This paper introduces the DeepATLAS foundational model for localization tasks in the domain of high-dimensional biomedical data. Upon convergence of the proposed self-supervised objective, a pretrained model maps an input to an anatomically-consistent embedding from which any point or set of points (e.g., boxes or segmentations) may be identified in a one-shot or few-shot approach. As a representative benchmark, a DeepATLAS model pretrained on a comprehensive cohort of 51,000+ unlabeled 3D computed tomography exams yields high one-shot segmentation performance on over 50 anatomic structures across four different external test sets, either matching or exceeding the performance of a standard supervised learning model. Further improvements in accuracy can be achieved by adding a small amount of labeled data using either a semisupervised or more conventional fine-tuning strategy.
University of North Carolina, Chapel Hill（北卡罗来纳大学教堂山分校）
Deep convolutional neural networks (CNNs) are state-of-the-art for semantic image segmentation, but typically require many labeled training samples. Obtaining 3D segmentations of medical images for supervised training is difficult and labor intensive. Motivated by classical approaches for joint segmentation and registration we therefore propose a deep learning framework that jointly learns networks for image registration and image segmentation. In contrast to previous work on deep unsupervised image registration, which showed the benefit of weak supervision via image segmentations, our approac…
BioVLM: Routing Prompts, Not Parameters, for Cross-Modality Generalization in Biomedical VLMs
University of Trento（特伦托大学）；Carnegie Mellon University（卡内基梅隆大学）；LNMIIT Jaipur（贾伊普尔 LNMIIT）；MBZUAI；Sunandan Divatia School of Science（Sunandan Divatia 科学学院）；IIT Bombay（博伊斯大学）
Does Bigger Mean Better? Comparitive Analysis of CNNs and Biomedical Vision Language Modles in Medical Diagnosis
University of Texas at Dallas（德克萨斯大学达拉斯分校）；Independent Researcher（独立研究者）；Duke University（杜克大学）；University of Michigan Ann Arbor（密歇根大学安娜堡分校）；Georgia Institute of Technology（佐治亚理工学院）；University of California, Irvine（加州大学 Irvine 分校）
Image segmentation is an important task in many medical applications. Methods based on convolutional neural networks attain state-of-the-art accuracy; however, they typically rely on supervised training with large labeled datasets. Labeling medical images requires significant expertise and time, and typical hand-tuned approaches for data augmentation fail to capture the complex variations in such images. We present an automated data augmentation method for synthesizing labeled medical images. We demonstrate our method on the task of segmenting magnetic resonance imaging (MRI) brain scans. Our …
Xiamen University（厦门大学）；Chinese PLA General Hospital（中国人民解放军总医院）；Deepwise AI Laboratory（深智云AI实验室）
Despite deep convolutional neural networks achieved impressive progress in medical image computing and analysis, its paradigm of supervised learning demands a large number of annotations for training to avoid overfitting and achieving promising results. In clinical practices, massive semantic annotations are difficult to acquire in some conditions where specialized biomedical expert knowledge is required, and it is also a common condition where only few annotated classes are available. In this work, we proposed a novel method for few-shot medical image segmentation, which enables a segmentatio…
Sparser2Sparse: Single-shot Sparser-to-Sparse Learning for Spatial Transcriptomics Imputation with Natural Image Co-learning
Department of Radiology, Northwestern University, Chicago, IL, USA（放射科，西北大学，芝加哥，伊利诺伊州，美国）；Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, USA（细胞与发育生物学系，西北大学，芝加哥，伊利诺伊州，美国）；Department of Pathology, Northwestern University, Chicago, IL, USA（病理学系，西北大学，芝加哥，伊利诺伊州，美国）
Prototype Correlation Matching and Class-Relation Reasoning for Few-Shot Medical Image Segmentation
The Hong Kong Polytechnic University（香港理工大学）；Shenyang Institute of Automation, Chinese Academy of Sciences（中国科学院沈阳自动化研究所）；Durham University（杜伦大学）；Jarvis Research Center, Tencent YouTu Lab（腾讯优图实验室贾维斯研究中心）
We propose a deep clustering architecture alongside image segmentation for medical image analysis. The main idea is based on unsupervised learning to cluster images on severity of the disease in the subject's sample, and this image is then segmented to highlight and outline regions of interest. We start with training an autoencoder on the images for segmentation. The encoder part from the autoencoder branches out to a clustering node and segmentation node. Deep clustering using Kmeans clustering is performed at the clustering branch and a lightweight model is used for segmentation. Each of the…
