Deep learning has achieved widespread success in medical image analysis, leading to an increasing demand for large-scale expert-annotated medical image datasets. Yet, the high cost of annotating medical images severely hampers the development of deep learning in this field. To reduce annotation costs, active learning aims to select the most informative samples for annotation and train high-performance models with as few labeled samples as possible. In this survey, we review the core methods of active learning, including the evaluation of informativeness and sampling strategy. For the first time, we provide a detailed summary of the integration of active learning with other label-efficient techniques, such as semi-supervised, self-supervised learning, and so on. We also summarize active learning works that are specifically tailored to medical image analysis. Additionally, we conduct a thorough comparative analysis of the performance of different AL methods in medical image analysis with experiments. In the end, we offer our perspectives on the future trends and challenges of active learning and its applications in medical image analysis.
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Recent advances unveiled physical neural networks as promising machine learning platforms, offering faster and more energy-efficient information processing. Compared with extensively-studied optical neural networks, the development of mechanical neural networks (MNNs) remains nascent and faces significant challenges, including heavy computational demands and learning with approximate gradients. Here, we introduce the mechanical analogue of in situ backpropagation to enable highly efficient training of MNNs. We demonstrate that the exact gradient can be obtained locally in MNNs, enabling learning through their immediate vicinity. With the gradient information, we showcase the successful training of MNNs for behavior learning and machine learning tasks, achieving high accuracy in regression and classification. Furthermore, we present the retrainability of MNNs involving task-switching and damage, demonstrating the resilience. Our findings, which integrate the theory for training MNNs and experimental and numerical validations, pave the way for mechanical machine learning hardware and autonomous self-learning material systems.
Deep learning methods are increasingly becoming instrumental as modeling tools in computational neuroscience, employing optimality principles to build bridges between neural responses and perception or behavior. Developing models that adequately represent uncertainty is however challenging for deep learning methods, which often suffer from calibration problems. This constitutes a difficulty in particular when modeling cortical circuits in terms of Bayesian inference, beyond single point estimates such as the posterior mean or the maximum a posteriori. In this work we systematically studied uncertainty representations in latent representations of variational auto-encoders (VAEs), both in a perceptual task from natural images and in two other canonical tasks of computer vision, finding a poor alignment between uncertainty and informativeness or ambiguities in the images. We next showed how a novel approach which we call explaining-away variational auto-encoders (EA-VAEs), fixes these issues, producing meaningful reports of uncertainty in a variety of scenarios, including interpolation, image corruption, and even out-of-distribution detection. We show EA-VAEs may prove useful both as models of perception in computational neuroscience and as inference tools in computer vision.
The use of machine learning algorithms to investigate phase transitions in physical systems is a valuable way to better understand the characteristics of these systems. Neural networks have been used to extract information of phases and phase transitions directly from many-body configurations. However, one limitation of neural networks is that they require the definition of the model architecture and parameters previous to their application, and such determination is itself a difficult problem. In this paper, we investigate for the first time the relationship between the accuracy of neural networks for information of phases and the network configuration (that comprises the architecture and hyperparameters). We formulate the phase analysis as a regression task, address the question of generating data that reflects the different states of the physical system, and evaluate the performance of neural architecture search for this task. After obtaining the optimized architectures, we further implement smart data processing and analytics by means of neuron coverage metrics, assessing the capability of these metrics to estimate phase transitions. Our results identify the neuron coverage metric as promising for detecting phase transitions in physical systems.
Training spiking neural networks to approximate complex functions is essential for studying information processing in the brain and neuromorphic computing. Yet, the binary nature of spikes constitutes a challenge for direct gradient-based training. To sidestep this problem, surrogate gradients have proven empirically successful, but their theoretical foundation remains elusive. Here, we investigate the relation of surrogate gradients to two theoretically well-founded approaches. On the one hand, we consider smoothed probabilistic models, which, due to lack of support for automatic differentiation, are impractical for training deep spiking neural networks, yet provide gradients equivalent to surrogate gradients in single neurons. On the other hand, we examine stochastic automatic differentiation, which is compatible with discrete randomness but has never been applied to spiking neural network training. We find that the latter provides the missing theoretical basis for surrogate gradients in stochastic spiking neural networks. We further show that surrogate gradients in deterministic networks correspond to a particular asymptotic case and numerically confirm the effectiveness of surrogate gradients in stochastic multi-layer spiking neural networks. Finally, we illustrate that surrogate gradients are not conservative fields and, thus, not gradients of a surrogate loss. Our work provides the missing theoretical foundation for surrogate gradients and an analytically well-founded solution for end-to-end training of stochastic spiking neural networks.
