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Authors = Flavia Grignaffini

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19 pages, 12083 KiB  
Article
An XAI Approach to Melanoma Diagnosis: Explaining the Output of Convolutional Neural Networks with Feature Injection
by Flavia Grignaffini, Enrico De Santis, Fabrizio Frezza and Antonello Rizzi
Information 2024, 15(12), 783; https://doi.org/10.3390/info15120783 - 5 Dec 2024
Cited by 1 | Viewed by 1266
Abstract
Computer-aided diagnosis (CAD) systems, which combine medical image processing with artificial intelligence (AI) to support experts in diagnosing various diseases, emerged from the need to solve some of the problems associated with medical diagnosis, such as long timelines and operator-related variability. The most [...] Read more.
Computer-aided diagnosis (CAD) systems, which combine medical image processing with artificial intelligence (AI) to support experts in diagnosing various diseases, emerged from the need to solve some of the problems associated with medical diagnosis, such as long timelines and operator-related variability. The most explored medical application is cancer detection, for which several CAD systems have been proposed. Among them, deep neural network (DNN)-based systems for skin cancer diagnosis have demonstrated comparable or superior performance to that of experienced dermatologists. However, the lack of transparency in the decision-making process of such approaches makes them “black boxes” and, therefore, not directly incorporable into clinical practice. Trying to explain and interpret the reasons for DNNs’ decisions can be performed by the emerging explainable AI (XAI) techniques. XAI has been successfully applied to DNNs for skin lesion image classification but never when additional information is incorporated during network training. This field is still unexplored; thus, in this paper, we aim to provide a method to explain, qualitatively and quantitatively, a convolutional neural network model with feature injection for melanoma diagnosis. The gradient-weighted class activation mapping and layer-wise relevance propagation methods were used to generate heat maps, highlighting the image regions and pixels that contributed most to the final prediction. In contrast, the Shapley additive explanations method was used to perform a feature importance analysis on the additional handcrafted information. To successfully integrate DNNs into the clinical and diagnostic workflow, ensuring their maximum reliability and transparency in whatever variant they are used is necessary. Full article
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41 pages, 2889 KiB  
Systematic Review
Alterations in Glutathione Redox Homeostasis in Metabolic Dysfunction-Associated Fatty Liver Disease: A Systematic Review
by Lucia Cesarini, Flavia Grignaffini, Anna Alisi and Anna Pastore
Antioxidants 2024, 13(12), 1461; https://doi.org/10.3390/antiox13121461 - 28 Nov 2024
Viewed by 2241
Abstract
Low molecular weight (LMW) thiols, particularly glutathione, play pathogenic roles in various multiorgan diseases. The liver is central for the production and systemic distribution of LMW thiols; thus, it is particularly susceptible to the imbalance of redox status that may determine increased oxidative [...] Read more.
Low molecular weight (LMW) thiols, particularly glutathione, play pathogenic roles in various multiorgan diseases. The liver is central for the production and systemic distribution of LMW thiols; thus, it is particularly susceptible to the imbalance of redox status that may determine increased oxidative stress and trigger the liver damage observed in metabolic dysfunction-associated steatotic liver disease (MASLD) models and humans. Indeed, increased LMW thiols at the cellular and extracellular levels may be associated with the severity of MASLD. Here, we present a systematic literature review of recent studies assessing the levels of LMW thiols in MASLD in in vivo and in vitro models and human subjects. Based on the PRISMA 2020 criteria, a search was conducted using PubMed and Scopus by applying inclusion/exclusion filters. The initial search returned 1012 documents, from which 165 eligible studies were selected, further described, and qualitatively analysed. Of these studies, most focused on animal and cellular models, while a minority used human fluids. The analysis of these studies revealed heterogeneity in the methods of sample processing and measurement of LMW thiol levels, which hinder cut-off values for diagnostic use. Standardisation of the analysis and measure of LMW thiol is necessary to facilitate future studies. Full article
(This article belongs to the Special Issue Oxidative Stress and Liver Disease)
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51 pages, 1540 KiB  
Systematic Review
Computer-Aided Diagnosis Systems for Automatic Malaria Parasite Detection and Classification: A Systematic Review
by Flavia Grignaffini, Patrizio Simeoni, Anna Alisi and Fabrizio Frezza
Electronics 2024, 13(16), 3174; https://doi.org/10.3390/electronics13163174 - 11 Aug 2024
Cited by 8 | Viewed by 3500
Abstract
Malaria is a disease that affects millions of people worldwide with a consistent mortality rate. The light microscope examination is the gold standard for detecting infection by malaria parasites. Still, it is limited by long timescales and requires a high level of expertise [...] Read more.
