Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention最新文献
Pub Date : 2023-07-04DOI: 10.48550/arXiv.2307.01798
Xiaojiao Xiao, Qinmin Hu, Guanghui Wang
Simultaneous multi-index quantification, segmentation, and uncertainty estimation of liver tumors on multi-modality non-contrast magnetic resonance imaging (NCMRI) are crucial for accurate diagnosis. However, existing methods lack an effective mechanism for multi-modality NCMRI fusion and accurate boundary information capture, making these tasks challenging. To address these issues, this paper proposes a unified framework, namely edge-aware multi-task network (EaMtNet), to associate multi-index quantification, segmentation, and uncertainty of liver tumors on the multi-modality NCMRI. The EaMtNet employs two parallel CNN encoders and the Sobel filters to extract local features and edge maps, respectively. The newly designed edge-aware feature aggregation module (EaFA) is used for feature fusion and selection, making the network edge-aware by capturing long-range dependency between feature and edge maps. Multi-tasking leverages prediction discrepancy to estimate uncertainty and improve segmentation and quantification performance. Extensive experiments are performed on multi-modality NCMRI with 250 clinical subjects. The proposed model outperforms the state-of-the-art by a large margin, achieving a dice similarity coefficient of 90.01$pm$1.23 and a mean absolute error of 2.72$pm$0.58 mm for MD. The results demonstrate the potential of EaMtNet as a reliable clinical-aided tool for medical image analysis.
{"title":"Edge-aware Multi-task Network for Integrating Quantification Segmentation and Uncertainty Prediction of Liver Tumor on Multi-modality Non-contrast MRI","authors":"Xiaojiao Xiao, Qinmin Hu, Guanghui Wang","doi":"10.48550/arXiv.2307.01798","DOIUrl":"https://doi.org/10.48550/arXiv.2307.01798","url":null,"abstract":"Simultaneous multi-index quantification, segmentation, and uncertainty estimation of liver tumors on multi-modality non-contrast magnetic resonance imaging (NCMRI) are crucial for accurate diagnosis. However, existing methods lack an effective mechanism for multi-modality NCMRI fusion and accurate boundary information capture, making these tasks challenging. To address these issues, this paper proposes a unified framework, namely edge-aware multi-task network (EaMtNet), to associate multi-index quantification, segmentation, and uncertainty of liver tumors on the multi-modality NCMRI. The EaMtNet employs two parallel CNN encoders and the Sobel filters to extract local features and edge maps, respectively. The newly designed edge-aware feature aggregation module (EaFA) is used for feature fusion and selection, making the network edge-aware by capturing long-range dependency between feature and edge maps. Multi-tasking leverages prediction discrepancy to estimate uncertainty and improve segmentation and quantification performance. Extensive experiments are performed on multi-modality NCMRI with 250 clinical subjects. The proposed model outperforms the state-of-the-art by a large margin, achieving a dice similarity coefficient of 90.01$pm$1.23 and a mean absolute error of 2.72$pm$0.58 mm for MD. The results demonstrate the potential of EaMtNet as a reliable clinical-aided tool for medical image analysis.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"13 1","pages":"652-661"},"PeriodicalIF":0.0,"publicationDate":"2023-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75993678","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 : 2023-07-04DOI: 10.48550/arXiv.2307.01738
Changjian Shui, Justin Szeto, Raghav Mehta, Douglas Arnold, T. Arbel
Trustworthy deployment of deep learning medical imaging models into real-world clinical practice requires that they be calibrated. However, models that are well calibrated overall can still be poorly calibrated for a sub-population, potentially resulting in a clinician unwittingly making poor decisions for this group based on the recommendations of the model. Although methods have been shown to successfully mitigate biases across subgroups in terms of model accuracy, this work focuses on the open problem of mitigating calibration biases in the context of medical image analysis. Our method does not require subgroup attributes during training, permitting the flexibility to mitigate biases for different choices of sensitive attributes without re-training. To this end, we propose a novel two-stage method: Cluster-Focal to first identify poorly calibrated samples, cluster them into groups, and then introduce group-wise focal loss to improve calibration bias. We evaluate our method on skin lesion classification with the public HAM10000 dataset, and on predicting future lesional activity for multiple sclerosis (MS) patients. In addition to considering traditional sensitive attributes (e.g. age, sex) with demographic subgroups, we also consider biases among groups with different image-derived attributes, such as lesion load, which are required in medical image analysis. Our results demonstrate that our method effectively controls calibration error in the worst-performing subgroups while preserving prediction performance, and outperforming recent baselines.
