Pub Date : 2023-08-24DOI: 10.48550/arXiv.2308.12679
A. Sadafi, Raheleh Salehi, A. Gruber, Sayedali Shetab Boushehri, Pascal Giehr, N. Navab, Carsten Marr
Accurate classification of white blood cells in peripheral blood is essential for diagnosing hematological diseases. Due to constantly evolving clinical settings, data sources, and disease classifications, it is necessary to update machine learning classification models regularly for practical real-world use. Such models significantly benefit from sequentially learning from incoming data streams without forgetting previously acquired knowledge. However, models can suffer from catastrophic forgetting, causing a drop in performance on previous tasks when fine-tuned on new data. Here, we propose a rehearsal-based continual learning approach for class incremental and domain incremental scenarios in white blood cell classification. To choose representative samples from previous tasks, we employ exemplar set selection based on the model's predictions. This involves selecting the most confident samples and the most challenging samples identified through uncertainty estimation of the model. We thoroughly evaluated our proposed approach on three white blood cell classification datasets that differ in color, resolution, and class composition, including scenarios where new domains or new classes are introduced to the model with every task. We also test a long class incremental experiment with both new domains and new classes. Our results demonstrate that our approach outperforms established baselines in continual learning, including existing iCaRL and EWC methods for classifying white blood cells in cross-domain environments.
{"title":"A Continual Learning Approach for Cross-Domain White Blood Cell Classification","authors":"A. Sadafi, Raheleh Salehi, A. Gruber, Sayedali Shetab Boushehri, Pascal Giehr, N. Navab, Carsten Marr","doi":"10.48550/arXiv.2308.12679","DOIUrl":"https://doi.org/10.48550/arXiv.2308.12679","url":null,"abstract":"Accurate classification of white blood cells in peripheral blood is essential for diagnosing hematological diseases. Due to constantly evolving clinical settings, data sources, and disease classifications, it is necessary to update machine learning classification models regularly for practical real-world use. Such models significantly benefit from sequentially learning from incoming data streams without forgetting previously acquired knowledge. However, models can suffer from catastrophic forgetting, causing a drop in performance on previous tasks when fine-tuned on new data. Here, we propose a rehearsal-based continual learning approach for class incremental and domain incremental scenarios in white blood cell classification. To choose representative samples from previous tasks, we employ exemplar set selection based on the model's predictions. This involves selecting the most confident samples and the most challenging samples identified through uncertainty estimation of the model. We thoroughly evaluated our proposed approach on three white blood cell classification datasets that differ in color, resolution, and class composition, including scenarios where new domains or new classes are introduced to the model with every task. We also test a long class incremental experiment with both new domains and new classes. Our results demonstrate that our approach outperforms established baselines in continual learning, including existing iCaRL and EWC methods for classifying white blood cells in cross-domain environments.","PeriodicalId":106540,"journal":{"name":"DART@MICCAI","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121232949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-15DOI: 10.48550/arXiv.2308.07624
Qi Wu, Yuyao Zhang, Marawan Elbatel
Recent advancements in large foundation models have shown promising potential in the medical industry due to their flexible prompting capability. One such model, the Segment Anything Model (SAM), a prompt-driven segmentation model, has shown remarkable performance improvements, surpassing state-of-the-art approaches in medical image segmentation. However, existing methods primarily rely on tuning strategies that require extensive data or prior prompts tailored to the specific task, making it particularly challenging when only a limited number of data samples are available. In this paper, we propose a novel perspective on self-prompting in medical vision applications. Specifically, we harness the embedding space of SAM to prompt itself through a simple yet effective linear pixel-wise classifier. By preserving the encoding capabilities of the large model, the contextual information from its decoder, and leveraging its interactive promptability, we achieve competitive results on multiple datasets (i.e. improvement of more than 15% compared to fine-tuning the mask decoder using a few images).
