Cited by 15Brain Tumor Detection and ClassificationMedical Image Segmentation TechniquesGlioma Diagnosis and Treatment

Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging

Open access
Capellán-Martín, Daniel, Jiang, Zhifan, Parida, Abhijeet, Liu, Xinyang, Lam, Van, Nisar, Hareem, Tapp, Austin, Elsharkawi, Sarah +3 more·2024·Lecture Notes in Computer Science

Abstract

Segmenting brain tumors in multi-parametric magnetic resonance imaging enables performing quantitative analysis in support of clinical trials and personalized patient care. This analysis provides the potential to impact clinical decision-making processes, including diagnosis and prognosis. In 2023, the well-established Brain Tumor Segmentation (BraTS) challenge presented a substantial expansion with eight tasks and 4,500 brain tumor cases. In this paper, we present a deep learning-based ensemble strategy that is evaluated for newly included tumor cases in three tasks: pediatric brain tumors (PED), intracranial meningioma (MEN), and brain metastases (MET). In particular, we ensemble outputs from state-of-the-art nnU-Net and Swin UNETR models on a region-wise basis. Furthermore, we implemented a targeted post-processing strategy based on a cross-validated threshold search to improve the segmentation results for tumor sub-regions. The evaluation of our proposed method on unseen test cases for the three tasks resulted in lesion-wise Dice scores for PED: 0.653, 0.809, 0.826; MEN: 0.876, 0.867, 0.849; and MET: 0.555, 0.6, 0.58; for the enhancing tumor, tumor core, and whole tumor, respectively. Our method was ranked first for PED, third for MEN, and fourth for MET, respectively.

AI snapshot

Written from the paper’s full text.

TL;DR

This paper presents a deep learning ensemble of nnU-Net and Swin UNETR with task-specific post-processing for brain tumor segmentation in the BraTS 2023 pediatric, meningioma, and metastasis tasks. It ranked first for PED, third for MEN, and fourth for MET on unseen test cases.

Key findings

  • On unseen test cases, lesion-wise Dice scores were PED: 0.653, 0.809, 0.826; MEN: 0.876, 0.867, 0.849; and MET: 0.555, 0.6, 0.58 for enhancing tumor, tumor core, and whole tumor, respectively.
  • The method ranked first for PED, third for MEN, and fourth for MET.
  • The combination of ensemble models and post-processing yielded clear improvements across PED, MEN, and MET, with the improvement more noticeable in pediatric tumor segmentation.
  • ET identification was the most challenging in PED, as shown by the lowest Dice coefficient for that region.

Methods

  • The authors ensembled nnU-Net and Swin UNETR outputs on a label-wise/region-wise basis, using five-fold cross-validation; for MET, only nnU-Net was used after experimental evaluation because Swin UNETR showed inferior performance.
  • Data were multi-parametric MRI including T1, T1CE, T2, and T2-FLAIR. Splits were PED: training n=99, validation n=45; MEN: training n=1,000, validation n=141; MET: training n=165, validation n=31, with additional testing datasets.
  • Post-processing removed disconnected regions smaller than 130 voxels for PED, 110 for MEN, and 15 for MET, and applied PED-specific label redefinition using cross-validated thresholds: ET/WT 0.04 and ED/WT 1.00.

Limitations

  • The paper states that PED and MET were conducted with limited available data, and that each task’s training was restricted to task-specific data per BraTS 2023 guidelines.
  • The authors state that additional pre-training outside the challenge could improve generalization, and they suggest self-supervised learning, foundation models, or generative AI to augment limited training sets.
  • Evident from the text: the ensemble did not use Swin UNETR for MET because it underperformed, so the final MET solution relied on nnU-Net alone.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1007/978-3-031-76163-8_20

Cites

29 of 29 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

6 of 7 cited sources checked · 3 supported · 0 flagged · accuracy not yet measured

  • Findingown data

    For the enhancing tumor (ET) label, the optimal post-processing threshold was 0.04.

