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STEFANO ALLEGRETTI

Docente a contratto
Dipartimento di Ingegneria "Enzo Ferrari"

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Pubblicazioni

2023 - Inferior Alveolar Canal Automatic Detection with Deep Learning CNNs on CBCTs: Development of a Novel Model and Release of Open-Source Dataset and Algorithm [Articolo su rivista]
Di Bartolomeo, Mattia; Pellacani, Arrigo; Bolelli, Federico; Cipriano, Marco; Lumetti, Luca; Negrello, Sara; Allegretti, Stefano; Minafra, Paolo; Pollastri, Federico; Nocini, Riccardo; Colletti, Giacomo; Chiarini, Luigi; Grana, Costantino; Anesi, Alexandre
abstract

Introduction: The need of accurate three-dimensional data of anatomical structures is increasing in the surgical field. The development of convolutional neural networks (CNNs) has been helping to fill this gap by trying to provide efficient tools to clinicians. Nonetheless, the lack of a fully accessible datasets and open-source algorithms is slowing the improvements in this field. In this paper, we focus on the fully automatic segmentation of the Inferior Alveolar Canal (IAC), which is of immense interest in the dental and maxillo-facial surgeries. Conventionally, only a bidimensional annotation of the IAC is used in common clinical practice. A reliable convolutional neural network (CNNs) might be timesaving in daily practice and improve the quality of assistance. Materials and methods: Cone Beam Computed Tomography (CBCT) volumes obtained from a single radiological center using the same machine were gathered and annotated. The course of the IAC was annotated on the CBCT volumes. A secondary dataset with sparse annotations and a primary dataset with both dense and sparse annotations were generated. Three separate experiments were conducted in order to evaluate the CNN. The IoU and Dice scores of every experiment were recorded as the primary endpoint, while the time needed to achieve the annotation was assessed as the secondary end-point. Results: A total of 347 CBCT volumes were collected, then divided into primary and secondary datasets. Among the three experiments, an IoU score of 0.64 and a Dice score of 0.79 were obtained thanks to the pre-training of the CNN on the secondary dataset and the creation of a novel deep label propagation model, followed by proper training on the primary dataset. To the best of our knowledge, these results are the best ever published in the segmentation of the IAC. The datasets is publicly available and algorithm is published as open-source software. On average, the CNN could produce a 3D annotation of the IAC in 6.33 s, compared to 87.3 s needed by the radiology technician to produce a bidimensional annotation. Conclusions: To resume, the following achievements have been reached. A new state of the art in terms of Dice score was achieved, overcoming the threshold commonly considered of 0.75 for the use in clinical practice. The CNN could fully automatically produce accurate three-dimensional segmentation of the IAC in a rapid setting, compared to the bidimensional annotations commonly used in the clinical practice and generated in a time-consuming manner. We introduced our innovative deep label propagation method to optimize the performance of the CNN in the segmentation of the IAC. For the first time in this field, the datasets and the source codes used were publicly released, granting reproducibility of the experiments and helping in the improvement of IAC segmentation.

2022 - Connected Components Labeling on Bitonal Images [Relazione in Atti di Convegno]
Bolelli, Federico; Allegretti, Stefano; Grana, Costantino
abstract

2022 - Deep Segmentation of the Mandibular Canal: a New 3D Annotated Dataset of CBCT Volumes [Articolo su rivista]
Cipriano, Marco; Allegretti, Stefano; Bolelli, Federico; Di Bartolomeo, Mattia; Pollastri, Federico; Pellacani, Arrigo; Minafra, Paolo; Anesi, Alexandre; Grana, Costantino
abstract

Inferior Alveolar Nerve (IAN) canal detection has been the focus of multiple recent works in dentistry and maxillofacial imaging. Deep learning-based techniques have reached interesting results in this research field, although the small size of 3D maxillofacial datasets has strongly limited the performance of these algorithms. Researchers have been forced to build their own private datasets, thus precluding any opportunity for reproducing results and fairly comparing proposals. This work describes a novel, large, and publicly available mandibular Cone Beam Computed Tomography (CBCT) dataset, with 2D and 3D manual annotations, provided by expert clinicians. Leveraging this dataset and employing deep learning techniques, we are able to improve the state of the art on the 3D mandibular canal segmentation. The source code which allows to exactly reproduce all the reported experiments is released as an open-source project, along with this article.

2022 - Improving Segmentation of the Inferior Alveolar Nerve through Deep Label Propagation [Relazione in Atti di Convegno]
Cipriano, Marco; Allegretti, Stefano; Bolelli, Federico; Pollastri, Federico; Grana, Costantino
abstract

2022 - One DAG to Rule Them All [Articolo su rivista]
Bolelli, Federico; Allegretti, Stefano; Grana, Costantino
abstract

In this paper, we present novel strategies for optimizing the performance of many binary image processing algorithms. These strategies are collected in an open-source framework, GRAPHGEN, that is able to automatically generate optimized C++ source code implementing the desired optimizations. Simply starting from a set of rules, the algorithms introduced with the GRAPHGEN framework can generate decision trees with minimum average path-length, possibly considering image pattern frequencies, apply state prediction and code compression by the use of Directed Rooted Acyclic Graphs (DRAGs). Moreover, the proposed algorithmic solutions allow to combine different optimization techniques and significantly improve performance. Our proposal is showcased on three classical and widely employed algorithms (namely Connected Components Labeling, Thinning, and Contour Tracing). When compared to existing approaches —in 2D and 3D—, implementations using the generated optimal DRAGs perform significantly better than previous state-of-the-art algorithms, both on CPU and GPU.

