Towards Machine Learning-based Quantitative Hyperspectral Image Guidance for Brain Tumor Resection

Complete resection of malignant gliomas is hampered by the difficulty in distinguishing tumor cells at the infiltration zone. Fluorescence guidance with 5-ALA assists in reaching this goal. Using hyperspectral imaging, previous work characterized five fluorophores' emission spectra in most human brain tumors. In this paper, the effectiveness of these five spectra was explored for different tumor and tissue classification tasks in 184 patients (891 hyperspectral measurements) harboring low- (n=30) and high-grade gliomas (n=115), non-glial primary brain tumors (n=19), radiation necrosis (n=2), miscellaneous (n=10) and metastases (n=8). Four machine learning models were trained to classify tumor type, grade, glioma margins and IDH mutation. Using random forests and multi-layer perceptrons, the classifiers achieved average test accuracies of 84-87%, 96%, 86%, and 93% respectively. All five fluorophore abundances varied between tumor margin types and tumor grades (p < 0.01). For tissue type, at least four of the five fluorophore abundances were found to be significantly different (p < 0.01) between all classes. These results demonstrate the fluorophores' differing abundances in different tissue classes, as well as the value of the five fluorophores as potential optical biomarkers, opening new opportunities for intraoperative classification systems in fluorescence-guided neurosurgery.

Multi-Scale Relational Graph Convolutional Network for Multiple Instance Learning in Histopathology Images

Graph convolutional neural networks have shown significant potential in natural and histopathology images. However, their use has only been studied in a single magnification or multi-magnification with late fusion. In order to leverage the multi-magnification information and early fusion with graph convolutional networks, we handle different embedding spaces at each magnification by introducing the Multi-Scale Relational Graph Convolutional Network (MS-RGCN) as a multiple instance learning method. We model histopathology image patches and their relation with neighboring patches and patches at other scales (i.e., magnifications) as a graph. To pass the information between different magnification embedding spaces, we define separate message-passing neural networks based on the node and edge type. We experiment on prostate cancer histopathology images to predict the grade groups based on the extracted features from patches. We also compare our MS-RGCN with multiple state-of-the-art methods with evaluations on both source and held-out datasets. Our method outperforms the state-of-the-art on both datasets and especially on the classification of grade groups 2 and 3, which are significant for clinical decisions for patient management. Through an ablation study, we test and show the value of the pertinent design features of the MS-RGCN.

ResNet Structure Simplification with the Convolutional Kernel Redundancy Measure

Deep learning, especially convolutional neural networks, has triggered accelerated advancements in computer vision, bringing changes into our daily practice. Furthermore, the standardized deep learning modules (also known as backbone networks), i.e., ResNet and EfficientNet, have enabled efficient and rapid development of new computer vision solutions. Yet, deep learning methods still suffer from several drawbacks. One of the most concerning problems is the high memory and computational cost, such that dedicated computing units, typically GPUs, have to be used for training and development. Therefore, in this paper, we propose a quantifiable evaluation method, the convolutional kernel redundancy measure, which is based on perceived image differences, for guiding the network structure simplification. When applying our method to the chest X-ray image classification problem with ResNet, our method can maintain the performance of the network and reduce the number of parameters from over $23$ million to approximately $128$ thousand (reducing $99.46\%$ of the parameters).

Generalizable Neural Radiance Fields for Novel View Synthesis with Transformer

We propose a Transformer-based NeRF (TransNeRF) to learn a generic neural radiance field conditioned on observed-view images for the novel view synthesis task. By contrast, existing MLP-based NeRFs are not able to directly receive observed views with an arbitrary number and require an auxiliary pooling-based operation to fuse source-view information, resulting in the missing of complicated relationships between source views and the target rendering view. Furthermore, current approaches process each 3D point individually and ignore the local consistency of a radiance field scene representation. These limitations potentially can reduce their performance in challenging real-world applications where large differences between source views and a novel rendering view may exist. To address these challenges, our TransNeRF utilizes the attention mechanism to naturally decode deep associations of an arbitrary number of source views into a coordinate-based scene representation. Local consistency of shape and appearance are considered in the ray-cast space and the surrounding-view space within a unified Transformer network. Experiments demonstrate that our TransNeRF, trained on a wide variety of scenes, can achieve better performance in comparison to state-of-the-art image-based neural rendering methods in both scene-agnostic and per-scene finetuning scenarios especially when there is a considerable gap between source views and a rendering view.

