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Single-Molecule Localization Microscopy (SMLM) has expanded our ability to visualize subcellular structures but is limited in its temporal resolution. Increasing emitter density will improve temporal resolution, but current analysis algorithms struggle as emitter images significantly overlap. Here we present a deep convolutional neural network called LUENN which utilizes a unique architecture that rejects the isolated emitter assumption; it can smoothly accommodate emitters that range from completely isolated to co-located. This architecture, alongside an accurate estimator of location uncertainty, extends the range of usable emitter densities by a factor of 6 to over 31 emitters per micrometer-squared with reduced penalty to localization precision and improved temporal resolution. Apart from providing uncertainty estimation, the algorithm improves usability in laboratories by reducing imaging times and easing requirements for successful experiments.

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Gaussianization is a simple generative model that can be trained without backpropagation. It has shown compelling performance on low dimensional data. As the dimension increases, however, it has been observed that the convergence speed slows down. We show analytically that the number of required layers scales linearly with the dimension for Gaussian input. We argue that this is because the model is unable to capture dependencies between dimensions. Empirically, we find the same linear increase in cost for arbitrary input $p(x)$, but observe favorable scaling for some distributions. We explore potential speed-ups and formulate challenges for further research.

We consider a symmetric mixture of linear regressions with random samples from the pairwise comparison design, which can be seen as a noisy version of a type of Euclidean distance geometry problem. We analyze the expectation-maximization (EM) algorithm locally around the ground truth and establish that the sequence converges linearly, providing an $\ell_\infty$-norm guarantee on the estimation error of the iterates. Furthermore, we show that the limit of the EM sequence achieves the sharp rate of estimation in the $\ell_2$-norm, matching the information-theoretically optimal constant. We also argue through simulation that convergence from a random initialization is much more delicate in this setting, and does not appear to occur in general. Our results show that the EM algorithm can exhibit several unique behaviors when the covariate distribution is suitably structured.

When analyzing real-world data it is common to work with event ensembles, which comprise sets of observations that collectively constrain the parameters of an underlying model of interest. Such models often have a hierarchical structure, where "local" parameters impact individual events and "global" parameters influence the entire dataset. We introduce practical approaches for optimal dataset-wide probabilistic inference in cases where the likelihood is intractable, but simulations can be realized via forward modeling. We construct neural estimators for the likelihood(-ratio) or posterior and show that explicitly accounting for the model's hierarchical structure can lead to tighter parameter constraints. We ground our discussion using case studies from the physical sciences, focusing on examples from particle physics (particle collider data) and astrophysics (strong gravitational lensing observations).

In the scenario of class-incremental learning (CIL), deep neural networks have to adapt their model parameters to non-stationary data distributions, e.g., the emergence of new classes over time. However, CIL models are challenged by the well-known catastrophic forgetting phenomenon. Typical methods such as rehearsal-based ones rely on storing exemplars of old classes to mitigate catastrophic forgetting, which limits real-world applications considering memory resources and privacy issues. In this paper, we propose a novel rehearsal-free CIL approach that learns continually via the synergy between two Complementary Learning Subnetworks. Our approach involves jointly optimizing a plastic CNN feature extractor and an analytical feed-forward classifier. The inaccessibility of historical data is tackled by holistically controlling the parameters of a well-trained model, ensuring that the decision boundary learned fits new classes while retaining recognition of previously learned classes. Specifically, the trainable CNN feature extractor provides task-dependent knowledge separately without interference; and the final classifier integrates task-specific knowledge incrementally for decision-making without forgetting. In each CIL session, it accommodates new tasks by attaching a tiny set of declarative parameters to its backbone, in which only one matrix per task or one vector per class is kept for knowledge retention. Extensive experiments on a variety of task sequences show that our method achieves competitive results against state-of-the-art methods, especially in accuracy gain, memory cost, training efficiency, and task-order robustness. Furthermore, to make the non-growing backbone (i.e., a model with limited network capacity) suffice to train on more incoming tasks, a graceful forgetting implementation on previously learned trivial tasks is empirically investigated.

Current deep learning research is dominated by benchmark evaluation. A method is regarded as favorable if it empirically performs well on the dedicated test set. This mentality is seamlessly reflected in the resurfacing area of continual learning, where consecutively arriving sets of benchmark data are investigated. The core challenge is framed as protecting previously acquired representations from being catastrophically forgotten due to the iterative parameter updates. However, comparison of individual methods is nevertheless treated in isolation from real world application and typically judged by monitoring accumulated test set performance. The closed world assumption remains predominant. It is assumed that during deployment a model is guaranteed to encounter data that stems from the same distribution as used for training. This poses a massive challenge as neural networks are well known to provide overconfident false predictions on unknown instances and break down in the face of corrupted data. In this work we argue that notable lessons from open set recognition, the identification of statistically deviating data outside of the observed dataset, and the adjacent field of active learning, where data is incrementally queried such that the expected performance gain is maximized, are frequently overlooked in the deep learning era. Based on these forgotten lessons, we propose a consolidated view to bridge continual learning, active learning and open set recognition in deep neural networks. Our results show that this not only benefits each individual paradigm, but highlights the natural synergies in a common framework. We empirically demonstrate improvements when alleviating catastrophic forgetting, querying data in active learning, selecting task orders, while exhibiting robust open world application where previously proposed methods fail.

