Hybrid method for the chemical master equation. - Andreas Hellander; Per Lötstedt (J. Comput. Phys., 2007)

A Hierarchy of Approximations of the Master Equation Scaled by a Size Parameter. - Lars Ferm; Per Lötstedt; Andreas Hellander (J. Sci. Comput., 2008)

Simulation of Stochastic Reaction-Diffusion Processes on Unstructured Meshes. - Stefan Engblom; Lars Ferm; Andreas Hellander; Per Lötstedt (SIAM J. Sci. Comput., 2009)

CellMC - a multiplatform model compiler for the Cell Broadband Engine and x86. - Emmet Caulfield; Andreas Hellander (Bioinform., 2010)

An adaptive algorithm for simulation of stochastic reaction-diffusion processes. - Lars Ferm; Andreas Hellander; Per Lötstedt (J. Comput. Phys., 2010)

Incorporating Active Transport of Cellular Cargo in Stochastic Mesoscopic Models of Living Cells. - Andreas Hellander; Per Lötstedt (Multiscale Model. Simul., 2010)

Abstractions for Scaling eScience Applications to Distributed Computing Environments - A StratUm Integration Case Study in Molecular Systems Biology. - Per-Olov Östberg; Andreas Hellander; Brian Drawert; Erik Elmroth; Sverker Holmgren; Linda R. Petzold (BIOINFORMATICS, 2012)

Reducing Complexity in Management of eScience Computations. - Per-Olov Östberg; Andreas Hellander; Brian Drawert; Erik Elmroth; Sverker Holmgren; Linda R. Petzold (CCGRID, 2012)

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries. - Brian Drawert; Stefan Engblom; Andreas Hellander (BMC Syst. Biol., 2012)

Coupled Mesoscopic and Microscopic Simulation of Stochastic Reaction-Diffusion Processes in Mixed Dimensions. - Andreas Hellander; Stefan Hellander; Per Lötstedt (Multiscale Model. Simul., 2012)

Scientific Analysis by Queries in Extended SPARQL over a Scalable e-Science Data Store. - Andrej Andrejev; Salman Zubair Toor; Andreas Hellander; Sverker Holmgren; Tore Risch (e-Science, 2013)

Automatic and portable cloud deployment for scientific simulations. - Christopher B. Horuk; Geoffrey Douglas; Anand Gupta; Chandra Krintz; Benjamin B. Bales; Giovanni Bellesia; Brian Drawert; Rich Wolski; Linda R. Petzold; Andreas Hellander (HPCS, 2014)

Local error estimates for adaptive simulation of the reaction-diffusion master equation via operator splitting. - Andreas Hellander; Michael J. Lawson; Brian Drawert; Linda R. Petzold (J. Comput. Phys., 2014)

Mesoscopic Modeling of Stochastic Reaction-Diffusion Kinetics in the Subdiffusive Regime. - Emilie Blanc; Stefan Engblom; Andreas Hellander; Per Lötstedt (Multiscale Model. Simul., 2016)

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist. - Brian Drawert; Andreas Hellander; Benjamin B. Bales; Debjani Banerjee; Giovanni Bellesia; Bernie J. Daigle Jr.; Geoffrey Douglas; Mengyuan Gu; Anand Gupta; Stefan Hellander; Christopher B. Horuk; Dibyendu Nath; et al. (PLoS Comput. Biol., 2016)

MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME. - Brian Drawert; Michael Trogdon; Salman Zubair Toor; Linda R. Petzold; Andreas Hellander (SIAM J. Sci. Comput., 2016)

Analysis and Design of Jump Coefficients in Discrete Stochastic Diffusion Models. - Lina Meinecke; Stefan Engblom; Andreas Hellander; Per Lötstedt (SIAM J. Sci. Comput., 2016)

Cost-aware Application Development and Management using CLOUD-METRIC. - Alieu Jallow; Andreas Hellander; Salman Zubair Toor (CLOSER, 2017)

