Despite the recent successes of deep learning, such models are still far from some human abilities like learning from few examples, reasoning and explaining decisions. In this paper, we focus on organ annotation in medical images and we introduce a reasoning framework that is based on learning fuzzy relations on a small dataset for generating explanations. Given a catalogue of relations, it efficiently induces the most relevant relations and combines them for building constraints in order to both solve the organ annotation task and generate explanations. We test our approach on a publicly available dataset of medical images where several organs are already segmented. A demonstration of our model is proposed with an example of explained annotations. It was trained on a small training set containing as few as a couple of examples.
University Medical Center Hamburg-Eppendorf（汉堡-埃彭多夫大学医学中心）；Universität Hamburg（汉堡大学）
Clinical decision support for histopathology image data mainly focuses on strongly supervised annotations, which offers intuitive interpretability, but is bound by expert performance. Here, we propose an explainable cancer relapse prediction network (eCaReNet) and show that end-to-end learning without strong annotations offers state-of-the-art performance while interpretability can be included through an attention mechanism. On the use case of prostate cancer survival prediction, using 14,479 images and only relapse times as annotations, we reach a cumulative dynamic AUC of 0.78 on a validatio…
MalariAI: A Label-Resilient Decoupled Framework for Annotation-Agnostic Cell Segmentation and Explainable Stage Classification in Dense Malaria Blood Smears
Understanding model predictions is critical in healthcare, to facilitate rapid verification of model correctness and to guard against use of models that exploit confounding variables. We introduce the challenging new task of explainable multiple abnormality classification in volumetric medical images, in which a model must indicate the regions used to predict each abnormality. To solve this task, we propose a multiple instance learning convolutional neural network, AxialNet, that allows identification of top slices for each abnormality. Next we incorporate HiResCAM, an attention mechanism, to …
Multi-organ segmentation: a progressive exploration of learning paradigms under scarce annotation
School of Basic Medical Science, Fudan University（复旦大学基础医学院）；Digital Medical Research Center（数字医学研究中心）；Shanghai Key Lab of Medical Image Computing and Computer Assisted Intervention（上海市医学影像计算与计算机辅助介入重点实验室）
Learning to Select Like Humans: Explainable Active Learning for Medical Imaging
AI Research, Department of Computer Science, University of South Dakota（人工智能研究，计算机科学系，南达科他大学）；Department of Computer Science and Software Engineering, Auburn University（计算机科学与软件工程系，阿伯丁大学）
Accurate segmentation of multiple organs of the head, neck, chest, and abdomen from medical images is an essential step in computer-aided diagnosis, surgical navigation, and radiation therapy. In the past few years, with a data-driven feature extraction approach and end-to-end training, automatic deep learning-based multi-organ segmentation method has far outperformed traditional methods and become a new research topic. This review systematically summarizes the latest research in this field. For the first time, from the perspective of full and imperfect annotation, we comprehensively compile 1…
Johns Hopkins University（约翰斯·霍普金斯大学）；University of Maryland Medical Intelligent Imaging (UM2ii) Center（马里兰大学医学智能成像（UM2ii）中心）
Segmentation is one of the most primary tasks in deep learning for medical imaging, owing to its multiple downstream clinical applications. However, generating manual annotations for medical images is time-consuming, requires high skill, and is an expensive effort, especially for 3D images. One potential solution is to aggregate knowledge from partially annotated datasets from multiple groups to collaboratively train global models using Federated Learning. To this end, we propose SegViz, a federated learning-based framework to train a segmentation model from distributed non-i.i.d datasets with…
