Convolutional Neural Networks (CNNs) with U-shaped architectures have dominated medical image segmentation, which is crucial for various clinical purposes. However, the inherent locality of convolution makes CNNs fail to fully exploit global context, essential for better recognition of some structures, e.g., brain lesions. Transformers have recently proven promising performance on vision tasks, including semantic segmentation, mainly due to their capability of modeling long-range dependencies. Nevertheless, the quadratic complexity of attention makes existing Transformer-based models use self-attention layers only after somehow reducing the image resolution, which limits the ability to capture global contexts present at higher resolutions. Therefore, this work introduces a family of models, dubbed Factorizer, which leverages the power of low-rank matrix factorization for constructing an end-to-end segmentation model. Specifically, we propose a linearly scalable approach to context modeling, formulating Nonnegative Matrix Factorization (NMF) as a differentiable layer integrated into a U-shaped architecture. The shifted window technique is also utilized in combination with NMF to effectively aggregate local information. Factorizers compete favorably with CNNs and Transformers in terms of accuracy, scalability, and interpretability, achieving state-of-the-art results on the BraTS dataset for brain tumor segmentation and ISLES'22 dataset for stroke lesion segmentation. Highly meaningful NMF components give an additional interpretability advantage to Factorizers over CNNs and Transformers. Moreover, our ablation studies reveal a distinctive feature of Factorizers that enables a significant speed-up in inference for a trained Factorizer without any extra steps and without sacrificing much accuracy. The code and models are publicly available at https://github.com/pashtari/factorizer.
Due to the cross-domain distribution shift aroused from diverse medical imaging systems, many deep learning segmentation methods fail to perform well on unseen data, which limits their real-world applicability. Recent works have shown the benefits of extracting domain-invariant representations on domain generalization. However, the interpretability of domain-invariant features remains a great challenge. To address this problem, we propose an interpretable Bayesian framework (BayeSeg) through Bayesian modeling of image and label statistics to enhance model generalizability for medical image seg…
TA-RNN-Medical-Hybrid: A Time-Aware and Interpretable Framework for Mortality Risk Prediction
Department of Computer Engineering, SRC.,Islamic Azad university（计算机工程系，伊斯兰教Azad大学）；School of Computer Engineering, Iran university of Science and technology（计算机工程学院，伊朗科学技术大学）
Implicit U-KAN2.0: Dynamic, Efficient and Interpretable Medical Image Segmentation
Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK（应用数学与理论物理系，剑桥大学）；Siebel School of Computing and Data Science, University of Illinois Urbana-Champaign, USA（计算与数据科学学院，伊利诺伊大学厄巴纳-香槟分校）；Zurich University of Applied Sciences, Switzerland（苏黎世应用科学大学）；Lucerne Cantonal Hospital, Switzerland（卢塞恩州立医院）；Lucerne University of Applied Sciences and Arts, Switzerland（卢塞恩应用科学与艺术大学）；Yau Mathematical Sciences Center, Tsinghua University, China（尤太数学科学中心，清华大学）
Principle-Guided Supervision for Interpretable Uncertainty in Medical Image Segmentation
School of Data Science, Fudan University（复旦大学数据科学学院）；Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University（复旦大学脑启发智能科学研究院）；National Heart and Lung Institute, Imperial College London（伦敦帝国理工学院国家心脏和肺研究所）
Interpretable Probabilistic Medical Image Segmentation via Gaussian Process with Explicit Modelling of Annotation Bias and Variability
University College London（伦敦大学学院）；Queen Mary University of London（伦敦玛丽女王大学）；University of Oxford（牛津大学）；University College London Hospitals NHS Trust（伦敦大学学院医院NHS信托基金会）；Imperial College Healthcare（帝国理工学院医疗保健）
Inception Institute of Artificial Intelligence（英赛普申人工智能研究院）
In many real world medical image classification settings we do not have access to samples of all possible disease classes, while a robust system is expected to give high performance in recognizing novel test data. We propose a generalized zero shot learning (GZSL) method that uses self supervised learning (SSL) for: 1) selecting anchor vectors of different disease classes; and 2) training a feature generator. Our approach does not require class attribute vectors which are available for natural images but not for medical images. SSL ensures that the anchor vectors are representative of each cla…
University of Copenhagen（哥本哈根大学）；Rigshospitalet（哥本哈根大学国立医院）
Generative models such as Generative Adversarial Networks (GANs) and Variational Autoencoders (VAEs) play an increasingly important role in medical image analysis. The latent spaces of these models often show semantically meaningful directions corresponding to human-interpretable image transformations. However, until now, their exploration for medical images has been limited due to the requirement of supervised data. Several methods for unsupervised discovery of interpretable directions in GAN latent spaces have shown interesting results on natural images. This work explores the potential of a…
Deep learning (DL) methods where interpretability is intrinsically considered as part of the model are required to better understand the relationship of clinical and imaging-based attributes with DL outcomes, thus facilitating their use in the reasoning behind medical decisions. Latent space representations built with variational autoencoders (VAE) do not ensure individual control of data attributes. Attribute-based methods enforcing attribute disentanglement have been proposed in the literature for classical computer vision tasks in benchmark data. In this paper, we propose a VAE approach, th…
Uppsala University（乌普萨拉大学）；Antaros Medical AB（安塔罗斯医疗公司）
