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2023
Journal article
Open Access
Brain metastases from NSCLC treated with stereotactic radiotherapy: prediction mismatch between two different radiomic platforms
Carloni G, Garibaldi C, Marvaso G, Volpe S, Zaffaroni M, Pepa M, Isaksson Lj, Colombo F, Durante S, Lo Presti G, Raimondi S, Spaggiari Lj, De Marinis F, Piperno G, Vigorito S, Gandini S, Cremonesi M, Positano V, Jereczekfossa Ba
Background and purpose. Radiomics enables the mining of quantitative features from medical images. The influence of the radiomic feature extraction software on the final performance of models is still a poorly understood topic. This study aimed to investigate the ability of radiomic features extracted by two different radiomic platforms to predict clinical outcomes in patients treated with radiosurgery for brain metastases from non-small cell lung cancer. We developed models integrating pre-treatment magnetic resonance imaging (MRI)-derived radiomic features and clinical data. Materials and methods. Pre-radiotherapy gadolinium enhanced axial T1-weighted MRI scans were used. MRI images were re-sampled, intensity-shifted, and histogram-matched before radiomic extraction by means of two different platforms (PyRadiomics and SOPHiA Radiomics). We adopted LASSO Cox regression models for multivariable analyses by creating radiomic, clinical, and combined models using three survival clinical endpoints (local control, distant progression, and overall survival). The statistical analysis was repeated 50 times with different random seeds and the median concordance index was used as performance metric of the models. Results. We analysed 276 metastases from 148 patients. The use of the two platforms resulted in differences in both the quality and the number of extractable features. That led to mismatches in terms of end-to-end performance, statistical significance of radiomic scores, and clinical covariates found significant in combined models. Conclusion. This study shed new light on how extracting radiomic features from the same images using two different platforms could yield several discrepancies. That may lead to acute consequences on drawing conclusions, comparing results across the literature, and translating radiomics into clinical practice.Source: RADIOTHERAPY AND ONCOLOGY, vol. 178
Carloni G, Garibaldi C, Marvaso G, Volpe S, Zaffaroni M, Pepa M, Isaksson Lj, Colombo F, Durante S, Lo Presti G, Raimondi S, Spaggiari Lj, De Marinis F, Piperno G, Vigorito S, Gandini S, Cremonesi M, Positano V, Jereczekfossa Ba
Background and purpose. Radiomics enables the mining of quantitative features from medical images. The influence of the radiomic feature extraction software on the final performance of models is still a poorly understood topic. This study aimed to investigate the ability of radiomic features extracted by two different radiomic platforms to predict clinical outcomes in patients treated with radiosurgery for brain metastases from non-small cell lung cancer. We developed models integrating pre-treatment magnetic resonance imaging (MRI)-derived radiomic features and clinical data. Materials and methods. Pre-radiotherapy gadolinium enhanced axial T1-weighted MRI scans were used. MRI images were re-sampled, intensity-shifted, and histogram-matched before radiomic extraction by means of two different platforms (PyRadiomics and SOPHiA Radiomics). We adopted LASSO Cox regression models for multivariable analyses by creating radiomic, clinical, and combined models using three survival clinical endpoints (local control, distant progression, and overall survival). The statistical analysis was repeated 50 times with different random seeds and the median concordance index was used as performance metric of the models. Results. We analysed 276 metastases from 148 patients. The use of the two platforms resulted in differences in both the quality and the number of extractable features. That led to mismatches in terms of end-to-end performance, statistical significance of radiomic scores, and clinical covariates found significant in combined models. Conclusion. This study shed new light on how extracting radiomic features from the same images using two different platforms could yield several discrepancies. That may lead to acute consequences on drawing conclusions, comparing results across the literature, and translating radiomics into clinical practice.Source: RADIOTHERAPY AND ONCOLOGY, vol. 178
See at:
CNR IRIS 
| ISTI Repository | www.sciencedirect.com | CNR IRIS 
| CNR IRIS
2024
Contribution to book
Open Access
Cine cardiac MRI reconstruction using a convolutional recurrent network with refinement
Xue Y, Du Y, Carloni G, Pachetti E, Jordan C, Tsaftaris Sa
Cine Magnetic Resonance Imaging (MRI) allows for understanding of the heart's function and condition in a non-invasive manner. Undersampling of the k-space is employed to reduce the scan duration, thus increasing patient comfort and reducing the risk of motion artefacts, at the cost of reduced image quality. In this challenge paper, we investigate the use of a convolutional recurrent neural network (CRNN) architecture to exploit temporal correlations in supervised cine cardiac MRI reconstruction. This is combined with a single-image super-resolution refinement module to improve single coil reconstruction by 4.4% in structural similarity and 3.9% in normalised mean square error compared to a plain CRNN implementation. We deploy a high-pass filter to our l1 loss to allow greater emphasis on high-frequency details which are missingin the original data. The proposed model demonstrates considerable enhancements compared to the baseline case and holds promising potential for further improving cardiac MRI reconstruction.Source: LECTURE NOTES IN COMPUTER SCIENCE, vol. 14507, pp. 421-432
Xue Y, Du Y, Carloni G, Pachetti E, Jordan C, Tsaftaris Sa
Cine Magnetic Resonance Imaging (MRI) allows for understanding of the heart's function and condition in a non-invasive manner. Undersampling of the k-space is employed to reduce the scan duration, thus increasing patient comfort and reducing the risk of motion artefacts, at the cost of reduced image quality. In this challenge paper, we investigate the use of a convolutional recurrent neural network (CRNN) architecture to exploit temporal correlations in supervised cine cardiac MRI reconstruction. This is combined with a single-image super-resolution refinement module to improve single coil reconstruction by 4.4% in structural similarity and 3.9% in normalised mean square error compared to a plain CRNN implementation. We deploy a high-pass filter to our l1 loss to allow greater emphasis on high-frequency details which are missingin the original data. The proposed model demonstrates considerable enhancements compared to the baseline case and holds promising potential for further improving cardiac MRI reconstruction.Source: LECTURE NOTES IN COMPUTER SCIENCE, vol. 14507, pp. 421-432
See at:
CNR IRIS | link.springer.com | CNR IRIS | CNR IRIS
2024
Conference article
Open Access
CROCODILE: Causality aids RObustness via COntrastive DIsentangled LEarning
Carloni G., Tsaftaris S. A., Colantonio S.