Malaria is a disease that affects millions of people worldwide with a consistent mortality rate. The light microscope examination is the gold standard for detecting infection by malaria parasites. Still, it is limited by long timescales and requires a high level of expertise from pathologists. Early diagnosis of this disease is necessary to achieve timely and effective treatment, which avoids tragic consequences, thus leading to the development of computer-aided diagnosis systems based on artificial intelligence (AI) for the detection and classification of blood cells infected with the malaria parasite in blood smear images. Such systems involve an articulated pipeline, culminating in the use of machine learning and deep learning approaches, the main branches of AI. Here, we present a systematic literature review of recent research on the use of automated algorithms to identify and classify malaria parasites in blood smear images. Based on the PRISMA 2020 criteria, a search was conducted using several electronic databases including PubMed, Scopus, and arXiv by applying inclusion/exclusion filters. From the 606 initial records identified, 135 eligible studies were selected and analyzed. Many promising results were achieved, and some mobile and web applications were developed to address resource and expertise limitations in developing countries. Full article
(This article belongs to the Special Issue Machine Learning for Biomedical Imaging Applications)
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23 pages, 6186 KiB  
Article
A Comparative Analysis of Machine Learning Algorithms for Identifying Cultural and Technological Groups in Archaeological Datasets through Clustering Analysis of Homogeneous Data
by Maurizio Troiano, Eugenio Nobile, Flavia Grignaffini, Fabio Mangini, Marco Mastrogiuseppe, Cecilia Conati Barbaro and Fabrizio Frezza
Electronics 2024, 13(14), 2752; https://doi.org/10.3390/electronics13142752 - 13 Jul 2024
Cited by 11 | Viewed by 2080
Abstract
Machine learning algorithms have revolutionized data analysis by uncovering hidden patterns and structures. Clustering algorithms play a crucial role in organizing data into coherent groups. We focused on K-Means, hierarchical, and Self-Organizing Map (SOM) clustering algorithms for analyzing homogeneous datasets based on archaeological [...] Read more.
Machine learning algorithms have revolutionized data analysis by uncovering hidden patterns and structures. Clustering algorithms play a crucial role in organizing data into coherent groups. We focused on K-Means, hierarchical, and Self-Organizing Map (SOM) clustering algorithms for analyzing homogeneous datasets based on archaeological finds from the middle phase of Pre-Pottery B Neolithic in Southern Levant (10,500–9500 cal B.P.). We aimed to assess the repeatability of these algorithms in identifying patterns using quantitative and qualitative evaluation criteria. Thorough experimentation and statistical analysis revealed the pros and cons of each algorithm, enabling us to determine their appropriateness for various clustering scenarios and data types. Preliminary results showed that traditional K-Means may not capture datasets’ intricate relationships and uncertainties. The hierarchical technique provided a more probabilistic approach, and SOM excelled at maintaining high-dimensional data structures. Our research provides valuable insights into balancing repeatability and interpretability for algorithm selection and allows professionals to identify ideal clustering solutions. Full article
(This article belongs to the Special Issue Data Retrieval and Data Mining)
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26 pages, 2639 KiB  
Systematic Review
The Use of Artificial Intelligence in the Liver Histopathology Field: A Systematic Review
by Flavia Grignaffini, Francesco Barbuto, Maurizio Troiano, Lorenzo Piazzo, Patrizio Simeoni, Fabio Mangini, Cristiano De Stefanis, Andrea Onetti Muda, Fabrizio Frezza and Anna Alisi
Diagnostics 2024, 14(4), 388; https://doi.org/10.3390/diagnostics14040388 - 10 Feb 2024
Cited by 8 | Viewed by 4370
Abstract
Digital pathology (DP) has begun to play a key role in the evaluation of liver specimens. Recent studies have shown that a workflow that combines DP and artificial intelligence (AI) applied to histopathology has potential value in supporting the diagnosis, treatment evaluation, and [...] Read more.
