Staging of liver fibrosis is important in the diagnosis and treatment planning of patients suffering from liver diseases. Current deep learning-based methods using abdominal magnetic resonance imaging (MRI) usually take a sub-region of the liver as an input, which nevertheless could miss critical information. To explore richer representations, we formulate this task as a multi-view learning problem and employ multiple sub-regions of the liver. Previously, features or predictions are usually combined in an implicit manner, and uncertainty-aware methods have been proposed. However, these methods could be challenged to capture cross-view representations, which can be important in the accurate prediction of staging. Therefore, we propose a reliable multi-view learning method with interpretable combination rules, which can model global representations to improve the accuracy of predictions. Specifically, the proposed method estimates uncertainties based on subjective logic to improve reliability, and an explicit combination rule is applied based on Dempster-Shafer's evidence theory with good power of interpretability. Moreover, a data-efficient transformer is introduced to capture representations in the global view. Results evaluated on enhanced MRI data show that our method delivers superior performance over existing multi-view learning methods.
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Stochastic gradient methods have been a popular and powerful choice of optimization methods, aimed at minimizing functions. Their advantage lies in the fact that that one approximates the gradient as opposed to using the full Jacobian matrix. One research direction, related to this, has been on the application to infinite-dimensional problems, where one may naturally have a Hilbert space framework. However, there has been limited work done on considering this in a more general setup, such as where the natural framework is that of a Banach space. This article aims to address this by the introduction of a novel stochastic method, the stochastic steepest descent method (SSD). The SSD will follow the spirit of stochastic gradient descent, which utilizes Riesz representation to identify gradients and derivatives. Our choice for using such a method is that it naturally allows one to adopt a Banach space setting, for which recent applications have exploited the benefit of this, such as in PDE-constrained shape optimization. We provide a convergence theory related to this under mild assumptions. Furthermore, we demonstrate the performance of this method on a couple of numerical applications, namely a $p$-Laplacian and an optimal control problem. Our assumptions are verified in these applications.
Deep neural networks are vulnerable to universal adversarial perturbation (UAP), an instance-agnostic perturbation capable of fooling the target model for most samples. Compared to instance-specific adversarial examples, UAP is more challenging as it needs to generalize across various samples and models. In this paper, we examine the serious dilemma of UAP generation methods from a generalization perspective -- the gradient vanishing problem using small-batch stochastic gradient optimization and the local optima problem using large-batch optimization. To address these problems, we propose a simple and effective method called Stochastic Gradient Aggregation (SGA), which alleviates the gradient vanishing and escapes from poor local optima at the same time. Specifically, SGA employs the small-batch training to perform multiple iterations of inner pre-search. Then, all the inner gradients are aggregated as a one-step gradient estimation to enhance the gradient stability and reduce quantization errors. Extensive experiments on the standard ImageNet dataset demonstrate that our method significantly enhances the generalization ability of UAP and outperforms other state-of-the-art methods. The code is available at //github.com/liuxuannan/Stochastic-Gradient-Aggregation.
Quantitative organ assessment is an essential step in automated abdominal disease diagnosis and treatment planning. Artificial intelligence (AI) has shown great potential to automatize this process. However, most existing AI algorithms rely on many expert annotations and lack a comprehensive evaluation of accuracy and efficiency in real-world multinational settings. To overcome these limitations, we organized the FLARE 2022 Challenge, the largest abdominal organ analysis challenge to date, to benchmark fast, low-resource, accurate, annotation-efficient, and generalized AI algorithms. We constructed an intercontinental and multinational dataset from more than 50 medical groups, including Computed Tomography (CT) scans with different races, diseases, phases, and manufacturers. We independently validated that a set of AI algorithms achieved a median Dice Similarity Coefficient (DSC) of 90.0\% by using 50 labeled scans and 2000 unlabeled scans, which can significantly reduce annotation requirements. The best-performing algorithms successfully generalized to holdout external validation sets, achieving a median DSC of 89.5\%, 90.9\%, and 88.3\% on North American, European, and Asian cohorts, respectively. They also enabled automatic extraction of key organ biology features, which was labor-intensive with traditional manual measurements. This opens the potential to use unlabeled data to boost performance and alleviate annotation shortages for modern AI models.
Many segmentation networks have been proposed for 3D volumetric segmentation of tumors and organs at risk. Hospitals and clinical institutions seek to accelerate and minimize the efforts of specialists in image segmentation. Still, in case of errors generated by these networks, clinicians would have to manually edit the generated segmentation maps. Given a 3D volume and its putative segmentation map, we propose an approach to identify and measure erroneous regions in the segmentation map. Our method can estimate error at any point or node in a 3D mesh generated from a possibly erroneous volumetric segmentation map, serving as a Quality Assurance tool. We propose a graph neural network-based transformer based on the Nodeformer architecture to measure and classify the segmentation errors at any point. We have evaluated our network on a high-resolution micro-CT dataset of the human inner-ear bony labyrinth structure by simulating erroneous 3D segmentation maps. Our network incorporates a convolutional encoder to compute node-centric features from the input micro-CT data, the Nodeformer to learn the latent graph embeddings, and a Multi-Layer Perceptron (MLP) to compute and classify the node-wise errors. Our network achieves a mean absolute error of ~0.042 over other Graph Neural Networks (GNN) and an accuracy of 79.53% over other GNNs in estimating and classifying the node-wise errors, respectively. We also put forth vertex-normal prediction as a custom pretext task for pre-training the CNN encoder to improve the network's overall performance. Qualitative analysis shows the efficiency of our network in correctly classifying errors and reducing misclassifications.