    “For ET, we obtained an optimal threshold of 0.04.”
    Quote in the paperNot a substantial claim
  • Findingown data

    For the MEN and MET tasks, a better balance between label segmentation was achieved.

    “For the MEN and MET tasks, a better balance between label segmentation was achieved.”
    Quote in the paperSubstantial claim
  • Findingown data

    For the edematous area (ED) label, the optimal post-processing threshold was 1.00.

    “On the other hand, Fig. 5b displays the lesion-wise Dice score vs ED/WT threshold curve obtained from the same process but applied to the ED label, which yielded an optimal threshold of 1.00.”
    Quote in the paperNot a substantial claim
  • Interpretationnone given

    The proposed strategy minimized undesired smaller contributions that would negatively impact lesion-wise performance.

    “Our strategy minimized undesired smaller contributions, which would negatively impact lesion-wise performance.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The BraTS 2023 challenge introduced new performance metrics that assess segmentation models at a lesion-wise level rather than over the entire/multiple tumor region(s).
  • Interpretationown data

    The ensemble prediction from nnU-Net and Swin UNETR provided better segmentation accuracy for all tumor types.

    “The ensemble prediction from nnU-net and Swin UNETR provided better segmentation accuracy for all tumor types.”
    Quote in the paperSubstantial claim
  • May combine two claims. 9
  • Classified as probably not a substantial claim. 5
  • The quote only partly states this claim. 1
  • May combine two claims.

    Premisecitation

    Swin UNETR's local window self-attention outperforms traditional ViT and is well suited to multiscale tasks.

    “Swin UNETR’s innovative local window self-attention outperforms traditional ViT, which is well suited to multiscale tasks.”
    Quote in the paperNot a substantial claim3 of 3 sources checked
    • cites [11] Hatamizadeh, A., Nath, V., Tang, Y., et al.: Swin UNETR: Swin transformers for semantic segmentation of brain tumors in MRI images. In: Crimi, A., Bakas, S. (eds.) Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries, pp. 272–284. Springer, Cham (2022). https://doi.org/10.1007/978-3-031-08999-2_22 source
    • cites [12] Hatamizadeh, A., Tang, Y., Nath, V., et al.: UNETR: transformers for 3D medical image segmentation. In: IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), pp. 574–584 (2022) source

      The Implementation Details (p. 5) describe UNETR’s encoder as following ViT-B16, while the Discussion (p. 7) reports UNETR’s performance. Our copy does not report Swin UNETR’s local-window self-attention, a comparison with traditional ViT, or its suitability for multiscale tasks (searched: Swin UNETR, local window self-attention, multiscale, ViT). (LLM, conf=0.76)

      Experimental — accuracy not yet measured
    • cites [27] Tang, Y., Yang, D., Li, W., Roth, H.R., et al.: Self-supervised pre-training of swin transformers for 3D medical image analysis. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, pp. 20730–20740 (2022) source
  • May combine two claims.

    Premisecitation

    Although a few previous works addressed pediatric brain tumors, their automatic segmentation remains challenging due to a lack of training data and variation in heterogeneous histologic sub-regions.

    “Although, a few previous works addressed pediatric brain tumors [10,14,20], their automatic segmentation remains challenging. This is due to a lack of training data and variation in heterogeneous histologic sub-regions including peritumoral edematous/invaded tissue, necrotic core, and enhancing tumor.”
    Quote in the paperSubstantial claim2 of 3 sources checked
    • cites [10] Fathi Kazerooni, A., Arif, S., Madhogarhia, R., et al.: Automated tumor segmentation and brain tissue extraction from multiparametric MRI of pediatric brain tumors: a multi-institutional study. Neuro-Oncol. Adv. 5(1), vdad027 (2023) source

