skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: MedShift: Automated Identification of Shift Data for Medical Image Dataset Curation
Automated curation of noisy external data in the medical domain has long been in high demand, as AI technologies need to be validated using various sources with clean, annotated data. Identifying the variance between internal and external sources is a fundamental step in curating a high-quality dataset, as the data distributions from different sources can vary significantly and subsequently affect the performance of AI models. The primary challenges for detecting data shifts are - (1) accessing private data across healthcare institutions for manual detection and (2) the lack of automated approaches to learn efficient shift-data representation without training samples. To overcome these problems, we propose an automated pipeline called MedShift to detect top-level shift samples and evaluate the significance of shift data without sharing data between internal and external organizations. MedShift employs unsupervised anomaly detectors to learn the internal distribution and identify samples showing significant shiftness for external datasets, and then compares their performance. To quantify the effects of detected shift data, we train a multi-class classifier that learns internal domain knowledge and evaluates the classification performance for each class in external domains after dropping the shift data. We also propose a data quality metric to quantify the dissimilarity between internal and external datasets. We verify the efficacy of MedShift using musculoskeletal radiographs (MURA) and chest X-ray datasets from multiple external sources. Our experiments show that our proposed shift data detection pipeline can be beneficial for medical centers to curate high-quality datasets more efficiently.  more » « less
Award ID(s):
1928481
PAR ID:
10488060
Author(s) / Creator(s):
; ; ; ;
Publisher / Repository:
IEEE
Date Published:
Journal Name:
IEEE Journal of Biomedical and Health Informatics
Volume:
27
Issue:
8
ISSN:
2168-2194
Page Range / eLocation ID:
3936 to 3947
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. null (Ed.)
    The novelty detection models learn a decision boundary around multiple categories of a given dataset. This helps such models in detecting any novel classes encountered during testing. However, in many cases, the test data distribution can be different from that of the training data. For such cases, the novelty detection models risk detecting a known class as novel due to the dataset distribution shift. This scenario is often ignored while working with novelty detection. To this end, we consider the problem of multiple class novelty detection under dataset distribution shift to improve the novelty detection performance. Firstly, we discuss the problem setting in detail and show how it affects the performance of current novelty detection methods. Secondly, we show that one could improve those novelty detection methods with a simple integration of domain adversarial loss. Finally, we propose a method which brings together the techniques from novelty detection and domain adaptation to improve generalization of multiple class novelty detection on different domains. We evaluate the proposed method on digits and object recognition datasets and show that it provides improvements over the baseline methods. 
    more » « less
  2. Abstract Light echoes (LEs) are the reflections of astrophysical transients off of interstellar dust. They are fascinating astronomical phenomena that enable studies of the scattering dust as well as of the original transients. LEs, however, are rare and extremely difficult to detect as they appear as faint, diffuse, time-evolving features. The detection of LEs still largely relies on human inspection of images, a method unfeasible in the era of large synoptic surveys. The Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) will generate an unprecedented amount of astronomical imaging data at high spatial resolution, exquisite image quality, and over tens of thousands of square degrees of sky: an ideal survey for LEs. However, the Rubin data processing pipelines are optimized for the detection of point sources and will entirely miss LEs. Over the past several years, artificial intelligence (AI) object-detection frameworks have achieved and surpassed real-time, human-level performance. In this work, we leverage a data set from the Asteroid Terrestrial-impact Last Alert System telescope to test a popular AI object-detection framework, You Only Look Once, or YOLO, developed by the computer-vision community, to demonstrate the potential of AI for the detection of LEs in astronomical images. We find that an AI framework can reach human-level performance even with a size- and quality-limited data set. We explore and highlight challenges, including class imbalance and label incompleteness, and road map the work required to build an end-to-end pipeline for the automated detection and study of LEs in high-throughput astronomical surveys. 
    more » « less
  3. Solving the domain shift problem during inference is essential in medical imaging as most deep-learning based solutions suffer from it. In practice, domain shifts are tackled by performing Unsupervised Domain Adaptation (UDA), where a model is adapted to an unlabeled target domain by leveraging the labelled source domain. In medical scenarios, the data comes with huge privacy concerns making it difficult to apply standard UDA techniques. Hence, a closer clinical setting is Source-Free UDA (SFUDA), where we have access to source trained model but not the source data during adaptation. Methods trying to solve SFUDA typically address the domain shift using pseudo-label based self-training techniques. However due to domain shift, these pseudo-labels are usually of high entropy and denoising them still does not make them perfect labels to supervise the model. Therefore, adapting the source model with noisy pseudo labels reduces its segmentation capability while addressing the domain shift. To this end, we propose a two-stage approach for source-free domain adaptive image segmentation: 1) Target-specific adaptation followed by 2) Task-specific adaptation. In the Stage-I, we focus on learning target-specific representation and generating high-quality pseudo labels by leveraging a proposed ensemble entropy minimization loss and selective voting strategy. In Stage II, we focus on improving segmentation performance by utilizing teacher-student self-training and augmentation-guided consistency loss, leveraging the pseudo labels obtained from Stage I. We evaluate our proposed method on both 2D fundus datasets and 3D MRI volumes across 7 different domain shifts where we achieve better performance than recent UDA and SF-UDA methods for medical image segmentation. Code is available at https://github.com/Vibashan/tt-sfuda. 
    more » « less
  4. We introduce the problem of domain adaptation under Open Set Label Shift (OSLS) where the label distribution can change arbitrarily and a new class may arrive during deployment, but the class-conditional distributions p(x|y) are domain-invariant. OSLS subsumes domain adaptation under label shift and Positive-Unlabeled (PU) learning. The learner's goals here are two-fold: (a) estimate the target label distribution, including the novel class; and (b) learn a target classifier. First, we establish necessary and sufficient conditions for identifying these quantities. Second, motivated by advances in label shift and PU learning, we propose practical methods for both tasks that leverage black-box predictors. Unlike typical Open Set Domain Adaptation (OSDA) problems, which tend to be ill-posed and amenable only to heuristics, OSLS offers a well-posed problem amenable to more principled machinery. Experiments across numerous semi-synthetic benchmarks on vision, language, and medical datasets demonstrate that our methods consistently outperform OSDA baselines, achieving 10--25% improvements in target domain accuracy. Finally, we analyze the proposed methods, establishing finite-sample convergence to the true label marginal and convergence to optimal classifier for linear models in a Gaussian setup. 
    more » « less
  5. The availability of large-scale electronic health record datasets has led to the development of artificial intel- ligence (AI) methods for clinical risk prediction that help improve patient care. However, existing studies have shown that AI models suffer from severe performance decay after several years of deployment, which might be caused by various temporal dataset shifts. When the shift occurs, we have access to large-scale pre-shift data and small-scale post-shift data that are not enough to train new models in the post-shift environment. In this study, we propose a new method to address the issue. We reweight patients from the pre-shift environ- ment to mitigate the distribution shift between pre- and post-shift environments. Moreover, we adopt a Kullback-Leibler divergence loss to force the models to learn similar patient representations in pre- and post-shift environments. Our experimental results show that our model efficiently mitigates temporal shifts, improving prediction performance. 
    more » « less