EXACT: an explainable anomaly-aware vision foundation model for analysis of 3D chest CT
School of Biomedical Engineering, Tsinghua University（清华大学生物医学工程学院）；Department of Radiology, Mianyang Central Hospital（绵阳市中心医院放射科）；Center for Biomedical Imaging Research, Tsinghua University（清华大学生物医学成像研究中心）
A Gradient Mapping Guided Explainable Deep Neural Network for Extracapsular Extension Identification in 3D Head and Neck Cancer Computed Tomography Images
Department of Industrial and Systems Engineering, Mississippi State University, Mississippi State, MS, 39762, USA（工业与系统工程系，密苏里州立大学）；Department of Radiation Oncology, University of Mississippi Medical Center, Jackson, MS, 39216, USA（放射肿瘤学系，密苏里大学医学中心）
Medical images are widely used in clinical practice for diagnosis. Automatically generating interpretable medical reports can reduce radiologists' burden and facilitate timely care. However, most existing approaches to automatic report generation require sufficient labeled data for training. In addition, the learned model can only generate reports for the training classes, lacking the ability to adapt to previously unseen novel diseases. To this end, we propose a lesion guided explainable few weak-shot medical report generation framework that learns correlation between seen and novel classes t…
TWLR: Text-Guided Weakly-Supervised Lesion Localization and Severity Regression for Explainable Diabetic Retinopathy Grading
Guangdong Provincial Key Laboratory of Interdisciplinary Research and Application for Data Science（广东省级交叉学科研究与数据科学应用重点实验室）；Department of Statistics and Data Science, Beijing Normal-Hong Kong Baptist University（北京师范大学-香港 Baptist大学统计与数据科学系）；Faculty of Science, Hong Kong Baptist University（香港 Baptist大学科学学院）；Data Science Research Center, Duke Kunshan University（杜克-昆山大学数据科学研究中心）；Shanxi Provincial People’s Hospital（山西人民医院）；The Fifth Clinical Medical school of Shanxi Medical University（山西医科大学第五临床医学院）；Research Center for Mathematics, Beijing Normal University（北京师范大学数学研究中心）；Department of Mathematics and Statistics, York University（约克大学数学与统计学系）
National Institutes of Health Clinical Center（美国国立卫生研究院临床中心）；NVIDIA（英伟达）
Radiologists in their daily work routinely find and annotate significant abnormalities on a large number of radiology images. Such abnormalities, or lesions, have collected over years and stored in hospitals' picture archiving and communication systems. However, they are basically unsorted and lack semantic annotations like type and location. In this paper, we aim to organize and explore them by learning a deep feature representation for each lesion. A large-scale and comprehensive dataset, DeepLesion, is introduced for this task. DeepLesion contains bounding boxes and size measurements of ove…
Centrum Wiskunde & Informatica（荷兰国家数学与计算机科学研究所）；Xomnia B.V.（Xomnia公司）；Erasmus University Medical Center（伊拉斯谟大学医学中心）；Delft University of Technology（代尔夫特理工大学）；Leiden University Medical Center（莱顿大学医学中心）
Deep learning models benefit from training with a large dataset (labeled or unlabeled). Following this motivation, we present an approach to learn a deep learning model for the automatic segmentation of Organs at Risk (OARs) in cervical cancer radiation treatment from a large clinically available dataset of Computed Tomography (CT) scans containing data inhomogeneity, label noise, and missing annotations. We employ simple heuristics for automatic data cleaning to minimize data inhomogeneity and label noise. Further, we develop a semi-supervised learning approach utilizing a teacher-student set…
Xiamen University（厦门大学）；The Hong Kong University of Science and Technology（香港科技大学）；Peking University（北京大学）；The Hong Kong Polytechnic University（香港理工大学）；Manteia Technologies Co.,Ltd（Manteia科技有限公司）
Automatic delineation of organ-at-risk (OAR) and gross-tumor-volume (GTV) is of great significance for radiotherapy planning. However, it is a challenging task to learn powerful representations for accurate delineation under limited pixel (voxel)-wise annotations. Contrastive learning at pixel-level can alleviate the dependency on annotations by learning dense representations from unlabeled data. Recent studies in this direction design various contrastive losses on the feature maps, to yield discriminative features for each pixel in the map. However, pixels in the same map inevitably share sem…