      The introductory passage (labeled Abstract > Conclusions; page unavailable) describes a few earlier pediatric segmentation studies and limitations in their performance and ability to distinguish subregions. The Methods and Results (pages unavailable) also describe difficulty distinguishing enhancing tumor, non-enhancing tumor, and edema; the Discussion links limited edema examples to class imbalance. The paper does not establish a general lack of training data as the cause of the challenge, and its listed subregions do not include the claim’s necrotic core or invaded tissue. (LLM, conf=0.84)

      Experimental — accuracy not yet measured
    • cites [14] Jiang, Z., Parida, A., Anwar, S.M., et al.: Automatic visual acuity loss prediction in children with optic pathway gliomas using magnetic resonance imaging. In: 2023 45th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), pp. 1–5 (2023) source

      The Introduction says automatic segmentation of the anterior visual pathway in children with optic pathway gliomas is difficult and that obtaining sufficient training data for rare pediatric brain tumors is challenging. The Methods list necrotic, peritumoral edematous, and enhancing regions as labels in an adult glioblastoma dataset; the paper does not say that variation among those regions causes the pediatric segmentation difficulty. (LLM, conf=0.87)

      Experimental — accuracy not yet measured
    • cites [20] Liu, X., Bonner, E., Jiang, Z., et al.: Automatic segmentation of rare pediatric brain tumors using knowledge transfer from adult data. In: 20th IEEE International Symposium on Biomedical Imaging (2023) source
  • May combine two claims.

    Premisecitation

    The nnU-Net framework autonomously adjusts its internal configurations according to the specific imaging modality and unique attributes of each dataset, resulting in improved segmentation performance and generalization compared to other state-of-the-art methods for biomedical image segmentation.

    “According to the specific imaging modality and unique attributes of each dataset, the framework autonomously adjusts its internal configurations [13]. This results in an improved segmentation performance and generalization when compared to other state-of-the-art methods for biomedical image segmentation.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [13] Isensee, F., Jaeger, P.F., Kohl, S.A., et al.: nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nat. Methods 18(2), 203–211 (2021) source
  • May combine two claims.

    Findingown data

    For the MET task, Swin UNETR showed inferior performance compared to nnU-Net, so only nnU-Net was used.

    “Finally, for the MET task, only nnU-Net, trained on all labels, was used after experimental evaluation, as Swin UNETR showed inferior performance in this scenario.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    On unseen test cases for the BraTS 2023 PED, MEN, and MET tasks, the proposed method achieved lesion-wise Dice scores for PED of 0.653, 0.809, and 0.826; for MEN of 0.876, 0.867, and 0.849; and for MET of 0.555, 0.6, and 0.58, for enhancing tumor, tumor core, and whole tumor, respectively.

    “The evaluation of our proposed method on unseen test cases for the three tasks resulted in lesion-wise Dice scores for PED: 0.653, 0.809, 0.826; MEN: 0.876, 0.867, 0.849; and MET: 0.555, 0.6, 0.58; for the enhancing tumor, tumor core, and whole tumor, respectively.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    The proposed method was ranked first for the PED task, third for the MEN task, and fourth for the MET task.

    “Our method was ranked first for PED, third for MEN, and fourth for MET, respectively.”
    • Also stated in: § Conclusion · boosted
      “The success of our method is demonstrated by the challenge ranking positions on unseen test cases, being the winner in PED task, ranked third for MEN, and fourth for MET task.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. May combine two claims. The quote only partly states this claim.

    Study design and conductown data

    For each of the three tasks, both the nnU-Net and Swin UNETR models were trained using a five-fold cross-validation approach.

    “For each of the three tasks, we trained a full-resolution 3D nnU-Net (v2) model using a five-fold cross-validation approach.”
    • Also stated in: § Deep Learning Models and Experimental Setup · plain
      “For each of the three tasks, we trained a full-resolution 3D Swin UNETR model using a five-fold cross-validation approach.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    The performance evaluation on the validation datasets was performed automatically by the challenge's digital platform, with no access to the validation ground truth data.

