BraSyn 2023 challenge: Missing MRI synthesis and the effect of different learning objectives

This work addresses the Brain Magnetic Resonance Image Synthesis for Tumor Segmentation (BraSyn) challenge, which was hosted as part of the Brain Tumor Segmentation (BraTS) challenge in 2023. In this challenge, researchers are invited to synthesize a missing magnetic resonance image sequence, given other available sequences, to facilitate tumor segmentation pipelines trained on complete sets of image sequences. This problem can be tackled using deep learning within the framework of paired image-to-image translation. In this study, we propose investigating the effectiveness of a commonly used deep learning framework, such as Pix2Pix, trained under the supervision of different image-quality loss functions. Our results indicate that the use of different loss functions significantly affects the synthesis quality. We systematically study the impact of various loss functions in the multi-sequence MR image synthesis setting of the BraSyn challenge. Furthermore, we demonstrate how image synthesis performance can be optimized by combining different learning objectives beneficially.

Benchmarking Pretrained Vision Embeddings for Near- and Duplicate Detection in Medical Images

Near- and duplicate image detection is a critical concern in the field of medical imaging. Medical datasets often contain similar or duplicate images from various sources, which can lead to significant performance issues and evaluation biases, especially in machine learning tasks due to data leakage between training and testing subsets. In this paper, we present an approach for identifying near- and duplicate 3D medical images leveraging publicly available 2D computer vision embeddings. We assessed our approach by comparing embeddings extracted from two state-of-the-art self-supervised pretrained models and two different vector index structures for similarity retrieval. We generate an experimental benchmark based on the publicly available Medical Segmentation Decathlon dataset. The proposed method yields promising results for near- and duplicate image detection achieving a mean sensitivity and specificity of 0.9645 and 0.8559, respectively.

Medical Image Retrieval Using Pretrained Embeddings

A wide range of imaging techniques and data formats available for medical images make accurate retrieval from image databases challenging. Efficient retrieval systems are crucial in advancing medical research, enabling large-scale studies and innovative diagnostic tools. Thus, addressing the challenges of medical image retrieval is essential for the continued enhancement of healthcare and research. In this study, we evaluated the feasibility of employing four state-of-the-art pretrained models for medical image retrieval at modality, body region, and organ levels and compared the results of two similarity indexing approaches. Since the employed networks take 2D images, we analyzed the impacts of weighting and sampling strategies to incorporate 3D information during retrieval of 3D volumes. We showed that medical image retrieval is feasible using pretrained networks without any additional training or fine-tuning steps. Using pretrained embeddings, we achieved a recall of 1 for various tasks at modality, body region, and organ level.

Uncertainty Estimation in Contrast-Enhanced MR Image Translation with Multi-Axis Fusion

In recent years, deep learning has been applied to a wide range of medical imaging and image processing tasks. In this work, we focus on the estimation of epistemic uncertainty for 3D medical image-to-image translation. We propose a novel model uncertainty quantification method, Multi-Axis Fusion (MAF), which relies on the integration of complementary information derived from multiple views on volumetric image data. The proposed approach is applied to the task of synthesizing contrast enhanced T1-weighted images based on native T1, T2 and T2-FLAIR scans. The quantitative findings indicate a strong correlation ($\rho_{\text healthy} = 0.89$) between the mean absolute image synthetization error and the mean uncertainty score for our MAF method. Hence, we consider MAF as a promising approach to solve the highly relevant task of detecting synthetization failures at inference time.

fRegGAN with K-space Loss Regularization for Medical Image Translation

Generative adversarial networks (GANs) have shown remarkable success in generating realistic images and are increasingly used in medical imaging for image-to-image translation tasks. However, GANs tend to suffer from a frequency bias towards low frequencies, which can lead to the removal of important structures in the generated images. To address this issue, we propose a novel frequency-aware image-to-image translation framework based on the supervised RegGAN approach, which we call fRegGAN. The framework employs a K-space loss to regularize the frequency content of the generated images and incorporates well-known properties of MRI K-space geometry to guide the network training process. By combine our method with the RegGAN approach, we can mitigate the effect of training with misaligned data and frequency bias at the same time. We evaluate our method on the public BraTS dataset and outperform the baseline methods in terms of both quantitative and qualitative metrics when synthesizing T2-weighted from T1-weighted MR images. Detailed ablation studies are provided to understand the effect of each modification on the final performance. The proposed method is a step towards improving the performance of image-to-image translation and synthesis in the medical domain and shows promise for other applications in the field of image processing and generation.