{"title":"Mitigating Calibration Bias Without Fixed Attribute Grouping for Improved Fairness in Medical Imaging Analysis","authors":"Changjian Shui, Justin Szeto, Raghav Mehta, Douglas Arnold, T. Arbel","doi":"10.48550/arXiv.2307.01738","DOIUrl":"https://doi.org/10.48550/arXiv.2307.01738","url":null,"abstract":"Trustworthy deployment of deep learning medical imaging models into real-world clinical practice requires that they be calibrated. However, models that are well calibrated overall can still be poorly calibrated for a sub-population, potentially resulting in a clinician unwittingly making poor decisions for this group based on the recommendations of the model. Although methods have been shown to successfully mitigate biases across subgroups in terms of model accuracy, this work focuses on the open problem of mitigating calibration biases in the context of medical image analysis. Our method does not require subgroup attributes during training, permitting the flexibility to mitigate biases for different choices of sensitive attributes without re-training. To this end, we propose a novel two-stage method: Cluster-Focal to first identify poorly calibrated samples, cluster them into groups, and then introduce group-wise focal loss to improve calibration bias. We evaluate our method on skin lesion classification with the public HAM10000 dataset, and on predicting future lesional activity for multiple sclerosis (MS) patients. In addition to considering traditional sensitive attributes (e.g. age, sex) with demographic subgroups, we also consider biases among groups with different image-derived attributes, such as lesion load, which are required in medical image analysis. Our results demonstrate that our method effectively controls calibration error in the worst-performing subgroups while preserving prediction performance, and outperforming recent baselines.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"2017 1","pages":"189-198"},"PeriodicalIF":0.0,"publicationDate":"2023-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73929508","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 : 2023-07-04DOI: 10.48550/arXiv.2307.01486
Jun Shi, Hongyu Kan, Shulan Ruan, Ziqi Zhu, Minfan Zhao, Liang Qiao, Zhaohui Wang, Hong An, Xudong Xue
Recently, deep learning methods have been widely used for tumor segmentation of multimodal medical images with promising results. However, most existing methods are limited by insufficient representational ability, specific modality number and high computational complexity. In this paper, we propose a hybrid densely connected network for tumor segmentation, named H-DenseFormer, which combines the representational power of the Convolutional Neural Network (CNN) and the Transformer structures. Specifically, H-DenseFormer integrates a Transformer-based Multi-path Parallel Embedding (MPE) module that can take an arbitrary number of modalities as input to extract the fusion features from different modalities. Then, the multimodal fusion features are delivered to different levels of the encoder to enhance multimodal learning representation. Besides, we design a lightweight Densely Connected Transformer (DCT) block to replace the standard Transformer block, thus significantly reducing computational complexity. We conduct extensive experiments on two public multimodal datasets, HECKTOR21 and PI-CAI22. The experimental results show that our proposed method outperforms the existing state-of-the-art methods while having lower computational complexity. The source code is available at https://github.com/shijun18/H-DenseFormer.
