Publications by Costantino Grana

Recently, the field of 3D medical segmentation has been dominated by deep learning models employing Convolutional Neural Networks (CNNs) and Transformer-based architectures, each with its distinctive strengths and limitations. CNNs are constrained by a local receptive field, whereas Transformer are hindered by their substantial memory requirements as well as their data hunger, making them not ideal for processing 3D medical volumes at a fine-grained level. For these reasons, fully convolutional neural networks, as nnU-Net, still dominate the scene when segmenting medical structures in large 3D medical volumes. Despite numerous advancements toward developing transformer variants with subquadratic time and memory complexity, these models still fall short in content-based reasoning. A recent breakthrough is Mamba, a Recurrent Neural Network (RNN) based on State Space Models (SSMs), outperforming Transformers in many long-context tasks (million-length sequences) on famous natural language processing and genomic benchmarks while keeping a linear complexity. In this paper, we evaluate the effectiveness of Mamba-based architectures in comparison to state-of-the-art convolutional and Transformer-based models for 3D medical image segmentation across three well-established datasets: Synapse Abdomen, MSD BrainTumor, and ACDC. Additionally, we address the primary limitations of existing Mamba-based architectures by proposing alternative architectural designs, hence improving segmentation performances. The source code is publicly available to ensure reproducibility and facilitate further research: https://github.com/LucaLumetti/TamingMambas.

Despite their remarkable success in medical image segmentation, the life cycle of deep neural networks remains a challenge in clinical applications. These models must be regularly updated to integrate new medical data and customized to meet evolving diagnostic standards, regulatory requirements, commercial needs, and privacy constraints. Model merging offers a promising solution, as it allows working with multiple specialized networks that can be created and combined dynamically instead of relying on monolithic models. While extensively studied in standard 2D classification, the potential of model merging for 3D segmentation remains unexplored. This paper presents an efficient framework that allows effective model merging in the domain of 3D image segmentation. Our approach builds upon theoretical analysis and encourages wide minima during pre-training, which we demonstrate to facilitate subsequent model merging. Using U-Net 3D, we evaluate the method on distinct anatomical structures with the ToothFairy2 and BTCV Abdomen datasets. To support further research, we release the source code and all the model weights in a dedicated repository: https://github.com/LucaLumetti/UNetTransplant

This article is about Connected Components Labeling (CCL) algorithms developed for GPU accelerators. The task itself is employed in many modern image-processing pipelines and represents a fundamental step in different scenarios, whenever object recognition is required. For this reason, a strong effort in the development of many different proposals devoted to improving algorithm performance using different kinds of hardware accelerators has been made. This paper focuses on GPU-based algorithmic solutions published in the last two decades, highlighting their distinctive traits and the improvements they leverage. The state-of-the-art review proposed is equipped with the source code, which allows to straightforwardly reproduce all the algorithms in different experimental settings. A comprehensive evaluation on multiple environments is also provided, including different operating systems, compilers, and GPUs. Our assessments are performed by means of several tests, including real-case images and synthetically generated ones, highlighting the strengths and weaknesses of each proposal. Overall, the experimental results revealed that block-based oriented algorithms outperform all the other algorithmic solutions on both 2D images and 3D volumes, regardless of the selected environment.

Since their invention in 1949, barcodes have remained the preferred method for automatic data capture, playing a crucial role in supply chain management. To detect a barcode in an image, multiple algorithms have been proposed in the literature, with a significant increase of interest in the topic since the rise of deep learning. However, research in the field suffers from many limitations, including the scarcity of public datasets and code implementations, which hampers the reproducibility and reliability of published results. For this reason, we developed "BarBeR" (Barcode Benchmark Repository), a benchmark designed for testing and comparing barcode detection algorithms. This benchmark includes the code implementation of various detection algorithms for barcodes, along with a suite of useful metrics. It offers a range of test setups and can be expanded to include any localization algorithm. In addition, we provide a large, annotated dataset of 8748 barcode images, combining multiple public barcode datasets with standardized annotation formats for both detection and segmentation tasks. Finally, we share the results obtained from running the benchmark on our dataset, offering valuable insights into the performance of different algorithms.

