Vim4Path: Self-Supervised Vision Mamba for Histopathology Images

Representation learning from Gigapixel Whole Slide Images (WSI) poses a significant challenge in computational pathology due to the complicated nature of tissue structures and the scarcity of labeled data. Multi-instance learning methods have addressed this challenge, leveraging image patches to classify slides utilizing pretrained models using Self-Supervised Learning (SSL) approaches. The performance of both SSL and MIL methods relies on the architecture of the feature encoder. This paper proposes leveraging the Vision Mamba (Vim) architecture, inspired by state space models, within the DINO framework for representation learning in computational pathology. We evaluate the performance of Vim against Vision Transformers (ViT) on the Camelyon16 dataset for both patch-level and slide-level classification. Our findings highlight Vim's enhanced performance compared to ViT, particularly at smaller scales, where Vim achieves an 8.21 increase in ROC AUC for models of similar size. An explainability analysis further highlights Vim's capabilities, which reveals that Vim uniquely emulates the pathologist workflow-unlike ViT. This alignment with human expert analysis highlights Vim's potential in practical diagnostic settings and contributes significantly to developing effective representation-learning algorithms in computational pathology. We release the codes and pretrained weights at \url{https://github.com/AtlasAnalyticsLab/Vim4Path}.

Joint chest X-ray diagnosis and clinical visual attention prediction with multi-stage cooperative learning: enhancing interpretability

As deep learning has become the state-of-the-art for computer-assisted diagnosis, interpretability of the automatic decisions is crucial for clinical deployment. While various methods were proposed in this domain, visual attention maps of clinicians during radiological screening offer a unique asset to provide important insights and can potentially enhance the quality of computer-assisted diagnosis. With this paper, we introduce a novel deep-learning framework for joint disease diagnosis and prediction of corresponding visual saliency maps for chest X-ray scans. Specifically, we designed a novel dual-encoder multi-task UNet, which leverages both a DenseNet201 backbone and a Residual and Squeeze-and-Excitation block-based encoder to extract diverse features for saliency map prediction, and a multi-scale feature-fusion classifier to perform disease classification. To tackle the issue of asynchronous training schedules of individual tasks in multi-task learning, we proposed a multi-stage cooperative learning strategy, with contrastive learning for feature encoder pretraining to boost performance. Experiments show that our proposed method outperformed existing techniques for chest X-ray diagnosis and the quality of visual saliency map prediction.

MedCLIP-SAM: Bridging Text and Image Towards Universal Medical Image Segmentation

Medical image segmentation of anatomical structures and pathology is crucial in modern clinical diagnosis, disease study, and treatment planning. To date, great progress has been made in deep learning-based segmentation techniques, but most methods still lack data efficiency, generalizability, and interactability. Consequently, the development of new, precise segmentation methods that demand fewer labeled datasets is of utmost importance in medical image analysis. Recently, the emergence of foundation models, such as CLIP and Segment-Anything-Model (SAM), with comprehensive cross-domain representation opened the door for interactive and universal image segmentation. However, exploration of these models for data-efficient medical image segmentation is still limited, but is highly necessary. In this paper, we propose a novel framework, called MedCLIP-SAM that combines CLIP and SAM models to generate segmentation of clinical scans using text prompts in both zero-shot and weakly supervised settings. To achieve this, we employed a new Decoupled Hard Negative Noise Contrastive Estimation (DHN-NCE) loss to fine-tune the BiomedCLIP model and the recent gScoreCAM to generate prompts to obtain segmentation masks from SAM in a zero-shot setting. Additionally, we explored the use of zero-shot segmentation labels in a weakly supervised paradigm to improve the segmentation quality further. By extensively testing three diverse segmentation tasks and medical image modalities (breast tumor ultrasound, brain tumor MRI, and lung X-ray), our proposed framework has demonstrated excellent accuracy.

Homodyned K-Distribution Parameter Estimation in Quantitative Ultrasound: Autoencoder and Bayesian Neural Network Approaches

Quantitative ultrasound (QUS) analyzes the ultrasound backscattered data to find the properties of scatterers that correlate with the tissue microstructure. Statistics of the envelope of the backscattered radiofrequency (RF) data can be utilized to estimate several QUS parameters. Different distributions have been proposed to model envelope data. The homodyned K-distribution (HK distribution) is one of the most comprehensive distributions that can model ultrasound backscattered envelope data under diverse scattering conditions (varying scatterer number density and coherent scattering). The scatterer clustering parameter (alpha) and the ratio of the coherent to diffuse scattering power (k) are the parameters of this distribution that have been used extensively for tissue characterization in diagnostic ultrasound. The estimation of these two parameters (which we refer to as HK parameters) is done using optimization algorithms in which statistical features such as the envelope point-wise signalto-noise ratio (SNR), skewness, kurtosis, and the log-based moments have been utilized as input to such algorithms. The optimization methods minimize the difference between features and their theoretical value from the HK model. We propose that the true value of these statistical features is a hyperplane that covers a small portion of the feature space. In this paper, we follow two approaches to reduce the effect of sample features' error. We propose a model projection neural network based on denoising autoencoders to project the noisy features into this space based on this assumption. We also investigate if the noise distribution can be learned by the deep estimators. We compare the proposed methods with conventional methods using simulations, an experimental phantom, and data from an in vivo animal model of hepatic steatosis. A demo code are available online at http://code.sonography.ai

Is visual explanation with Grad-CAM more reliable for deeper neural networks? a case study with automatic pneumothorax diagnosis