{"title":"H-DenseFormer: An Efficient Hybrid Densely Connected Transformer for Multimodal Tumor Segmentation","authors":"Jun Shi, Hongyu Kan, Shulan Ruan, Ziqi Zhu, Minfan Zhao, Liang Qiao, Zhaohui Wang, Hong An, Xudong Xue","doi":"10.48550/arXiv.2307.01486","DOIUrl":"https://doi.org/10.48550/arXiv.2307.01486","url":null,"abstract":"Recently, deep learning methods have been widely used for tumor segmentation of multimodal medical images with promising results. However, most existing methods are limited by insufficient representational ability, specific modality number and high computational complexity. In this paper, we propose a hybrid densely connected network for tumor segmentation, named H-DenseFormer, which combines the representational power of the Convolutional Neural Network (CNN) and the Transformer structures. Specifically, H-DenseFormer integrates a Transformer-based Multi-path Parallel Embedding (MPE) module that can take an arbitrary number of modalities as input to extract the fusion features from different modalities. Then, the multimodal fusion features are delivered to different levels of the encoder to enhance multimodal learning representation. Besides, we design a lightweight Densely Connected Transformer (DCT) block to replace the standard Transformer block, thus significantly reducing computational complexity. We conduct extensive experiments on two public multimodal datasets, HECKTOR21 and PI-CAI22. The experimental results show that our proposed method outperforms the existing state-of-the-art methods while having lower computational complexity. The source code is available at https://github.com/shijun18/H-DenseFormer.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"20 1","pages":"692-702"},"PeriodicalIF":0.0,"publicationDate":"2023-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90949288","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 : 2023-07-03DOI: 10.48550/arXiv.2307.00885
Luyi Han, Tianyu Zhang, Yunzhi Huang, Haoran Dou, Xin Wang, Yuan Gao, Chun-Ta Lu, Tan Tao, R. Mann
Multi-sequence MRI is valuable in clinical settings for reliable diagnosis and treatment prognosis, but some sequences may be unusable or missing for various reasons. To address this issue, MRI synthesis is a potential solution. Recent deep learning-based methods have achieved good performance in combining multiple available sequences for missing sequence synthesis. Despite their success, these methods lack the ability to quantify the contributions of different input sequences and estimate the quality of generated images, making it hard to be practical. Hence, we propose an explainable task-specific synthesis network, which adapts weights automatically for specific sequence generation tasks and provides interpretability and reliability from two sides: (1) visualize the contribution of each input sequence in the fusion stage by a trainable task-specific weighted average module; (2) highlight the area the network tried to refine during synthesizing by a task-specific attention module. We conduct experiments on the BraTS2021 dataset of 1251 subjects, and results on arbitrary sequence synthesis indicate that the proposed method achieves better performance than the state-of-the-art methods. Our code is available at url{https://github.com/fiy2W/mri_seq2seq}.
{"title":"An Explainable Deep Framework: Towards Task-Specific Fusion for Multi-to-One MRI Synthesis","authors":"Luyi Han, Tianyu Zhang, Yunzhi Huang, Haoran Dou, Xin Wang, Yuan Gao, Chun-Ta Lu, Tan Tao, R. Mann","doi":"10.48550/arXiv.2307.00885","DOIUrl":"https://doi.org/10.48550/arXiv.2307.00885","url":null,"abstract":"Multi-sequence MRI is valuable in clinical settings for reliable diagnosis and treatment prognosis, but some sequences may be unusable or missing for various reasons. To address this issue, MRI synthesis is a potential solution. Recent deep learning-based methods have achieved good performance in combining multiple available sequences for missing sequence synthesis. Despite their success, these methods lack the ability to quantify the contributions of different input sequences and estimate the quality of generated images, making it hard to be practical. Hence, we propose an explainable task-specific synthesis network, which adapts weights automatically for specific sequence generation tasks and provides interpretability and reliability from two sides: (1) visualize the contribution of each input sequence in the fusion stage by a trainable task-specific weighted average module; (2) highlight the area the network tried to refine during synthesizing by a task-specific attention module. We conduct experiments on the BraTS2021 dataset of 1251 subjects, and results on arbitrary sequence synthesis indicate that the proposed method achieves better performance than the state-of-the-art methods. Our code is available at url{https://github.com/fiy2W/mri_seq2seq}.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"130 1","pages":"45-55"},"PeriodicalIF":0.0,"publicationDate":"2023-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75120314","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 : 2023-07-03DOI: 10.48550/arXiv.2307.00899
