CXR-LT: Multi-Label Long-Tailed Classification on Chest X-Rays

Abstract

Many real-world problems, including diagnostic medical imaging exams, are “long-tailed” – there are a few common findings followed by more relatively rare conditions. In chest radiography, diagnosis is both a long-tailed and multi-label problem, as patients often present with multiple disease findings simultaneously. This is distinct from most large-scale image classification benchmarks, where each image only belongs to one label and the distribution of labels is relatively balanced. While researchers have begun to study the problem of long-tailed learning in medical image recognition, few have studied its interplay with label co-occurrence. This competition will provide a challenging large-scale multi-label long-tailed learning task on chest X-rays (CXRs), encouraging community engagement with this emerging interdisciplinary topic. This project contains labels for the CXR-LT 2023 competition dataset, containing 377,110 CXRs from 26 classes, and a related subset used in the MICCAI 2023 paper, "How Does Pruning Impact Multi-Label Long-Tailed Learning?" containing 257,018 frontal CXRs from 19 classes.

Objective

Background

Chest radiography, like many diagnostic medical exams, produces a long-tailed distribution of clinical findings; while a small subset of diseases are routinely observed, the vast majority of diseases are relatively rare [1]. This poses a challenge for standard deep learning methods, which exhibit bias toward the most common classes at the expense of the important, but rare, “tail” classes [2]. Many existing methods [3] have been proposed to tackle this specific type of imbalance, though only recently with attention to long-tailed medical image recognition problems [4-6]. Diagnosis on chest X-rays (CXRs) is also a multi-label problem, as patients often present with multiple disease findings simultaneously; however, only a select few studies incorporate knowledge of label co-occurrence into the learning process [7-9, 12].

Since most large-scale image classification benchmarks contain single-label images with a mostly balanced distribution of labels, many standard deep learning methods fail to accommodate the class imbalance and co-occurrence problems posed by the long-tailed, multi-label nature of tasks like disease diagnosis on CXRs [2].

To develop a benchmark for long-tailed, multi-label medical image classification, we expand upon the MIMIC-CXR-JPG [10,11] dataset by enlarging the set of target classes from 14 to 26 (see full details in “Data Description”), generating labels for 12 new disease findings by parsing radiology reports. This follows the procedure of Holste et al. [2], who added 5 new findings to MIMIC-CXR-JPG – Calcification of the Aorta, Subcutaneous Emphysema, Tortuous Aorta, Pneumomediastinum, and Pneumoperitoneum – to study long-tailed learning approaches for CXRs and Moukheiber et al. [12], who added 5 new classes – Chronic obstructive pulmonary disease, Emphysema, Interstitial lung disease, Calcification, Fibrosis – to study ensemble methods for few-shot learning on CXRs.

CXR-LT challenge task

Given a CXR, detect all clinical findings. If no findings are present, predict "No Finding" (with the exception that "No Finding" can co-occur with "Support Devices"). To do this, participants will train multi-label thorax disease classifiers on the provided labeled training data.

ICCV 2023 CVAMD workshop

This shared task is hosted in conjunction with the ICCV 2023 [13] workshop, Computer Vision for Automated Medical Diagnosis (CVAMD) [14]. Upon completion of the competition, we will invite participants to submit their solutions for potential presentation at CVAMD 2023 and publication in the ICCV 2023 workshop proceedings. We intend to accept 5-6 papers for publication and select 2-3 of the accepted papers for oral presentation at CVAMD in Paris.

Participation

This shared task will be conducted on CodaLab [15]. Participants must have credentialed access to MIMIC-CXR-JPG v2.0.0 [10,11] (more details in the "Data Description" section) and register for the competition on CodaLab.

Tentative timeline

• 05/01/2023: Development Phase begins. Participants can begin making submissions and tracking results on the public leaderboard.
• 07/14/2023: Testing Phase begins. Unlabeled test data will be released to registered participants. The leaderboard will be kept private for this phase.
• 07/17/2023: Competition ends. Participants are invited to submit their solutions as 8-page papers to ICCV CVAMD 2023!
• 07/28/2023: ICCV CVAMD 2023 submission deadline. (Competition participants may receive an extension if needed.)
• 08/04/2023: ICCV CVAMD 2023 acceptance notification.
• 10/02/2023: ICCV CVAMD 2023 workshop.