Multi-task UNet: Jointly Boosting Saliency Prediction and Disease Classification on Chest X-ray Images

Human visual attention has recently shown its distinct capability in boosting machine learning models. However, studies that aim to facilitate medical tasks with human visual attention are still scarce. To support the use of visual attention, this paper describes a novel deep learning model for visual saliency prediction on chest X-ray (CXR) images. To cope with data deficiency, we exploit the multi-task learning method and tackles disease classification on CXR simultaneously. For a more robust training process, we propose a further optimized multi-task learning scheme to better handle model overfitting. Experiments show our proposed deep learning model with our new learning scheme can outperform existing methods dedicated either for saliency prediction or image classification. The code used in this paper is available at https://github.com/hz-zhu/MT-UNet.

Gaze-Guided Class Activation Mapping: Leveraging Human Attention for Network Attention in Chest X-rays Classification

The increased availability and accuracy of eye-gaze tracking technology has sparked attention-related research in psychology, neuroscience, and, more recently, computer vision and artificial intelligence. The attention mechanism in artificial neural networks is known to improve learning tasks. However, no previous research has combined the network attention and human attention. This paper describes a gaze-guided class activation mapping (GG-CAM) method to directly regulate the formation of network attention based on expert radiologists' visual attention for the chest X-ray pathology classification problem, which remains challenging due to the complex and often nuanced differences among images. GG-CAM is a lightweight ($3$ additional trainable parameters for regulating the learning process) and generic extension that can be easily applied to most classification convolutional neural networks (CNN). GG-CAM-modified CNNs do not require human attention as an input when fully trained. Comparative experiments suggest that two standard CNNs with the GG-CAM extension achieve significantly greater classification performance. The median area under the curve (AUC) metrics for ResNet50 increases from $0.721$ to $0.776$. For EfficientNetv2 (s), the median AUC increases from $0.723$ to $0.801$. The GG-CAM also brings better interpretability of the network that facilitates the weakly-supervised pathology localization and analysis.

Multifrequency 3D Elasticity Reconstruction withStructured Sparsity and ADMM

We introduce a model-based iterative method to obtain shear modulus images of tissue using magnetic resonance elastography. The method jointly finds the displacement field that best fits multifrequency tissue displacement data and the corresponding shear modulus. The displacement satisfies a viscoelastic wave equation constraint, discretized using the finite element method. Sparsifying regularization terms in both shear modulus and the displacement are used in the cost function minimized for the best fit. The formulated problem is bi-convex. Its solution can be obtained iteratively by using the alternating direction method of multipliers. Sparsifying regularizations and the wave equation constraint filter out sensor noise and compressional waves. Our method does not require bandpass filtering as a preprocessing step and converges fast irrespective of the initialization. We evaluate our new method in multiple in silico and phantom experiments, with comparisons with existing methods, and we show improvements in contrast to noise and signal to noise ratios. Results from an in vivo liver imaging study show elastograms with mean elasticity comparable to other values reported in the literature.

Automatic Segmentation of the Prostate on 3D Trans-rectal Ultrasound Images using Statistical Shape Models and Convolutional Neural Networks

In this work we propose to segment the prostate on a challenging dataset of trans-rectal ultrasound (TRUS) images using convolutional neural networks (CNNs) and statistical shape models (SSMs). TRUS is commonly used for a number of image-guided interventions on the prostate. Fast and accurate segmentation on the organ in these images is crucial to planning and fusion with other modalities such as magnetic resonance images (MRIs) . However, TRUS has limited soft tissue contrast and signal to noise ratio which makes the task of segmenting the prostate challenging and subject to inter-observer and intra-observer variability. This is especially problematic at the base and apex where the gland boundary is hard to define. In this paper, we aim to tackle this problem by taking advantage of shape priors learnt on an MR dataset which has higher soft tissue contrast allowing the prostate to be contoured more accurately. We use this shape prior in combination with a prostate tissue probability map computed by a CNN for segmentation.

Multi-view 3D Reconstruction with Transformer

Deep CNN-based methods have so far achieved the state of the art results in multi-view 3D object reconstruction. Despite the considerable progress, the two core modules of these methods - multi-view feature extraction and fusion, are usually investigated separately, and the object relations in different views are rarely explored. In this paper, inspired by the recent great success in self-attention-based Transformer models, we reformulate the multi-view 3D reconstruction as a sequence-to-sequence prediction problem and propose a new framework named 3D Volume Transformer (VolT) for such a task. Unlike previous CNN-based methods using a separate design, we unify the feature extraction and view fusion in a single Transformer network. A natural advantage of our design lies in the exploration of view-to-view relationships using self-attention among multiple unordered inputs. On ShapeNet - a large-scale 3D reconstruction benchmark dataset, our method achieves a new state-of-the-art accuracy in multi-view reconstruction with fewer parameters ($70\%$ less) than other CNN-based methods. Experimental results also suggest the strong scaling capability of our method. Our code will be made publicly available.