While deep learning techniques have provided the state-of-the-art performance in various clinical tasks, explainability regarding their decision-making process can greatly enhance the credence of these methods for safer and quicker clinical adoption. With high flexibility, Gradient-weighted Class Activation Mapping (Grad-CAM) has been widely adopted to offer intuitive visual interpretation of various deep learning models' reasoning processes in computer-assisted diagnosis. However, despite the popularity of the technique, there is still a lack of systematic study on Grad-CAM's performance on different deep learning architectures. In this study, we investigate its robustness and effectiveness across different popular deep learning models, with a focus on the impact of the networks' depths and architecture types, by using a case study of automatic pneumothorax diagnosis in X-ray scans. Our results show that deeper neural networks do not necessarily contribute to a strong improvement of pneumothorax diagnosis accuracy, and the effectiveness of GradCAM also varies among different network architectures.

VesselShot: Few-shot learning for cerebral blood vessel segmentation

Angiography is widely used to detect, diagnose, and treat cerebrovascular diseases. While numerous techniques have been proposed to segment the vascular network from different imaging modalities, deep learning (DL) has emerged as a promising approach. However, existing DL methods often depend on proprietary datasets and extensive manual annotation. Moreover, the availability of pre-trained networks specifically for medical domains and 3D volumes is limited. To overcome these challenges, we propose a few-shot learning approach called VesselShot for cerebrovascular segmentation. VesselShot leverages knowledge from a few annotated support images and mitigates the scarcity of labeled data and the need for extensive annotation in cerebral blood vessel segmentation. We evaluated the performance of VesselShot using the publicly available TubeTK dataset for the segmentation task, achieving a mean Dice coefficient (DC) of 0.62(0.03).

Robust RF Data Normalization for Deep Learning

Radio frequency (RF) data contain richer information compared to other data types, such as envelope or B-mode, and employing RF data for training deep neural networks has attracted growing interest in ultrasound image processing. However, RF data is highly fluctuating and additionally has a high dynamic range. Most previous studies in the literature have relied on conventional data normalization, which has been adopted within the computer vision community. We demonstrate the inadequacy of those techniques for normalizing RF data and propose that individual standardization of each image substantially enhances the performance of deep neural networks by utilizing the data more efficiently. We compare conventional and proposed normalizations in a phase aberration correction task and illustrate how the former enhances the generality of trained models.

Phase Aberration Correction: A Deep Learning-Based Aberration to Aberration Approach

One of the primary sources of suboptimal image quality in ultrasound imaging is phase aberration. It is caused by spatial changes in sound speed over a heterogeneous medium, which disturbs the transmitted waves and prevents coherent summation of echo signals. Obtaining non-aberrated ground truths in real-world scenarios can be extremely challenging, if not impossible. This challenge hinders training of deep learning-based techniques' performance due to the presence of domain shift between simulated and experimental data. Here, for the first time, we propose a deep learning-based method that does not require ground truth to correct the phase aberration problem, and as such, can be directly trained on real data. We train a network wherein both the input and target output are randomly aberrated radio frequency (RF) data. Moreover, we demonstrate that a conventional loss function such as mean square error is inadequate for training such a network to achieve optimal performance. Instead, we propose an adaptive mixed loss function that employs both B-mode and RF data, resulting in more efficient convergence and enhanced performance. Finally, we publicly release our dataset, including 161,701 single plane-wave images (RF data). This dataset serves to mitigate the data scarcity problem in the development of deep learning-based techniques for phase aberration correction.

Frequency-Space Prediction Filtering for Phase Aberration Correction in Plane-Wave Ultrasound

Ultrasound imaging often suffers from image degradation stemming from phase aberration, which represents a significant contributing factor to the overall image degradation in ultrasound imaging. Frequency-space prediction filtering or FXPF is a technique that has been applied within focused ultrasound imaging to alleviate the phase aberration effect. It presupposes the existence of an autoregressive (AR) model across the signals received at the transducer elements and removes any components that do not conform to the established model. In this study, we illustrate the challenge of applying this technique to plane-wave imaging, where, at shallower depths, signals from more distant elements lose relevance, and a fewer number of elements contribute to image reconstruction. While the number of contributing signals varies, adopting a fixed-order AR model across all depths, results in suboptimal performance. To address this challenge, we propose an AR model with an adaptive order and quantify its effectiveness using contrast and generalized contrast-to-noise ratio metrics.

Dense Error Map Estimation for MRI-Ultrasound Registration in Brain Tumor Surgery Using Swin UNETR

Early surgical treatment of brain tumors is crucial in reducing patient mortality rates. However, brain tissue deformation (called brain shift) occurs during the surgery, rendering pre-operative images invalid. As a cost-effective and portable tool, intra-operative ultrasound (iUS) can track brain shift, and accurate MRI-iUS registration techniques can update pre-surgical plans and facilitate the interpretation of iUS. This can boost surgical safety and outcomes by maximizing tumor removal while avoiding eloquent regions. However, manual assessment of MRI-iUS registration results in real-time is difficult and prone to errors due to the 3D nature of the data. Automatic algorithms that can quantify the quality of inter-modal medical image registration outcomes can be highly beneficial. Therefore, we propose a novel deep-learning (DL) based framework with the Swin UNETR to automatically assess 3D-patch-wise dense error maps for MRI-iUS registration in iUS-guided brain tumor resection and show its performance with real clinical data for the first time.