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The robustness of supervised deep learning-based medical image classification is significantly undermined by label noise. Although several methods have been proposed to enhance classification performance in the presence of noisy labels, they face some challenges: 1) a struggle with class-imbalanced datasets, leading to the frequent overlooking of minority classes as noisy samples; 2) a singular focus on maximizing performance using noisy datasets, without incorporating experts-in-the-loop for actively cleaning the noisy labels. To mitigate these challenges, we propose a two-phase approach that combines Learning with Noisy Labels (LNL) and active learning. This approach not only improves the robustness of medical image classification in the presence of noisy labels, but also iteratively improves the quality of the dataset by relabeling the important incorrect labels, under a limited annotation budget. Furthermore, we introduce a novel Variance of Gradients approach in LNL phase, which complements the loss-based sample selection by also sampling under-represented samples. Using two imbalanced noisy medical classification datasets, we demonstrate that that our proposed technique is superior to its predecessors at handling class imbalance by not misidentifying clean samples from minority classes as mostly noisy samples., Comment: Accepted at MICCAI 2024

In image-guided liver surgery, 3D-3D non-rigid registration methods play a crucial role in estimating the mapping between the preoperative model and the intraoperative surface represented as point clouds, addressing the challenge of tissue deformation. Typically, these methods incorporate a biomechanical model, represented as a finite element model (FEM), used to regularize a surface matching term. This paper introduces a novel 3D-3D non-rigid registration method. In contrast to the preceding techniques, our method uniquely incorporates the FEM within the surface matching term itself, ensuring that the estimated deformation maintains geometric consistency throughout the registration process. Additionally, we eliminate the need to determine zero-boundary conditions and applied force locations in the FEM. We achieve this by integrating soft springs into the stiffness matrix and allowing forces to be distributed across the entire liver surface. To further improve robustness, we introduce a regularization technique focused on the gradient of the force magnitudes. This regularization imposes spatial smoothness and helps prevent the overfitting of irregular noise in intraoperative data. Optimization is achieved through an accelerated proximal gradient algorithm, further enhanced by our proposed method for determining the optimal step size. Our method is evaluated and compared to both a learning-based method and a traditional method that features FEM regularization using data collected on our custom-developed phantom, as well as two publicly available datasets. Our method consistently outperforms or is comparable to the baseline techniques. Both the code and dataset will be made publicly available.

Label noise in medical image classification datasets significantly hampers the training of supervised deep learning methods, undermining their generalizability. The test performance of a model tends to decrease as the label noise rate increases. Over recent years, several methods have been proposed to mitigate the impact of label noise in medical image classification and enhance the robustness of the model. Predominantly, these works have employed CNN-based architectures as the backbone of their classifiers for feature extraction. However, in recent years, Vision Transformer (ViT)-based backbones have replaced CNNs, demonstrating improved performance and a greater ability to learn more generalizable features, especially when the dataset is large. Nevertheless, no prior work has rigorously investigated how transformer-based backbones handle the impact of label noise in medical image classification. In this paper, we investigate the architectural robustness of ViT against label noise and compare it to that of CNNs. We use two medical image classification datasets -- COVID-DU-Ex, and NCT-CRC-HE-100K -- both corrupted by injecting label noise at various rates. Additionally, we show that pretraining is crucial for ensuring ViT's improved robustness against label noise in supervised training.

Medical Vision Language Pretraining (VLP) has recently emerged as a promising solution to the scarcity of labeled data in the medical domain. By leveraging paired/unpaired vision and text datasets through self-supervised learning, models can be trained to acquire vast knowledge and learn robust feature representations. Such pretrained models have the potential to enhance multiple downstream medical tasks simultaneously, reducing the dependency on labeled data. However, despite recent progress and its potential, there is no such comprehensive survey paper that has explored the various aspects and advancements in medical VLP. In this paper, we specifically review existing works through the lens of different pretraining objectives, architectures, downstream evaluation tasks, and datasets utilized for pretraining and downstream tasks. Subsequently, we delve into current challenges in medical VLP, discussing existing and potential solutions, and conclude by highlighting future directions. To the best of our knowledge, this is the first survey focused on medical VLP.

