DeepMiCa: Automatic segmentation and classification of breast MIcroCAlcifications from mammograms. (June 2023)

• Record Type: Journal Article
• Authors: Gerbasi, Alessia; Clementi, Greta; Corsi, Fabio; Albasini, Sara; Malovini, Alberto; Quaglini, Silvana; Bellazzi, Riccardo
• Is Part Of: Computer methods and programs in biomedicine. Volume 235(2023)
• Publication Date: 2023-06
• Subjects: Microcalcifications -- Mammograms -- Deep learning -- Segmentation -- Classification -- Explainability; Medicine -- Computer programs -- Periodicals; Biology -- Computer programs -- Periodicals; Computers -- Periodicals; Medicine -- Periodicals; Médecine -- Logiciels -- Périodiques; Biologie -- Logiciels -- Périodiques; Biology -- Computer programs; Medicine -- Computer programs; Periodicals; Electronic journals; 610.28
• DOI: 10.1016/j.cmpb.2023.107483
• Languages: English
• ISSNs: 0169-2607

Abstract

Highlights: Development of a fully automated and easily customisable pipeline for microcalcifications analysis requiring only the raw mammograms as input and limited computational resources. Automatic patch-based semantic segmentation using a UNet based network with a custom loss function appositely designed to deal with extremely small lesions. Classification model for breast microcalcifications malignancy detection trained with a deep transfer-learning approach on a dataset with biopsy-proven labels. Output classification predictions are analysed with state-of-the-art explainable AI algorithms to visually inspect the contribution of each area of the image to the final classification. Abstract: Background and objective: Breast cancer is the world's most prevalent form of cancer. The survival rates have increased in the last years mainly due to factors such as screening programs for early detection, new insights on the disease mechanisms as well as personalised treatments. Microcalcifications are the only first detectable sign of breast cancer and diagnosis timing is strongly related to the chances of survival. Nevertheless microcalcifications detection and classification as benign or malignant lesions is still a challenging clinical task and their malignancy can only be proven after a biopsy procedure. We propose DeepMiCa, a fully automated and visually explainable deep-learning based pipeline for the analysis of raw mammograms with microcalcifications. Our aim is to propose a reliable decision support system able to guide the diagnosis and help the clinicians to better inspect borderline difficult cases. Methods: DeepMiCa is composed by three main steps: (1) Preprocessing of the raw scans (2) Automatic patch-based Semantic Segmentation using a UNet based network with a custom loss function appositely designed to deal with extremely small lesions (3) Classification of the detected lesions with a deep transfer-learning approach. Finally, state-of-the-art explainable AI methods are used to produce maps for a visual interpretation of the classification results. Each step of DeepMiCa is designed to address the main limitations of the previous proposed works resulting in a novel automated and accurate pipeline easily customisable to meet radiologists' needs. Results: The proposed segmentation and classification algorithms achieve an area under the ROC curve of 0.95 and 0.89 respectively. Compared to previously proposed works, this method does not require high performance computational resources and provides a visual explanation of the final classification results. Conclusion: To conclude, we designed a novel fully automated pipeline for detection and classification of breast microcalcifications. We believe that the proposed system has the potential to provide a second opinion in the diagnosis process giving the clinicians the opportunity to quickly visualise and inspect relevant imaging characteristics. In the clinical practice the proposed decision support system could help reduce the rate of misclassified lesions and consequently the number of unnecessary biopsies.