2022 - Quest for Speed: The Epic Saga of Record-Breaking on OpenCV Connected Components Extraction [Relazione in Atti di Convegno]
Bolelli, Federico; Allegretti, Stefano; Grana, Costantino
abstract

Connected Components Labeling (CCL) represents an essential part of many Image Processing and Computer Vision pipelines. Given its relevance on the field, it has been part of most cutting-edge Computer Vision libraries. In this paper, all the algorithms included in the OpenCV during the years are reviewed, from sequential to parallel/GPU-based implementations. Our goal is to provide a better understanding of what has changed and why one algorithm should be preferred to another both in terms of memory usage and execution speed.

2021 - A Heuristic-Based Decision Tree for Connected Components Labeling of 3D Volumes [Relazione in Atti di Convegno]
Söchting, Maximilian; Allegretti, Stefano; Bolelli, Federico; Grana, Costantino
abstract

Connected Components Labeling represents a fundamental step for many Computer Vision and Image Processing pipelines. Since the first appearance of the task in the sixties, many algorithmic solutions to optimize the computational load needed to label an image have been proposed. Among them, block-based scan approaches and decision trees revealed to be some of the most valuable strategies. However, due to the cost of the manual construction of optimal decision trees and the computational limitations of automatic strategies employed in the past, the application of blocks and decision trees has been restricted to small masks, and thus to 2D algorithms. With this paper we present a novel heuristic algorithm based on decision tree learning methodology, called Entropy Partitioning Decision Tree (EPDT). It allows to compute near-optimal decision trees for large scan masks. Experimental results demonstrate that algorithms based on the generated decision trees outperform state-of-the-art competitors.

2021 - A Heuristic-Based Decision Tree for Connected Components Labeling of 3D Volumes: Implementation and Reproducibility Notes [Relazione in Atti di Convegno]
Bolelli, Federico; Allegretti, Stefano; Grana, Costantino
abstract

This paper provides a detailed description of how to install, setup, and use the YACCLAB benchmark to test the algorithms published in "A Heuristic-Based Decision Tree for Connected Components Labeling of 3D Volumes," underlying how the parameters affect and influence experimental results.

2021 - Fast Run-Based Connected Components Labeling for Bitonal Images [Relazione in Atti di Convegno]
Wonsang, Lee; Allegretti, Stefano; Bolelli, Federico; Grana, Costantino
abstract

Connected Components Labeling (CCL) is a fundamental task in binary image processing. Since its introduction in the sixties, several algorithmic strategies have been proposed to optimize its execution time. Most CCL algorithms in literature, including the current state-of-the-art, are designed to work on an input stored with 1-byte per pixel, even if the most memory-efficient format for a binary input only uses 1-bit per pixel. This paper deals with connected components labeling on 1-bit per pixel images, also known as 1bpp or bitonal images. An existing run-based CCL strategy is adapted to this input format, and optimized with Find First Set hardware operations and a smart management of provisional labels, giving birth to an efficient solution called Bit-Run Two Scan (BRTS). Then, BRTS is further optimized by merging pairs of consecutive lines through bitwise OR, and finding runs on this reduced data. This modification is the basis for another new algorithm on bitonal images, Bit-Merge-Run Scan (BMRS). When evaluated on a public benchmark, the two proposals outperform all the fastest competitors in literature, and therefore represent the new state-of-the-art for connected components labeling on bitonal images.

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
abstract

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.

2021 - The DeepHealth Toolkit: A Unified Framework to Boost Biomedical Applications [Relazione in Atti di Convegno]
Cancilla, Michele; Canalini, Laura; Bolelli, Federico; Allegretti, Stefano; Carrión, Salvador; Paredes, Roberto; Ander Gómez, Jon; Leo, Simone; Enrico Piras, Marco; Pireddu, Luca; Badouh, Asaf; Marco-Sola, Santiago; Alvarez, Lluc; Moreto, Miquel; Grana, Costantino
abstract

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.

2020 - A Warp Speed Chain-Code Algorithm Based on Binary Decision Trees [Relazione in Atti di Convegno]
Allegretti, Stefano; Bolelli, Federico; Grana, Costantino
abstract

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.

2020 - Optimized Block-Based Algorithms to Label Connected Components on GPUs [Articolo su rivista]
Allegretti, Stefano; Bolelli, Federico; Grana, Costantino
abstract

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.

2020 - Spaghetti Labeling: Directed Acyclic Graphs for Block-Based Connected Components Labeling [Articolo su rivista]
Bolelli, Federico; Allegretti, Stefano; Baraldi, Lorenzo; Grana, Costantino
abstract

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.

2019 - A Block-Based Union-Find Algorithm to Label Connected Components on GPUs [Relazione in Atti di Convegno]
Allegretti, Stefano; Bolelli, Federico; Cancilla, Michele; Grana, Costantino
abstract

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.

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
abstract

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
abstract

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 - Optimizing GPU-Based Connected Components Labeling Algorithms [Relazione in Atti di Convegno]
Allegretti, Stefano; Bolelli, Federico; Cancilla, Michele; Grana, Costantino
abstract

Connected Components Labeling (CCL) is a fundamental image processing technique, widely used in various application areas. Computational throughput of Graphical Processing Units (GPUs) makes them eligible for such a kind of algorithms. In the last decade, many approaches to compute CCL on GPUs have been proposed. Unfortunately, most of them have focused on 4-way connectivity neglecting the importance of 8-way connectivity. This paper aims to extend state-of-the-art GPU-based algorithms from 4 to 8-way connectivity and to improve them with additional optimizations. Experimental results revealed the effectiveness of the proposed strategies.