Due to domain shift, deep learning image classifiers perform poorly whenapplied to a domain different from the training one. For instance, a classifiertrained on chest X-ray (CXR) images from one hospital may not generalize toimages from another hospital due to variations in scanner settings or patientcharacteristics. In this paper, we introduce our CROCODILE framework, showinghow tools from causality can foster a model's robustness to domain shift viafeature disentanglement, contrastive learning losses, and the injection ofprior knowledge. This way, the model relies less on spurious correlations,learns the mechanism bringing from images to prediction better, and outperformsbaselines on out-of-distribution (OOD) data. We apply our method to multi-labellung disease classification from CXRs, utilizing over 750000 images from fourdatasets. Our bias-mitigation method improves domain generalization andfairness, broadening the applicability and reliability of deep learning modelsfor a safer medical image analysis. Find our code at:https://github.com/gianlucarloni/crocodile.Source: LECTURE NOTES IN COMPUTER SCIENCE, vol. 15167, pp. 105-116. Marrakech, Morocco, 6-10/10/2024
Carloni G., Tsaftaris S. A., Colantonio S.
Due to domain shift, deep learning image classifiers perform poorly whenapplied to a domain different from the training one. For instance, a classifiertrained on chest X-ray (CXR) images from one hospital may not generalize toimages from another hospital due to variations in scanner settings or patientcharacteristics. In this paper, we introduce our CROCODILE framework, showinghow tools from causality can foster a model's robustness to domain shift viafeature disentanglement, contrastive learning losses, and the injection ofprior knowledge. This way, the model relies less on spurious correlations,learns the mechanism bringing from images to prediction better, and outperformsbaselines on out-of-distribution (OOD) data. We apply our method to multi-labellung disease classification from CXRs, utilizing over 750000 images from fourdatasets. Our bias-mitigation method improves domain generalization andfairness, broadening the applicability and reliability of deep learning modelsfor a safer medical image analysis. Find our code at:https://github.com/gianlucarloni/crocodile.Source: LECTURE NOTES IN COMPUTER SCIENCE, vol. 15167, pp. 105-116. Marrakech, Morocco, 6-10/10/2024
See at:
CNR IRIS | link.springer.com | CNR IRIS | CNR IRIS
2024
Conference article
Open Access
Connectivity-inspired network for context-aware recognition
Carloni G., Colantonio S.
The aim of this paper is threefold. We inform the AI practitioner about thehuman visual system with an extensive literature review; we propose a novelbiologically motivated neural network for image classification; and, finally,we present a new plug-and-play module to model context awareness. We focus onthe effect of incorporating circuit motifs found in biological brains toaddress visual recognition. Our convolutional architecture is inspired by theconnectivity of human cortical and subcortical streams, and we implementbottom-up and top-down modulations that mimic the extensive afferent andefferent connections between visual and cognitive areas. Our ContextualAttention Block is simple and effective and can be integrated with anyfeed-forward neural network. It infers weights that multiply the feature mapsaccording to their causal influence on the scene, modeling the co-occurrence ofdifferent objects in the image. We place our module at different bottlenecks toinfuse a hierarchical context awareness into the model. We validated ourproposals through image classification experiments on benchmark data and founda consistent improvement in performance and the robustness of the producedexplanations via class activation. Our code is available at https://github.com/gianlucarloni/CoCoReco.Source: LECTURE NOTES IN COMPUTER SCIENCE, vol. 15138. Milano, Italia, 29/09-04/10/2024
Project(s): ProCAncer-I
, PAR FAS Tuscany - PRAMA
Carloni G., Colantonio S.
