Publications

You can also find my publications on my ORCiD profile.

Journal Articles

Modelling the impact of anthropogenic aerosols on CCN concentrations over a rural boreal forest environment

Published in Atmospheric Chemistry and Physics, 2026

We use a novel Lagrangian modelling framework to examine the origins and history of gas and aerosol components observed at the boreal forest measurement site SMEAR II, and their potential to act as CCN.

Recommended citation: Clusius, P., Baykara, M., Xavier, C., Zhou, P., Tyree, J., Foreback, B., Äijälä, M., Graeffe, F., Petäjä, T., Kulmala, M., Paasonen, P., Palmer, P. I., and Boy, M. (2026) Modelling the impact of anthropogenic aerosols on CCN concentrations over a rural boreal forest environment. Atmospheric Chemistry and Physics. 26, 1967–1992. Available from: doi:10.5194/acp-26-1967-2026.
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A decoupled, modular and scriptable architecture for tools to curate data platforms

Published in Bioinformatics, 2021

cmd-iaso is a decoupled, modular and scriptable curation tool built on top of the existing identifiers.org platform.

Recommended citation: Tyree, J. & Hermjakob, H. & Llinares, M. B. (2021) A decoupled, modular and scriptable architecture for tools to curate data platforms. Bioinformatics. btab233. Available from: doi:10.1093/bioinformatics/btab233.
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Conference Papers

χiplot: Web-First Visualisation Platform for Multidimensional Data

Published in Lecture Notes in Computer Science, 2023

χiplot is an HTML5-based system for interactive exploration of data and machine learning models.

Recommended citation: Tanaka, A., Tyree, J., Björklund, A., Mäkelä, J., and Puolamäki, K. (2023) χiplot: Web-First Visualisation Platform for Multidimensional Data. In: De Francisci Morales, G., Perlich, C., Ruchansky, N., Kourtellis, N., Baralis, E., Bonchi, F. (eds) Machine Learning and Knowledge Discovery in Databases: Applied Data Science and Demo Track. ECML PKDD 2023. Lecture Notes in Computer Science, 14175. Available from: doi:10.1007/978-3-031-43430-3_26.
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Theses

Prudent Response Surface Models: Exploring a Framework for Approximating Simulations with Confidence and Certainty

Published in University of Helsinki, 2023

The Icarus Response Surface Model architecture combines an out-of-distribution detector, a prediction model, and an uncertainty quantifier.

Recommended citation: Tyree, J. (2023) Prudent Response Surface Models: Exploring a Framework for Approximating Simulations with Confidence and Certainty. Master’s Thesis. Available from: URN:NBN:fi:hulib-202305151941.
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Communication-free and Parallel Simulation of Neutral Biodiversity Models

Published in Imperial College London, 2021

necsim-rust implements a novel communication-free algorithm for individual-based probabilistic neutral biodiversity simulations.

Recommended citation: Tyree, J. (2021) Communication-free and Parallel Simulation of Neutral Biodiversity Models. Master’s Thesis. Available from: doi:10.48550/arXiv.2108.05815.
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Technical Reports

ESiWACE3 Deliverable D3.3 - Report on the online version of the data sets

Published in Zenodo, 2024

This deliverable documents the development of an Online Laboratory for Data Compression in Climate Science and Meteorology and the publication of the data compression datasets that allow the testing of various compression methods for output of both weather and climate models.

Recommended citation: Faghih-Naini, S., Tyree, J., Yepes-Arbós, X., Peters-von Gehlen, K., Dueben, P., Järvinen, H. J. (2024) ESiWACE3 Deliverable D3.3 - Report on the online version of the data sets. Available from: doi:10.5281/zenodo.14622238.
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Preprints

ClimateBenchPress (v1.0): A Benchmark for Lossy Compression of Climate Data

Published in EGUsphere, 2026

We address this gap by presenting ClimateBenchPress, a benchmark suite for lossy compression of climate data, which defines both data sets and evaluation techniques.

Recommended citation: Reichelt, T., Tyree, J., Klöwer, M., Dueben, P., Lawrence, B. N., Baker, A. H., Faghih-Naini, S., Hoefler, T., and Stier, P. (2026). ClimateBenchPress (v1.0): A Benchmark for Lossy Compression of Climate Data. EGUsphere [preprint]. Available from: doi:10.5194/egusphere-2026-60.
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phepy: Visual Benchmarks and Improvements for Out-of-Distribution Detectors

Published in arXiv, 2023

phepy is a benchmark for out-of-distribution detection, which includes three novel and easily-visualisable toy examples.

Recommended citation: Tyree, J., Rupp, A., Clusius, P. S., Boy, M. H. (2023) phepy: Visual Benchmarks and Improvements for Out-of-Distribution Detectors. Preprint. Available from: doi:10.48550/arXiv.2503.05169.
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