Publications by Federico Bolelli

Testicular ultrasound imaging is vital for assessing male infertility, with testicular inhomogeneity serving as a key biomarker. However, subjective interpretation and the scarcity of publicly available datasets pose challenges to automated classification. In this study, we explore supervised and unsupervised pretraining strategies using a ResNet-based architecture, supplemented by diffusion-based generative models to synthesize realistic ultrasound images. Our results demonstrate that pretraining significantly enhances classification performance compared to training from scratch, and synthetic data can effectively substitute real images in the pretraining process, alleviating data-sharing constraints. These methods offer promising advancements toward robust, clinically valuable automated analysis of male infertility. The source code is publicly available at https://github.com/AImageLab-zip/TesticulUS/.

Brain tumor segmentation is a crucial task in medical imaging that involves the integrated modeling of four distinct imaging modalities to identify tumor regions accurately. Unfortunately, in real-life scenarios, the full availability of such four modalities is often violated due to scanning cost, time, and patient condition. Consequently, several deep learning models have been developed to address the challenge of brain tumor segmentation under conditions of missing imaging modalities. However, the majority of these models have been evaluated using the 2018 version of the BraTS dataset, which comprises only $285$ volumes. In this study, we reproduce and extensively analyze the most relevant models using BraTS2023, which includes 1,250 volumes, thereby providing a more comprehensive and reliable comparison of their performance. Furthermore, we propose and evaluate the adoption of Mamba as an alternative fusion mechanism for brain tumor segmentation in the presence of missing modalities. Experimental results demonstrate that transformer-based architectures achieve leading performance on BraTS2023, outperforming purely convolutional models that were instead superior in BraTS2018. Meanwhile, the proposed Mamba-based architecture exhibits promising performance in comparison to state-of-the-art models, competing and even outperforming transformers. The source code of the proposed approach is publicly released alongside the benchmark developed for the evaluation: https://github.com/AImageLab-zip/IM-Fuse.

Convolutional Neural Networks (CNNs) have been broadly employed in dermoscopic image analysis, mainly due to the large amount of data gathered by the International Skin Imaging Collaboration (ISIC). But where do neural networks look? Several authors have claimed that the ISIC dataset is affected by strong biases, i.e. spurious correlations between samples that machine learning models unfairly exploit while discarding the useful patterns they are expected to learn. These strong claims have been supported by showing that deep learning models maintain excellent performance even when "no information about the lesion remains" in the debased input images. With this paper, we explore the interpretability of CNNs in dermoscopic image analysis by analyzing which characteristics are considered by autonomous classification algorithms. Starting from a standard setting, experiments presented in this paper gradually conceal well-known crucial dermoscopic features and thoroughly investigate how CNNs performance subsequently evolves. Experimental results carried out on two well-known CNNs, EfficientNet-B3, and ResNet-152, demonstrate that neural networks autonomously learn to extract features that are notoriously important for melanoma detection. Even when some of such features are removed, the others are still enough to achieve satisfactory classification performance. Obtained results demonstrate that literature claims on biases are not supported by carried-out experiments. Finally, to demonstrate the generalization capabilities of state-of-the-art CNN models for skin lesion classification, a large private dataset has been employed as an additional test set.

The segmentation of the Inferior Alveolar Canal (IAC) plays a central role in maxillofacial surgery, drawing significant attention in the current research. Because of their outstanding results, deep learning methods are widely adopted in the segmentation of 3D medical volumes, including the IAC in Cone Beam Computed Tomography (CBCT) data. One of the main challenges when segmenting large volumes, including those obtained through CBCT scans, arises from the use of patch-based techniques, mandatory to fit memory constraints. Such training approaches compromise neural network performance due to a reduction in the global contextual information. Performance degradation is prominently evident when the target objects are small with respect to the background, as it happens with the inferior alveolar nerve that develops across the mandible, but involves only a few voxels of the entire scan. In order to target this issue and push state-of-the-art performance in the segmentation of the IAC, we propose an innovative approach that exploits spatial information of extracted patches and integrates it into a Transformer architecture. By incorporating prior knowledge about patch location, our model improves state of the art by ~2 points on the Dice score when integrated with the standard U-Net architecture. The source code of our proposal is publicly released.

Overcrowding in Emergency Departments (EDs) is a pressing concern driven by high patient demand and limited resources. Prolonged Length of Stay (pLOS), a major contributor to this congestion, may lead to adverse outcomes, including patients leaving without being seen, suboptimal clinical care, increased mortality rates, provider burnout, and escalating healthcare costs. This study investigates the application of various Machine Learning (ML) algorithms to predict both LOS and pLOS. A retrospective analysis examined 32,967 accesses at a northern Italian hospital’s ED between 2022 and 2024. Twelve classification algorithms were evaluated in forecasting pLOS, using clinically relevant thresholds. Two data variants were employed for model comparison: one containing only structured data (e.g., demographics and clinical information), while a second one also including features extracted from free-text nursing notes. To enhance the accuracy of LOS prediction, novel queue-based variables capturing the real-time state of the ED were incorporated as additional dynamic predictors. Compared to single-algorithm models, ensemble models demonstrated superior robustness in forecasting both ED-LOS and ED-pLOS. These findings highlight the potential for integrating ML into EDs practices as auxiliary tools to provide valuable insights into patient flow. By identifying patients at high risk of pLOS, healthcare professionals can proactively implement strategies to expedite care, optimize resource allocation, and ultimately improve patient outcomes and ED efficiency, promoting a more effective and sustainable public healthcare delivery.

