Xiao Yang

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PhD student in the Department of Computer Science, Research Assistant at Pennsylvania State University

  • Fast Predictive Simple Geodesic Regression

    Deformable image registration and regression are important tasks in medical image analysis. However, they are computationally expensive, especially when analyzing large-scale datasets that contain thousands of images. Hence, cluster computing is typically used, making the approaches dependent on such computational infrastructure. Even larger computational resources are required as study sizes increase. This limits the use of deformable image registration and regression for clinical applications and as component algorithms for other image analysis approaches. We therefore propose using a fast predictive approach to perform image registrations. In particular, we employ these fast registration predictions to approximate a simplified geodesic regression model to capture longitudinal brain changes. The resulting method is orders of magnitude faster than the standard optimization-based regression model and hence facilitates large-scale analysis on a single graphics processing unit (GPU). We evaluate our results on 3D brain magnetic resonance images (MRI) from the ADNI datasets.

    11/15/2017 ∙ by Zhipeng Ding, et al. ∙ 0 share

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  • Learning non-parametric Markov networks with mutual information

    We propose a method for learning Markov network structures for continuous data without invoking any assumptions about the distribution of the variables. The method makes use of previous work on a non-parametric estimator for mutual information which is used to create a non-parametric test for multivariate conditional independence. This independence test is then combined with an efficient constraint-based algorithm for learning the graph structure. The performance of the method is evaluated on several synthetic data sets and it is shown to learn considerably more accurate structures than competing methods when the dependencies between the variables involve non-linearities.

    08/08/2017 ∙ by Janne Leppä-aho, et al. ∙ 0 share

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  • Prolongation of SMAP to Spatio-temporally Seamless Coverage of Continental US Using a Deep Learning Neural Network

    The Soil Moisture Active Passive (SMAP) mission has delivered valuable sensing of surface soil moisture since 2015. However, it has a short time span and irregular revisit schedule. Utilizing a state-of-the-art time-series deep learning neural network, Long Short-Term Memory (LSTM), we created a system that predicts SMAP level-3 soil moisture data with atmospheric forcing, model-simulated moisture, and static physiographic attributes as inputs. The system removes most of the bias with model simulations and improves predicted moisture climatology, achieving small test root-mean-squared error (<0.035) and high correlation coefficient >0.87 for over 75% of Continental United States, including the forested Southeast. As the first application of LSTM in hydrology, we show the proposed network avoids overfitting and is robust for both temporal and spatial extrapolation tests. LSTM generalizes well across regions with distinct climates and physiography. With high fidelity to SMAP, LSTM shows great potential for hindcasting, data assimilation, and weather forecasting.

    07/20/2017 ∙ by Kuai Fang, et al. ∙ 0 share

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  • Learning to Extract Semantic Structure from Documents Using Multimodal Fully Convolutional Neural Network

    We present an end-to-end, multimodal, fully convolutional network for extracting semantic structures from document images. We consider document semantic structure extraction as a pixel-wise segmentation task, and propose a unified model that classifies pixels based not only on their visual appearance, as in the traditional page segmentation task, but also on the content of underlying text. Moreover, we propose an efficient synthetic document generation process that we use to generate pretraining data for our network. Once the network is trained on a large set of synthetic documents, we fine-tune the network on unlabeled real documents using a semi-supervised approach. We systematically study the optimum network architecture and show that both our multimodal approach and the synthetic data pretraining significantly boost the performance.

    06/07/2017 ∙ by Xiao Yang, et al. ∙ 0 share

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  • Efficient Registration of Pathological Images: A Joint PCA/Image-Reconstruction Approach

    Registration involving one or more images containing pathologies is challenging, as standard image similarity measures and spatial transforms cannot account for common changes due to pathologies. Low-rank/Sparse (LRS) decomposition removes pathologies prior to registration; however, LRS is memory-demanding and slow, which limits its use on larger data sets. Additionally, LRS blurs normal tissue regions, which may degrade registration performance. This paper proposes an efficient alternative to LRS: (1) normal tissue appearance is captured by principal component analysis (PCA) and (2) blurring is avoided by an integrated model for pathology removal and image reconstruction. Results on synthetic and BRATS 2015 data demonstrate its utility.

    03/31/2017 ∙ by Xu Han, et al. ∙ 0 share

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  • Quicksilver: Fast Predictive Image Registration - a Deep Learning Approach

    This paper introduces Quicksilver, a fast deformable image registration method. Quicksilver registration for image-pairs works by patch-wise prediction of a deformation model based directly on image appearance. A deep encoder-decoder network is used as the prediction model. While the prediction strategy is general, we focus on predictions for the Large Deformation Diffeomorphic Metric Mapping (LDDMM) model. Specifically, we predict the momentum-parameterization of LDDMM, which facilitates a patch-wise prediction strategy while maintaining the theoretical properties of LDDMM, such as guaranteed diffeomorphic mappings for sufficiently strong regularization. We also provide a probabilistic version of our prediction network which can be sampled during the testing time to calculate uncertainties in the predicted deformations. Finally, we introduce a new correction network which greatly increases the prediction accuracy of an already existing prediction network. We show experimental results for uni-modal atlas-to-image as well as uni- / multi- modal image-to-image registrations. These experiments demonstrate that our method accurately predicts registrations obtained by numerical optimization, is very fast, achieves state-of-the-art registration results on four standard validation datasets, and can jointly learn an image similarity measure. Quicksilver is freely available as an open-source software.