{"title":"Self-Prompting Large Vision Models for Few-Shot Medical Image Segmentation","authors":"Qi Wu, Yuyao Zhang, Marawan Elbatel","doi":"10.48550/arXiv.2308.07624","DOIUrl":"https://doi.org/10.48550/arXiv.2308.07624","url":null,"abstract":"Recent advancements in large foundation models have shown promising potential in the medical industry due to their flexible prompting capability. One such model, the Segment Anything Model (SAM), a prompt-driven segmentation model, has shown remarkable performance improvements, surpassing state-of-the-art approaches in medical image segmentation. However, existing methods primarily rely on tuning strategies that require extensive data or prior prompts tailored to the specific task, making it particularly challenging when only a limited number of data samples are available. In this paper, we propose a novel perspective on self-prompting in medical vision applications. Specifically, we harness the embedding space of SAM to prompt itself through a simple yet effective linear pixel-wise classifier. By preserving the encoding capabilities of the large model, the contextual information from its decoder, and leveraging its interactive promptability, we achieve competitive results on multiple datasets (i.e. improvement of more than 15% compared to fine-tuning the mask decoder using a few images).","PeriodicalId":106540,"journal":{"name":"DART@MICCAI","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133891375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-14DOI: 10.48550/arXiv.2308.07444
Levy G. Chaves, Alceu Bissoto, Eduardo Valle, S. Avila
Transfer learning boosts the performance of medical image analysis by enabling deep learning (DL) on small datasets through the knowledge acquired from large ones. As the number of DL architectures explodes, exhaustively attempting all candidates becomes unfeasible, motivating cheaper alternatives for choosing them. Transferability scoring methods emerge as an enticing solution, allowing to efficiently calculate a score that correlates with the architecture accuracy on any target dataset. However, since transferability scores have not been evaluated on medical datasets, their use in this context remains uncertain, preventing them from benefiting practitioners. We fill that gap in this work, thoroughly evaluating seven transferability scores in three medical applications, including out-of-distribution scenarios. Despite promising results in general-purpose datasets, our results show that no transferability score can reliably and consistently estimate target performance in medical contexts, inviting further work in that direction.
{"title":"The Performance of Transferability Metrics does not Translate to Medical Tasks","authors":"Levy G. Chaves, Alceu Bissoto, Eduardo Valle, S. Avila","doi":"10.48550/arXiv.2308.07444","DOIUrl":"https://doi.org/10.48550/arXiv.2308.07444","url":null,"abstract":"Transfer learning boosts the performance of medical image analysis by enabling deep learning (DL) on small datasets through the knowledge acquired from large ones. As the number of DL architectures explodes, exhaustively attempting all candidates becomes unfeasible, motivating cheaper alternatives for choosing them. Transferability scoring methods emerge as an enticing solution, allowing to efficiently calculate a score that correlates with the architecture accuracy on any target dataset. However, since transferability scores have not been evaluated on medical datasets, their use in this context remains uncertain, preventing them from benefiting practitioners. We fill that gap in this work, thoroughly evaluating seven transferability scores in three medical applications, including out-of-distribution scenarios. Despite promising results in general-purpose datasets, our results show that no transferability score can reliably and consistently estimate target performance in medical contexts, inviting further work in that direction.","PeriodicalId":106540,"journal":{"name":"DART@MICCAI","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117350643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-08-05DOI: 10.48550/arXiv.2208.03327
Marawan Elbatel, Christina Bornberg, Manasi Kattel, E. Almar, C. Marrocco, A. Bria
. In-vitro tests are an alternative to animal testing for the toxicity of medical devices. Detecting cells as a first step, a cell expert evaluates the growth of cells according to cytotoxicity grade under the microscope. Thus, human fatigue plays a role in error making, making the use of deep learning appealing. Due to the high cost of training data annotation, an approach without manual annotation is needed. We propose Seamless Iterative Semi-Supervised correction of Imperfect labels (SISSI) , a new method for training object detection models with noisy and missing annotations in a semi-supervised fashion. Our network learns from noisy labels generated with simple image processing algorithms, which are iteratively corrected during self-training. Due to the nature of missing bounding boxes in the pseudo labels, which would negatively affect the training, we propose to train on dynamically generated synthetic-like images using seamless cloning. Our method successfully provides an adaptive early learning correction technique for object detection. The combination of early learning correction that has been applied in classification and semantic segmentation before and synthetic-like image generation proves to be more effective than the usual semi-supervised approach by > 15% AP and > 20% AR across three different readers. Our code is available at https://github.com/marwankefah/SISSI.
