Generating 3D Brain Tumor Regions in MRI using Vector-Quantization Generative Adversarial Networks

Medical image analysis has significantly benefited from advancements in deep learning, particularly in the application of Generative Adversarial Networks (GANs) for generating realistic and diverse images that can augment training datasets. However, the effectiveness of such approaches is often limited by the amount of available data in clinical settings. Additionally, the common GAN-based approach is to generate entire image volumes, rather than solely the region of interest (ROI). Research on deep learning-based brain tumor classification using MRI has shown that it is easier to classify the tumor ROIs compared to the entire image volumes. In this work, we present a novel framework that uses vector-quantization GAN and a transformer incorporating masked token modeling to generate high-resolution and diverse 3D brain tumor ROIs that can be directly used as augmented data for the classification of brain tumor ROI. We apply our method to two imbalanced datasets where we augment the minority class: (1) the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2019 dataset to generate new low-grade glioma (LGG) ROIs to balance with high-grade glioma (HGG) class; (2) the internal pediatric LGG (pLGG) dataset tumor ROIs with BRAF V600E Mutation genetic marker to balance with BRAF Fusion genetic marker class. We show that the proposed method outperforms various baseline models in both qualitative and quantitative measurements. The generated data was used to balance the data in the brain tumor types classification task. Using the augmented data, our approach surpasses baseline models by 6.4% in AUC on the BraTS 2019 dataset and 4.3% in AUC on our internal pLGG dataset. The results indicate the generated tumor ROIs can effectively address the imbalanced data problem. Our proposed method has the potential to facilitate an accurate diagnosis of rare brain tumors using MRI scans.

Domain Transfer Through Image-to-Image Translation for Uncertainty-Aware Prostate Cancer Classification

Prostate Cancer (PCa) is often diagnosed using High-resolution 3.0 Tesla(T) MRI, which has been widely established in clinics. However, there are still many medical centers that use 1.5T MRI units in the actual diagnostic process of PCa. In the past few years, deep learning-based models have been proven to be efficient on the PCa classification task and can be successfully used to support radiologists during the diagnostic process. However, training such models often requires a vast amount of data, and sometimes it is unobtainable in practice. Additionally, multi-source MRIs can pose challenges due to cross-domain distribution differences. In this paper, we have presented a novel approach for unpaired image-to-image translation of prostate mp-MRI for classifying clinically significant PCa, to be applied in data-constrained settings. First, we introduce domain transfer, a novel pipeline to translate unpaired 3.0T multi-parametric prostate MRIs to 1.5T, to increase the number of training data. Second, we estimate the uncertainty of our models through an evidential deep learning approach; and leverage the dataset filtering technique during the training process. Furthermore, we introduce a simple, yet efficient Evidential Focal Loss that incorporates the focal loss with evidential uncertainty to train our model. Our experiments demonstrate that the proposed method significantly improves the Area Under ROC Curve (AUC) by over 20% compared to the previous work (98.4% vs. 76.2%). We envision that providing prediction uncertainty to radiologists may help them focus more on uncertain cases and thus expedite the diagnostic process effectively. Our code is available at https://github.com/med-i-lab/DT_UE_PCa

From Clozing to Comprehending: Retrofitting Pre-trained Language Model to Pre-trained Machine Reader

We present Pre-trained Machine Reader (PMR), a novel method to retrofit Pre-trained Language Models (PLMs) into Machine Reading Comprehension (MRC) models without acquiring labeled data. PMR is capable of resolving the discrepancy between model pre-training and downstream fine-tuning of existing PLMs, and provides a unified solver for tackling various extraction tasks. To achieve this, we construct a large volume of general-purpose and high-quality MRC-style training data with the help of Wikipedia hyperlinks and design a Wiki Anchor Extraction task to guide the MRC-style pre-training process. Although conceptually simple, PMR is particularly effective in solving extraction tasks including Extractive Question Answering and Named Entity Recognition, where it shows tremendous improvements over previous approaches especially under low-resource settings. Moreover, viewing sequence classification task as a special case of extraction task in our MRC formulation, PMR is even capable to extract high-quality rationales to explain the classification process, providing more explainability of the predictions.