Transfer Learning for Segmentation Problems: Choose the Right Encoder and Skip the Decoder

It is common practice to reuse models initially trained on different data to increase downstream task performance. Especially in the computer vision domain, ImageNet-pretrained weights have been successfully used for various tasks. In this work, we investigate the impact of transfer learning for segmentation problems, being pixel-wise classification problems that can be tackled with encoder-decoder architectures. We find that transfer learning the decoder does not help downstream segmentation tasks, while transfer learning the encoder is truly beneficial. We demonstrate that pretrained weights for a decoder may yield faster convergence, but they do not improve the overall model performance as one can obtain equivalent results with randomly initialized decoders. However, we show that it is more effective to reuse encoder weights trained on a segmentation or reconstruction task than reusing encoder weights trained on classification tasks. This finding implicates that using ImageNet-pretrained encoders for downstream segmentation problems is suboptimal. We also propose a contrastive self-supervised approach with multiple self-reconstruction tasks, which provides encoders that are suitable for transfer learning in segmentation problems in the absence of segmentation labels.

FAIR4Cov: Fused Audio Instance and Representation for COVID-19 Detection

Audio-based classification techniques on body sounds have long been studied to support diagnostic decisions, particularly in pulmonary diseases. In response to the urgency of the COVID-19 pandemic, a growing number of models are developed to identify COVID-19 patients based on acoustic input. Most models focus on cough because the dry cough is the best-known symptom of COVID-19. However, other body sounds, such as breath and speech, have also been revealed to correlate with COVID-19 as well. In this work, rather than relying on a specific body sound, we propose Fused Audio Instance and Representation for COVID-19 Detection (FAIR4Cov). It relies on constructing a joint feature vector obtained from a plurality of body sounds in waveform and spectrogram representation. The core component of FAIR4Cov is a self-attention fusion unit that is trained to establish the relation of multiple body sounds and audio representations and integrate it into a compact feature vector. We set up our experiments on different combinations of body sounds using only waveform, spectrogram, and a joint representation of waveform and spectrogram. Our findings show that the use of self-attention to combine extracted features from cough, breath, and speech sounds leads to the best performance with an Area Under the Receiver Operating Characteristic Curve (AUC) score of 0.8658, a sensitivity of 0.8057, and a specificity of 0.7958. This AUC is 0.0227 higher than the one of the models trained on spectrograms only and 0.0847 higher than the one of the models trained on waveforms only. The results demonstrate that the combination of spectrogram with waveform representation helps to enrich the extracted features and outperforms the models with single representation.

How Transferable Are Self-supervised Features in Medical Image Classification Tasks?

Transfer learning has become a standard practice to mitigate the lack of labeled data in medical classification tasks. Whereas finetuning a downstream task using supervised ImageNet pretrained features is straightforward and extensively investigated in many works, there is little study on the usefulness of self-supervised pretraining. In this paper, we assess the transferability of ImageNet self-supervisedpretraining by evaluating the performance of models initialized with pretrained features from three self-supervised techniques (SimCLR, SwAV, and DINO) on selected medical classification tasks. The chosen tasks cover tumor detection in sentinel axillary lymph node images, diabetic retinopathy classification in fundus images, and multiple pathological condition classification in chest X-ray images. We demonstrate that self-supervised pretrained models yield richer embeddings than their supervised counterpart, which benefits downstream tasks in view of both linear evaluation and finetuning. For example, in view of linear evaluation at acritically small subset of the data, we see an improvement up to 14.79% in Kappa score in the diabetic retinopathy classification task, 5.4% in AUC in the tumor classification task, 7.03% AUC in the pneumonia detection, and 9.4% in AUC in the detection of pathological conditions in chest X-ray. In addition, we introduce Dynamic Visual Meta-Embedding (DVME) as an end-to-end transfer learning approach that fuses pretrained embeddings from multiple models. We show that the collective representation obtained by DVME leads to a significant improvement in the performance of selected tasks compared to using a single pretrained model approach and can be generalized to any combination of pretrained models.

Multi-Resolution 3D Convolutional Neural Networks for Automatic Coronary Centerline Extraction in Cardiac CT Angiography Scans

We propose a deep learning-based automatic coronary artery tree centerline tracker (AuCoTrack) extending the vessel tracker by Wolterink (arXiv:1810.03143). A dual pathway Convolutional Neural Network (CNN) operating on multi-scale 3D inputs predicts the direction of the coronary arteries as well as the presence of a bifurcation. A similar multi-scale dual pathway 3D CNN is trained to identify coronary artery endpoints for terminating the tracking process. Two or more continuation directions are derived based on the bifurcation detection. The iterative tracker detects the entire left and right coronary artery trees based on only two ostium landmarks derived from a model-based segmentation of the heart. The 3D CNNs were trained on a proprietary dataset consisting of 43 CCTA scans. An average sensitivity of 87.1% and clinically relevant overlap of 89.1% was obtained relative to a refined manual segmentation. In addition, the MICCAI 2008 Coronary Artery Tracking Challenge (CAT08) training and test datasets were used to benchmark the algorithm and to assess its generalization. An average overlap of 93.6% and a clinically relevant overlap of 96.4% were obtained. The proposed method achieved better overlap scores than the current state-of-the-art automatic centerline extraction techniques on the CAT08 dataset with a vessel detection rate of 95%.