Segmentation of the Inferior Alveolar Canal (IAC) is a critical aspect of dentistry and maxillofacial imaging, garnering considerable attention in recent research endeavors. Deep learning techniques have shown promising results in this domain, yet their efficacy is still significantly hindered by the limited availability of 3D maxillofacial datasets. An inherent challenge is posed by the size of input volumes, which necessitates a patch-based processing approach that compromises the neural network performance due to the absence of global contextual information. This study introduces a novel approach that harnesses the spatial information within the extracted patches and incorporates it into a Transformer architecture, thereby enhancing the segmentation process through the use of prior knowledge about the patch location. Our method significantly improves the Dice score by a factor of 4 points, with respect to the previous work proposed by Cipriano et al., while also reducing the training steps required by the entire pipeline. By integrating spatial information and leveraging the power of Transformer architectures, this research not only advances the accuracy of IAC segmentation, but also streamlines the training process, offering a promising direction for improving dental and maxillofacial image analysis.

The presence of visible particles in pharmaceutical products is a critical quality issue that demands strict monitoring. Recently, Convolutional Neural Networks (CNNs) have been widely used in industrial settings to detect defects, but there remains a gap in the literature concerning the detection of particles floating in liquid substances, mainly due to the lack of publicly available datasets. In this study, we focus on the detection of foreign particles in pharmaceutical liquid vials, leveraging two state-of-the-art deep-learning approaches adapted to our specific multiclass problem. The first methodology employs a standard ResNet-18 architecture, while the second exploits a Multi-Instance Learning (MIL) technique to efficiently deal with multiple images (sequences) of the same sample. To address the issue of no data availability, we devised and partially released an annotated dataset consisting of sequences containing 19 images for each sample, captured from rotating vials, both with and without impurities. The dataset comprises 2,426 sequences for a total of 46,094 images labeled at the sequence level and including five distinct classes. The proposed methodologies, trained on this new extensive dataset, represent advancements in the field, offering promising strategies to improve the safety and quality control of pharmaceutical products and setting a benchmark for future comparisons.

Introduction. Length of Stay (LOS) and Prolonged Length of Stay (pLOS) are critical indicators of hospital efficiency. Reducing pLOS is crucial for patient safety, autonomy, and bed allocation. This study investigates different machine learning (ML) models to predict LOS and pLOS. Methods. We analyzed a dataset of patients discharged from a northern Italian hospital between 2022 and 2023 as a retrospective cohort study. We compared sixteen regression algorithms and twelve classification methods for predicting LOS as either a continuous or multi-class variable (1-3 days, 4-10 days, >10 days). We also evaluated pLOS prediction using the same models, having pLOS defined as any hospitalization with LOS longer than 8 days. We further analyzed all models using two versions of the same dataset: one containing only structured data (e.g. demographics and clinical information), whereas the second one also containing features extracted from free-text diagnosis. Results. Our results indicate that ensemble models achieved the highest prediction accuracy for both LOS and pLOS, outperforming traditional single-algorithm models, particularly when using both structured and unstructured data extracted from diagnoses. Discussion. The integration of ML, particularly ensemble models, can significantly improve LOS prediction and identify patients at increased risk of pLOS. This information can guide healthcare professionals and bed managers in making informed decisions to enhance patient care and optimize resource allocation.

The Inferior Alveolar Nerve (IAN) is of main interest in the maxillofacial field, as an accurate localization of such nerve reduces the risks of injury during surgical procedures. Although recent literature has focused on developing novel deep learning techniques to produce accurate segmentation masks of the canal containing the IAN, there are still strong limitations due to the scarce amount of publicly available 3D maxillofacial datasets. In this paper, we present an improved version of a previously released tool, IACAT (Inferior Alveolar Canal Annotation Tool), today used by medical experts to produce 3D ground truth annotation. In addition, we release a new dataset, ToothFairy, which is part of the homonymous MICCAI2023 challenge hosted by the Grand-Challenge platform, as an extension of the previously released Maxillo dataset, which was the only publicly available. With ToothFairy, the number of annotations has been increased as well as the quality of existing data.