The aim of this paper is threefold. We inform the AI practitioner about thehuman visual system with an extensive literature review; we propose a novelbiologically motivated neural network for image classification; and, finally,we present a new plug-and-play module to model context awareness. We focus onthe effect of incorporating circuit motifs found in biological brains toaddress visual recognition. Our convolutional architecture is inspired by theconnectivity of human cortical and subcortical streams, and we implementbottom-up and top-down modulations that mimic the extensive afferent andefferent connections between visual and cognitive areas. Our ContextualAttention Block is simple and effective and can be integrated with anyfeed-forward neural network. It infers weights that multiply the feature mapsaccording to their causal influence on the scene, modeling the co-occurrence ofdifferent objects in the image. We place our module at different bottlenecks toinfuse a hierarchical context awareness into the model. We validated ourproposals through image classification experiments on benchmark data and founda consistent improvement in performance and the robustness of the producedexplanations via class activation. Our code is available at https://github.com/gianlucarloni/CoCoReco.Source: LECTURE NOTES IN COMPUTER SCIENCE, vol. 15138. Milano, Italia, 29/09-04/10/2024
Project(s): ProCAncer-I
, PAR FAS Tuscany - PRAMA
2024
Journal article
Open Access
Exploiting causality signals in medical images: a pilot study with empirical results
Carloni Gianluca, Colantonio Sara
We present a novel technique to discover and exploit weak causal signals directly from images via neural networks for classification purposes. This way, we model how the presence of a feature in one part of the image affects the appearance of another feature in a different part of the image. Our method consists of a convolutional neural network backbone and a causality-factors extractor module, which computes weights to enhance each feature map according to its causal influence in the scene. We develop different architecture variants and empirically evaluate all the models on two public datasets of prostate MRI images and breast histopathology slides for cancer diagnosis. We study the effectiveness of our module both in fully-supervised and few-shot learning, we assess its addition to existing attention-based solutions, we conduct ablation studies, and investigate the explainability of our models via class activation maps. Our findings show that our lightweight block extracts meaningful information and improves the overall classification, together with producing more robust predictions that focus on relevant parts of the image. That is crucial in medical imaging, where accurate and reliable classifications are essential for effective diagnosis and treatment planning.Source: EXPERT SYSTEMS WITH APPLICATIONS, vol. 249 (issue Part A)
Project(s): ProCAncer-I, NAVIGATOR: An Imaging Biobank to Precisely Prevent and Predict cancer, and facilitate the Participation of oncologic patients to Diagnosis and Treatment
Carloni Gianluca, Colantonio Sara
We present a novel technique to discover and exploit weak causal signals directly from images via neural networks for classification purposes. This way, we model how the presence of a feature in one part of the image affects the appearance of another feature in a different part of the image. Our method consists of a convolutional neural network backbone and a causality-factors extractor module, which computes weights to enhance each feature map according to its causal influence in the scene. We develop different architecture variants and empirically evaluate all the models on two public datasets of prostate MRI images and breast histopathology slides for cancer diagnosis. We study the effectiveness of our module both in fully-supervised and few-shot learning, we assess its addition to existing attention-based solutions, we conduct ablation studies, and investigate the explainability of our models via class activation maps. Our findings show that our lightweight block extracts meaningful information and improves the overall classification, together with producing more robust predictions that focus on relevant parts of the image. That is crucial in medical imaging, where accurate and reliable classifications are essential for effective diagnosis and treatment planning.Source: EXPERT SYSTEMS WITH APPLICATIONS, vol. 249 (issue Part A)
Project(s): ProCAncer-I
, NAVIGATOR: An Imaging Biobank to Precisely Prevent and Predict cancer, and facilitate the Participation of oncologic patients to Diagnosis and Treatment
See at:
CNR IRIS | www.sciencedirect.com | CNR IRIS
2023
Conference article
Open Access
On the applicability of prototypical part learning in medical images: breast masses classification using ProtoPNet
Carloni G, Berti A, Iacconi C, Pascali Ma, Colantonio S
Deep learning models have become state-of-the-art in many areas, ranging from computer vision to agriculture research. However, concerns have been raised with respect to the transparency of their decisions, especially in the image domain. In this regard, Explainable Artificial Intelligence has been gaining popularity in recent years. The ProtoPNet model, which breaks down an image into prototypes and uses evidence gathered from the prototypes to classify an image, represents an appealing approach. Still, questions regarding its effectiveness arise when the application domain changes from real-world natural images to gray-scale medical images. This work explores the applicability of prototypical part learning in medical imaging by experimenting with ProtoPNet on a breast masses classification task. The two considered aspects were the classification capabilities and the validity of explanations. We looked for the optimal model's hyperparameter configuration via a random search. We trained the model in a five-fold CV supervised framework, with mammogram images cropped around the lesions and ground-truth labels of benign/malignant masses. Then, we compared the performance metrics of ProtoPNet to that of the corresponding base architecture, which was ResNet18, trained under the same framework. In addition, an experienced radiologist provided a clinical viewpoint on the quality of the learned prototypes, the patch activations, and the global explanations. We achieved a Recall of 0.769 and an area under the receiver operating characteristic curve of 0.719 in our experiments. Even though our findings are non-optimal for entering the clinical practice yet, the radiologist found ProtoPNet's explanations very intuitive, reporting a high level of satisfaction. Therefore, we believe that prototypical part learning offers a reasonable and promising trade-off between classification performance and the quality of the related explanation.