SNIC Science Cloud (SSC): A National-Scale Cloud Infrastructure for Swedish Academia. - Salman Zubair Toor; Mathias Lindberg; Ingemar Falman; Andreas Vallin; Olof Mohill; Pontus Freyhult; Linus Nilsson; Martin Agback; Lars Viklund; Henric Zazzik; Ola Spjuth; Marco Capuccini; et al. (eScience, 2017)

Surrogate assisted model reduction for stochastic biochemical reaction networks. - Prashant Singh; Andreas Hellander (WSC, 2017)

Robustness Analysis of Spatiotemporal Models in the Presence of Extrinsic Fluctuations. - Andreas Hellander; Jan Klosa; Per Lötstedt; Shev MacNamara (SIAM J. Appl. Math., 2017)

HarmonicIO: Scalable Data Stream Processing for Scientific Datasets. - Preechakorn Torruangwatthana; Håkan Wieslander; Ben Blamey; Andreas Hellander; Salman Zubair Toor (IEEE CLOUD, 2018)

Orchestral: A Lightweight Framework for Parallel Simulations of Cell-Cell Communication. - Adrien Coulier; Andreas Hellander (eScience, 2018)

Hyperparameter Optimization for Approximate Bayesian Computation. - Prashant Singh; Andreas Hellander (WSC, 2018)

BAMSI: a multi-cloud service for scalable distributed filtering of massive genome data. - Kristiina Ausmees; Aji John; Salman Zubair Toor; Andreas Hellander; Carl Nettelblad (BMC Bioinform., 2018)

Multi-Statistic Approximate Bayesian Computation with Multi-Armed Bandits. - Prashant Singh; Andreas Hellander (CoRR, 2018)

Apache Spark Streaming and HarmonicIO: A Performance and Architecture Comparison. - Ben Blamey; Andreas Hellander; Salman Zubair Toor (CoRR, 2018)

Apache Spark Streaming, Kafka and HarmonicIO: A Performance Benchmark and Architecture Comparison for Enterprise and Scientific Computing. - Ben Blamey; Andreas Hellander; Salman Toor (Bench, 2019)

Adapting the Secretary Hiring Problem for Optimal Hot-Cold Tier Placement Under Top-K Workloads. - Ben Blamey; Fredrik Wrede; Johan Karlsson; Andreas Hellander; Salman Toor (CCGRID, 2019)

Smart computational exploration of stochastic gene regulatory network models using human-in-the-loop semi-supervised learning. - Fredrik Wrede; Andreas Hellander (Bioinform., 2019)

Resource- and Message Size-Aware Scheduling of Stream Processing at the Edge with application to Realtime Microscopy. - Ben Blamey; Ida-Maria Sintorn; Andreas Hellander; Salman Toor (CoRR, 2019)

Smart Resource Management for Data Streaming using an Online Bin-packing Strategy. - Oliver Stein; Ben Blamey; Johan Karlsson; Alan Sabirsh; Ola Spjuth; Andreas Hellander; Salman Toor (IEEE BigData, 2020)

Epidemiological modeling in StochSS Live! - Richard M. Jiang 002; Bruno Jacob; Matthew Geiger; Sean Matthew; Bryan Rumsey; Prashant Singh; Fredrik Wrede; Tau-Mu Yi; Brian Drawert; Andreas Hellander; Linda R. Petzold (Bioinform., 2021)

Scalable machine learning-assisted model exploration and inference using Sciope. - Prashant Singh; Fredrik Wrede; Andreas Hellander (Bioinform., 2021)

Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators. - Richard M. Jiang 002; Fredrik Wrede; Prashant Singh; Andreas Hellander; Linda R. Petzold (BMC Bioinform., 2021)

Scalable federated machine learning with FEDn. - Morgan Ekmefjord; Addi Ait-Mlouk; Sadi Alawadi; Mattias Åkesson; Desislava Stoyanova; Ola Spjuth; Salman Toor; Andreas Hellander (CoRR, 2021)

