Publications

Publications from ISCL PIs and members.

2022

Mays F AL-Naday, Martin J Reed, Vlad Dobre, Salman Toor, Bruno Volckaert and Filip De Turck (2023) Service-based Federated Deep Reinforcement Learning for Anomaly Detection in Fog Ecosystems, 26th Conference on Innovation in Clouds, Internet and Networks and Workshops (ICIN) (Link)

Adrien Coulier, Prashant Singh, Marc Sturrock and Andreas Hellander (2022) Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation, PLOS Computational Biology (to appear). (bioRxiv preprint)

Markéta Kaucká, Alberto Joven Araus, Marketa Tesarova, Joshua Currie, Johan Boström, Michaela Kavkova, Julian Petersen, Zeyu Yao, Anass Bouchnita, Andreas Hellander, Tomáš Zikmund, Ahmed Elewa, Phillip Newton, Ji-Feng Fei, Andrei Chagin, Kaj Fried, Elly Tanaka, Jozef Kaiser, Andras Simon, and Igor Adameyko (2022), Altered developmental programs and oriented cell divisions lead to bulky bones during salamander limb regeneration, Nature Communications (to appear)

Thibault Bouderlique, Julian Petersen, Louis Faure, Daniel Abed-Navandi, Anass Bouchnita, Benjamin Mueller, Murtazo Nazarov, Lukas Englmaier, Marketa Tesarova, Pedro R. Frade, Tomas Zikmund, Till Koehne, Jozef Kaiser, Kaj Fried, Christian Wild, Olga Pantos, Andreas Hellander, John Bythell, Igor Adameyko (2022), Surface flow for colonial integration in reef-building corals, Current Biology, 2022.

Markéta Tesařová, Lucia Mancini, Edgardo Mauri, Gregor Aljančič, Magdalena Năpăruş-Aljančič, Rok Kostanjšek, Lilijana Bizjak Mali, Tomáš Zikmund, Markéta Kaucká, Federica Papi, Jana Goyens, Anass Bouchnita, Andreas Hellander, Igor Adameyko, Jozef Kaiser, Living in darkness: Exploring adaptation of Proteus anguinus in 3 dimensions by X-ray imaging, GigaScience, Volume 11, 2022, giac030, https://doi.org/10.1093/gigascience/giac030

Tianru Zhang, Salman Toor, Andreas Hellander (2022), Efficient Hierarchical Storage Management Framework Empowered by Reinforcement Learning, in IEEE Transactions on Knowledge and Data Engineering, doi: 10.1109/TKDE.2022.3176753 (ArXiv preprint)

Addi Ait-Mlouk, Sadi Alawadi, Salman Toor, Andreas Hellander (2022), FedQAS: Privacy-aware machine reading comprehension with federated learning, Applied Sciences, 12(6), 3130 (ArXiv preprint)

Richard Jiang, Prashant Singh, Fredrik Wrede, Andreas Hellander, Linda Petzold (2022) Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods, PLOS Computational Biology, 18(1): e1009830 .

2021

Li Ju, Prashant Singh and Salman Toor (2022), Proactive Autoscaling for Edge Computing Systems with Kubernetes, 14th IEEE/ACM International Conference on Utility and Cloud Computing UCC 2021 (ArXiv preprint)

O. Javed, W. Binder and S. Toor. The Good and the Bad: Understanding the Quality of Contrainer Security Vulnerability Detection Tools. (ArXiv preprint) . Accepted in the 5th International Conference on Cloud and Big Data Computing.

Felix Morsbach and Salman Toor (2021), DecFL: An Ubiquitous Decentralized Model Training Protocol and Framework Empowered by Blockchain, BSCI ’21: Proceedings of the 3rd ACM International Symposium on Blockchain and Secure Critical Infrastructure.

Ola Spjuth, Jens Frid, Andreas Hellander (2021), The Machine Learning Life Cycle and the Cloud: Implications for Drug Discovery, Expert Opinion on Drug Discovery, 2021 Sep;16(9):1071-1079.

