computational expert and the biologist
Part of PloS Computational Biology, 2016
Part of SIAM Journal on Scientific Computing, 2016
Mesoscopic modeling of stochastic reaction–diffusion kinetics in the subdiffusive regime
Part of Multiscale Modeling & simulation, p. 668-707, 2016
Analysis and design of jump coefficients in discrete stochastic diffusion models
Part of SIAM Journal on Scientific Computing, 2016
- DOI for Analysis and design of jump coefficients in discrete stochastic diffusion models
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Analysis of neural crest-derived clones reveals novel aspects of facial development
Part of Science Advances, 2016
Reaction rates for mesoscopic reaction-diffusion kinetics
Part of Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 2015
- DOI for Reaction rates for mesoscopic reaction-diffusion kinetics
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Accuracy of the Michaelis–Menten approximation when analysing effects of molecular noise
Part of Journal of the Royal Society Interface, 2015
- DOI for Accuracy of the Michaelis–Menten approximation when analysing effects of molecular noise
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Part of Journal of Computational Physics, p. 89-100, 2014
Part of Multiscale Modeling & simulation, p. 585-611, 2012
Part of BMC Systems Biology, 2012
Reaction-diffusion master equation in the microscopic limit
Part of Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 2012
CellMC: a multiplatform model compiler for the Cell Broadband Engine and x86
Part of Bioinformatics, p. 426-428, 2010
Incorporating active transport of cellular cargo in stochastic mesoscopic models of living cells
Part of Multiscale Modeling & simulation, p. 1691-1714, 2010
An adaptive algorithm for simulation of stochastic reaction-diffusion processes
Part of Journal of Computational Physics, p. 343-360, 2010
Simulation of stochastic reaction-diffusion processes on unstructured meshes
Part of SIAM Journal on Scientific Computing, p. 1774-1797, 2009
Sparse grids and hybrid methods for the chemical master equation
Part of BIT Numerical Mathematics, p. 265-283, 2008
Part of Journal of Chemical Physics, 2008
A hierarchy of approximations of the master equation scaled by a size parameter
Part of Journal of Scientific Computing, p. 127-151, 2008
Hybrid method for the chemical master equation
Part of Journal of Computational Physics, p. 100-122, 2007
Chapters in book
Multiscale simulation of stochastic reaction–diffusion networks
Part of Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology, p. 55-79, Springer, 2017
Comprehensive doctoral thesis
Comprehensive licentiate thesis
Conference papers
Efficient Hierarchical Storage Management Empowered by Reinforcement Learning Extended Abstract
p. 3869-3870, 2023
Robust and integrative Bayesian neural networks for likelihood-free parameter inference
Part of 2022 International Joint Conference on Neural Networks (IJCNN), p. 1-10, 2022
Scalable federated machine learning with FEDn
Part of 2022 22nd IEEE/ACM International Symposium on Cluster, Cloud and Internet Computing (CCGrid 2022), p. 555-564, 2022
Smart Resource Management for Data Streaming using an Online Bin-packing Strategy
Part of 2020 IEEE International Conference on Big Data (Big Data), p. 2207-2216, 2020
Part of Benchmarking, Measuring, and Optimizing, p. 335-347, 2020
Adapting the secretary hiring problem for optimal hot–cold tier placement under top-K workloads
Part of Proc. 19th International Symposium on Cluster, Cloud, and Grid Computing, p. 576-583, 2019
Orchestral: a lightweight framework for parallel simulations of cell–cell communication
Part of Proc. 14th International Conference on e-Science, p. 168-176, 2018
Hyperparameter optimization for approximate Bayesian computation
Part of Proc. 50th Winter Simulation Conference, p. 1718-1729, 2018
HarmonicIO: Scalable data stream processing for scientific datasets
Part of Proc. 11th International Conference on Cloud Computing, p. 879-882, 2018
Part of Proc. 32nd European Simulation and Modelling Conference, p. 22-27, 2018
Cost-aware application development and management using CLOUD-METRIC
Part of Proc. 7th International Conference on Cloud Computing and Services Science, p. 515-522, 2017
Surrogate assisted model reduction for stochastic biochemical reaction networks
Part of Proc. 49th Winter Simulation Conference, p. 1773-1783, 2017
SNIC Science Cloud (SSC): A national-scale cloud infrastructure for Swedish academia
Part of Proc. 13th International Conference on e-Science, p. 219-227, 2017
Automatic and portable cloud deployment for scientific simulations
Part of Proc. 12th International Conference on High Performance Computing and Simulation, p. 374-381, 2014
Scientific analysis by queries in extended SPARQL over a scalable e-Science data store
Part of Proc. 9th International Conference on e-Science, p. 98-106, 2013
Part of Proc. 3rd International Conference on Bioinformatics Models, Methods and Algorithms, p. 290-294, 2012
Reducing complexity in management of eScience computations
Part of Proc. 12th International Symposium on Cluster, Cloud and Grid Computing, p. 845-852, 2012
Adaptive stochastic hybrid simulation of biochemical reaction-diffusion models
Part of Proc. 3rd International Conference on Foundations of Systems Biology in Engineering, p. 4, 2009
Manuscripts (preprints)
Reports
2011
Incorporating active transport of cellular cargo in stochastic mesoscopic models of living cells
2010
An adaptive algorithm for simulation of stochastic reaction-diffusion processes
2009
Simulation of stochastic reaction-diffusion processes on unstructured meshes
2008
2007
A hierarchy of approximations of the master equation scaled by a size parameter
2007
Hybrid method for the chemical master equation
2006