Matthew Baugh, Jeremy Tan, Johanna P. Muller, Mischa Dombrowski, James Batten, Bernhard Kainz
There is a growing interest in single-class modelling and out-of-distribution detection as fully supervised machine learning models cannot reliably identify classes not included in their training. The long tail of infinitely many out-of-distribution classes in real-world scenarios, e.g., for screening, triage, and quality control, means that it is often necessary to train single-class models that represent an expected feature distribution, e.g., from only strictly healthy volunteer data. Conventional supervised machine learning would require the collection of datasets that contain enough samples of all possible diseases in every imaging modality, which is not realistic. Self-supervised learning methods with synthetic anomalies are currently amongst the most promising approaches, alongside generative auto-encoders that analyse the residual reconstruction error. However, all methods suffer from a lack of structured validation, which makes calibration for deployment difficult and dataset-dependant. Our method alleviates this by making use of multiple visually-distinct synthetic anomaly learning tasks for both training and validation. This enables more robust training and generalisation. With our approach we can readily outperform state-of-the-art methods, which we demonstrate on exemplars in brain MRI and chest X-rays. Code is available at https://github.com/matt-baugh/many-tasks-make-light-work .
{"title":"Many tasks make light work: Learning to localise medical anomalies from multiple synthetic tasks","authors":"Matthew Baugh, Jeremy Tan, Johanna P. Muller, Mischa Dombrowski, James Batten, Bernhard Kainz","doi":"10.48550/arXiv.2307.00899","DOIUrl":"https://doi.org/10.48550/arXiv.2307.00899","url":null,"abstract":"There is a growing interest in single-class modelling and out-of-distribution detection as fully supervised machine learning models cannot reliably identify classes not included in their training. The long tail of infinitely many out-of-distribution classes in real-world scenarios, e.g., for screening, triage, and quality control, means that it is often necessary to train single-class models that represent an expected feature distribution, e.g., from only strictly healthy volunteer data. Conventional supervised machine learning would require the collection of datasets that contain enough samples of all possible diseases in every imaging modality, which is not realistic. Self-supervised learning methods with synthetic anomalies are currently amongst the most promising approaches, alongside generative auto-encoders that analyse the residual reconstruction error. However, all methods suffer from a lack of structured validation, which makes calibration for deployment difficult and dataset-dependant. Our method alleviates this by making use of multiple visually-distinct synthetic anomaly learning tasks for both training and validation. This enables more robust training and generalisation. With our approach we can readily outperform state-of-the-art methods, which we demonstrate on exemplars in brain MRI and chest X-rays. Code is available at https://github.com/matt-baugh/many-tasks-make-light-work .","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"56 1","pages":"162-172"},"PeriodicalIF":0.0,"publicationDate":"2023-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85394326","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 : 2023-07-01DOI: 10.48550/arXiv.2307.00257
Linrui Dai, Wenhui Lei, Xiaofan Zhang
As research interests in medical image analysis become increasingly fine-grained, the cost for extensive annotation also rises. One feasible way to reduce the cost is to annotate with coarse-grained superclass labels while using limited fine-grained annotations as a complement. In this way, fine-grained data learning is assisted by ample coarse annotations. Recent studies in classification tasks have adopted this method to achieve satisfactory results. However, there is a lack of research on efficient learning of fine-grained subclasses in semantic segmentation tasks. In this paper, we propose a novel approach that leverages the hierarchical structure of categories to design network architecture. Meanwhile, a task-driven data generation method is presented to make it easier for the network to recognize different subclass categories. Specifically, we introduce a Prior Concatenation module that enhances confidence in subclass segmentation by concatenating predicted logits from the superclass classifier, a Separate Normalization module that stretches the intra-class distance within the same superclass to facilitate subclass segmentation, and a HierarchicalMix model that generates high-quality pseudo labels for unlabeled samples by fusing only similar superclass regions from labeled and unlabeled images. Our experiments on the BraTS2021 and ACDC datasets demonstrate that our approach achieves comparable accuracy to a model trained with full subclass annotations, with limited subclass annotations and sufficient superclass annotations. Our approach offers a promising solution for efficient fine-grained subclass segmentation in medical images. Our code is publicly available here.
