Preliminary diagnosis of fungal infections can rely on microscopic examination. However, in many cases, it does not allow unambiguous identification of the species due to their visual similarity. Therefore, it is usually necessary to use additional biochemical tests. That involves additional costs and extends the identification process up to 10 days. Such a delay in the implementation of targeted therapy may be grave in consequence as the mortality rate for immunosuppressed patients is high. In this paper, we apply a machine learning approach based on deep neural networks and bag-of-words to classify microscopic images of various fungi species. Our approach makes the last stage of biochemical identification redundant, shortening the identification process by 2-3 days, and reducing the cost of the diagnosis.

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Multiple Instance Learning (MIL) is weakly supervised learning, which assumes that there is only one label provided for the entire bag of instances. As such, it appears in many problems of medical image analysis, like the whole-slide images classification of biopsy. Most recently, MIL was also applied to deep architectures by introducing the aggregation operator, which focuses on crucial instances of a bag. In this paper, we enrich this idea with the self-attention mechanism to take into account dependencies across the instances. We conduct several experiments and show that our method with various types of kernels increases the accuracy, especially in the case of non-standard MIL assumptions. This is of importance for real-word medical problems, which usually satisfy presence-based or threshold-based assumptions.