    03/31/2017 ∙ by Xiao Yang, et al. ∙ 0 share

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  • Fast Predictive Multimodal Image Registration

    We introduce a deep encoder-decoder architecture for image deformation prediction from multimodal images. Specifically, we design an image-patch-based deep network that jointly (i) learns an image similarity measure and (ii) the relationship between image patches and deformation parameters. While our method can be applied to general image registration formulations, we focus on the Large Deformation Diffeomorphic Metric Mapping (LDDMM) registration model. By predicting the initial momentum of the shooting formulation of LDDMM, we preserve its mathematical properties and drastically reduce the computation time, compared to optimization-based approaches. Furthermore, we create a Bayesian probabilistic version of the network that allows evaluation of registration uncertainty via sampling of the network at test time. We evaluate our method on a 3D brain MRI dataset using both T1- and T2-weighted images. Our experiments show that our method generates accurate predictions and that learning the similarity measure leads to more consistent registrations than relying on generic multimodal image similarity measures, such as mutual information. Our approach is an order of magnitude faster than optimization-based LDDMM.

    03/31/2017 ∙ by Xiao Yang, et al. ∙ 0 share

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  • Smart Library: Identifying Books in a Library using Richly Supervised Deep Scene Text Reading

    Physical library collections are valuable and long standing resources for knowledge and learning. However, managing books in a large bookshelf and finding books on it often leads to tedious manual work, especially for large book collections where books might be missing or misplaced. Recently, deep neural models, such as Convolutional Neural Networks (CNN) and Recurrent Neural Networks (RNN) have achieved great success for scene text detection and recognition. Motivated by these recent successes, we aim to investigate their viability in facilitating book management, a task that introduces further challenges including large amounts of cluttered scene text, distortion, and varied lighting conditions. In this paper, we present a library inventory building and retrieval system based on scene text reading methods. We specifically design our scene text recognition model using rich supervision to accelerate training and achieve state-of-the-art performance on several benchmark datasets. Our proposed system has the potential to greatly reduce the amount of human labor required in managing book inventories as well as the space needed to store book information.

    11/22/2016 ∙ by Xiao Yang, et al. ∙ 0 share

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  • Fast Predictive Image Registration

    We present a method to predict image deformations based on patch-wise image appearance. Specifically, we design a patch-based deep encoder-decoder network which learns the pixel/voxel-wise mapping between image appearance and registration parameters. Our approach can predict general deformation parameterizations, however, we focus on the large deformation diffeomorphic metric mapping (LDDMM) registration model. By predicting the LDDMM momentum-parameterization we retain the desirable theoretical properties of LDDMM, while reducing computation time by orders of magnitude: combined with patch pruning, we achieve a 1500x/66x speed up compared to GPU-based optimization for 2D/3D image registration. Our approach has better prediction accuracy than predicting deformation or velocity fields and results in diffeomorphic transformations. Additionally, we create a Bayesian probabilistic version of our network, which allows evaluation of deformation field uncertainty through Monte Carlo sampling using dropout at test time. We show that deformation uncertainty highlights areas of ambiguous deformations. We test our method on the OASIS brain image dataset in 2D and 3D.

    07/08/2016 ∙ by Xiao Yang, et al. ∙ 0 share

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  • Using Word Embeddings in Twitter Election Classification

    Word embeddings and convolutional neural networks (CNN) have attracted extensive attention in various classification tasks for Twitter, e.g. sentiment classification. However, the effect of the configuration used to train and generate the word embeddings on the classification performance has not been studied in the existing literature. In this paper, using a Twitter election classification task that aims to detect election-related tweets, we investigate the impact of the background dataset used to train the embedding models, the context window size and the dimensionality of word embeddings on the classification performance. By comparing the classification results of two word embedding models, which are trained using different background corpora (e.g. Wikipedia articles and Twitter microposts), we show that the background data type should align with the Twitter classification dataset to achieve a better performance. Moreover, by evaluating the results of word embeddings models trained using various context window sizes and dimensionalities, we found that large context window and dimension sizes are preferable to improve the performance. Our experimental results also show that using word embeddings and CNN leads to statistically significant improvements over various baselines such as random, SVM with TF-IDF and SVM with word embeddings.

    06/22/2016 ∙ by Xiao Yang, et al. ∙ 0 share

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  • Adversarial Training for Community Question Answer Selection Based on Multi-scale Matching

    Community-based question answering (CQA) websites represent an important source of information. As a result, the problem of matching the most valuable answers to their corresponding questions has become an increasingly popular research topic. We frame this task as a binary (relevant/irrelevant) classification problem, and propose a Multi-scale Matching model that inspects the correlation between words and ngrams (word-to-ngrams) of different levels of granularity. This is in addition to word-to-word correlations which are used in most prior work. In this way, our model is able to capture rich context information conveyed in ngrams, therefore can better differentiate good answers from bad ones. Furthermore, we present an adversarial training framework to iteratively generate challenging negative samples to fool the proposed classification model. This is completely different from previous methods, where negative samples are uniformly sampled from the dataset during training process. The proposed method is evaluated on SemEval 2017 and Yahoo Answer dataset and achieves state-of-the-art performance.

    04/22/2018 ∙ by Xiao Yang, et al. ∙ 0 share

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