{"title":"Efficient Subclass Segmentation in Medical Images","authors":"Linrui Dai, Wenhui Lei, Xiaofan Zhang","doi":"10.48550/arXiv.2307.00257","DOIUrl":"https://doi.org/10.48550/arXiv.2307.00257","url":null,"abstract":"As research interests in medical image analysis become increasingly fine-grained, the cost for extensive annotation also rises. One feasible way to reduce the cost is to annotate with coarse-grained superclass labels while using limited fine-grained annotations as a complement. In this way, fine-grained data learning is assisted by ample coarse annotations. Recent studies in classification tasks have adopted this method to achieve satisfactory results. However, there is a lack of research on efficient learning of fine-grained subclasses in semantic segmentation tasks. In this paper, we propose a novel approach that leverages the hierarchical structure of categories to design network architecture. Meanwhile, a task-driven data generation method is presented to make it easier for the network to recognize different subclass categories. Specifically, we introduce a Prior Concatenation module that enhances confidence in subclass segmentation by concatenating predicted logits from the superclass classifier, a Separate Normalization module that stretches the intra-class distance within the same superclass to facilitate subclass segmentation, and a HierarchicalMix model that generates high-quality pseudo labels for unlabeled samples by fusing only similar superclass regions from labeled and unlabeled images. Our experiments on the BraTS2021 and ACDC datasets demonstrate that our approach achieves comparable accuracy to a model trained with full subclass annotations, with limited subclass annotations and sufficient superclass annotations. Our approach offers a promising solution for efficient fine-grained subclass segmentation in medical images. Our code is publicly available here.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"130 1","pages":"266-275"},"PeriodicalIF":0.0,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86363943","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}
Anterior segment optical coherence tomography (AS-OCT) is a non-invasive imaging technique that is highly valuable for ophthalmic diagnosis. However, speckles in AS-OCT images can often degrade the image quality and affect clinical analysis. As a result, removing speckles in AS-OCT images can greatly benefit automatic ophthalmology analysis. Unfortunately, challenges still exist in deploying effective AS-OCT image denoising algorithms, including collecting sufficient paired training data and the requirement to preserve consistent content in medical images. To address these practical issues, we propose an unsupervised AS-OCT despeckling algorithm via Content Preserving Diffusion Model (CPDM) with statistical knowledge. At the training stage, a Markov chain transforms clean images to white Gaussian noise by repeatedly adding random noise and removes the predicted noise in a reverse procedure. At the inference stage, we first analyze the statistical distribution of speckles and convert it into a Gaussian distribution, aiming to match the fast truncated reverse diffusion process. We then explore the posterior distribution of observed images as a fidelity term to ensure content consistency in the iterative procedure. Our experimental results show that CPDM significantly improves image quality compared to competitive methods. Furthermore, we validate the benefits of CPDM for subsequent clinical analysis, including ciliary muscle (CM) segmentation and scleral spur (SS) localization.