Carloni G, Berti A, Iacconi C, Pascali Ma, Colantonio S
Deep learning models have become state-of-the-art in many areas, ranging from computer vision to agriculture research. However, concerns have been raised with respect to the transparency of their decisions, especially in the image domain. In this regard, Explainable Artificial Intelligence has been gaining popularity in recent years. The ProtoPNet model, which breaks down an image into prototypes and uses evidence gathered from the prototypes to classify an image, represents an appealing approach. Still, questions regarding its effectiveness arise when the application domain changes from real-world natural images to gray-scale medical images. This work explores the applicability of prototypical part learning in medical imaging by experimenting with ProtoPNet on a breast masses classification task. The two considered aspects were the classification capabilities and the validity of explanations. We looked for the optimal model's hyperparameter configuration via a random search. We trained the model in a five-fold CV supervised framework, with mammogram images cropped around the lesions and ground-truth labels of benign/malignant masses. Then, we compared the performance metrics of ProtoPNet to that of the corresponding base architecture, which was ResNet18, trained under the same framework. In addition, an experienced radiologist provided a clinical viewpoint on the quality of the learned prototypes, the patch activations, and the global explanations. We achieved a Recall of 0.769 and an area under the receiver operating characteristic curve of 0.719 in our experiments. Even though our findings are non-optimal for entering the clinical practice yet, the radiologist found ProtoPNet's explanations very intuitive, reporting a high level of satisfaction. Therefore, we believe that prototypical part learning offers a reasonable and promising trade-off between classification performance and the quality of the related explanation.
See at:
CNR IRIS | link.springer.com | ISTI Repository | CNR IRIS | CNR IRIS
2023
Journal article
Open Access
The role of causality in explainable artificial intelligence
Carloni G, Berti A, Colantonio S
Causality and eXplainable Artificial Intelligence (XAI) have developed as separate fields in computer science, even though the underlying concepts of causation and explanation share common ancient roots. This is further enforced by the lack of review works jointly covering these two fields. In this paper, we investigate the literature to try to understand how and to what extent causality and XAI are intertwined. More precisely, we seek to uncover what kinds of relationships exist between the two concepts and how one can benefit from them, for instance, in building trust in AI systems. As a result, three main perspectives are identified. In the first one, the lack of causality is seen as one of the major limitations of current AI and XAI approaches, and the "optimal" form of explanations is investigated. The second is a pragmatic perspective and considers XAI as a tool to foster scientific exploration for causal inquiry, via the identification of pursue-worthy experimental manipulations. Finally, the third perspective supports the idea that causality is propaedeutic to XAI in three possible manners: exploiting concepts borrowed from causality to support or improve XAI, utilizing counterfactuals for explainability, and considering accessing a causal model as explaining itself. To complement our analysis, we also provide relevant software solutions used to automate causal tasks. We believe our work provides a unified view of the two fields of causality and XAI by highlighting potential domain bridges and uncovering possible limitations.Source: WILEY INTERDISCIPLINARY REVIEWS. DATA MINING AND KNOWLEDGE DISCOVERY
Project(s): ProCAncer-I
Carloni G, Berti A, Colantonio S
Causality and eXplainable Artificial Intelligence (XAI) have developed as separate fields in computer science, even though the underlying concepts of causation and explanation share common ancient roots. This is further enforced by the lack of review works jointly covering these two fields. In this paper, we investigate the literature to try to understand how and to what extent causality and XAI are intertwined. More precisely, we seek to uncover what kinds of relationships exist between the two concepts and how one can benefit from them, for instance, in building trust in AI systems. As a result, three main perspectives are identified. In the first one, the lack of causality is seen as one of the major limitations of current AI and XAI approaches, and the "optimal" form of explanations is investigated. The second is a pragmatic perspective and considers XAI as a tool to foster scientific exploration for causal inquiry, via the identification of pursue-worthy experimental manipulations. Finally, the third perspective supports the idea that causality is propaedeutic to XAI in three possible manners: exploiting concepts borrowed from causality to support or improve XAI, utilizing counterfactuals for explainability, and considering accessing a causal model as explaining itself. To complement our analysis, we also provide relevant software solutions used to automate causal tasks. We believe our work provides a unified view of the two fields of causality and XAI by highlighting potential domain bridges and uncovering possible limitations.Source: WILEY INTERDISCIPLINARY REVIEWS. DATA MINING AND KNOWLEDGE DISCOVERY
Project(s): ProCAncer-I
See at:
arxiv.org | CNR IRIS | ISTI Repository | CNR IRIS
2023
Conference article
Open Access
Causality-driven one-shot learning for prostate cancer grading from MRI
Carloni G, Pachetti E, Colantonio S
In this paper, we present a novel method to automatically classify medical images that learns and leverages weak causal signals in the image. Our framework consists of a convolutional neural network backbone and a causality-extractor module that extracts cause-effect relationships between feature maps that can inform the model on the appearance of a feature in one place of the image, given the presence of another feature within some other place of the image. To evaluate the effectiveness of our approach in low-data scenarios, we train our causality-driven architecture in a One-shot learning scheme, where we propose a new meta-learning procedure entailing meta-training and meta-testing tasks that are designed using related classes but at different levels of granularity. We conduct binary and multi-class classification experiments on a publicly available dataset of prostate MRI images. To validate the effectiveness of the proposed causality-driven module, we perform an ablation study and conduct qualitative assessments using class activation maps to highlight regions strongly influencing the network's decision-making process. Our findings show that causal relationships among features play a crucial role in enhancing the model's ability to discern relevant information and yielding more reliable and interpretable predictions. This would make it a promising approach for medical image classification tasks.