Digital pathology (DP) has begun to play a key role in the evaluation of liver specimens. Recent studies have shown that a workflow that combines DP and artificial intelligence (AI) applied to histopathology has potential value in supporting the diagnosis, treatment evaluation, and prognosis prediction of liver diseases. Here, we provide a systematic review of the use of this workflow in the field of hepatology. Based on the PRISMA 2020 criteria, a search of the PubMed, SCOPUS, and Embase electronic databases was conducted, applying inclusion/exclusion filters. The articles were evaluated by two independent reviewers, who extracted the specifications and objectives of each study, the AI tools used, and the results obtained. From the 266 initial records identified, 25 eligible studies were selected, mainly conducted on human liver tissues. Most of the studies were performed using whole-slide imaging systems for imaging acquisition and applying different machine learning and deep learning methods for image pre-processing, segmentation, feature extractions, and classification. Of note, most of the studies selected demonstrated good performance as classifiers of liver histological images compared to pathologist annotations. Promising results to date bode well for the not-too-distant inclusion of these techniques in clinical practice. Full article
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24 pages, 7769 KiB  
Article
Anomaly Detection for Skin Lesion Images Using Convolutional Neural Network and Injection of Handcrafted Features: A Method That Bypasses the Preprocessing of Dermoscopic Images
by Flavia Grignaffini, Maurizio Troiano, Francesco Barbuto, Patrizio Simeoni, Fabio Mangini, Gabriele D’Andrea, Lorenzo Piazzo, Carmen Cantisani, Noah Musolff, Costantino Ricciuti and Fabrizio Frezza
Algorithms 2023, 16(10), 466; https://doi.org/10.3390/a16100466 - 2 Oct 2023
Cited by 9 | Viewed by 4269
Abstract
Skin cancer (SC) is one of the most common cancers in the world and is a leading cause of death in humans. Melanoma (M) is the most aggressive form of skin cancer and has an increasing incidence rate. Early and accurate diagnosis of [...] Read more.
Skin cancer (SC) is one of the most common cancers in the world and is a leading cause of death in humans. Melanoma (M) is the most aggressive form of skin cancer and has an increasing incidence rate. Early and accurate diagnosis of M is critical to increase patient survival rates; however, its clinical evaluation is limited by the long timelines, variety of interpretations, and difficulty in distinguishing it from nevi (N) because of striking similarities. To overcome these problems and to support dermatologists, several machine-learning (ML) and deep-learning (DL) approaches have been developed. In the proposed work, melanoma detection, understood as an anomaly detection task with respect to the normal condition consisting of nevi, is performed with the help of a convolutional neural network (CNN) along with the handcrafted texture features of the dermoscopic images as additional input in the training phase. The aim is to evaluate whether the preprocessing and segmentation steps of dermoscopic images can be bypassed while maintaining high classification performance. Network training is performed on the ISIC2018 and ISIC2019 datasets, from which only melanomas and nevi are considered. The proposed network is compared with the most widely used pre-trained networks in the field of dermatology and shows better results in terms of classification and computational cost. It is also tested on the ISIC2016 dataset to provide a comparison with the literature: it achieves high performance in terms of accuracy, sensitivity, and specificity. Full article
(This article belongs to the Special Issue Deep Learning for Anomaly Detection)
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30 pages, 2252 KiB  
Systematic Review
Machine Learning Approaches for Skin Cancer Classification from Dermoscopic Images: A Systematic Review
by Flavia Grignaffini, Francesco Barbuto, Lorenzo Piazzo, Maurizio Troiano, Patrizio Simeoni, Fabio Mangini, Giovanni Pellacani, Carmen Cantisani and Fabrizio Frezza
Algorithms 2022, 15(11), 438; https://doi.org/10.3390/a15110438 - 21 Nov 2022
Cited by 38 | Viewed by 8431
Abstract
Skin cancer (SC) is one of the most prevalent cancers worldwide. Clinical evaluation of skin lesions is necessary to assess the characteristics of the disease; however, it is limited by long timelines and variety in interpretation. As early and accurate diagnosis of SC [...] Read more.