{"title":"Content-Preserving Diffusion Model for Unsupervised AS-OCT image Despeckling","authors":"Sanqian Li, Risa Higashita, Huazhu Fu, Heng Li, Jingxuan Liu, Jiang Liu","doi":"10.48550/arXiv.2306.17717","DOIUrl":"https://doi.org/10.48550/arXiv.2306.17717","url":null,"abstract":"Anterior segment optical coherence tomography (AS-OCT) is a non-invasive imaging technique that is highly valuable for ophthalmic diagnosis. However, speckles in AS-OCT images can often degrade the image quality and affect clinical analysis. As a result, removing speckles in AS-OCT images can greatly benefit automatic ophthalmology analysis. Unfortunately, challenges still exist in deploying effective AS-OCT image denoising algorithms, including collecting sufficient paired training data and the requirement to preserve consistent content in medical images. To address these practical issues, we propose an unsupervised AS-OCT despeckling algorithm via Content Preserving Diffusion Model (CPDM) with statistical knowledge. At the training stage, a Markov chain transforms clean images to white Gaussian noise by repeatedly adding random noise and removes the predicted noise in a reverse procedure. At the inference stage, we first analyze the statistical distribution of speckles and convert it into a Gaussian distribution, aiming to match the fast truncated reverse diffusion process. We then explore the posterior distribution of observed images as a fidelity term to ensure content consistency in the iterative procedure. Our experimental results show that CPDM significantly improves image quality compared to competitive methods. Furthermore, we validate the benefits of CPDM for subsequent clinical analysis, including ciliary muscle (CM) segmentation and scleral spur (SS) localization.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"72 1","pages":"660-670"},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86351285","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 : 2023-06-29DOI: 10.48550/arXiv.2306.16714
Yu-Min Zhong, Yi Wang
Breast dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) plays an important role in the screening and prognosis assessment of high-risk breast cancer. The segmentation of cancerous regions is essential useful for the subsequent analysis of breast MRI. To alleviate the annotation effort to train the segmentation networks, we propose a weakly-supervised strategy using extreme points as annotations for breast cancer segmentation. Without using any bells and whistles, our strategy focuses on fully exploiting the learning capability of the routine training procedure, i.e., the train - fine-tune - retrain process. The network first utilizes the pseudo-masks generated using the extreme points to train itself, by minimizing a contrastive loss, which encourages the network to learn more representative features for cancerous voxels. Then the trained network fine-tunes itself by using a similarity-aware propagation learning (SimPLe) strategy, which leverages feature similarity between unlabeled and positive voxels to propagate labels. Finally the network retrains itself by employing the pseudo-masks generated using previous fine-tuned network. The proposed method is evaluated on our collected DCE-MRI dataset containing 206 patients with biopsy-proven breast cancers. Experimental results demonstrate our method effectively fine-tunes the network by using the SimPLe strategy, and achieves a mean Dice value of 81%.
{"title":"SimPLe: Similarity-Aware Propagation Learning for Weakly-Supervised Breast Cancer Segmentation in DCE-MRI","authors":"Yu-Min Zhong, Yi Wang","doi":"10.48550/arXiv.2306.16714","DOIUrl":"https://doi.org/10.48550/arXiv.2306.16714","url":null,"abstract":"Breast dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) plays an important role in the screening and prognosis assessment of high-risk breast cancer. The segmentation of cancerous regions is essential useful for the subsequent analysis of breast MRI. To alleviate the annotation effort to train the segmentation networks, we propose a weakly-supervised strategy using extreme points as annotations for breast cancer segmentation. Without using any bells and whistles, our strategy focuses on fully exploiting the learning capability of the routine training procedure, i.e., the train - fine-tune - retrain process. The network first utilizes the pseudo-masks generated using the extreme points to train itself, by minimizing a contrastive loss, which encourages the network to learn more representative features for cancerous voxels. Then the trained network fine-tunes itself by using a similarity-aware propagation learning (SimPLe) strategy, which leverages feature similarity between unlabeled and positive voxels to propagate labels. Finally the network retrains itself by employing the pseudo-masks generated using previous fine-tuned network. The proposed method is evaluated on our collected DCE-MRI dataset containing 206 patients with biopsy-proven breast cancers. Experimental results demonstrate our method effectively fine-tunes the network by using the SimPLe strategy, and achieves a mean Dice value of 81%.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"19 1","pages":"567-577"},"PeriodicalIF":0.0,"publicationDate":"2023-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73990162","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}
