Publications by Federico Bolelli

Given the overwhelming impact of machine learning on the last decade, several libraries and frameworks have been developed in recent years to simplify the design and training of neural networks, providing array-based programming, automatic differentiation and user-friendly access to hardware accelerators. None of those tools, however, was designed with native and transparent support for Cloud Computing or heterogeneous High-Performance Computing (HPC). The DeepHealth Toolkit is an open source Deep Learning toolkit aimed at boosting productivity of data scientists operating in the medical field by providing a unified framework for the distributed training of neural networks, which is able to leverage hybrid HPC and cloud environments in a transparent way for the user. The toolkit is composed of a Computer Vision library, a Deep Learning library, and a front-end for non-expert users; all of the components are focused on the medical domain, but they are general purpose and can be applied to any other field. In this paper, the principles driving the design of the DeepHealth libraries are described, along with details about the implementation and the interaction between the different elements composing the toolkit. Finally, experiments on common benchmarks prove the efficiency of each separate component and of the DeepHealth Toolkit overall.

Contours extraction, also known as chain-code extraction, is one of the most common algorithms of binary image processing. Despite being the raster way the most cache friendly and, consequently, fast way to scan an image, most commonly used chain-code algorithms perform contours tracing, and therefore tend to be fairly inefficient. In this paper, we took a rarely used algorithm that extracts contours in raster scan, and optimized its execution time through template functions, look-up tables and decision trees, in order to reduce code branches and the average number of load/store operations required. The result is a very fast solution that outspeeds the state-of-the-art contours extraction algorithm implemented in OpenCV, on a collection of real case datasets. Contribution: This paper significantly improves the performance of existing chain-code algorithms, by smartly introducing decision trees to reduce code branches and the average number of load/store operations required.

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.

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.

Connected Components Labeling (CCL) is a crucial step of several image processing and computer vision pipelines. Many efficient sequential strategies exist, among which one of the most effective is the use of a block-based mask to drastically cut the number of memory accesses. In the last decade, aided by the fast development of Graphics Processing Units (GPUs), a lot of data parallel CCL algorithms have been proposed along with sequential ones. Applications that entirely run in GPU can benefit from parallel implementations of CCL that allow to avoid expensive memory transfers between host and device. In this paper, two new eight-connectivity CCL algorithms are proposed, namely Block-based Union Find (BUF) and Block-based Komura Equivalence (BKE). These algorithms optimize existing GPU solutions introducing a block-based approach. Extensions for three-dimensional datasets are also discussed. In order to produce a fair comparison with previously proposed alternatives, YACCLAB, a public CCL benchmarking framework, has been extended and made suitable for evaluating also GPU algorithms. Moreover, three-dimensional datasets have been added to its collection. Experimental results on real cases and synthetically generated datasets demonstrate the superiority of the new proposals with respect to state-of-the-art, both on 2D and 3D scenarios.

La procedura che rende un algoritmo più efficiente in termini di requisiti di memoria o tempo di esecuzione si chiama ottimizzazione e rappresenta un passaggio cruciale nell'elaborazione di immagini e video. È raro che il processo di ottimizzazione produca un algoritmo ottimo in senso assoluto, ma spesso occorre raggiungere un compromesso tra i requisiti di tempo e quelli di memoria. Ad ogni modo, esistono molti scenari in cui il tempo di esecuzione totale richiesto per completare un'attività è il vincolo più restrittivo. Gli algoritmi di elaborazione di immagini binarie, ad esempio, rappresentano un'operazione fondamentale nella maggior parte dei sistemi di analisi di immagini e video all'avanguardia, anche quando questi sono basati su tecniche di deep learning. Avere un'implementazione efficiente è quindi essenziale, specialmente quando questi sistemi devono essere impiegati in scenari con vincoli temporali, dove compromettere la qualità del risultato, o fare affidamento su hardware più performante, non è una strada percorribile. Questa tesi introduce ed esplora diversi approcci per l'ottimizzazione degli algoritmi di elaborazione di immagini binarie modellabili con tabelle decisionali. Esistono diversi problemi che possono essere definiti in questo modo: l’etichettatura delle componenti connesse, il thinning, il chain code e gli operatori morfologici sono alcuni di questi. In generale, tutti gli algoritmi in cui il valore di output per ciascun pixel dell'immagine è ottenuto dal valore del pixel stesso e di alcuni dei suoi vicini possono essere definiti utilizzando tabelle decisionali. Concentrandosi sull'etichettatura delle componenti connesse, vengono analizzati gli approcci all'avanguardia sia per ambienti sequenziali basati su CPU che per ambienti paralleli basati su CPU e GPU, focalizzandosi su come misurare in modo equo le prestazioni. Vengono quindi introdotti nuovi approcci per migliorare ulteriormente le prestazioni in termini di tempo totale di esecuzione, mostrando come queste tecniche possano essere generalizzate per migliorare qualsiasi algoritmo modellabile con tabelle decisionali. Infine, viene presentato un framework che consente di applicare automaticamente molte delle strategie di ottimizzazione precedentemente descritte ed analizzate ad un determinato algoritmo. Il framework, chiamato GRAPHGEN, prende come input una definizione del problema in termini di condizioni da verificare e azioni da eseguire ed è in grado di produrre come output il codice C/C++ che include tutte le ottimizzazioni necessarie. Rispetto agli approcci esistenti, gli algoritmi generati con GRAPHGEN hanno prestazioni significativamente migliori, sia su set di dati reali che su quelli sintetici.

Connected Components Labeling is an essential step of many Image Processing and Computer Vision tasks. Since the first proposal of a labeling algorithm, which dates back to the sixties, many approaches have optimized the computational load needed to label an image. In particular, the use of decision forests and state prediction have recently appeared as valuable strategies to improve performance. However, due to the overhead of the manual construction of prediction states and the size of the resulting machine code, the application of these strategies has been restricted to small masks, thus ignoring the benefit of using a block-based approach. In this paper, we combine a block-based mask with state prediction and code compression: the resulting algorithm is modeled as a Directed Rooted Acyclic Graph with multiple entry points, which is automatically generated without manual intervention. When tested on synthetic and real datasets, in comparison with optimized implementations of state-of-the-art algorithms, the proposed approach shows superior performance, surpassing the results obtained by all compared approaches in all settings.

The problem of labeling the connected components of a binary image is well-defined and several proposals have been presented in the past. Since an exact solution to the problem exists, algorithms mainly differ on their execution speed. In this paper, we propose and describe YACCLAB, Yet Another Connected Components Labeling Benchmark. Together with a rich and varied dataset, YACCLAB contains an open source platform to test new proposals and to compare them with publicly available competitors. Textual and graphical outputs are automatically generated for many kinds of tests, which analyze the methods from different perspectives. An extensive set of experiments among state-of-the-art techniques is reported and discussed.

In this paper, we introduce a novel GPU-based Connected Components Labeling algorithm: the Block-based Union Find. The proposed strategy significantly improves an existing GPU algorithm, taking advantage of a block-based approach. Experimental results on real cases and synthetically generated datasets demonstrate the superiority of the new proposal with respect to state-of-the-art.

In this paper we describe the algorithmic implementation details of "Connected Components Labeling on DRAGs'' (Directed Rooted Acyclic Graphs), studying the influence of parameters on the results. Moreover, a detailed description of how to install, setup and use YACCLAB (Yet Another Connected Components LAbeling Benchmark) to test DRAG is provided.