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In this work, we analyze if it is possible to distinguish between differentclones of the same bacteria species (Klebsiella pneumoniae) based only onmicroscopic images. It is a challenging task, previously considered impossibledue to the high clones similarity. For this purpose, we apply a multi-stepalgorithm with attention-based multiple instance learning. Except for obtainingaccuracy at the level of 0.9, we introduce extensive interpretability based onCellProfiler and persistence homology, increasing the understandability andtrust in the model.

Classifying bacteria clones using attention-based deep multiple instance learning interpreted by persistence homology