Department Systems Analysis, Integrated Assessment and Modelling



We test a big data workflow for understanding and predicting plankton dynamics using monitoring data. This is a timely case study, given the current streaming of plankton images
from automated monitoring, which need to be classified and analysed. Automated
classification of plankton pictures is challenging , due to the scarcity of labeled data for
training classifiers and the uneven frequency of detection among species. We propose a new
dataset construction and classification strategy based on semi-supervised, active, and
ensemble learning.
The outcoming classifiers are be used to create a large database of taxa abundances, their
features, and environmental conditions as a function of time. With this dataset, we test a
novel data- and modeling-oriented approach to cope with measurement choices, in such a
way that the modeling potential of the dataset is maximized. The whole workflow of the
proposal, from dataset construction and classification to data-oriented sampling, is explicitly
devised in order to be applicable to different kinds of environmental studies.



Dr. Marco Baity Jesi Group Leader (he/him) Tel. +41 58 765 5793 Send Mail
Marta Reyes Research Technician Tel. +41 58 765 6725 Send Mail


Kyathanahally, S. P.; Hardeman, T.; Reyes, M.; Merz, E.; Bulas, T.; Brun, P.; Pomati, F.; Baity-Jesi, M. (2022) Ensembles of data-efficient vision transformers as a new paradigm for automated classification in ecology, Scientific Reports, 12, 18590 (11 pp.), doi:10.1038/s41598-022-21910-0, Institutional Repository
Kyathanahally, S. P.; Hardeman, T.; Merz, E.; Bulas, T.; Reyes, M.; Isles, P.; Pomati, F.; Baity-Jesi, M. (2021) Deep learning classification of Lake Zooplankton, Frontiers in Microbiology, 12, 746297 (13 pp.), doi:10.3389/fmicb.2021.746297, Institutional Repository
Merz, E.; Kozakiewicz, T.; Reyes, M.; Ebi, C.; Isles, P.; Baity-Jesi, M.; Roberts, P.; Jaffe, J. S.; Dennis, S. R.; Hardeman, T.; Stevens, N.; Lorimer, T.; Pomati, F. (2021) Underwater dual-magnification imaging for automated lake plankton monitoring, Water Research, 203, 117524 (12 pp.), doi:10.1016/j.watres.2021.117524, Institutional Repository


Dr. Marco Baity Jesi Group Leader (he/him) Tel. +41 58 765 5793 Send Mail