arXiv subjects

Xiaoxiao Li

Publications and source records attributed to Xiaoxiao Li.

At least 181 records · Page 10Linked to original sources

arXiv2019

Decision Explanation and Feature Importance for Invertible Networks

Deep neural networks are vulnerable to adversarial attacks and hard to interpret because of their black-box nature. The recently proposed invertible network is able to accurately reconstruct the inputs to a layer from its outputs, thus has the potential to unravel the black-box model. An invertible network classifier can be viewed as a two-stage model: (1) invertible transformation from input space to the feature space; (2) a linear classifier in the feature space. We can determine the decision boundary of a linear classifier in the feature space; since the transform is invertible, we can invert the decision boundary from the feature space to the input space. Furthermore, we propose to determine the projection of a data point onto the decision boundary, and define explanation as the difference between data and its projection. Finally, we propose to locally approximate a neural network with its first-order Taylor expansion, and define feature importance using a local linear model. We provide the implementation of our method: \url{https://github.com/juntang-zhuang/explain_invertible}.

cs.LG↗

arXiv2019

Jointly Discriminative and Generative Recurrent Neural Networks for Learning from fMRI

Recurrent neural networks (RNNs) were designed for dealing with time-series data and have recently been used for creating predictive models from functional magnetic resonance imaging (fMRI) data. However, gathering large fMRI datasets for learning is a difficult task. Furthermore, network interpretability is unclear. To address these issues, we utilize multitask learning and design a novel RNN-based model that learns to discriminate between classes while simultaneously learning to generate the fMRI time-series data. Employing the long short-term memory (LSTM) structure, we develop a discriminative model based on the hidden state and a generative model based on the cell state. The addition of the generative model constrains the network to learn functional communities represented by the LSTM nodes that are both consistent with the data generation as well as useful for the classification task. We apply our approach to the classification of subjects with autism vs. healthy controls using several datasets from the Autism Brain Imaging Data Exchange. Experiments show that our jointly discriminative and generative model improves classification learning while also producing robust and meaningful functional communities for better model understanding.

eess.IV↗

arXiv2019

Preparing squeezed spin states in a spin-mechanical hybrid system with silicon-vacancy centers

We present and analyze an effective scheme for preparing squeezed spin states in a novel spin-mechanical hybrid device, which is realized by a single crystal diamond waveguide with built-in silicon-vacancy (SiV) centers. After studying the strain couplings between the SiV spins and the propagating phonon modes, we show that long-range spin-spin interactions can be achieved under large detuning condition. We model these nonlinear spin-spin couplings with an effective one-axis twisting Hamiltonian, and find that the system can be steered to the squeezed spin states in the practical situations. This work may have interesting applications in high-precision metrology and quantum information.

quant-ph↗

arXiv2019

REFUGE Challenge: A Unified Framework for Evaluating Automated Methods for Glaucoma Assessment from Fundus Photographs

Glaucoma is one of the leading causes of irreversible but preventable blindness in working age populations. Color fundus photography (CFP) is the most cost-effective imaging modality to screen for retinal disorders. However, its application to glaucoma has been limited to the computation of a few related biomarkers such as the vertical cup-to-disc ratio. Deep learning approaches, although widely applied for medical image analysis, have not been extensively used for glaucoma assessment due to the limited size of the available data sets. Furthermore, the lack of a standardize benchmark strategy makes difficult to compare existing methods in a uniform way. In order to overcome these issues we set up the Retinal Fundus Glaucoma Challenge, REFUGE (\url{https://refuge.grand-challenge.org}), held in conjunction with MICCAI 2018. The challenge consisted of two primary tasks, namely optic disc/cup segmentation and glaucoma classification. As part of REFUGE, we have publicly released a data set of 1200 fundus images with ground truth segmentations and clinical glaucoma labels, currently the largest existing one. We have also built an evaluation framework to ease and ensure fairness in the comparison of different models, encouraging the development of novel techniques in the field. 12 teams qualified and participated in the online challenge. This paper summarizes their methods and analyzes their corresponding results. In particular, we observed that two of the top-ranked teams outperformed two human experts in the glaucoma classification task. Furthermore, the segmentation results were in general consistent with the ground truth annotations, with complementary outcomes that can be further exploited by ensembling the results.