Noisy labels hurt deep learning-based supervised image classification performance as the models may overfit the noise and learn corrupted feature extractors. For natural image classification training with noisy labeled data, model initialization with contrastive self-supervised pretrained weights has shown to reduce feature corruption and improve classification performance. However, no works have explored: i) how other self-supervised approaches, such as pretext task-based pretraining, impact the learning with noisy label, and ii) any self-supervised pretraining methods alone for medical images in noisy label settings. Medical images often feature smaller datasets and subtle inter class variations, requiring human expertise to ensure correct classification. Thus, it is not clear if the methods improving learning with noisy labels in natural image datasets such as CIFAR would also help with medical images. In this work, we explore contrastive and pretext task-based self-supervised pretraining to initialize the weights of a deep learning classification model for two medical datasets with self-induced noisy labels -- NCT-CRC-HE-100K tissue histological images and COVID-QU-Ex chest X-ray images. Our results show that models initialized with pretrained weights obtained from self-supervised learning can effectively learn better features and improve robustness against noisy labels., Comment: Accepted at MICCAI 2023 DEMI Workshop

Acquiring properly annotated data is expensive in the medical field as it requires experts, time-consuming protocols, and rigorous validation. Active learning attempts to minimize the need for large annotated samples by actively sampling the most informative examples for annotation. These examples contribute significantly to improving the performance of supervised machine learning models, and thus, active learning can play an essential role in selecting the most appropriate information in deep learning-based diagnosis, clinical assessments, and treatment planning. Although some existing works have proposed methods for sampling the best examples for annotation in medical image analysis, they are not task-agnostic and do not use multimodal auxiliary information in the sampler, which has the potential to increase robustness. Therefore, in this work, we propose a Multimodal Variational Adversarial Active Learning (M-VAAL) method that uses auxiliary information from additional modalities to enhance the active sampling. We applied our method to two datasets: i) brain tumor segmentation and multi-label classification using the BraTS2018 dataset, and ii) chest X-ray image classification using the COVID-QU-Ex dataset. Our results show a promising direction toward data-efficient learning under limited annotations.

Purpose: Stereo matching methods that enable depth estimation are crucial for visualization enhancement applications in computer-assisted surgery (CAS). Learning-based stereo matching methods are promising to predict accurate results on laparoscopic images. However, they require a large amount of training data, and their performance may be degraded due to domain shifts. Methods: Maintaining robustness and improving the accuracy of learning-based methods are still open problems. To overcome the limitations of learning-based methods, we propose a disparity refinement framework consisting of a local disparity refinement method and a global disparity refinement method to improve the results of learning-based stereo matching methods in a cross-domain setting. Those learning-based stereo matching methods are pre-trained on a large public dataset of natural images and are tested on two datasets of laparoscopic images. Results: Qualitative and quantitative results suggest that our proposed disparity framework can effectively refine disparity maps when they are noise-corrupted on an unseen dataset, without compromising prediction accuracy when the network can generalize well on an unseen dataset. Conclusion: Our proposed disparity refinement framework could work with learning-based methods to achieve robust and accurate disparity prediction. Yet, as a large laparoscopic dataset for training learning-based methods does not exist and the generalization ability of networks remains to be improved, the incorporation of the proposed disparity refinement framework into existing networks will contribute to improving their overall accuracy and robustness associated with depth estimation.

Purpose: In laparoscopic liver surgery (LLS), pre-operative information can be overlaid onto the intra-operative scene by registering a 3D pre-operative model to the intra-operative partial surface reconstructed from the laparoscopic video. To assist with this task, we explore the use of learning-based feature descriptors, which, to our best knowledge, have not been explored for use in laparoscopic liver registration. Furthermore, a dataset to train and evaluate the use of learning-based descriptors does not exist. Methods: We present the LiverMatch dataset consisting of 16 preoperative models and their simulated intra-operative 3D surfaces. We also propose the LiverMatch network designed for this task, which outputs per-point feature descriptors, visibility scores, and matched points. Results: We compare the proposed LiverMatch network with anetwork closest to LiverMatch, and a histogram-based 3D descriptor on the testing split of the LiverMatch dataset, which includes two unseen pre-operative models and 1400 intra-operative surfaces. Results suggest that our LiverMatch network can predict more accurate and dense matches than the other two methods and can be seamlessly integrated with a RANSAC-ICP-based registration algorithm to achieve an accurate initial alignment. Conclusion: The use of learning-based feature descriptors in LLR is promising, as it can help achieve an accurate initial rigid alignment, which, in turn, serves as an initialization for subsequent non-rigid registration. We will release the dataset and code upon acceptance.