Skin cancer (SC) is one of the most prevalent cancers worldwide. Clinical evaluation of skin lesions is necessary to assess the characteristics of the disease; however, it is limited by long timelines and variety in interpretation. As early and accurate diagnosis of SC is crucial to increase patient survival rates, machine-learning (ML) and deep-learning (DL) approaches have been developed to overcome these issues and support dermatologists. We present a systematic literature review of recent research on the use of machine learning to classify skin lesions with the aim of providing a solid starting point for researchers beginning to work in this area. A search was conducted in several electronic databases by applying inclusion/exclusion filters and for this review, only those documents that clearly and completely described the procedures performed and reported the results obtained were selected. Sixty-eight articles were selected, of which the majority use DL approaches, in particular convolutional neural networks (CNN), while a smaller portion rely on ML techniques or hybrid ML/DL approaches for skin cancer detection and classification. Many ML and DL methods show high performance as classifiers of skin lesions. The promising results obtained to date bode well for the not-too-distant inclusion of these techniques in clinical practice. Full article
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6 pages, 241 KiB  
Communication
Melanoma Detection by Non-Specialists: An Untapped Potential for Triage?
by Carmen Cantisani, Luca Ambrosio, Carlotta Cucchi, Fanni Adél Meznerics, Norbert Kiss, András Bánvölgyi, Federica Rega, Flavia Grignaffini, Francesco Barbuto, Fabrizio Frezza and Giovanni Pellacani
Diagnostics 2022, 12(11), 2821; https://doi.org/10.3390/diagnostics12112821 - 16 Nov 2022
Cited by 15 | Viewed by 2076
Abstract
Introduction: The incidence of melanoma increased considerably in recent decades, representing a significant public health problem. We aimed to evaluate the ability of non-specialists for the preliminary screening of skin lesions to identify melanoma-suspect lesions. Materials and Methods: A medical student and a [...] Read more.
Introduction: The incidence of melanoma increased considerably in recent decades, representing a significant public health problem. We aimed to evaluate the ability of non-specialists for the preliminary screening of skin lesions to identify melanoma-suspect lesions. Materials and Methods: A medical student and a dermatologist specialist examined the total body scans of 50 patients. Results: The agreement between the expert and the non-specialist was 87.75% (κ = 0.65) regarding the assessment of clinical significance. The four parameters of the ABCD rule were evaluated on the 129 lesions rated as clinically significant by both observers. Asymmetry was evaluated similarly in 79.9% (κ = 0.59), irregular borders in 74.4% (κ = 0.50), color in 81.4% (κ = 0.57), and diameter in 89.9% (κ = 0.77) of the cases. The concordance of the two groups was 96.9% (κ = 0.83) in the case of the detection of the Ugly Duckling Sign. Conclusions: Although the involvement of GPs is part of routine care worldwide, emphasizing the importance of educating medical students and general practitioners is crucial, as many European countries lack structured melanoma screening training programs targeting non-dermatologists. Full article
(This article belongs to the Special Issue Imaging Diagnosis for Melanoma 2.0)
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