Carloni G, Pachetti E, Colantonio S
In this paper, we present a novel method to automatically classify medical images that learns and leverages weak causal signals in the image. Our framework consists of a convolutional neural network backbone and a causality-extractor module that extracts cause-effect relationships between feature maps that can inform the model on the appearance of a feature in one place of the image, given the presence of another feature within some other place of the image. To evaluate the effectiveness of our approach in low-data scenarios, we train our causality-driven architecture in a One-shot learning scheme, where we propose a new meta-learning procedure entailing meta-training and meta-testing tasks that are designed using related classes but at different levels of granularity. We conduct binary and multi-class classification experiments on a publicly available dataset of prostate MRI images. To validate the effectiveness of the proposed causality-driven module, we perform an ablation study and conduct qualitative assessments using class activation maps to highlight regions strongly influencing the network's decision-making process. Our findings show that causal relationships among features play a crucial role in enhancing the model's ability to discern relevant information and yielding more reliable and interpretable predictions. This would make it a promising approach for medical image classification tasks.
See at:
CNR IRIS | ieeexplore.ieee.org | ISTI Repository | CNR IRIS | CNR IRIS
2024
Journal article
Open Access
Optimizing radiomics for prostate cancer diagnosis: feature selection strategies, machine learning classifiers, and MRI sequences
Mylona E., Zaridis D. I., Kalantzopoulos C., Tachos N. S., Regge D., Papanikolaou N., Tsiknakis M., Marias K., Marquez R., Henne T., Saillant C., Mora J. M., Pastor A. J., Agraniotis D., Pollalis C., Giavri Z., Hernandez W., Correia J., Bridge C., Kalpathy-Cramer J., Carloni G., Berti A., Germanese D., Del Corso G., Pachetti E., Pascali M. A., Colantonio S., Napolitano V., Maimone G., Cappello G., Mazzetti S., Giannini V., García-Martí G., Jacobs T., Doran S., Ribeiro A., Vit S., Emsley R., Koh D. M., Georgios G., Vasilis K., Slidevska K., Untanas A., Briediene R., Usinskiene J., Vilanova J. C., Karcaaltincaba M., Atak F., Karaosmanoglu A. D., Özmen M., Akata D., Nan, Mendola V., Tumminello L., Aringhieri G., Neri E., Marfil M., Navarro S., Ribas G., Cerdá-Alberich L., Martí-Bonmatí L., Futterer J., Twilt J. J., Saha A., De Rooij M., Huisman H., Chambel M., Rodrigues N., Rodrigues A. C., Verde A. C., De Almeida J. G., Dimitriadis A., Kalliatakis G., Trivizakis E., Kalokyri V., Sfakianakis S., Fotiadis D. I.
Objectives: Radiomics-based analyses encompass multiple steps, leading to ambiguity regarding the optimal approaches for enhancing model performance. This study compares the effect of several feature selection methods, machine learning (ML) classifiers, and sources of radiomic features, on models' performance for the diagnosis of clinically significant prostate cancer (csPCa) from bi-parametric MRI. Methods: Two multi-centric datasets, with 465 and 204 patients each, were used to extract 1246 radiomic features per patient and MRI sequence. Ten feature selection methods, such as Boruta, mRMRe, ReliefF, recursive feature elimination (RFE), random forest (RF) variable importance, L1-lasso, etc., four ML classifiers, namely SVM, RF, LASSO, and boosted generalized linear model (GLM), and three sets of radiomics features, derived from T2w images, ADC maps, and their combination, were used to develop predictive models of csPCa. Their performance was evaluated in a nested cross-validation and externally, using seven performance metrics. Results: In total, 480 models were developed. In nested cross-validation, the best model combined Boruta with Boosted GLM (AUC = 0.71, F1 = 0.76). In external validation, the best model combined L1-lasso with boosted GLM (AUC = 0.71, F1 = 0.47). Overall, Boruta, RFE, L1-lasso, and RF variable importance were the top-performing feature selection methods, while the choice of ML classifier didn't significantly affect the results. The ADC-derived features showed the highest discriminatory power with T2w-derived features being less informative, while their combination did not lead to improved performance. Conclusion: The choice of feature selection method and the source of radiomic features have a profound effect on the models' performance for csPCa diagnosis. Critical relevance statement: This work may guide future radiomic research, paving the way for the development of more effective and reliable radiomic models; not only for advancing prostate cancer diagnostic strategies, but also for informing broader applications of radiomics in different medical contexts. Key points: Radiomics is a growing field that can still be optimized. Feature selection method impacts radiomics models' performance more than ML algorithms. Best feature selection methods: RFE, LASSO, RF, and Boruta. ADC-derived radiomic features yield more robust models compared to T2w-derived radiomic features.Source: INSIGHTS INTO IMAGING, vol. 15 (issue 1)
Project(s): ProCAncer-I