    “This performance evaluation was performed automatically by the challenge’s digital platform, with no access to the validation ground truth data.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Premisenone given

    Binary metrics disproportionately penalize false positive predictions.

    “Consequently, binary metrics disproportionately penalize false positive predictions.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: The BraTS 2023 challenge introduced new performance metrics that assess segmentation models at a lesion-wise level rather than over the entire/multiple tumor region(s).
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Each task's training process was restricted to the usage of task-specific data, adhering to the predefined guidelines of the BraTS 2023 challenge.

    “Each task’s training process was restricted to the usage of task-specific data, adhering to the predefined guidelines of the BraTS 2023 challenge.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationreasoning

    The targeted post-processing strategy based on cross-validated thresholding search improved performance in all tasks, with the improvement being more noticeable in pediatric tumor segmentation.

    “Furthermore, our targeted post-processing strategy based on cross-validated thresholding search improved the performance in all tasks, being more noticeable in pediatric tumor segmentation due to the label-wise targeted post-processing steps.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The BraTS 2023 challenge introduced new performance metrics that assess segmentation models at a lesion-wise level rather than over the entire/multiple tumor region(s).
  • Classified as probably not a substantial claim.

    Study design and conductown data

    The optimal post-processing threshold values were determined by experimenting with the cross-validation data.

    “These optimal threshold values were determined by experimenting with the cross-validation data.”
    • Also stated in: § Post-processing · plain
      “These optimal threshold values were also determined by experimenting with the cross-validation data.”
    Quote in the paperSubstantial claim
12 of 12
  • The paper relies on this without support.

    The BraTS 2023 challenge introduced new performance metrics that assess segmentation models at a lesion-wise level rather than over the entire/multiple tumor region(s).

    “New performance metrics were introduced in this year’s BraTS challenge to assess segmentation models at a lesion-wise level rather than over the entire/multiple tumor region(s).”
1 of 1

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Conclusion credits an ensemble for MET, but MET used only nnU-Net

    Major

    The conclusion attributes better segmentation accuracy for all tumor types to an ensemble of nnU-Net and Swin UNETR. The methods state that the MET task used only nnU-Net, so its results cannot demonstrate a benefit from that ensemble.

1 of 1

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Authors
Capellán-Martín, D., Jiang, Z., Parida, A., Liu, X., Lam, V., Nisar, H., Tapp, A., Elsharkawi, S., Ledesma-Carbayo, M. J., Anwar, S. M., & Linguraru, M. G.
Affiliations
Children's National (US)
Corresponding author
Linguraru, Marius George
Venue
Lecture Notes in Computer Science
Published
2024
Volume
14669
Pages
221-232
ISSN
  • 0302-9743 (ISSN-L)
  • 1611-3349
OpenAlex
W4405823737
Cited by
15
References
22
Citations by year
2026: 9 · 2025: 5 · 2024: 1
FWCI
6.97
Type
conference paper
Language
en
Open access
Locations
  • Lecture notes in computer science (publishedVersion)
  • PubMed (publishedVersion)
  • arXiv (Cornell University) (submittedVersion, cc-by-nc-nd)
  • PubMed Central (submittedVersion)
  • arXiv (Cornell University)
Funders
  • European Commission (101100633)
  • Universidad Politécnica de Madrid
  • Ministerio de Ciencia e Innovación (PDC2022, PID2022)
  • Agencia Estatal de Investigación (PDC2022-133865-I00)
  • National Cancer Institute (UG3CA236536)
Topics
  • Life Sciences › Neuroscience › Neurology › Brain Tumor Detection and Classification
  • Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Medical Image Segmentation Techniques
  • Health Sciences › Medicine › Genetics › Glioma Diagnosis and Treatment
Keywords
brain tumor segmentation, ensemble learning, BraTS, pediatric brain tumors, intracranial meningioma, brain metastases, nnU-Net, Swin UNETR, post-processing, multiparametric MRI

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