Ultrasound (US) imaging is a popular tool in clinical diagnosis, offering safety, repeatability, and real-time capabilities. Freehand 3D US is a technique that provides a deeper understanding of scanned regions without increasing complexity. However, estimating elevation displacement and accumulation error remains challenging, making it difficult to infer the relative position using images alone. The addition of external lightweight sensors has been proposed to enhance reconstruction performance without adding complexity, which has been shown to be beneficial. We propose a novel online self-consistency network (OSCNet) using multiple inertial measurement units (IMUs) to improve reconstruction performance. OSCNet utilizes a modal-level self-supervised strategy to fuse multiple IMU information and reduce differences between reconstruction results obtained from each IMU data. Additionally, a sequence-level self-consistency strategy is proposed to improve the hierarchical consistency of prediction results among the scanning sequence and its sub-sequences. Experiments on large-scale arm and carotid datasets with multiple scanning tactics demonstrate that our OSCNet outperforms previous methods, achieving state-of-the-art reconstruction performance.
{"title":"Multi-IMU with Online Self-Consistency for Freehand 3D Ultrasound Reconstruction","authors":"Mingyuan Luo, Xin Yang, Zhongnuo Yan, Yuanji Zhang, Junyu Li, Jiongquan Chen, Xindi Hu, Jikuan Qian, Junda Cheng, Dong Ni","doi":"10.48550/arXiv.2306.16197","DOIUrl":"https://doi.org/10.48550/arXiv.2306.16197","url":null,"abstract":"Ultrasound (US) imaging is a popular tool in clinical diagnosis, offering safety, repeatability, and real-time capabilities. Freehand 3D US is a technique that provides a deeper understanding of scanned regions without increasing complexity. However, estimating elevation displacement and accumulation error remains challenging, making it difficult to infer the relative position using images alone. The addition of external lightweight sensors has been proposed to enhance reconstruction performance without adding complexity, which has been shown to be beneficial. We propose a novel online self-consistency network (OSCNet) using multiple inertial measurement units (IMUs) to improve reconstruction performance. OSCNet utilizes a modal-level self-supervised strategy to fuse multiple IMU information and reduce differences between reconstruction results obtained from each IMU data. Additionally, a sequence-level self-consistency strategy is proposed to improve the hierarchical consistency of prediction results among the scanning sequence and its sub-sequences. Experiments on large-scale arm and carotid datasets with multiple scanning tactics demonstrate that our OSCNet outperforms previous methods, achieving state-of-the-art reconstruction performance.","PeriodicalId":18289,"journal":{"name":"Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention","volume":"1 1","pages":"342-351"},"PeriodicalIF":0.0,"publicationDate":"2023-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90223479","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 : 2023-06-28DOI: 10.48550/arXiv.2306.15971
Yoni Choukroun, Lior Golgher, P. Blinder, L. Wolf
The relationship between blood flow and neuronal activity is widely recognized, with blood flow frequently serving as a surrogate for neuronal activity in fMRI studies. At the microscopic level, neuronal activity has been shown to influence blood flow in nearby blood vessels. This study introduces the first predictive model that addresses this issue directly at the explicit neuronal population level. Using in vivo recordings in awake mice, we employ a novel spatiotemporal bimodal transformer architecture to infer current blood flow based on both historical blood flow and ongoing spontaneous neuronal activity. Our findings indicate that incorporating neuronal activity significantly enhances the model's ability to predict blood flow values. Through analysis of the model's behavior, we propose hypotheses regarding the largely unexplored nature of the hemodynamic response to neuronal activity.
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Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention
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