An Attention-based Multi-Scale Feature Learning Network for Multimodal Medical Image Fusion

Medical images play an important role in clinical applications. Multimodal medical images could provide rich information about patients for physicians to diagnose. The image fusion technique is able to synthesize complementary information from multimodal images into a single image. This technique will prevent radiologists switch back and forth between different images and save lots of time in the diagnostic process. In this paper, we introduce a novel Dilated Residual Attention Network for the medical image fusion task. Our network is capable to extract multi-scale deep semantic features. Furthermore, we propose a novel fixed fusion strategy termed Softmax-based weighted strategy based on the Softmax weights and matrix nuclear norm. Extensive experiments show our proposed network and fusion strategy exceed the state-of-the-art performance compared with reference image fusion methods on four commonly used fusion metrics.

Towards Theoretical Analysis of Transformation Complexity of ReLU DNNs

This paper aims to theoretically analyze the complexity of feature transformations encoded in DNNs with ReLU layers. We propose metrics to measure three types of complexities of transformations based on the information theory. We further discover and prove the strong correlation between the complexity and the disentanglement of transformations. Based on the proposed metrics, we analyze two typical phenomena of the change of the transformation complexity during the training process, and explore the ceiling of a DNN's complexity. The proposed metrics can also be used as a loss to learn a DNN with the minimum complexity, which also controls the over-fitting level of the DNN and influences adversarial robustness, adversarial transferability, and knowledge consistency. Comprehensive comparative studies have provided new perspectives to understand the DNN.

Enhancing Cross-lingual Prompting with Mask Token Augmentation

Prompting shows promising results in few-shot scenarios. However, its strength for multilingual/cross-lingual problems has not been fully exploited. Zhao and Sch\"utze (2021) made initial explorations in this direction by presenting that cross-lingual prompting outperforms cross-lingual finetuning. In this paper, we conduct empirical analysis on the effect of each component in cross-lingual prompting and derive Universal Prompting across languages, which helps alleviate the discrepancies between source-language training and target-language inference. Based on this, we propose a mask token augmentation framework to further improve the performance of prompt-based cross-lingual transfer. Notably, for XNLI, our method achieves 46.54% with only 16 English training examples per class, significantly better than 34.99% of finetuning.

Heuristic Hyperparameter Optimization for Convolutional Neural Networks using Genetic Algorithm

In recent years, people from all over the world are suffering from one of the most severe diseases in history, known as Coronavirus disease 2019, COVID-19 for short. When the virus reaches the lungs, it has a higher probability to cause lung pneumonia and sepsis. X-ray image is a powerful tool in identifying the typical features of the infection for COVID-19 patients. The radiologists and pathologists observe that ground-glass opacity appears in the chest X-ray for infected patient \cite{cozzi2021ground}, and it could be used as one of the criteria during the diagnosis process. In the past few years, deep learning has proven to be one of the most powerful methods in the field of image classification. Due to significant differences in Chest X-Ray between normal and infected people \cite{rousan2020chest}, deep models could be used to identify the presence of the disease given a patient's Chest X-Ray. Many deep models are complex, and it evolves with lots of input parameters. Designers sometimes struggle with the tuning process for deep models, especially when they build up the model from scratch. Genetic Algorithm, inspired by the biological evolution process, plays a key role in solving such complex problems. In this paper, I proposed a genetic-based approach to optimize the Convolutional Neural Network(CNN) for the Chest X-Ray classification task.

A Unified Game-Theoretic Interpretation of Adversarial Robustness

This paper provides a unified view to explain different adversarial attacks and defense methods, \emph{i.e.} the view of multi-order interactions between input variables of DNNs. Based on the multi-order interaction, we discover that adversarial attacks mainly affect high-order interactions to fool the DNN. Furthermore, we find that the robustness of adversarially trained DNNs comes from category-specific low-order interactions. Our findings provide a potential method to unify adversarial perturbations and robustness, which can explain the existing defense methods in a principle way. Besides, our findings also make a revision of previous inaccurate understanding of the shape bias of adversarially learned features.

Shoulder Implant X-Ray Manufacturer Classification: Exploring with Vision Transformer

Shoulder replacement surgery, also called total shoulder replacement, is a common and complex surgery in Orthopedics discipline. It involves replacing a dead shoulder joint with an artificial implant. In the market, there are many artificial implant manufacturers and each of them may produce different implants with different structures compares to other providers. The problem arises in the following situation: a patient has some problems with the shoulder implant accessory and the manufacturer of that implant maybe unknown to either the patient or the doctor, therefore, correctly identification of the manufacturer is the key prior to the treatment. In this paper, we will demonstrate different methods for classifying the manufacturer of a shoulder implant. We will use Vision Transformer approach to this task for the first time ever