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Dottorando presso: Dipartimento di Ingegneria "Enzo Ferrari"

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2021 - A Cone Beam Computed Tomography Annotation Tool for Automatic Detection of the Inferior Alveolar Nerve Canal [Relazione in Atti di Convegno]
Mercadante, Cristian; Cipriano, Marco; Bolelli, Federico; Pollastri, Federico; Di Bartolomeo, Mattia; Anesi, Alexandre; Grana, Costantino

In recent years, deep learning has been employed in several medical fields, achieving impressive results. Unfortunately, these algorithms require a huge amount of annotated data to ensure the correct learning process. When dealing with medical imaging, collecting and annotating data can be cumbersome and expensive. This is mainly related to the nature of data, often three-dimensional, and to the need for well-trained expert technicians. In maxillofacial imagery, recent works have been focused on the detection of the Inferior Alveolar Nerve (IAN), since its position is of great relevance for avoiding severe injuries during surgery operations such as third molar extraction or implant installation. In this work, we introduce a novel tool for analyzing and labeling the alveolar nerve from Cone Beam Computed Tomography (CBCT) 3D volumes.

2021 - A Deep Analysis on High Resolution Dermoscopic Image Classification [Articolo su rivista]
Pollastri, Federico; Parreño, Mario; Maroñas, Juan; Bolelli, Federico; Paredes, Roberto; Ramos, Daniel; Grana, Costantino

Convolutional Neural Networks (CNNs) have been broadly employed in dermoscopic image analysis, mainly as a result of the large amount of data gathered by the International Skin Imaging Collaboration (ISIC). Like in many other medical imaging domains, state-of-the-art methods take advantage of architectures developed for other tasks, frequently assuming full transferability between enormous sets of natural images (eg{} ImageNet) and dermoscopic images, which is not always the case. With this paper we provide a comprehensive analysis on the effectiveness of state-of-the-art deep learning techniques when applied to dermoscopic image analysis. In order to achieve this goal, we consider several CNNs architectures and analyze how their performance is affected by the size of the network, image resolution, data augmentation process, amount of available data, and model calibration. Moreover, taking advantage of the analysis performed, we design a novel ensemble method to further increase the classification accuracy. The proposed solution achieved the third best result in the 2019 official ISIC challenge, with an accuracy of 0.593.

2021 - Confidence Calibration for Deep Renal Biopsy Immunofluorescence Image Classification [Relazione in Atti di Convegno]
Pollastri, Federico; Maroñas, Juan; Bolelli, Federico; Ligabue, Giulia; Paredes, Roberto; Magistroni, Riccardo; Grana, Costantino

With this work we tackle immunofluorescence classification in renal biopsy, employing state-of-the-art Convolutional Neural Networks. In this setting, the aim of the probabilistic model is to assist an expert practitioner towards identifying the location pattern of antibody deposits within a glomerulus. Since modern neural networks often provide overconfident outputs, we stress the importance of having a reliable prediction, demonstrating that Temperature Scaling (TS), a recently introduced re-calibration technique, can be successfully applied to immunofluorescence classification in renal biopsy. Experimental results demonstrate that the designed model yields good accuracy on the specific task, and that TS is able to provide reliable probabilities, which are highly valuable for such a task given the low inter-rater agreement.

2021 - Supporting Skin Lesion Diagnosis with Content-Based Image Retrieval [Relazione in Atti di Convegno]
Allegretti, Stefano; Bolelli, Federico; Pollastri, Federico; Longhitano, Sabrina; Pellacani, Giovanni; Grana, Costantino

In recent years, many attempts have been dedicated to the creation of automated devices that could assist both expert and beginner dermatologists towards fast and early diagnosis of skin lesions. Tasks such as skin lesion classification and segmentation have been extensively addressed with deep learning algorithms, which in some cases reach a diagnostic accuracy comparable to that of expert physicians. However, the general lack of interpretability and reliability severely hinders the ability of those approaches to actually support dermatologists in the diagnosis process. In this paper a novel skin image retrieval system is presented, which exploits features extracted by Convolutional Neural Networks to gather similar images from a publicly available dataset, in order to assist the diagnosis process of both expert and novice practitioners. In the proposed framework, ResNet-50 is initially trained for the classification of dermoscopic images; then, the feature extraction part is isolated, and an embedding network is built on top of it. The embedding learns an alternative representation, which allows to check image similarity by means of a distance measure. Experimental results reveal that the proposed method is able to select meaningful images, which can effectively boost the classification accuracy of human dermatologists.

2020 - Augmenting data with GANs to segment melanoma skin lesions [Articolo su rivista]
Pollastri, Federico; Bolelli, Federico; Paredes Palacios, Roberto; Grana, Costantino

This paper presents a novel strategy that employs Generative Adversarial Networks (GANs) to augment data in the skin lesion segmentation task, which is a fundamental first step in the automated melanoma detection process. The proposed framework generates both skin lesion images and their segmentation masks, making the data augmentation process extremely straightforward. In order to thoroughly analyze how the quality and diversity of synthetic images impact the efficiency of the method, we remodel two different well known GANs: a Deep Convolutional GAN (DCGAN) and a Laplacian GAN (LAPGAN). Experimental results reveal that, by introducing such kind of synthetic data into the training process, the overall accuracy of a state-of-the-art Convolutional/Deconvolutional Neural Network for melanoma skin lesion segmentation is increased.