Mylona E., Zaridis D. I., Kalantzopoulos C., Tachos N. S., Regge D., Papanikolaou N., Tsiknakis M., Marias K., Marquez R., Henne T., Saillant C., Mora J. M., Pastor A. J., Agraniotis D., Pollalis C., Giavri Z., Hernandez W., Correia J., Bridge C., Kalpathy-Cramer J., Carloni G., Berti A., Germanese D., Del Corso G., Pachetti E., Pascali M. A., Colantonio S., Napolitano V., Maimone G., Cappello G., Mazzetti S., Giannini V., García-Martí G., Jacobs T., Doran S., Ribeiro A., Vit S., Emsley R., Koh D. M., Georgios G., Vasilis K., Slidevska K., Untanas A., Briediene R., Usinskiene J., Vilanova J. C., Karcaaltincaba M., Atak F., Karaosmanoglu A. D., Özmen M., Akata D., Nan, Mendola V., Tumminello L., Aringhieri G., Neri E., Marfil M., Navarro S., Ribas G., Cerdá-Alberich L., Martí-Bonmatí L., Futterer J., Twilt J. J., Saha A., De Rooij M., Huisman H., Chambel M., Rodrigues N., Rodrigues A. C., Verde A. C., De Almeida J. G., Dimitriadis A., Kalliatakis G., Trivizakis E., Kalokyri V., Sfakianakis S., Fotiadis D. I.
Objectives: Radiomics-based analyses encompass multiple steps, leading to ambiguity regarding the optimal approaches for enhancing model performance. This study compares the effect of several feature selection methods, machine learning (ML) classifiers, and sources of radiomic features, on models' performance for the diagnosis of clinically significant prostate cancer (csPCa) from bi-parametric MRI. Methods: Two multi-centric datasets, with 465 and 204 patients each, were used to extract 1246 radiomic features per patient and MRI sequence. Ten feature selection methods, such as Boruta, mRMRe, ReliefF, recursive feature elimination (RFE), random forest (RF) variable importance, L1-lasso, etc., four ML classifiers, namely SVM, RF, LASSO, and boosted generalized linear model (GLM), and three sets of radiomics features, derived from T2w images, ADC maps, and their combination, were used to develop predictive models of csPCa. Their performance was evaluated in a nested cross-validation and externally, using seven performance metrics. Results: In total, 480 models were developed. In nested cross-validation, the best model combined Boruta with Boosted GLM (AUC = 0.71, F1 = 0.76). In external validation, the best model combined L1-lasso with boosted GLM (AUC = 0.71, F1 = 0.47). Overall, Boruta, RFE, L1-lasso, and RF variable importance were the top-performing feature selection methods, while the choice of ML classifier didn't significantly affect the results. The ADC-derived features showed the highest discriminatory power with T2w-derived features being less informative, while their combination did not lead to improved performance. Conclusion: The choice of feature selection method and the source of radiomic features have a profound effect on the models' performance for csPCa diagnosis. Critical relevance statement: This work may guide future radiomic research, paving the way for the development of more effective and reliable radiomic models; not only for advancing prostate cancer diagnostic strategies, but also for informing broader applications of radiomics in different medical contexts. Key points: Radiomics is a growing field that can still be optimized. Feature selection method impacts radiomics models' performance more than ML algorithms. Best feature selection methods: RFE, LASSO, RF, and Boruta. ADC-derived radiomic features yield more robust models compared to T2w-derived radiomic features.Source: INSIGHTS INTO IMAGING, vol. 15 (issue 1)
Project(s): ProCAncer-I
See at:
CNR IRIS | insightsimaging.springeropen.com | CNR IRIS
2022
Conference article
Open Access
Data models for an imaging bio-bank for colorectal, prostate and gastric cancer: the NAVIGATOR project
Berti A, Carloni G, Colantonio S, Pascali Ma, Manghi P, Pagano P, Buongiorno R, Pachetti E, Caudai C, Di Gangi D, Carlini E, Falaschi Z, Ciarrocchi E, Neri E, Bertelli E, Miele V, Carpi R, Bagnacci G, Di Meglio N, Mazzei Ma, Barucci A
Researchers nowadays may take advantage of broad collections of medical data to develop personalized medicine solutions. Imaging bio-banks play a fundamental role, in this regard, by serving as organized repositories of medical images associated with imaging biomarkers. In this context, the NAVIGATOR Project aims to advance colorectal, prostate, and gastric oncology translational research by leveraging quantitative imaging and multi-omics analyses. As Project's core, an imaging bio-bank is being designed and implemented in a web-accessible Virtual Research Environment (VRE). The VRE serves to extract the imaging biomarkers and further process them within prediction algorithms. In our work, we present the realization of the data models for the three cancer use-cases of the Project. First, we carried out an extensive requirements analysis to fulfill the necessities of the clinical partners involved in the Project. Then, we designed three separate data models utilizing entity-relationship diagrams. We found diagrams' modeling for colorectal and prostate cancers to be more straightforward, while gastric cancer required a higher level of complexity. Future developments of this work would include designing a common data model following the Observational Medical Outcomes Partnership Standards. Indeed, a common data model would standardize the logical infrastructure of data models and make the bio-bank easily interoperable with other bio-banks.