Sonja Mathias, Adrien Coulier and Andreas Hellander (2021), CBMOS: a GPU-enabled Python framework for the numerical study of center-based models, BMC Bioinformatics (to appear) (bioRxiv preprint)

Fredrik Wrede, Robin Eriksson, Richard Jiang, Linda Petzold, Stefan Engblom, Andreas Hellander, Prashant Singh (2021), Robust and integrative Bayesian neural networks for likelihood-free parameter inference, IEEE International Joint Conference on Neural Networks (IJCNN 2022) (to apper) (ArXiv preprint)

Harrison PJ, Wieslander H, Sabirsh A,  Karlsson J, Malmsjö V, Hellander A, Wählby C,  Spjuth O. (2021) Deep learning models for lipid-nanoparticle-based drug delivery, Nanomedicine, Vol 16 No. 13.

Richard Jiang, Bruno Jacob, Matthew Geiger, Sean Matthew, Bryan Rumsey, Prashant Singh, Fredrik Wrede, Tau-Mu Yi, Brian Drawert, Andreas Hellander, Linda Petzold (2021) Epidemiological modeling in StochSS Live!, 2021, Bioinformatics btab061

Morgan Ekmefjord, Addi Ait-Mlouk, Sadi Alawadi, Mattias Åkesson, Prashant Singh, Ola Spjuth, Salman Toor, Andreas Hellander (2021) Scalable federated learning with FEDn, to appear in the 2022 IEEE/ACM International Conference on Cluster, Cloud and Grid Computing (CCGrid), (ArXiv preprint)

Ben Blamey, Ida-Maria Sintorn, Andres Hellander and Salman Toor (2021) Resource- and Message Size-Aware Scheduling of Stream Processing at the Edge with application to Realtime Microscopy. (ArXiv preprint).

Adrien Coulier, Stefan Hellander and Andreas Hellander (2021), A multiscale compartment-based model of stochastic gene regulatory networks using hitting-time analysis, J. Chem. Phys. 154, 184105.

2020

Richard Jiang, Fredrik Wrede, Prashant Singh, Andreas Hellander and Linda R Petzold (2021), Accelerated Regression-Based Summary Statistic for Discrete Stochastic Systems via Approximate Simulations, BMC Bioinformatics, 22, Article number: 339 .

Mattias Åkesson, Prashant Singh, Fredrik Wrede, Andreas Hellander, Convolutional Neural Networks as Summary Statistics for Approximate Bayesian Computation, IEEE/ACM Transactions on Computational Biology and Bioinformatics, doi: 10.1109/TCBB.2021.3108695 ArXiv preprint.

Oliver Stein, Ben Blamey, Johan Karlsson, Alan Sabirsh, Ola Spjuth, Andreas Hellander, Salman Toor (2020) Smart Resource Management for Data Streaming using an Online Bin-packing Strategy, 2020 IEEE International Conference on Big Data (Big Data), Atlanta, GA, USA, 2020, pp. 2207-2216 ArXiv preprint.

Ben Blamey, Salman Toor, Martin Dahlö, Håkan Wieslander, Philip J Harrison, Ida-Maria Sintorn, Alan Sabirsh, Carolina Wählby, Ola Spjuth, Andreas Hellander, Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit, Gigascience 10(3) BioRxiv preprint.

S. Mathias, A. Coulier, A. Bouchnita, A. Hellander (2020), Impact of force functions on the numerical simulation of centre-based models, Bulletin of Mathematical Biology 82, 132. BioRxiv preprint.

A. Bouchnita, V. Volpert, M.J. Koury, A. Hellander (2020) A multiscale model to design therapeutic strategies that overcome drug resistance in multiple myeloma, Mathematical Biosciences, 319, pp. 108293.

2019

B. Blamey, I-M. Sintorn, A. Hellander, S. Toor (2019) Resource- and Message Size-Aware Scheduling of Stream Processing at the Edge with application to Real-time Microscopy ArXiv preprint: https://arxiv.org/abs/1912.09088  Dataset

B. Blamey, A. Hellander, and S. Toor, Apache Spark Streaming, Kafka and HarmonicIO: A Performance Benchmark and Architecture Comparison for Enterprise and Scientific Computing, in Bench’19, Denver, Colorado, USA, 2019. ArXiv preprint

S. Hellander and A. Hellander (2019) Hierarchical Reaction-Diffusion Master Equation, J. Chem. Phys, 152(3) pp. 034104.  ArXiv preprint

A. Bouchnita, S. Hellander, A. Hellander (2019),   A 3D Multiscale Model to Explore the Role of EGFR Overexpression in Tumourigenesis, Bull. Math. Biol. 81(7):2323-2344

B. Blamey, F. Wrede, J. Karlsson, A. Hellander, S. Toor (2019), Adapting The Secretary Hiring Problem for Optimal Hot-Cold Tier Placement under Top-K Workloads, in 19th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID). ArXiv preprint.