A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.

Graph Neural Networks (GNNs), which generalize deep neural networks to graph-structured data, have drawn considerable attention and achieved state-of-the-art performance in numerous graph related tasks. However, existing GNN models mainly focus on designing graph convolution operations. The graph pooling (or downsampling) operations, that play an important role in learning hierarchical representations, are usually overlooked. In this paper, we propose a novel graph pooling operator, called Hierarchical Graph Pooling with Structure Learning (HGP-SL), which can be integrated into various graph neural network architectures. HGP-SL incorporates graph pooling and structure learning into a unified module to generate hierarchical representations of graphs. More specifically, the graph pooling operation adaptively selects a subset of nodes to form an induced subgraph for the subsequent layers. To preserve the integrity of graph's topological information, we further introduce a structure learning mechanism to learn a refined graph structure for the pooled graph at each layer. By combining HGP-SL operator with graph neural networks, we perform graph level representation learning with focus on graph classification task. Experimental results on six widely used benchmarks demonstrate the effectiveness of our proposed model.

Deep convolutional neural networks (CNNs) have recently achieved great success in many visual recognition tasks. However, existing deep neural network models are computationally expensive and memory intensive, hindering their deployment in devices with low memory resources or in applications with strict latency requirements. Therefore, a natural thought is to perform model compression and acceleration in deep networks without significantly decreasing the model performance. During the past few years, tremendous progress has been made in this area. In this paper, we survey the recent advanced techniques for compacting and accelerating CNNs model developed. These techniques are roughly categorized into four schemes: parameter pruning and sharing, low-rank factorization, transferred/compact convolutional filters, and knowledge distillation. Methods of parameter pruning and sharing will be described at the beginning, after that the other techniques will be introduced. For each scheme, we provide insightful analysis regarding the performance, related applications, advantages, and drawbacks etc. Then we will go through a few very recent additional successful methods, for example, dynamic capacity networks and stochastic depths networks. After that, we survey the evaluation matrix, the main datasets used for evaluating the model performance and recent benchmarking efforts. Finally, we conclude this paper, discuss remaining challenges and possible directions on this topic.

Deep Convolutional Neural Networks (CNNs) are a special type of Neural Networks, which have shown state-of-the-art results on various competitive benchmarks. The powerful learning ability of deep CNN is largely achieved with the use of multiple non-linear feature extraction stages that can automatically learn hierarchical representation from the data. Availability of a large amount of data and improvements in the hardware processing units have accelerated the research in CNNs and recently very interesting deep CNN architectures are reported. The recent race in deep CNN architectures for achieving high performance on the challenging benchmarks has shown that the innovative architectural ideas, as well as parameter optimization, can improve the CNN performance on various vision-related tasks. In this regard, different ideas in the CNN design have been explored such as use of different activation and loss functions, parameter optimization, regularization, and restructuring of processing units. However, the major improvement in representational capacity is achieved by the restructuring of the processing units. Especially, the idea of using a block as a structural unit instead of a layer is gaining substantial appreciation. This survey thus focuses on the intrinsic taxonomy present in the recently reported CNN architectures and consequently, classifies the recent innovations in CNN architectures into seven different categories. These seven categories are based on spatial exploitation, depth, multi-path, width, feature map exploitation, channel boosting and attention. Additionally, it covers the elementary understanding of the CNN components and sheds light on the current challenges and applications of CNNs.

Recently, deep learning has achieved very promising results in visual object tracking. Deep neural networks in existing tracking methods require a lot of training data to learn a large number of parameters. However, training data is not sufficient for visual object tracking as annotations of a target object are only available in the first frame of a test sequence. In this paper, we propose to learn hierarchical features for visual object tracking by using tree structure based Recursive Neural Networks (RNN), which have fewer parameters than other deep neural networks, e.g. Convolutional Neural Networks (CNN). First, we learn RNN parameters to discriminate between the target object and background in the first frame of a test sequence. Tree structure over local patches of an exemplar region is randomly generated by using a bottom-up greedy search strategy. Given the learned RNN parameters, we create two dictionaries regarding target regions and corresponding local patches based on the learned hierarchical features from both top and leaf nodes of multiple random trees. In each of the subsequent frames, we conduct sparse dictionary coding on all candidates to select the best candidate as the new target location. In addition, we online update two dictionaries to handle appearance changes of target objects. Experimental results demonstrate that our feature learning algorithm can significantly improve tracking performance on benchmark datasets.

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