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Graph Neural Networks (GNNs) have been widely applied to various fields for learning over graph-structured data. They have shown significant improvements over traditional heuristic methods in various tasks such as node classification and graph classification. However, since GNNs heavily rely on smoothed node features rather than graph structure, they often show poor performance than simple heuristic methods in link prediction where the structural information, e.g., overlapped neighborhoods, degrees, and shortest paths, is crucial. To address this limitation, we propose Neighborhood Overlap-aware Graph Neural Networks (Neo-GNNs) that learn useful structural features from an adjacency matrix and estimate overlapped neighborhoods for link prediction. Our Neo-GNNs generalize neighborhood overlap-based heuristic methods and handle overlapped multi-hop neighborhoods. Our extensive experiments on Open Graph Benchmark datasets (OGB) demonstrate that Neo-GNNs consistently achieve state-of-the-art performance in link prediction. Our code is publicly available at //github.com/seongjunyun/Neo_GNNs.

Objective: Knowledge based planning (KBP) typically involves training an end-to-end deep learning model to predict dose distributions. However, training end-to-end KBP methods may be associated with practical limitations due to the limited size of medical datasets that are often used. To address these limitations, we propose a content based image retrieval (CBIR) method for retrieving dose distributions of previously planned patients based on anatomical similarity. Approach: Our proposed CBIR method trains a representation model that produces latent space embeddings of a patient's anatomical information. The latent space embeddings of new patients are then compared against those of previous patients in a database for image retrieval of dose distributions. Summary metrics (e.g. dose-volume histogram, conformity index, homogeneity index, etc.) are computed and can then be utilized in subsequent automated planning. All source code for this project is available on github. Main Results: The retrieval performance of various CBIR methods is evaluated on a dataset consisting of both publicly available plans and clinical plans from our institution. This study compares various encoding methods, ranging from simple autoencoders to more recent Siamese networks like SimSiam, and the best performance was observed for the multitask Siamese network. Significance: Applying CBIR to inform subsequent treatment planning potentially addresses many limitations associated with end-to-end KBP. Our current results demonstrate that excellent image retrieval performance can be obtained through slight changes to previously developed Siamese networks. We hope to integrate CBIR into automated planning workflow in future works, potentially through methods like the MetaPlanner framework.

As a scene graph compactly summarizes the high-level content of an image in a structured and symbolic manner, the similarity between scene graphs of two images reflects the relevance of their contents. Based on this idea, we propose a novel approach for image-to-image retrieval using scene graph similarity measured by graph neural networks. In our approach, graph neural networks are trained to predict the proxy image relevance measure, computed from human-annotated captions using a pre-trained sentence similarity model. We collect and publish the dataset for image relevance measured by human annotators to evaluate retrieval algorithms. The collected dataset shows that our method agrees well with the human perception of image similarity than other competitive baselines.

Data augmentation has been widely used to improve generalizability of machine learning models. However, comparatively little work studies data augmentation for graphs. This is largely due to the complex, non-Euclidean structure of graphs, which limits possible manipulation operations. Augmentation operations commonly used in vision and language have no analogs for graphs. Our work studies graph data augmentation for graph neural networks (GNNs) in the context of improving semi-supervised node-classification. We discuss practical and theoretical motivations, considerations and strategies for graph data augmentation. Our work shows that neural edge predictors can effectively encode class-homophilic structure to promote intra-class edges and demote inter-class edges in given graph structure, and our main contribution introduces the GAug graph data augmentation framework, which leverages these insights to improve performance in GNN-based node classification via edge prediction. Extensive experiments on multiple benchmarks show that augmentation via GAug improves performance across GNN architectures and datasets.

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.

Answering questions that require reading texts in an image is challenging for current models. One key difficulty of this task is that rare, polysemous, and ambiguous words frequently appear in images, e.g., names of places, products, and sports teams. To overcome this difficulty, only resorting to pre-trained word embedding models is far from enough. A desired model should utilize the rich information in multiple modalities of the image to help understand the meaning of scene texts, e.g., the prominent text on a bottle is most likely to be the brand. Following this idea, we propose a novel VQA approach, Multi-Modal Graph Neural Network (MM-GNN). It first represents an image as a graph consisting of three sub-graphs, depicting visual, semantic, and numeric modalities respectively. Then, we introduce three aggregators which guide the message passing from one graph to another to utilize the contexts in various modalities, so as to refine the features of nodes. The updated nodes have better features for the downstream question answering module. Experimental evaluations show that our MM-GNN represents the scene texts better and obviously facilitates the performances on two VQA tasks that require reading scene texts.

