In microbiology it is diagnostically useful to recognize various genera and species of bacteria. It can be achieved using computer-aided methods, which make the recognition processes more automatic and thus significantly reduce the time necessary for the classification. Moreover, in case of diagnostic uncertainty (the misleading similarity in shape or structure of bacterial cells), such methods can minimize the risk of incorrect recognition. In this article, we apply the state of the art method for texture analysis to classify genera and species of bacteria. This method uses deep Convolutional Neural Networks to obtain image descriptors, which are then encoded and classified with Support Vector Machine or Random Forest. To evaluate this approach and to make it comparable with other approaches, we provide a new dataset of images. DIBaS dataset (Digital Image of Bacterial Species) contains 660 images with 33 different genera and species of bacteria.
We build a general and highly applicable clustering theory, which we call cross-entropy clustering (shortly CEC) which joins advantages of classical kmeans (easy implementation and speed) with those of EM (affine invariance and ability to adapt to clusters of desired shapes). Moreover, contrary to k-means and EM, CEC finds the optimal number of clusters by automatically removing groups which carry no information.Although CEC, similarly like EM, can be build on an arbitrary family of densities, in the most important case of Gaussian CEC the division into clusters is affine invariant, while the numerical complexity is comparable to that of k-means.
We present a mechanism for detecting adversarial examples based on data representations taken from the hidden layers of the target network. For this purpose, we train individual autoencoders at intermediate layers of the target network. This allows us to describe the manifold of true data and, in consequence, decide whether a given example has the same characteristics as true data. It also gives us insight into the behavior of adversarial examples and their flow through the layers of a deep neural network. Experimental results show that our method outperforms the state of the art in supervised and unsupervised settings.Preprint. Under review.
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