Berti A, Carloni G, Colantonio S, Pascali Ma, Manghi P, Pagano P, Buongiorno R, Pachetti E, Caudai C, Di Gangi D, Carlini E, Falaschi Z, Ciarrocchi E, Neri E, Bertelli E, Miele V, Carpi R, Bagnacci G, Di Meglio N, Mazzei Ma, Barucci A
Researchers nowadays may take advantage of broad collections of medical data to develop personalized medicine solutions. Imaging bio-banks play a fundamental role, in this regard, by serving as organized repositories of medical images associated with imaging biomarkers. In this context, the NAVIGATOR Project aims to advance colorectal, prostate, and gastric oncology translational research by leveraging quantitative imaging and multi-omics analyses. As Project's core, an imaging bio-bank is being designed and implemented in a web-accessible Virtual Research Environment (VRE). The VRE serves to extract the imaging biomarkers and further process them within prediction algorithms. In our work, we present the realization of the data models for the three cancer use-cases of the Project. First, we carried out an extensive requirements analysis to fulfill the necessities of the clinical partners involved in the Project. Then, we designed three separate data models utilizing entity-relationship diagrams. We found diagrams' modeling for colorectal and prostate cancers to be more straightforward, while gastric cancer required a higher level of complexity. Future developments of this work would include designing a common data model following the Observational Medical Outcomes Partnership Standards. Indeed, a common data model would standardize the logical infrastructure of data models and make the bio-bank easily interoperable with other bio-banks.
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CNR IRIS | ieeexplore.ieee.org | ISTI Repository | CNR IRIS | CNR IRIS
2023
Conference article
Open Access
Exploring the potentials and challenges of AI in supporting clinical diagnostics and remote assistance for the health and well-being of individuals
Berti A, Buongiorno R, Carloni G, Caudai C, Del Corso G, Germanese D, Pachetti E, Pascali Ma, Colantonio S
Innovative technologies powered by Artificial Intelligence have the big potential to support new models of care delivery, disease prevention and quality of life promotion. The ultimate goal is a paradigm shift towards more personalized, accessible, effective, and sustainable care and health systems. Nevertheless, despite the advances in the field over the last years, the adoption and deployment of AI technologies remains limited in clinical practice and real-world settings. This paper summarizes the activities that a multidisciplinary research group within the Signals and Images Lab of the Institute of Information Science and Technologies of the National Research Council of Italy is carrying out for exploring both the potential of AI in health and well-being as well as the challenges to their uptake in real-world settingsSource: CEUR WORKSHOP PROCEEDINGS. Pisa, Italy, 29-30/05/2023
Project(s): ProCAncer-I
Berti A, Buongiorno R, Carloni G, Caudai C, Del Corso G, Germanese D, Pachetti E, Pascali Ma, Colantonio S
Innovative technologies powered by Artificial Intelligence have the big potential to support new models of care delivery, disease prevention and quality of life promotion. The ultimate goal is a paradigm shift towards more personalized, accessible, effective, and sustainable care and health systems. Nevertheless, despite the advances in the field over the last years, the adoption and deployment of AI technologies remains limited in clinical practice and real-world settings. This paper summarizes the activities that a multidisciplinary research group within the Signals and Images Lab of the Institute of Information Science and Technologies of the National Research Council of Italy is carrying out for exploring both the potential of AI in health and well-being as well as the challenges to their uptake in real-world settingsSource: CEUR WORKSHOP PROCEEDINGS. Pisa, Italy, 29-30/05/2023
Project(s): ProCAncer-I
See at:
ceur-ws.org | CNR IRIS | ISTI Repository | CNR IRIS
2023
Conference article
Open Access
Exploring the potentials and challenges of Artificial Intelligence in supporting clinical diagnostics and remote assistance for the health and well-being of individuals
Berti A., Buongiorno R., Carloni G., Caudai C., Del Corso G., Germanese D., Pachetti E., Pascali M. A., Colantonio S.
Innovative technologies powered by Artificial Intelligence have the big potential to support new models of care delivery, disease prevention and quality of life promotion. The ultimate goal is a paradigm shift towards more personalized, accessible, effective, and sustainable care and health systems. Nevertheless, despite the advances in the field over the last years, the adoption and deployment of AI technologies remains limited in clinical practice and real-world settings. This paper summarizes the activities that a multidisciplinary research group within the Signals and Images Lab of the Institute of Information Science and Technologies of the National Research Council of Italy is carrying out for exploring both the potential of AI in health and well-being as well as the challenges to their uptake in real-world settings.Source: CEUR WORKSHOP PROCEEDINGS, vol. 3486. Pisa, Italy, 29-30/05/2023
Berti A., Buongiorno R., Carloni G., Caudai C., Del Corso G., Germanese D., Pachetti E., Pascali M. A., Colantonio S.