Average calibration of the prediction uncertainties of machine learning regression tasks can be tested in two ways: one is to estimate the calibration error (CE) as the difference between the mean absolute error (MSE) and the mean variance (MV) or mean squared uncertainty; the alternative is to compare the mean squared z-scores (ZMS) or scaled errors to 1. The problem is that both approaches might lead to different conclusions, as illustrated in this study for an ensemble of datasets from the recent machine learning uncertainty quantification (ML-UQ) literature. It is shown that the estimation of MV, MSE and their confidence intervals can become unreliable for heavy-tailed uncertainty and error distributions, which seems to be a common issue for ML-UQ datasets. By contrast, the ZMS statistic is less sensitive and offers the most reliable approach in this context. Unfortunately, the same problem affects also conditional calibrations statistics, such as the popular ENCE, and very likely post-hoc calibration methods based on similar statistics. As not much can be done to relieve this issue, except for a change of paradigm to intervals- or distribution-based UQ metrics, robust tailedness metrics are proposed to detect the potentially problematic datasets.
While computer modeling and simulation are crucial for understanding scientometrics, their practical use in literature remains somewhat limited. In this study, we establish a joint coauthorship and citation network using preferential attachment. As papers get published, we update the coauthorship network based on each paper's author list, representing the collaborative team behind it. This team is formed considering the number of collaborations each author has, and we introduce new authors at a fixed probability, expanding the coauthorship network. Simultaneously, as each paper cites a specific number of references, we add an equivalent number of citations to the citation network upon publication. The likelihood of a paper being cited depends on its existing citations, fitness value, and age. Then we calculate the journal impact factor and h-index, using them as examples of scientific impact indicators. After thorough validation, we conduct case studies to analyze the impact of different parameters on the journal impact factor and h-index. The findings reveal that increasing the reference number N or reducing the paper's lifetime {\theta} significantly boosts the journal impact factor and average h-index. On the other hand, enlarging the team size m without introducing new authors or decreasing the probability of newcomers p notably increases the average h-index. In conclusion, it is evident that various parameters influence scientific impact indicators, and their interpretation can be manipulated by authors. Thus, exploring the impact of these parameters and continually refining scientific impact indicators are essential. The modeling and simulation method serves as a powerful tool in this ongoing process, and the model can be easily extended to include other scientific impact indicators and scenarios.
Most state-of-the-art machine learning techniques revolve around the optimisation of loss functions. Defining appropriate loss functions is therefore critical to successfully solving problems in this field. We present a survey of the most commonly used loss functions for a wide range of different applications, divided into classification, regression, ranking, sample generation and energy based modelling. Overall, we introduce 33 different loss functions and we organise them into an intuitive taxonomy. Each loss function is given a theoretical backing and we describe where it is best used. This survey aims to provide a reference of the most essential loss functions for both beginner and advanced machine learning practitioners.
Deep learning is usually described as an experiment-driven field under continuous criticizes of lacking theoretical foundations. This problem has been partially fixed by a large volume of literature which has so far not been well organized. This paper reviews and organizes the recent advances in deep learning theory. The literature is categorized in six groups: (1) complexity and capacity-based approaches for analyzing the generalizability of deep learning; (2) stochastic differential equations and their dynamic systems for modelling stochastic gradient descent and its variants, which characterize the optimization and generalization of deep learning, partially inspired by Bayesian inference; (3) the geometrical structures of the loss landscape that drives the trajectories of the dynamic systems; (4) the roles of over-parameterization of deep neural networks from both positive and negative perspectives; (5) theoretical foundations of several special structures in network architectures; and (6) the increasingly intensive concerns in ethics and security and their relationships with generalizability.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
Deep learning constitutes a recent, modern technique for image processing and data analysis, with promising results and large potential. As deep learning has been successfully applied in various domains, it has recently entered also the domain of agriculture. In this paper, we perform a survey of 40 research efforts that employ deep learning techniques, applied to various agricultural and food production challenges. We examine the particular agricultural problems under study, the specific models and frameworks employed, the sources, nature and pre-processing of data used, and the overall performance achieved according to the metrics used at each work under study. Moreover, we study comparisons of deep learning with other existing popular techniques, in respect to differences in classification or regression performance. Our findings indicate that deep learning provides high accuracy, outperforming existing commonly used image processing techniques.
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