Objectives: The shape is commonly used to describe the objects. State-of-the-art algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surfacemodels are used. This is seen from the growing popularity of ShapeNet (51,300 models) and Princeton ModelNet (127,915 models). However, a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instruments is missing. Methods: We present MedShapeNet to translate datadriven vision algorithms to medical applications and to adapt state-of-the-art vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. We present use cases in classifying brain tumors, skull reconstructions, multi-class anatomy completion, education, and 3D printing. Results: By now, MedShapeNet includes 23 datasets with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via aweb interface and a Python application programming interface and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Conclusions: MedShapeNet contains medical shapes from anatomy and surgical instruments and will continue to collect data for benchmarks and applications. The project page is: https://medshapenet.ikim.nrw/.

Recently, Multimodal Large Language Models (MLLMs) have emerged as a leading framework for enhancing the ability of Large Language Models (LLMs) to interpret non-linguistic modalities. Despite their impressive capabilities, the robustness of MLLMs under conditions where one or more modalities are missing remains largely unexplored. In this paper, we investigate the extent to which MLLMs can maintain performance when faced with missing modality inputs. Moreover, we propose a novel framework to mitigate the aforementioned issue called Retrieval-Augmented Generation for missing modalities (MissRAG). It consists of a novel multimodal RAG technique alongside a tailored prompt engineering strategy designed to enhance model robustness by mitigating the impact of absent modalities while preventing the burden of additional instruction tuning. To demonstrate the effectiveness of our techniques, we conducted comprehensive evaluations across five diverse datasets, covering tasks such as audio-visual question answering, audio-visual captioning, and multimodal sentiment analysis.

QR and Datamatrix codes are widely used in warehouse logistics and high-speed production pipelines. Still, distant or small barcodes often yield low-pixel-density images that are hard to read. Conventional solutions rely on costly hardware or enhanced lighting, raising expenses and potentially reducing depth of field. We propose Mosaic-SR, a multi-step, adaptive super-resolution (SR) method that devotes more computation to barcode regions than uniform backgrounds. For each patch, it predicts an uncertainty value to decide how many refinement steps are required. Our experiments show that Mosaic-SR surpasses state-of-the-art SR models on 2D barcode images, achieving higher PSNR and decoding rates in less time. All code and trained models are publicly available at https://github.com/Henvezz95/mosaic-sr.

The synthesis of missing MRI modalities has emerged as a critical solution to address incomplete multi-parametric imaging in brain tumor diagnosis and treatment planning. While recent advances in generative models, especially GANs and diffusion-based approaches, have demonstrated promising results in cross-modality MRI generation, challenges remain in preserving anatomical fidelity and minimizing synthesis artifacts. In this work, we build upon the Hybrid Fusion GAN (\hfgan) framework, introducing several enhancements aimed at improving synthesis quality and generalization across tumor types. Specifically, we incorporate z-score normalization, optimize network components for faster and more stable training, and extend the pipeline to support multi-view generation across various brain tumor categories, including gliomas, metastases, and meningiomas. Our approach focuses on refining 2D slice-based generation to ensure intra-slice coherence and reduce intensity inconsistencies, ultimately supporting more accurate and robust tumor segmentation in scenarios with missing imaging modalities. Our source code is available at https://github.com/AImageLab-zip/BraSyn25.

Effective hospital resource management hinges on established metrics such as Length of Stay (LOS) and Prolonged Length of Stay (pLOS). Reducing pLOS is associated with improved patient outcomes and optimized resource utilization (e.g., bed allocation). This study investigates several Machine Learning (ML) models for both LOS and pLOS prediction. We conducted a retrospective study analyzing data from general inpatients discharged between 2022 and 2023 at a northern Italian hospital. Sixteen regression and twelve classification algorithms were compared in forecasting LOS as either a continuous or multi-class variable (1-3 days, 4-10 days, >10 days). Additionally, the same models were assessed for pLOS prediction (defined as LOS exceeding 8 days). All models were evaluated using two variants of the same dataset: one containing only structured data (e.g., demographics and clinical information), and a second one also containing features extracted from free-text diagnosis. Ensemble models, leveraging the combined strengths of multiple ML algorithms, demonstrated superior accuracy in predicting both LOS and pLOS compared to single-algorithm models, particularly when utilizing both structured and unstructured data extracted from diagnoses. Integration of ML, particularly ensemble models, has the potential to significantly improve LOS prediction and identify patients at high risk of pLOS. Such insights can empower healthcare professionals and bed managers to optimize patient care and resource allocation, promoting overall healthcare efficiency and sustainability.