Innovative technologies powered by Artificial Intelligence have the big potential to support new models of care delivery, disease prevention and quality of life promotion. The ultimate goal is a paradigm shift towards more personalized, accessible, effective, and sustainable care and health systems. Nevertheless, despite the advances in the field over the last years, the adoption and deployment of AI technologies remains limited in clinical practice and real-world settings. This paper summarizes the activities that a multidisciplinary research group within the Signals and Images Lab of the Institute of Information Science and Technologies of the National Research Council of Italy is carrying out for exploring both the potential of AI in health and well-being as well as the challenges to their uptake in real-world settings.Source: CEUR WORKSHOP PROCEEDINGS, vol. 3486. Pisa, Italy, 29-30/05/2023
See at:
ceur-ws.org | CNR IRIS | CNR IRIS
2024
Conference article
Open Access
From Covid-19 detection to cancer grading: how medical-AI is boosting clinical diagnostics and may improve treatment
Berti A., Buongiorno R., Carloni G., Caudai C., Conti F., Del Corso G., Germanese D., Moroni D., Pachetti E., Pascali M. A., Colantonio S.
The integration of artificial intelligence (AI) into medical imaging has guided an era of transformation in healthcare. This paper presents the research activities that a multidisciplinary research group within the Signals and Images Lab of the Institute of Information Science and Technologies of the National Research Council of Italy is carrying out to explore the great potential of AI in medical imaging. From the convolutional neural network-based segmentation of Covid-19 lung patterns to the radiomic signature for benign/malignant breast nodule discrimination, to the automatic grading of prostate cancer, this work highlights the paradigm shift that AI has brought to medical imaging, revolutionizing diagnosis and patient care.Source: CEUR WORKSHOP PROCEEDINGS, vol. 3762, pp. 336-341. Naples, Italy, 29-30/05/2024
Berti A., Buongiorno R., Carloni G., Caudai C., Conti F., Del Corso G., Germanese D., Moroni D., Pachetti E., Pascali M. A., Colantonio S.
The integration of artificial intelligence (AI) into medical imaging has guided an era of transformation in healthcare. This paper presents the research activities that a multidisciplinary research group within the Signals and Images Lab of the Institute of Information Science and Technologies of the National Research Council of Italy is carrying out to explore the great potential of AI in medical imaging. From the convolutional neural network-based segmentation of Covid-19 lung patterns to the radiomic signature for benign/malignant breast nodule discrimination, to the automatic grading of prostate cancer, this work highlights the paradigm shift that AI has brought to medical imaging, revolutionizing diagnosis and patient care.Source: CEUR WORKSHOP PROCEEDINGS, vol. 3762, pp. 336-341. Naples, Italy, 29-30/05/2024
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ceur-ws.org | CNR IRIS | CNR IRIS
2022
Other
Open Access
SI-Lab annual research report 2021
Righi M, Leone G R, Carboni A, Caudai C, Colantonio S, Kuruoglu E E, Leporini B, Magrini M, Paradisi P, Pascali M A, Pieri G, Reggiannini M, Salerno E, Scozzari A, Tonazzini A, Fusco G, Galesi G, Martinelli M, Pardini F, Tampucci M, Berti A, Bruno A, Buongiorno R, Carloni G, Conti F, Germanese D, Ignesti G, Matarese F, Omrani A, Pachetti E, Papini O, Benassi A, Bertini G, Coltelli P, Tarabella L, Straface S, Salvetti O, Moroni D
The Signal & Images Laboratory is an interdisciplinary research group in computer vision, signal analysis, intelligent vision systems and multimedia data understanding. It is part of the Institute of Information Science and Technologies (ISTI) of the National Research Council of Italy (CNR). This report accounts for the research activities of the Signal and Images Laboratory of the Institute of Information Science and Technologies during the year 2021.DOI: 10.32079/isti-ar-2022/003
Metrics:
Righi M, Leone G R, Carboni A, Caudai C, Colantonio S, Kuruoglu E E, Leporini B, Magrini M, Paradisi P, Pascali M A, Pieri G, Reggiannini M, Salerno E, Scozzari A, Tonazzini A, Fusco G, Galesi G, Martinelli M, Pardini F, Tampucci M, Berti A, Bruno A, Buongiorno R, Carloni G, Conti F, Germanese D, Ignesti G, Matarese F, Omrani A, Pachetti E, Papini O, Benassi A, Bertini G, Coltelli P, Tarabella L, Straface S, Salvetti O, Moroni D
The Signal & Images Laboratory is an interdisciplinary research group in computer vision, signal analysis, intelligent vision systems and multimedia data understanding. It is part of the Institute of Information Science and Technologies (ISTI) of the National Research Council of Italy (CNR). This report accounts for the research activities of the Signal and Images Laboratory of the Institute of Information Science and Technologies during the year 2021.DOI: 10.32079/isti-ar-2022/003
Metrics:
See at:
CNR IRIS | ISTI Repository | CNR IRIS