{"title":"Seamless Iterative Semi-Supervised Correction of Imperfect Labels in Microscopy Images","authors":"Marawan Elbatel, Christina Bornberg, Manasi Kattel, E. Almar, C. Marrocco, A. Bria","doi":"10.48550/arXiv.2208.03327","DOIUrl":"https://doi.org/10.48550/arXiv.2208.03327","url":null,"abstract":". In-vitro tests are an alternative to animal testing for the toxicity of medical devices. Detecting cells as a first step, a cell expert evaluates the growth of cells according to cytotoxicity grade under the microscope. Thus, human fatigue plays a role in error making, making the use of deep learning appealing. Due to the high cost of training data annotation, an approach without manual annotation is needed. We propose Seamless Iterative Semi-Supervised correction of Imperfect labels (SISSI) , a new method for training object detection models with noisy and missing annotations in a semi-supervised fashion. Our network learns from noisy labels generated with simple image processing algorithms, which are iteratively corrected during self-training. Due to the nature of missing bounding boxes in the pseudo labels, which would negatively affect the training, we propose to train on dynamically generated synthetic-like images using seamless cloning. Our method successfully provides an adaptive early learning correction technique for object detection. The combination of early learning correction that has been applied in classification and semantic segmentation before and synthetic-like image generation proves to be more effective than the usual semi-supervised approach by > 15% AP and > 20% AR across three different readers. Our code is available at https://github.com/marwankefah/SISSI.","PeriodicalId":106540,"journal":{"name":"DART@MICCAI","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124349106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-07-31DOI: 10.48550/arXiv.2208.00474
Ivan Zakazov, V. Shaposhnikov, Iaroslav Bespalov, D. Dylov
Generalizability of deep learning models may be severely affected by the difference in the distributions of the train (source domain) and the test (target domain) sets, e.g., when the sets are produced by different hardware. As a consequence of this domain shift, a certain model might perform well on data from one clinic, and then fail when deployed in another. We propose a very light and transparent approach to perform test-time domain adaptation. The idea is to substitute the target low-frequency Fourier space components that are deemed to reflect the style of an image. To maximize the performance, we implement the"optimal style donor"selection technique, and use a number of source data points for altering a single target scan appearance (Multi-Source Transferring). We study the effect of severity of domain shift on the performance of the method, and show that our training-free approach reaches the state-of-the-art level of complicated deep domain adaptation models. The code for our experiments is released.
{"title":"Feather-Light Fourier Domain Adaptation in Magnetic Resonance Imaging","authors":"Ivan Zakazov, V. Shaposhnikov, Iaroslav Bespalov, D. Dylov","doi":"10.48550/arXiv.2208.00474","DOIUrl":"https://doi.org/10.48550/arXiv.2208.00474","url":null,"abstract":"Generalizability of deep learning models may be severely affected by the difference in the distributions of the train (source domain) and the test (target domain) sets, e.g., when the sets are produced by different hardware. As a consequence of this domain shift, a certain model might perform well on data from one clinic, and then fail when deployed in another. We propose a very light and transparent approach to perform test-time domain adaptation. The idea is to substitute the target low-frequency Fourier space components that are deemed to reflect the style of an image. To maximize the performance, we implement the\"optimal style donor\"selection technique, and use a number of source data points for altering a single target scan appearance (Multi-Source Transferring). We study the effect of severity of domain shift on the performance of the method, and show that our training-free approach reaches the state-of-the-art level of complicated deep domain adaptation models. The code for our experiments is released.","PeriodicalId":106540,"journal":{"name":"DART@MICCAI","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129037154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-02-06DOI: 10.1007/978-3-031-16852-9_1
Peter J. Bevan, Amir Atapour-Abarghouei
{"title":"Detecting Melanoma Fairly: Skin Tone Detection and Debiasing for Skin Lesion Classification","authors":"Peter J. Bevan, Amir Atapour-Abarghouei","doi":"10.1007/978-3-031-16852-9_1","DOIUrl":"https://doi.org/10.1007/978-3-031-16852-9_1","url":null,"abstract":"","PeriodicalId":106540,"journal":{"name":"DART@MICCAI","volume":"36 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114160043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 1900-01-01DOI: 10.1007/978-3-031-16852-9_12
Rasha Sheikh, Morris Klasen, T. Schultz
{"title":"Adaptive Optimization with Fewer Epochs Improves Across-Scanner Generalization of U-Net Based Medical Image Segmentation","authors":"Rasha Sheikh, Morris Klasen, T. Schultz","doi":"10.1007/978-3-031-16852-9_12","DOIUrl":"https://doi.org/10.1007/978-3-031-16852-9_12","url":null,"abstract":"","PeriodicalId":106540,"journal":{"name":"DART@MICCAI","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125682642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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