The application of machine learning techniques to histopathology images enables advances in the field, providing valuable tools that can speed up and facilitate the diagnosis process. The classification of these images is a relevant aid for physicians who have to process a large number of images in long and repetitive tasks. This work proposes the adoption of metric learning that, beyond the task of classifying images, can provide additional information able to support the decision of the classification system. In particular, triplet networks have been employed to create a representation in the embedding space that gathers together images of the same class while tending to separate images with different labels. The obtained representation shows an evident separation of the classes with the possibility of evaluating the similarity and the dissimilarity among input images according to distance criteria. The model has been tested on the BreakHis dataset, a reference and largely used dataset that collects breast cancer images with eight pathology labels and four magnification levels. Our proposed classification model achieves relevant performance on the patient level, with the advantage of providing interpretable information for the obtained results, which represent a specific feature missed by the all the recent methodologies proposed for the same purpose.

The automatic analysis of histology images is an open research field where machine learning techniques and neural networks, especially deep architectures, are considered successful tools due to their abilities in image classification. This paper proposes a granular computing methodology for histopathological image classification. It is based on embedding tiles of histopathology images using deep metric learning, where a self-organizing map is adopted to generate the granular structure in this learned embedding space. The SOM enables the implementation of an explainable mechanism by visualizing a knowledge space that the experts can use to analyze and classify the new images. Additionally, it provides confidence in the classification results while highlighting each important image fragment, with the benefit of reducing the number of false negatives. An exemplary case is when an image detail is indicated, with small confidence, as malignant in an image globally classified as benign. Another implemented feature is the proposal of additional labelled image tiles sharing the same characteristics to specify the context of the output decision. The proposed system was tested using three histopathology image datasets, obtaining the accuracy of the state-of-the-art black-box methods based on deep learning neural networks. Differently from the methodologies proposed so far for the same purpose, this paper introduces a novel explainable method for medical image analysis where the advantages of the deep learning neural networks used to build the embedding space for the image tiles are combined with the intrinsic explainability of the granular process obtained using the clustering property of a self-organizing map.

Background: Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that nucleosomes are determined by the combined effects of several factors, including DNA sequence organization. Interestingly, the identification of nucleosomes on a genomic scale has been successfully performed by computational methods using DNA sequence as input data. Results: In this work, we propose CORENup, a deep learning model for nucleosome identification. CORENup processes a DNA sequence as input using one-hot representation and combines in a parallel fashion a fully convolutional neural network and a recurrent layer. These two parallel levels are devoted to catching both non periodic and periodic DNA string features. A dense layer is devoted to their combination to give a final classification. Conclusions: Results computed on public data sets of different organisms show that CORENup is a state of the art methodology for nucleosome positioning identification based on a Deep Neural Network architecture. The comparisons have been carried out using two groups of datasets, currently adopted by the best performing methods, and CORENup has shown top performance both in terms of classification metrics and elapsed computation time.

The new area ofLearned Data Structuresconsists of mixing Machine Learning techniques with those specific to Data Structures, with the purpose to achieve time/space gains in the performance of those latter. The perceived paradigm shift in computer architectures, that would favor the employment of graphics/tensor units over traditional central processing units, is one of the driving forces behind this new area. The advent of the corresponding branch-free programming paradigm would then favor the adoption of Neural Networks as the fundamental units of Classic Data Structures. This is the case of Learned Bloom Filters. The equally important field of Learned Indexes does not appear to make use of Neural Networks at all. In this paper, we offer a comparative experimental investigation regarding the potential uses of Neural Networks as a fundamental building block of Learned Indexes. Our results provide a solid and much-needed evaluation of the role Neural Networks can play in Learned Indexing. Based on our findings, we highlight the need for the creation of highly specialised Neural Networks customised to Learned Indexes. Because of the methodological significance of our findings and application of Learned Indexes in strategic domains, such as Computer Networks and Databases, care has been taken to make the presentation of our results accessible to the general audience of scientists and engineers working in Neural Networks and with no background about Learned Indexing.