Image-to-image translation aims to learn the mapping between two visual domains. There are two main challenges for many applications: 1) the lack of aligned training pairs and 2) multiple possible outputs from a single input image. In this work, we present an approach based on disentangled representation for producing diverse outputs without paired training images. To achieve diversity, we propose to embed images onto two spaces: a domain-invariant content space capturing shared information across domains and a domain-specific attribute space. Our model takes the encoded content features extracted from a given input and the attribute vectors sampled from the attribute space to produce diverse outputs at test time. To handle unpaired training data, we introduce a novel cross-cycle consistency loss based on disentangled representations. Qualitative results show that our model can generate diverse and realistic images on a wide range of tasks without paired training data. For quantitative comparisons, we measure realism with user study and diversity with a perceptual distance metric. We apply the proposed model to domain adaptation and show competitive performance when compared to the state-of-the-art on the MNIST-M and the LineMod datasets.

We investigate the problem of automatically determining what type of shoe left an impression found at a crime scene. This recognition problem is made difficult by the variability in types of crime scene evidence (ranging from traces of dust or oil on hard surfaces to impressions made in soil) and the lack of comprehensive databases of shoe outsole tread patterns. We find that mid-level features extracted by pre-trained convolutional neural nets are surprisingly effective descriptors for this specialized domains. However, the choice of similarity measure for matching exemplars to a query image is essential to good performance. For matching multi-channel deep features, we propose the use of multi-channel normalized cross-correlation and analyze its effectiveness. Our proposed metric significantly improves performance in matching crime scene shoeprints to laboratory test impressions. We also show its effectiveness in other cross-domain image retrieval problems: matching facade images to segmentation labels and aerial photos to map images. Finally, we introduce a discriminatively trained variant and fine-tune our system through our proposed metric, obtaining state-of-the-art performance.

Deep learning (DL) based semantic segmentation methods have been providing state-of-the-art performance in the last few years. More specifically, these techniques have been successfully applied to medical image classification, segmentation, and detection tasks. One deep learning technique, U-Net, has become one of the most popular for these applications. In this paper, we propose a Recurrent Convolutional Neural Network (RCNN) based on U-Net as well as a Recurrent Residual Convolutional Neural Network (RRCNN) based on U-Net models, which are named RU-Net and R2U-Net respectively. The proposed models utilize the power of U-Net, Residual Network, as well as RCNN. There are several advantages of these proposed architectures for segmentation tasks. First, a residual unit helps when training deep architecture. Second, feature accumulation with recurrent residual convolutional layers ensures better feature representation for segmentation tasks. Third, it allows us to design better U-Net architecture with same number of network parameters with better performance for medical image segmentation. The proposed models are tested on three benchmark datasets such as blood vessel segmentation in retina images, skin cancer segmentation, and lung lesion segmentation. The experimental results show superior performance on segmentation tasks compared to equivalent models including U-Net and residual U-Net (ResU-Net).

Learning from a few examples remains a key challenge in machine learning. Despite recent advances in important domains such as vision and language, the standard supervised deep learning paradigm does not offer a satisfactory solution for learning new concepts rapidly from little data. In this work, we employ ideas from metric learning based on deep neural features and from recent advances that augment neural networks with external memories. Our framework learns a network that maps a small labelled support set and an unlabelled example to its label, obviating the need for fine-tuning to adapt to new class types. We then define one-shot learning problems on vision (using Omniglot, ImageNet) and language tasks. Our algorithm improves one-shot accuracy on ImageNet from 87.6% to 93.2% and from 88.0% to 93.8% on Omniglot compared to competing approaches. We also demonstrate the usefulness of the same model on language modeling by introducing a one-shot task on the Penn Treebank.