Approaches for containerized scientific workflows in cloud environments with applications in life science. - Ola Spjuth; Marco Capuccini; Matteo Carone; Anders Larsson; Wesley Schaal; Jon Ander Novella; Oliver Stein; Morgan Ekmefjord; Paolo Di Tommaso; Evan W. Floden; Cédric Notredame; Pablo A. Moreno; et al. (F1000Research, 2021)

Scalable federated machine learning with FEDn. - Morgan Ekmefjord; Addi Ait-Mlouk; Sadi Alawadi; Mattias Åkesson; Prashant Singh; Ola Spjuth; Salman Toor; Andreas Hellander (CCGRID, 2022)

Robust and integrative Bayesian neural networks for likelihood-free parameter inference. - Fredrik Wrede; Robin Eriksson; Richard M. Jiang 002; Linda R. Petzold; Stefan Engblom; Andreas Hellander; Prashant Singh (IJCNN, 2022)

CBMOS: a GPU-enabled Python framework for the numerical study of center-based models. - Sonja Mathias; Adrien Coulier; Andreas Hellander (BMC Bioinform., 2022)

Efficient Hierarchical Storage Management Framework Empowered by Reinforcement Learning. - Tianru Zhang; Salman Toor; Andreas Hellander (CoRR, 2022)

FedQAS: Privacy-aware machine reading comprehension with federated learning. - Addi Ait-Mlouk; Sadi Alawadi; Salman Toor; Andreas Hellander (CoRR, 2022)

Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods. - Richard M. Jiang 002; Prashant Singh; Fredrik Wrede; Andreas Hellander; Linda R. Petzold (PLoS Comput. Biol., 2022)

Convolutional Neural Networks as Summary Statistics for Approximate Bayesian Computation. - Mattias Åkesson; Prashant Singh; Fredrik Wrede; Andreas Hellander (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation. - Adrien Coulier; Prashant Singh; Marc Sturrock; Andreas Hellander (PLoS Comput. Biol., 2022)

Efficient Hierarchical Storage Management Empowered by Reinforcement Learning Extended Abstract. - Tianru Zhang; Andreas Hellander; Salman Toor (ICDE, 2023)

Accelerating Fair Federated Learning: Adaptive Federated Adam. - Li Ju; Tianru Zhang; Salman Toor; Andreas Hellander (CoRR, 2023)

FedBot: Enhancing Privacy in Chatbots with Federated Learning. - Addi Ait-Mlouk; Sadi Alawadi; Salman Toor; Andreas Hellander (CoRR, 2023)

Efficient Hierarchical Storage Management Empowered by Reinforcement Learning. - Tianru Zhang; Andreas Hellander; Salman Toor (IEEE Trans. Knowl. Data Eng., 2023)

Contributions of cell behavior to geometric order in embryonic cartilage. - Sonja Mathias; Igor Adameyko; Andreas Hellander; Jochen Kursawe (PLoS Comput. Biol., 2023)

Variational Autoencoders for Efficient Simulation-Based Inference. - Mayank Nautiyal; Andrey Shternshis; Andreas Hellander; Prashant Singh (CoRR, 2024)

Data management of scientific applications in a reinforcement learning-based hierarchical storage system. - Tianru Zhang; Ankit Gupta 018; María Andreína Francisco Rodríguez; Ola Spjuth; Andreas Hellander; Salman Toor (Expert Syst. Appl., 2024)

Toward efficient resource utilization at edge nodes in federated learning. - Sadi Alawadi; Addi Ait-Mlouk; Salman Toor; Andreas Hellander (Prog. Artif. Intell., 2024)

ConDiSim: Conditional Diffusion Models for Simulation Based Inference. - Mayank Nautiyal; Andreas Hellander; Prashant Singh (CoRR, 2025)

Exploiting the Asymmetric Uncertainty Structure of Pre-trained VLMs on the Unit Hypersphere. - Li Ju; Max Andersson; Stina Fredriksson; Edward Glöckner; Andreas Hellander; Ekta Vats; Prashant Singh (CoRR, 2025)