Muhammad Aqib Javed , Muhammad Khuram Shahzad , Hafiz Syed Muhammad Bilal Ali
{"title":"一种用于减少生物医学图像分割中实例不平衡的损失函数正则化方法","authors":"Muhammad Aqib Javed , Muhammad Khuram Shahzad , Hafiz Syed Muhammad Bilal Ali","doi":"10.1016/j.compbiolchem.2025.108555","DOIUrl":null,"url":null,"abstract":"<div><div>Biomedical Image Segmentation applications have witnessed mushroom growth in the last two decades. Current state-of-the-art approaches face challenges when dealing with instance imbalances in datasets. Various functions, such as Blob Loss, Lesion-wise Loss, and Dice Loss limitations, were addressed by Instance-wise loss and Center-of-Instance loss (ICI). ICI is the result of Instance loss, and the center of instance loss suffers from highly unregulated labels and outputs, resulting in low accuracy of aforementioned loss functions. We introduce a novel dual-coefficient regularization approach for loss functions that modifies both predicted outputs and labels before loss computation. This addresses instance imbalance more effectively than previous pixel-level or class-level weighting strategies. The proposed approach resulted in the enhancement of existing loss functions: (1) RIW (regularized instance-wise loss), (2) RCI (regularized center of instance loss), and (3) RPW (regularized pixel-wise loss). The simulation experiments on the ATLAS R2.0 (MICCAI, 2022) and BraTS’20 (MICCAI, 2020) datasets validated our approach in comparison with the state-of-the-art loss functions resulting in significant improvements in RIW (up to 69.16%), RCI ( up to 16.58%), RPW (67.82%), subsequently decreased false detection rate up to (97.78%), and number of missed instances.</div></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":"119 ","pages":"Article 108555"},"PeriodicalIF":3.1000,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"A novel regularization approach for loss functions to reduce instance imbalance in biomedical image segmentation\",\"authors\":\"Muhammad Aqib Javed , Muhammad Khuram Shahzad , Hafiz Syed Muhammad Bilal Ali\",\"doi\":\"10.1016/j.compbiolchem.2025.108555\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div>Biomedical Image Segmentation applications have witnessed mushroom growth in the last two decades. Current state-of-the-art approaches face challenges when dealing with instance imbalances in datasets. Various functions, such as Blob Loss, Lesion-wise Loss, and Dice Loss limitations, were addressed by Instance-wise loss and Center-of-Instance loss (ICI). ICI is the result of Instance loss, and the center of instance loss suffers from highly unregulated labels and outputs, resulting in low accuracy of aforementioned loss functions. We introduce a novel dual-coefficient regularization approach for loss functions that modifies both predicted outputs and labels before loss computation. This addresses instance imbalance more effectively than previous pixel-level or class-level weighting strategies. The proposed approach resulted in the enhancement of existing loss functions: (1) RIW (regularized instance-wise loss), (2) RCI (regularized center of instance loss), and (3) RPW (regularized pixel-wise loss). The simulation experiments on the ATLAS R2.0 (MICCAI, 2022) and BraTS’20 (MICCAI, 2020) datasets validated our approach in comparison with the state-of-the-art loss functions resulting in significant improvements in RIW (up to 69.16%), RCI ( up to 16.58%), RPW (67.82%), subsequently decreased false detection rate up to (97.78%), and number of missed instances.</div></div>\",\"PeriodicalId\":10616,\"journal\":{\"name\":\"Computational Biology and Chemistry\",\"volume\":\"119 \",\"pages\":\"Article 108555\"},\"PeriodicalIF\":3.1000,\"publicationDate\":\"2025-07-23\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Computational Biology and Chemistry\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1476927125002154\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computational Biology and Chemistry","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1476927125002154","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOLOGY","Score":null,"Total":0}
A novel regularization approach for loss functions to reduce instance imbalance in biomedical image segmentation
Biomedical Image Segmentation applications have witnessed mushroom growth in the last two decades. Current state-of-the-art approaches face challenges when dealing with instance imbalances in datasets. Various functions, such as Blob Loss, Lesion-wise Loss, and Dice Loss limitations, were addressed by Instance-wise loss and Center-of-Instance loss (ICI). ICI is the result of Instance loss, and the center of instance loss suffers from highly unregulated labels and outputs, resulting in low accuracy of aforementioned loss functions. We introduce a novel dual-coefficient regularization approach for loss functions that modifies both predicted outputs and labels before loss computation. This addresses instance imbalance more effectively than previous pixel-level or class-level weighting strategies. The proposed approach resulted in the enhancement of existing loss functions: (1) RIW (regularized instance-wise loss), (2) RCI (regularized center of instance loss), and (3) RPW (regularized pixel-wise loss). The simulation experiments on the ATLAS R2.0 (MICCAI, 2022) and BraTS’20 (MICCAI, 2020) datasets validated our approach in comparison with the state-of-the-art loss functions resulting in significant improvements in RIW (up to 69.16%), RCI ( up to 16.58%), RPW (67.82%), subsequently decreased false detection rate up to (97.78%), and number of missed instances.
期刊介绍:
Computational Biology and Chemistry publishes original research papers and review articles in all areas of computational life sciences. High quality research contributions with a major computational component in the areas of nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins are particularly welcome. Exceptionally high quality research work in bioinformatics, systems biology, ecology, computational pharmacology, metabolism, biomedical engineering, epidemiology, and statistical genetics will also be considered.
Given their inherent uncertainty, protein modeling and molecular docking studies should be thoroughly validated. In the absence of experimental results for validation, the use of molecular dynamics simulations along with detailed free energy calculations, for example, should be used as complementary techniques to support the major conclusions. Submissions of premature modeling exercises without additional biological insights will not be considered.
Review articles will generally be commissioned by the editors and should not be submitted to the journal without explicit invitation. However prospective authors are welcome to send a brief (one to three pages) synopsis, which will be evaluated by the editors.