Functionally significant coronary artery disease (CAD) is caused by plaque buildup in the coronary arteries, potentially leading to narrowing of the arterial lumen, i.e. coronary stenosis, that significantly obstructs blood flow to the myocardium. The current reference for establishing the presence of a functionally significant stenosis is invasive fractional flow reserve (FFR) measurement. To avoid invasive measurements, non-invasive prediction of FFR from coronary CT angiography (CCTA) has emerged. For this, machine learning approaches, characterized by fast inference, are increasingly developed. However, these methods predict a single FFR value per artery i.e. they don't provide information about the stenosis location or treatment strategy. We propose a deep learning-based method to predict the FFR along the artery from CCTA scans. This study includes CCTA images of 110 patients who underwent invasive FFR pullback measurement in 112 arteries. First, a multi planar reconstruction (MPR) of the artery is fed to a variational autoencoder to characterize the artery, i.e. through the lumen area and unsupervised artery encodings. Thereafter, a convolutional neural network (CNN) predicts the FFR along the artery. The CNN is supervised by multiple loss functions, notably a loss function inspired by the Earth Mover's Distance (EMD) to predict the correct location of FFR drops and a histogram-based loss to explicitly supervise the slope of the FFR curve. To train and evaluate our model, eight-fold cross-validation was performed. The resulting FFR curves show good agreement with the reference allowing the distinction between diffuse and focal CAD distributions in most cases. Quantitative evaluation yielded a mean absolute difference in the area under the FFR pullback curve (AUPC) of 1.7. The method may pave the way towards fast, accurate, automatic prediction of FFR along the artery from CCTA.
Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.
Human-in-the-loop aims to train an accurate prediction model with minimum cost by integrating human knowledge and experience. Humans can provide training data for machine learning applications and directly accomplish some tasks that are hard for computers in the pipeline with the help of machine-based approaches. In this paper, we survey existing works on human-in-the-loop from a data perspective and classify them into three categories with a progressive relationship: (1) the work of improving model performance from data processing, (2) the work of improving model performance through interventional model training, and (3) the design of the system independent human-in-the-loop. Using the above categorization, we summarize major approaches in the field, along with their technical strengths/ weaknesses, we have simple classification and discussion in natural language processing, computer vision, and others. Besides, we provide some open challenges and opportunities. This survey intends to provide a high-level summarization for human-in-the-loop and motivates interested readers to consider approaches for designing effective human-in-the-loop solutions.
We consider the problem of explaining the predictions of graph neural networks (GNNs), which otherwise are considered as black boxes. Existing methods invariably focus on explaining the importance of graph nodes or edges but ignore the substructures of graphs, which are more intuitive and human-intelligible. In this work, we propose a novel method, known as SubgraphX, to explain GNNs by identifying important subgraphs. Given a trained GNN model and an input graph, our SubgraphX explains its predictions by efficiently exploring different subgraphs with Monte Carlo tree search. To make the tree search more effective, we propose to use Shapley values as a measure of subgraph importance, which can also capture the interactions among different subgraphs. To expedite computations, we propose efficient approximation schemes to compute Shapley values for graph data. Our work represents the first attempt to explain GNNs via identifying subgraphs explicitly and directly. Experimental results show that our SubgraphX achieves significantly improved explanations, while keeping computations at a reasonable level.
Deep neural networks (DNNs) are successful in many computer vision tasks. However, the most accurate DNNs require millions of parameters and operations, making them energy, computation and memory intensive. This impedes the deployment of large DNNs in low-power devices with limited compute resources. Recent research improves DNN models by reducing the memory requirement, energy consumption, and number of operations without significantly decreasing the accuracy. This paper surveys the progress of low-power deep learning and computer vision, specifically in regards to inference, and discusses the methods for compacting and accelerating DNN models. The techniques can be divided into four major categories: (1) parameter quantization and pruning, (2) compressed convolutional filters and matrix factorization, (3) network architecture search, and (4) knowledge distillation. We analyze the accuracy, advantages, disadvantages, and potential solutions to the problems with the techniques in each category. We also discuss new evaluation metrics as a guideline for future research.
Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translational research. In recent years, deep neural networks have achieved significant success in named entity recognition and many other Natural Language Processing (NLP) tasks. Most of these algorithms are trained end to end, and can automatically learn features from large scale labeled datasets. However, these data-driven methods typically lack the capability of processing rare or unseen entities. Previous statistical methods and feature engineering practice have demonstrated that human knowledge can provide valuable information for handling rare and unseen cases. In this paper, we address the problem by incorporating dictionaries into deep neural networks for the Chinese CNER task. Two different architectures that extend the Bi-directional Long Short-Term Memory (Bi-LSTM) neural network and five different feature representation schemes are proposed to handle the task. Computational results on the CCKS-2017 Task 2 benchmark dataset show that the proposed method achieves the highly competitive performance compared with the state-of-the-art deep learning methods.
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