Data Description

CXR-LT 2023 challenge data

This challenge will use an expanded version of MIMIC-CXR-JPG v2.0.0 [10,11], a large benchmark dataset for automated thorax disease classification. Following Holste et al. [2], each CXR study in the dataset was labeled with 12 newly added disease findings extracted from the associated radiology reports. The resulting long-tailed (LT) dataset contains 377,110 CXRs, each labeled with at least one of 26 clinical findings (including a "No Finding" class). In addition to the 13 clinical findings in the original MIMIC-CXR-JPG v2.0.0 dataset, the following 12 new findings have been added:

• Calcification of the Aorta
• Emphysema
• Fibrosis
• Hernia
• Infiltration
• Mass
• Nodule
• Pleural Thickening
• Pneumomediastinum
• Pneumoperitoneum
• Subcutaneous Emphysema
• Tortuous Aorta

Within the cxr-lt-2023/ directory, training set and validation set image IDs, metadata, and labels can be found in train.csv and development.csv, respectively. Alternatively, these files are available to registered participants on CodaLab [15] under "Participate" -> "Files". Test set image IDs, metadata, and labels can be found in test.csv after the conclusion of the competition.

MICCAI 2023 PruneCXR data

Additionally, a subset of this dataset used in the forthcoming MICCAI 2023 paper, "How Does Pruning Impact Long-Tailed Multi-Label Medical Image Classifiers?" [16] is provided here to ensure reproducibility; please see the accompanying Github repository [17] for full details on implementation and reproducibility. This study consists of 257,018 frontal CXRS, each labeled with one of 19 clinical findings (including a "No Findings" class). The following 5 findings are included in the label set in addition to the original 13 found in MIMIC-CXR-JPG v2.0.0:

• Calcification of the Aorta
• Pneumomediastinum
• Pneumoperitoneum
• Subcutaneous Emphysema
• Tortuous Aorta

Within the miccai-2023_mimic-cxr-lt/ directory, the training, validation, and test set image IDs and labels for this study can be found, respectively, in miccai2023_mimic-cxr-lt_labels_train.csv, miccai2023_mimic-cxr-lt_labels_val.csv, and miccai2023_mimic-cxr-lt_labels_test.csv.

Evaluation

Participants will upload image-level predictions on the provided test sets for evaluation. Since this is a multi-label classification problem with severe imbalance, the primary evaluation metric will be mean Average Precision (mAP) (i.e., "macro-averaged" AP across the 26 classes). While Area Under the Receiver Operating Characteristic Curve (AUC) is a standard metric for related datasets, AUC can be heavily inflated in the presence of strong imbalance. Instead, mAP is more appropriate for the long-tailed, multi-label setting since it both (i) measures performance across decision thresholds and (ii) does not degrade under class imbalance. For thoroughness, mean AUC (mAUC) and mean F1 score (mF1) — using a threshold of 0.5 for each class — will be calculated and appear on the leaderboard, but not contribute to team rankings.

A sample submission .csv for the development phase can be found in development_sample_submission.csv or on CodaLab [15] under "Participate" -> "Files". A sample submission for the test phase (test_sample_submission.csv) will be released when the testing phase begins on 07/14/2023. Reproducible code is required for this challenge, so all final submissions must contain all necessary code for preprocessing, training, inference, etc. See instructions below for how to successfully submit on CodaLab.

Submission file structure

All CodaLab submissions are required to be in .zip format. For this competition, this compressed .zip file must contain (i) a predictions .csv file and (ii) a "code/" directory with all of your training and inference code. The required file structure is as follows:

    
        xxx.csv  # predictions .csv file
        code/  # code directory
        ├── yyy.py
        ├── zzz.py
        ├── ...
    

To create the final submission .zip file, you might then run zip -r submission.zip xxx.csv code. Please note that the names of your individual submission files do not matter, though the code directory must be named "code".

Predictions .csv file requirements

Your predictions .csv file must contain image-level predictions of the probability that each of the 26 classes are present in a given image. Specifically,

• You must have a "dicom_id" column with the provided unique image IDs for the given evaluation set.
  • Entries must be strings.
• You must have a column for each of the 26 class labels ("Atelectasis", "Calcification of the Aorta", etc.).
  • Entries must be floats or integers in the interval [0, 1].

Release Notes

Version 1.1.0: This is an update to the CXR-LT 2023 challenge dataset now that the competition has concluded. All test phase image IDs, metadata, and labels have been added. Additionally, a subset of the CXR-LT challenge dataset used in Holste et al. [16] has been included for reproducibility.

Ethics

This shared task uses image data from MIMIC-CXR-JPG v2.0.0 and generates labels from free-text radiology reports in MIMIC-CXR, a de-identified dataset that we gained access to through a PhysioNet Credentialed Health Data Use Agreement (v1.5.0).

Acknowledgements

We thank our steering committee for their support of this project: Leo Anthony Celi, Zhiyong Lu, George Shih, and Ronald Summers.

Conflicts of Interest

The authors have no conflicts of interest to declare.

References

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