2020 - Evaluation of the Classification Accuracy of the Kidney Biopsy Direct Immunofluorescence through Convolutional Neural Networks [Articolo su rivista]
Ligabue, Giulia; Pollastri, Federico; Fontana, Francesco; Leonelli, Marco; Furci, Luciana; Giovanella, Silvia; Alfano, Gaetano; Cappelli, Gianni; Testa, Francesca; Bolelli, Federico; Grana, Costantino; Magistroni, Riccardo

Background and objectives: Immunohistopathology is an essential technique in the diagnostic workflow of a kidney biopsy. Deep learning is an effective tool in the elaboration of medical imaging. We wanted to evaluate the role of a convolutional neural network as a support tool for kidney immunofluorescence reporting. Design, setting, participants, & measurements: High-magnification (×400) immunofluorescence images of kidney biopsies performed from the year 2001 to 2018 were collected. The report, adopted at the Division of Nephrology of the AOU Policlinico di Modena, describes the specimen in terms of “appearance,” “distribution,” “location,” and “intensity” of the glomerular deposits identified with fluorescent antibodies against IgG, IgA, IgM, C1q and C3 complement fractions, fibrinogen, and κ- and λ-light chains. The report was used as ground truth for the training of the convolutional neural networks. Results: In total, 12,259 immunofluorescence images of 2542 subjects undergoing kidney biopsy were collected. The test set analysis showed accuracy values between 0.79 (“irregular capillary wall” feature) and 0.94 (“fine granular” feature). The agreement test of the results obtained by the convolutional neural networks with respect to the ground truth showed similar values to three pathologists of our center. Convolutional neural networks were 117 times faster than human evaluators in analyzing 180 test images. A web platform, where it is possible to upload digitized images of immunofluorescence specimens, is available to evaluate the potential of our approach. Conclusions: The data showed that the accuracy of convolutional neural networks is comparable with that of pathologists experienced in the field.

2019 - How does Connected Components Labeling with Decision Trees perform on GPUs? [Relazione in Atti di Convegno]
Allegretti, Stefano; Bolelli, Federico; Cancilla, Michele; Pollastri, Federico; Canalini, Laura; Grana, Costantino

In this paper the problem of Connected Components Labeling (CCL) in binary images using Graphic Processing Units (GPUs) is tackled by a different perspective. In the last decade, many novel algorithms have been released, specifically designed for GPUs. Because CCL literature concerning sequential algorithms is very rich, and includes many efficient solutions, designers of parallel algorithms were often inspired by techniques that had already proved successful in a sequential environment, such as the Union-Find paradigm for solving equivalences between provisional labels. However, the use of decision trees to minimize memory accesses, which is one of the main feature of the best performing sequential algorithms, was never taken into account when designing parallel CCL solutions. In fact, branches in the code tend to cause thread divergence, which usually leads to inefficiency. Anyway, this consideration does not necessarily apply to every possible scenario. Are we sure that the advantages of decision trees do not compensate for the cost of thread divergence? In order to answer this question, we chose three well-known sequential CCL algorithms, which employ decision trees as the cornerstone of their strategy, and we built a data-parallel version of each of them. Experimental tests on real case datasets show that, in most cases, these solutions outperform state-of-the-art algorithms, thus demonstrating the effectiveness of decision trees also in a parallel environment.

2019 - Skin Lesion Segmentation Ensemble with Diverse Training Strategies [Relazione in Atti di Convegno]
Canalini, Laura; Pollastri, Federico; Bolelli, Federico; Cancilla, Michele; Allegretti, Stefano; Grana, Costantino

This paper presents a novel strategy to perform skin lesion segmentation from dermoscopic images. We design an effective segmentation pipeline, and explore several pre-training methods to initialize the features extractor, highlighting how different procedures lead the Convolutional Neural Network (CNN) to focus on different features. An encoder-decoder segmentation CNN is employed to take advantage of each pre-trained features extractor. Experimental results reveal how multiple initialization strategies can be exploited, by means of an ensemble method, to obtain state-of-the-art skin lesion segmentation accuracy.

2018 - Improving Skin Lesion Segmentation with Generative Adversarial Networks [Relazione in Atti di Convegno]
Pollastri, Federico; Bolelli, Federico; Paredes, Roberto; Grana, Costantino

This paper proposes a novel strategy that employs Generative Adversarial Networks (GANs) to augment data in the image segmentation field, and a Convolutional-Deconvolutional Neural Network (CDNN) to automatically generate lesion segmentation mask from dermoscopic images. Training the CDNN with our GAN generated data effectively improves the state-of-the-art.