Filippo Bargagna

Mr. Filippo Bargagna

orcid

Research Focus & Metrics

Academic Career Length

4Years (2023-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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3 October 2023 in Journal of Digital Imaging
Verified
Journal Article
Open access
PDF file
FBFilippo Bargagna
Filippo Bargagna
LSLisa Anita De Santi
Lisa Anita De Santi
NMNicola Martini
Nicola Martini
DGDario Genovesi
Dario Genovesi
BFBrunella Favilli
Brunella Favilli
MSMaria Filomena Santarelli
Maria Filomena Santarelli
Deep neural networks (DNNs) have already impacted the field of medicine in data analysis, classification, and image processing. Unfortunately, their performance is drastically reduced when datasets are scarce in nature (e.g., rare diseases or early-research data). In such scenarios, DNNs display poor capacity for generalization and often lead to highly biased estimates and silent failures. Moreover, deterministic systems cannot provide epistemic uncertainty, a key component to asserting the model’s reliability. In this work, we developed a probabilistic system for classification as a framework for addressing the aforementioned criticalities. Specifically, we implemented a Bayesian convolutional neural network (BCNN) for the classification of cardiac amyloidosis (CA) subtypes. We prepared four different CNNs: base-deterministic, dropout-deterministic, dropout-Bayesian, and Bayesian. We then trained them on a dataset of 1107 PET images from 47 CA and control patients (data scarcity scenario). The Bayesian model achieved performances (78.28 (1.99) % test accuracy) comparable to the base-deterministic, dropout-deterministic, and dropout-Bayesian ones, while showing strongly increased “Out of Distribution” input detection (validation-test accuracy mismatch reduction). Additionally, both the dropout-Bayesian and the Bayesian models enriched the classification through confidence estimates, while reducing the criticalities of the dropout-deterministic and base-deterministic approaches. This in turn increased the model’s reliability, also providing much needed insights into the network’s estimates. The obtained results suggest that a Bayesian CNN can be a promising solution for addressing the challenges posed by data scarcity in medical imaging classification tasks.

28 October 2024 in BioMedInformatics
Verified
Journal Article
Open access
PDF file
LSLisa Anita De Santi
Lisa Anita De Santi
FPFranco Italo Piparo
Franco Italo Piparo
FBFilippo Bargagna
Filippo Bargagna
Maria Filomena SantarelliMaria Filomena Santarelli
Maria Filomena Santarelli
Simona CeliSimona Celi
Simona Celi
Vincenzo PositanoVincenzo Positano
Vincenzo Positano
Recent developments in Artificial Intelligence have increasingly focused on explainability research. The potential of Explainable Artificial Intelligence (XAI) in producing trustworthy computer-aided diagnosis systems and its usage for knowledge discovery are gaining interest in the medical imaging (MI) community to support the diagnostic process and the discovery of image biomarkers. Most of the existing XAI applications in MI are focused on interpreting the predictions made using deep neural networks, typically including attribution techniques with saliency map approaches and other feature visualization methods. However, these are often criticized for providing incorrect and incomplete representations of the black-box models’ behaviour. This highlights the importance of proposing models intentionally designed to be self-explanatory. In particular, part-prototype (PP) models are interpretable-by-design computer vision (CV) models that base their decision process on learning and identifying representative prototypical parts from input images, and they are gaining increasing interest and results in MI applications. However, the medical field has unique characteristics that could benefit from more advanced implementations of these types of architectures. This narrative review summarizes existing PP networks, their application in MI analysis, and current challenges.

2 October 2024 in Journal of Imaging Informatics in Medicine
Verified
Journal Article
Open access
PDF file
FBFilippo Bargagna
Filippo Bargagna
DZDonato Zigrino
Donato Zigrino
LSLisa Anita De Santi
Lisa Anita De Santi
DGDario Genovesi
Dario Genovesi
MSMichele Scipioni
Michele Scipioni
MSMaria Filomena Santarelli
Maria Filomena Santarelli
Medical image classification using convolutional neural networks (CNNs) is promising but often requires extensive manual tuning for optimal model definition. Neural architecture search (NAS) automates this process, reducing human intervention significantly. This study applies NAS to [18F]-Florbetaben PET cardiac images for classifying cardiac amyloidosis (CA) sub-types (amyloid light chain (AL) and transthyretin amyloid (ATTR)) and controls. Following data preprocessing and augmentation, an evolutionary cell-based NAS approach with a fixed network macro-structure is employed, automatically deriving cells’ micro-structure. The algorithm is executed five times, evaluating 100 mutating architectures per run on an augmented dataset of 4048 images (originally 597), totaling 5000 architectures evaluated. The best network (NAS-Net) achieves 76.95% overall accuracy. K-fold analysis yields mean ± SD percentages of sensitivity, specificity, and accuracy on the test dataset: AL subjects (98.7 ± 2.9, 99.3 ± 1.1, 99.7 ± 0.7), ATTR-CA subjects (93.3 ± 7.8, 78.0 ± 2.9, 70.9 ± 3.7), and controls (35.8 ± 14.6, 77.1 ± 2.0, 96.7 ± 4.4). NAS-derived network performance rivals manually determined networks in the literature while using fewer parameters, validating its automatic approach’s efficacy.

10 September 2024 in Preprints.org
Verified
Preprint
Open access
PDF file
LSLisa Anita De Santi
Lisa Anita De Santi
FPFranco Italo Piparo
Franco Italo Piparo
FBFilippo Bargagna
Filippo Bargagna
Maria Filomena SantarelliMaria Filomena Santarelli
Maria Filomena Santarelli
Simona CeliSimona Celi
Simona Celi
Vincenzo PositanoVincenzo Positano
Vincenzo Positano
The last wave of Artificial Intelligence is dedicating particular emphasis to the line of explainability research. The potential of Explainable Artificial Intelligence (XAI) in producing trustworthy computer-aided-diagnosis systems and its usage for knowledge discovery are collecting interest in the Medical Imaging (MI) community to support the diagnostic process and the discovery of image biomarkers. Most of the existing XAI applications in MI were focused on interpreting the predictions returned by deep neural networks, typically including attribution techniques with saliency map approaches and other feature visualization methods. However, these are often criticized for providing incorrect and incomplete representations of the black-box models’ behaviour. This raises the attention in proposing models intentionally designed to be self-explanatory. In particular, part-prototype (PP) models are interpretable-by-design computer vision (CV) models that base their decision process in learning and identifying representative prototypical parts from the input images, and they are collecting increasing interest and results in MI applications. This narrative review provides a summary of existing PP networks, their application in MI analysis and current challenges.