Large-scale medical studies such as the UK Biobank examine thousands of volunteer participants with medical imaging techniques. Combined with the vast amount of collected metadata, anatomical information from these images has the potential for medical analyses at unprecedented scale. However, their evaluation often requires manual input and long processing times, limiting the amount of reference values for biomarkers and other measurements available for research. Recent approaches with convolutional neural networks for regression can perform these evaluations automatically. On magnetic resonan…
Peter Munk Cardiac Center（彼得·芒克心脏中心）；University of Toronto（多伦多大学）；Vector Institute（向量研究所）；University of Waterloo（滑铁卢大学）
Medical image segmentation is a difficult but important task for many clinical operations such as cardiac bi-ventricular volume estimation. More recently, there has been a shift to utilizing deep learning and fully convolutional neural networks (CNNs) to perform image segmentation that has yielded state-of-the-art results in many public benchmark datasets. Despite the progress of deep learning in medical image segmentation, standard CNNs are still not fully adopted in clinical settings as they lack robustness and interpretability. Shapes are generally more meaningful features than solely textu…
GFSR-Net: Guided Focus via Segment-Wise Relevance Network for Interpretable Deep Learning in Medical Imaging
Institute of Physical Chemistry (IPC) and Abbe Center of Photonics (ACP), Friedrich Schiller University Jena（耶拿弗里德里希·席勒大学物理化学研究所与阿贝光子学中心）；Leibniz Institute of Photonic Technology（莱布尼茨光子技术研究所）
AmbientCycleGAN for Establishing Interpretable Stochastic Object Models Based on Mathematical Phantoms and Medical Imaging Measurements
Global Institute of Future Technology, Shanghai Jiao Tong University（上海交通大学未来科技研究院）；University of Michigan-Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University（上海交通大学密歇根大学联合学院）
REACT-KD: Region-Aware Cross-modal Topological Knowledge Distillation for Interpretable Medical Image Classification
Department of Health Technology and Informatics, Hong Kong Polytechnic University（健康科技与信息技术系，香港理工大学）；Department of Nuclear Medicine and PET, Hong Kong Sanatorium and Hospital（核医学与PET部门，香港疗养院及医院）
Center for Public Health Genomics（公共卫生基因组学中心）；Department of Biomedical Engineering University of Virginia（弗吉尼亚大学生物医学工程系）；University of Virginia（弗吉尼亚大学）
White Blood Cell (WBC) Leukaemia is detected through image-based classification. Convolutional Neural Networks are used to learn the features needed to classify images of cells a malignant or healthy. However, this type of model requires learning a large number of parameters and is difficult to interpret and explain. Explainable AI (XAI) attempts to alleviate this issue by providing insights to how models make decisions. Therefore, we present an XAI model which uses only 24 explainable and interpretable features and is highly competitive to other approaches by outperforming them by about 4.38\…
Uppsala University（乌普萨拉大学）；Antaros Medical AB（安塔罗斯医疗公司）
In a large-scale medical examination, the UK Biobank study has successfully imaged more than 32,000 volunteer participants with magnetic resonance imaging (MRI). Each scan is linked to extensive metadata, providing a comprehensive medical survey of imaged anatomy and related health states. Despite its potential for research, this vast amount of data presents a challenge to established methods of evaluation, which often rely on manual input. To date, the range of reference values for cardiovascular and metabolic risk factors is therefore incomplete. In this work, neural networks were trained fo…
Wellcome Centre for Human Neuroimaging（惠康人类神经影像中心）；UCL（伦敦大学学院）；UCL Institute of Neurology（伦敦大学学院神经学研究所）
Automatically generating one medical imaging modality from another is known as medical image translation, and has numerous interesting applications. This paper presents an interpretable generative modelling approach to medical image translation. By allowing a common model for group-wise normalisation and segmentation of brain scans to handle missing data, the model allows for predicting entirely missing modalities from one, or a few, MR contrasts. Furthermore, the model can be trained on a fairly small number of subjects. The proposed model is validated on three clinically relevant scenarios. …
Center for Data Science, New York University（纽约大学数据科学中心）；Department of Computer Science, Courant Institute, New York University（纽约大学库朗研究所计算机科学系）；Department of Radiology, NYU School of Medicine（纽约大学医学院放射科）；Perlmutter Cancer Center, NYU Langone Health（纽约大学朗格尼健康系统珀尔马特癌症中心）；Center for Advanced Imaging Innovation and Research, NYU Langone Health（纽约大学朗格尼健康系统先进成像创新与研究中心）；CIFAR Associate Fellow（CIFAR研究员（注：CIFAR是加拿大英属哥伦比亚大学的一个研究机构，但根据提取规则，此处仅提取“CIFAR”相关部分，严格按英文保留））
Medical images differ from natural images in significantly higher resolutions and smaller regions of interest. Because of these differences, neural network architectures that work well for natural images might not be applicable to medical image analysis. In this work, we extend the globally-aware multiple instance classifier, a framework we proposed to address these unique properties of medical images. This model first uses a low-capacity, yet memory-efficient, network on the whole image to identify the most informative regions. It then applies another higher-capacity network to collect detail…
The use of convolutional neural networks (CNNs) for classification tasks has become dominant in various medical imaging applications. At the same time, recent advances in interpretable machine learning techniques have shown great potential in explaining classifiers' decisions. Layer-wise relevance propagation (LRP) has been introduced as one of these novel methods that aim to provide visual interpretation for the network's decisions. In this work we propose the application of 3D CNNs with LRP for the first time for neonatal T2-weighted magnetic resonance imaging (MRI) data analysis. Through LR…