F. Wrede and  A. Hellander (2019), Smart computational exploration of stochastic gene regulatory network models using human-in-the-loop semi-supervised learning, Bioinformatics btz420.  

2018

A. Coulier and A. Hellander (2018), Orchestral: a lightweight framework for parallel simulations of cell-cell communication, in IEEE 14th International Conference on e-Science.

P. Singh and A. Hellander (2018), Hyperparameter Optimization for Approximate Bayesian Computation, Proceedings of the Winter Simulation Conference 2018,  pp. 1718-1729.

P. Singh, E. Vats and A. Hast (2018), Learning surrogate models of document image quality metrics for automated document image processing, I Proc. 13th International Workshop on Document Analysis Systems.

P. Torruangwatthana, H. Wieslander, B. Blamey, A. Hellander and S. Toor (2018), HarmonicIO: Scalable data stream processing for scientific datasets, In. proc. 2018 IEEE 11th International Conference on Cloud Computing (CLOUD)

K. Ausmees, A. John, S. Toor, A. Hellander  and C. Nettelblad (2017), BAMSI: A multi-cloud service for scalable distributed filtering of massive genome data,  BMC Bioinformatics 19, Article number: 240.

2017

E. Vats, A. Hast and P. Singh (2017), Automatic document image binarization using Bayesian optimization, I Proc. 4th International Workshop on Historical Document Imaging and Processing, New York: ACM Press. 89-94

S. Hellander,  A. Hellander and L. Petzold (2017), Mesocopic-microscopic spatial stochastic simulation with automatic system partitioning, J. Chem. Phys. 147, 234101.

S. Engblom,  A. Hellander and P. Lötstedt (2017), Multiscale simulation of stochastic reaction–diffusion networks, In: Stochastic Processes, Multiscale Modeling, and Numerical Methods for Computational Cellular Biology, Springer, 2017, 55-79 p.

S. Toor, M. Lindberg, I. Fällman, A. Vallin, O. Mohill, P. Freyhult, L. Nilsson, M. Agback, L. Viklund, H. Zazzi, O. Spjuth, M. Capuccini, J. Moller, D. Murtagh and A. Hellander (2017).  SNIC Science Cloud (SSC): A National-scale Cloud Infrastructure for Swedish Academia, Proc. of the 13th IEEE international conference on eScience, 2017.

P. Singh and A. Hellander (2017), ’Surrogate assisted model reduction for stochastic biochemical reaction networks’, I Proc. 49th Winter Simulation Conference, Piscataway, NJ: IEEE. 1773-1783

Marketa Kaucka, Tomas Zikmund, Marketa Tesarova, Daniel Gyllborg, Andreas Hellander, Josef Jaros, Jozef Kaiser, Julian Petersen, Bara Szarowska, Phillip T. Newton, Vyacheslav Dyachuk, Lei Li, Hong Qian, Anne-Sofie Johansson, Yuji Mishina, Joshua D. Currie, Elly M. Tanaka, Alek Erickson, Andrew Dudley, Hjalmar Brismar , Paul Southam, Enrico Coen, Min Chen, Lee S. Weinstein, Ales Hampl, Ernest Arenas, Andrei S. Chagin, Kaj Fried, Igor Adameyko (2017), Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage, eLife 2017;6:e25902.

Alieu Jallow, Andreas Hellander and Salman Toor (2017), Cost-aware Application Development and Management using CLOUD-METRIC, In Proceedings of the 7th International Conference on Cloud Computing and Services Science – Volume 1: CLOSER, ISBN 978-989-758-243-1, pages 515-522. DOI: 10.5220/0006307505150522.

J. H. Abel, B. Drawert, A. Hellander, and L. R. Petzold (2017). GillesPy: A Python package for stochastic model building and simulation, IEEE Life Science Letters PP(99)

A. Hellander, J. Klosa, P. Lötstedt and S. MacNamara (2017) Robustness analysis of spatiotemporal models in the presence of extrinsic fluctuations, SIAM J. Appl. Math., 77(4), 1157–1183.

2016

2015

2014

2013

2012

2011

2010

2009

2008