The First Affiliated Hospital of Anhui Medical University（安徽医科大学第一附属医院）；Huawei Cloud Computing Technology Co. Ltd（华为云计算技术有限公司）；University of Science and Technology of China（中国科学技术大学）
There exists a large number of datasets for organ segmentation, which are partially annotated and sequentially constructed. A typical dataset is constructed at a certain time by curating medical images and annotating the organs of interest. In other words, new datasets with annotations of new organ categories are built over time. To unleash the potential behind these partially labeled, sequentially-constructed datasets, we propose to incrementally learn a multi-organ segmentation model. In each incremental learning (IL) stage, we lose the access to previous data and annotations, whose knowledg…
From Classification to Segmentation with Explainable AI: A Study on Crack Detection and Growth Monitoring
Intelligent Maintenance and Operations Systems (IMOS), EPFL（智能维护与运营系统研究所（IMOS），洛桑联邦理工学院）；Environmental Computational Science and Earth Observation (ECEO), EPFL（环境计算科学与地球观测研究所（ECEO），洛桑联邦理工学院）
University of Electronic Science and Technology of China（电子科技大学）；Shanghai Artificial Intelligence Laboratory（上海人工智能实验室）；Sichuan Cancer Hospital and Institute（四川省肿瘤医院（四川省肿瘤研究所））；Sichuan Cancer Center（四川省癌症中心）；Sichuan University（四川大学）；West China Hospital（华西医院）；Johns Hopkins University（约翰斯·霍普金斯大学）；SenseTime Research（商汤科技研究院）；Rutgers University（罗格斯大学）
Whole abdominal organ segmentation is important in diagnosing abdomen lesions, radiotherapy, and follow-up. However, oncologists' delineating all abdominal organs from 3D volumes is time-consuming and very expensive. Deep learning-based medical image segmentation has shown the potential to reduce manual delineation efforts, but it still requires a large-scale fine annotated dataset for training, and there is a lack of large-scale datasets covering the whole abdomen region with accurate and detailed annotations for the whole abdominal organ segmentation. In this work, we establish a new large-s…
Senckenberg Biodiversity and Climate Research Centre (SBiK-F)（森肯伯格生物多样性与气候研究中心）；Philipps-University Marburg（马尔堡菲利普斯大学）；Palmengarten der Stadt Frankfurt（法兰克福棕榈园）；Senckenberg Research Institute and Natural History Museum（森肯伯格研究所与自然历史博物馆）
As herbarium specimens are increasingly becoming digitized and accessible in online repositories, advanced computer vision techniques are being used to extract information from them. The presence of certain plant organs on herbarium sheets is useful information in various scientific contexts and automatic recognition of these organs will help mobilize such information. In our study we use deep learning to detect plant organs on digitized herbarium specimens with Faster R-CNN. For our experiment we manually annotated hundreds of herbarium scans with thousands of bounding boxes for six types of …
Reliable and automated 3D plant shoot segmentation is a core prerequisite for the extraction of plant phenotypic traits at the organ level. Combining deep learning and point clouds can provide effective ways to address the challenge. However, fully supervised deep learning methods require datasets to be point-wise annotated, which is extremely expensive and time-consuming. In our work, we proposed a novel weakly supervised framework, Eff-3DPSeg, for 3D plant shoot segmentation. First, high-resolution point clouds of soybean were reconstructed using a low-cost photogrammetry system, and the Mes…
Carleton University（卡尔顿大学）；Canada CIFAR AI Chair（加拿大CIFAR人工智能讲席）
Medical image segmentation methods typically rely on numerous dense annotated images for model training, which are notoriously expensive and time-consuming to collect. To alleviate this burden, weakly supervised techniques have been exploited to train segmentation models with less expensive annotations. In this paper, we propose a novel point-supervised contrastive variance method (PSCV) for medical image semantic segmentation, which only requires one pixel-point from each organ category to be annotated. The proposed method trains the base segmentation network by using a novel contrastive vari…
