Disentangled Multimodal Brain MR Image Translation via Transformer-based Modality Infuser

Multimodal Magnetic Resonance (MR) Imaging plays a crucial role in disease diagnosis due to its ability to provide complementary information by analyzing a relationship between multimodal images on the same subject. Acquiring all MR modalities, however, can be expensive, and, during a scanning session, certain MR images may be missed depending on the study protocol. The typical solution would be to synthesize the missing modalities from the acquired images such as using generative adversarial networks (GANs). Yet, GANs constructed with convolutional neural networks (CNNs) are likely to suffer from a lack of global relationships and mechanisms to condition the desired modality. To address this, in this work, we propose a transformer-based modality infuser designed to synthesize multimodal brain MR images. In our method, we extract modality-agnostic features from the encoder and then transform them into modality-specific features using the modality infuser. Furthermore, the modality infuser captures long-range relationships among all brain structures, leading to the generation of more realistic images. We carried out experiments on the BraTS 2018 dataset, translating between four MR modalities, and our experimental results demonstrate the superiority of our proposed method in terms of synthesis quality. In addition, we conducted experiments on a brain tumor segmentation task and different conditioning methods.

Hybrid-Fusion Transformer for Multisequence MRI

Medical segmentation has grown exponentially through the advent of a fully convolutional network (FCN), and we have now reached a turning point through the success of Transformer. However, the different characteristics of the modality have not been fully integrated into Transformer for medical segmentation. In this work, we propose the novel hybrid fusion Transformer (HFTrans) for multisequence MRI image segmentation. We take advantage of the differences among multimodal MRI sequences and utilize the Transformer layers to integrate the features extracted from each modality as well as the features of the early fused modalities. We validate the effectiveness of our hybrid-fusion method in three-dimensional (3D) medical segmentation. Experiments on two public datasets, BraTS2020 and MRBrainS18, show that the proposed method outperforms previous state-of-the-art methods on the task of brain tumor segmentation and brain structure segmentation.

Why is the winner the best?

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

SOS: Score-based Oversampling for Tabular Data

Score-based generative models (SGMs) are a recent breakthrough in generating fake images. SGMs are known to surpass other generative models, e.g., generative adversarial networks (GANs) and variational autoencoders (VAEs). Being inspired by their big success, in this work, we fully customize them for generating fake tabular data. In particular, we are interested in oversampling minor classes since imbalanced classes frequently lead to sub-optimal training outcomes. To our knowledge, we are the first presenting a score-based tabular data oversampling method. Firstly, we re-design our own score network since we have to process tabular data. Secondly, we propose two options for our generation method: the former is equivalent to a style transfer for tabular data and the latter uses the standard generative policy of SGMs. Lastly, we define a fine-tuning method, which further enhances the oversampling quality. In our experiments with 6 datasets and 10 baselines, our method outperforms other oversampling methods in all cases.

Invertible Tabular GANs: Killing Two Birds with OneStone for Tabular Data Synthesis

Tabular data synthesis has received wide attention in the literature. This is because available data is often limited, incomplete, or cannot be obtained easily, and data privacy is becoming increasingly important. In this work, we present a generalized GAN framework for tabular synthesis, which combines the adversarial training of GANs and the negative log-density regularization of invertible neural networks. The proposed framework can be used for two distinctive objectives. First, we can further improve the synthesis quality, by decreasing the negative log-density of real records in the process of adversarial training. On the other hand, by increasing the negative log-density of real records, realistic fake records can be synthesized in a way that they are not too much close to real records and reduce the chance of potential information leakage. We conduct experiments with real-world datasets for classification, regression, and privacy attacks. In general, the proposed method demonstrates the best synthesis quality (in terms of task-oriented evaluation metrics, e.g., F1) when decreasing the negative log-density during the adversarial training. If increasing the negative log-density, our experimental results show that the distance between real and fake records increases, enhancing robustness against privacy attacks.

Domain-Robust Mitotic Figure Detection with Style Transfer

We propose a new training scheme for domain generalization in mitotic figure detection. Mitotic figures show different characteristics for each scanner. We consider each scanner as a 'domain' and the image distribution specified for each domain as 'style'. The goal is to train our network to be robust on scanner types by using various 'style' images. To expand the style variance, we transfer a style of the training image into arbitrary styles, by defining a module based on StarGAN. Our model with the proposed training scheme shows positive performance on MIDOG Preliminary Test-Set containing scanners never seen before.

Domain-Robust Mitotic Figure Detection with StyleGAN

We propose a new training scheme for domain generalization in mitotic figure detection. By considering the image variance due to different scanner types as different image styles, we have trained our detection network to be robust on scanner types. To expand the image variance, domain of training image is transferred into arbitrary domain. The proposed style transfer module generates different styled images from an input image with random code, eventually generating variously styled images. Our model with the proposed training scheme shows good performance on MIDOG Preliminary Test-Set containing scanners never seen before.