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Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{//github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.

As an effective strategy, data augmentation (DA) alleviates data scarcity scenarios where deep learning techniques may fail. It is widely applied in computer vision then introduced to natural language processing and achieves improvements in many tasks. One of the main focuses of the DA methods is to improve the diversity of training data, thereby helping the model to better generalize to unseen testing data. In this survey, we frame DA methods into three categories based on the diversity of augmented data, including paraphrasing, noising, and sampling. Our paper sets out to analyze DA methods in detail according to the above categories. Further, we also introduce their applications in NLP tasks as well as the challenges.

We present CoDEx, a set of knowledge graph completion datasets extracted from Wikidata and Wikipedia that improve upon existing knowledge graph completion benchmarks in scope and level of difficulty. In terms of scope, CoDEx comprises three knowledge graphs varying in size and structure, multilingual descriptions of entities and relations, and tens of thousands of hard negative triples that are plausible but verified to be false. To characterize CoDEx, we contribute thorough empirical analyses and benchmarking experiments. First, we analyze each CoDEx dataset in terms of logical relation patterns. Next, we report baseline link prediction and triple classification results on CoDEx for five extensively tuned embedding models. Finally, we differentiate CoDEx from the popular FB15K-237 knowledge graph completion dataset by showing that CoDEx covers more diverse and interpretable content, and is a more difficult link prediction benchmark. Data, code, and pretrained models are available at //bit.ly/2EPbrJs.

This paper surveys the field of transfer learning in the problem setting of Reinforcement Learning (RL). RL has been the key solution to sequential decision-making problems. Along with the fast advance of RL in various domains. including robotics and game-playing, transfer learning arises as an important technique to assist RL by leveraging and transferring external expertise to boost the learning process. In this survey, we review the central issues of transfer learning in the RL domain, providing a systematic categorization of its state-of-the-art techniques. We analyze their goals, methodologies, applications, and the RL frameworks under which these transfer learning techniques would be approachable. We discuss the relationship between transfer learning and other relevant topics from an RL perspective and also explore the potential challenges as well as future development directions for transfer learning in RL.

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at \url{//github.com/IBM/EvolveGCN}.

We present MMKG, a collection of three knowledge graphs that contain both numerical features and (links to) images for all entities as well as entity alignments between pairs of KGs. Therefore, multi-relational link prediction and entity matching communities can benefit from this resource. We believe this data set has the potential to facilitate the development of novel multi-modal learning approaches for knowledge graphs.We validate the utility ofMMKG in the sameAs link prediction task with an extensive set of experiments. These experiments show that the task at hand benefits from learning of multiple feature types.

This paper surveys the machine learning literature and presents machine learning as optimization models. Such models can benefit from the advancement of numerical optimization techniques which have already played a distinctive role in several machine learning settings. Particularly, mathematical optimization models are presented for commonly used machine learning approaches for regression, classification, clustering, and deep neural networks as well new emerging applications in machine teaching and empirical model learning. The strengths and the shortcomings of these models are discussed and potential research directions are highlighted.

With the advent of deep neural networks, learning-based approaches for 3D reconstruction have gained popularity. However, unlike for images, in 3D there is no canonical representation which is both computationally and memory efficient yet allows for representing high-resolution geometry of arbitrary topology. Many of the state-of-the-art learning-based 3D reconstruction approaches can hence only represent very coarse 3D geometry or are limited to a restricted domain. In this paper, we propose occupancy networks, a new representation for learning-based 3D reconstruction methods. Occupancy networks implicitly represent the 3D surface as the continuous decision boundary of a deep neural network classifier. In contrast to existing approaches, our representation encodes a description of the 3D output at infinite resolution without excessive memory footprint. We validate that our representation can efficiently encode 3D structure and can be inferred from various kinds of input. Our experiments demonstrate competitive results, both qualitatively and quantitatively, for the challenging tasks of 3D reconstruction from single images, noisy point clouds and coarse discrete voxel grids. We believe that occupancy networks will become a useful tool in a wide variety of learning-based 3D tasks.

Generative Adversarial networks (GANs) have obtained remarkable success in many unsupervised learning tasks and unarguably, clustering is an important unsupervised learning problem. While one can potentially exploit the latent-space back-projection in GANs to cluster, we demonstrate that the cluster structure is not retained in the GAN latent space. In this paper, we propose ClusterGAN as a new mechanism for clustering using GANs. By sampling latent variables from a mixture of one-hot encoded variables and continuous latent variables, coupled with an inverse network (which projects the data to the latent space) trained jointly with a clustering specific loss, we are able to achieve clustering in the latent space. Our results show a remarkable phenomenon that GANs can preserve latent space interpolation across categories, even though the discriminator is never exposed to such vectors. We compare our results with various clustering baselines and demonstrate superior performance on both synthetic and real datasets.

We study the problem of learning to reason in large scale knowledge graphs (KGs). More specifically, we describe a novel reinforcement learning framework for learning multi-hop relational paths: we use a policy-based agent with continuous states based on knowledge graph embeddings, which reasons in a KG vector space by sampling the most promising relation to extend its path. In contrast to prior work, our approach includes a reward function that takes the accuracy, diversity, and efficiency into consideration. Experimentally, we show that our proposed method outperforms a path-ranking based algorithm and knowledge graph embedding methods on Freebase and Never-Ending Language Learning datasets.