Semantic segmentation is an import task in the medical field to identify the exact extent and orientation of significant structures like organs and pathology. Deep neural networks can perform this task well by leveraging the information from a large well-labeled data-set. This paper aims to present a method that mitigates the necessity of an extensive well-labeled data-set. This method also addresses semi-supervision by enabling segmentation based on bounding box annotations, avoiding the need for full pixel-level annotations. The network presented consists of a single U-Net based unbranched a…
SenseTime Research（商汤科技研究院）；School of Information Science and Engineering at Shandong Normal University（山东师范大学信息科学与工程学院）；CUHK-SenseTime Joint Laboratory, The Chinese University of Hong Kong（香港中文大学-商汤科技联合实验室）
Multi-organ segmentation has extensive applications in many clinical applications. To segment multiple organs of interest, it is generally quite difficult to collect full annotations of all the organs on the same images, as some medical centers might only annotate a portion of the organs due to their own clinical practice. In most scenarios, one might obtain annotations of a single or a few organs from one training set, and obtain annotations of the the other organs from another set of training images. Existing approaches mostly train and deploy a single model for each subset of organs, which …
Segmentation of organs of interest in 3D medical images is necessary for accurate diagnosis and longitudinal studies. Though recent advances using deep learning have shown success for many segmentation tasks, large datasets are required for high performance and the annotation process is both time consuming and labor intensive. In this paper, we propose a 3D few shot segmentation framework for accurate organ segmentation using limited training samples of the target organ annotation. To achieve this, a U-Net like network is designed to predict segmentation by learning the relationship between 2D…
FunnyNodules: A Customizable Medical Dataset Tailored for Evaluating Explainable AI
Ulm University Medical Center（乌尔姆大学医学中心）；XAIRAD - Cooperation for Artificial Intelligence in Experimental Radiology（XAIRAD——实验放射学人工智能合作）；Department of Diagnostic and Interventional Radiology（诊断与介入放射学系）
Zero-Shot 3D Plant Organ Segmentation with SAM3 and Semantic NeRFs
Fraunhofer Institute for Integrated Circuits (IIS)（弗劳恩霍夫集成电路研究所）；Otto-Friedrich-Universität Bamberg（班贝格奥托·弗里德里希大学）；Friedrich-Alexander-Universität Erlangen-Nürnberg（埃尔朗根-纽伦堡弗里德里希-亚历山大大学）
XEmoGPT: An Explainable Multimodal Emotion Recognition Framework with Cue-Level Perception and Reasoning
School of Computer Science and Engineering, University of Electronic Science and Technology of China（电子科技大学计算机科学与工程学院）；th Research Institute, China Electronics Technology Group Corporation（中国电子科技集团第五十四研究所）
Person-Centric Annotations of LAION-400M: Auditing Bias and Its Transfer to Models
Technical University of Munich, Munich Center for Machine Learning (MCML), MDSI（慕尼黑工业大学，慕尼黑机器学习中心（MCML），MDSI）；LTCI, Télécom Paris, Institut Polytechnique de Paris, France（法国巴黎理工学院，巴黎电信学院，LTCI）；Helmholtz Munich（亥姆霍兹慕尼黑中心）；University of California, Berkeley（加州大学伯克利分校）
The Chinese University of Hong Kong（香港中文大学）；The First Hospital of Jilin University（吉林大学第一医院）
Despite the remarkable success on medical image analysis with deep learning, it is still under exploration regarding how to rapidly transfer AI models from one dataset to another for clinical applications. This paper presents a novel and generic human-in-the-loop scheme for efficiently transferring a segmentation model from a small-scale labelled dataset to a larger-scale unlabelled dataset for multi-organ segmentation in CT. To achieve this, we propose to use an igniter network which can learn from a small-scale labelled dataset and generate coarse annotations to start the process of human-ma…