cs.CV↗

arXiv2019

Asymptotic expansions of solutions of the Yamabe equation and the $σ_k$-Yamabe equation near isolated singular points

We study asymptotic behaviors of positive solutions to the Yamabe equation and the $σ$k-Yamabe equation near isolated singular points and establish expansions up to arbitrary orders. Such results generalize an earlier pioneering work by Caffarelli, Gidas, and Spruck, and a work by Korevaar, Mazzeo, Pacard, and Schoen, on the Yamabe equation, and a work by Han, Li, and Teixeira on the $σ_k$-Yamabe equation. The study is based on a combination of classification of global singular solutions and an analysis of linearized operators at these global singular solutions. Such linearized equations are uniformly elliptic near singular points for $1 \leq k \leq n/2$ and become degenerate for $n/2 < k \leq n$. In a significant portion of the paper, we establish a degree 1 expansion for the $σ_k$-Yamabe equation for $n/2 < k < n$, generalizing a similar result for $k = 1$ by Korevaar, Mazzeo, Pacard, and Schoen and for $2 \leq k \leq n/2$ by Han, Li, and Teixeira.

math.DG↗

arXiv2019

Graph Embedding Using Infomax for ASD Classification and Brain Functional Difference Detection

Significant progress has been made using fMRI to characterize the brain changes that occur in ASD, a complex neuro-developmental disorder. However, due to the high dimensionality and low signal-to-noise ratio of fMRI, embedding informative and robust brain regional fMRI representations for both graph-level classification and region-level functional difference detection tasks between ASD and healthy control (HC) groups is difficult. Here, we model the whole brain fMRI as a graph, which preserves geometrical and temporal information and use a Graph Neural Network (GNN) to learn from the graph-structured fMRI data. We investigate the potential of including mutual information (MI) loss (Infomax), which is an unsupervised term encouraging large MI of each nodal representation and its corresponding graph-level summarized representation to learn a better graph embedding. Specifically, this work developed a pipeline including a GNN encoder, a classifier and a discriminator, which forces the encoded nodal representations to both benefit classification and reveal the common nodal patterns in a graph. We simultaneously optimize graph-level classification loss and Infomax. We demonstrated that Infomax graph embedding improves classification performance as a regularization term. Furthermore, we found separable nodal representations of ASD and HC groups in prefrontal cortex, cingulate cortex, visual regions, and other social, emotional and execution related brain regions. In contrast with GNN with classification loss only, the proposed pipeline can facilitate training more robust ASD classification models. Moreover, the separable nodal representations can detect the functional differences between the two groups and contribute to revealing new ASD biomarkers.

eess.IV↗

arXiv2019

Invertible Network for Classification and Biomarker Selection for ASD

Determining biomarkers for autism spectrum disorder (ASD) is crucial to understanding its mechanisms. Recently deep learning methods have achieved success in the classification task of ASD using fMRI data. However, due to the black-box nature of most deep learning models, it's hard to perform biomarker selection and interpret model decisions. The recently proposed invertible networks can accurately reconstruct the input from its output, and have the potential to unravel the black-box representation. Therefore, we propose a novel method to classify ASD and identify biomarkers for ASD using the connectivity matrix calculated from fMRI as the input. Specifically, with invertible networks, we explicitly determine the decision boundary and the projection of data points onto the boundary. Like linear classifiers, the difference between a point and its projection onto the decision boundary can be viewed as the explanation. We then define the importance as the explanation weighted by the gradient of prediction $w.r.t$ the input, and identify biomarkers based on this importance measure. We perform a regression task to further validate our biomarker selection: compared to using all edges in the connectivity matrix, using the top 10\% important edges we generate a lower regression error on 6 different severity scores. Our experiments show that the invertible network is both effective at ASD classification and interpretable, allowing for discovery of reliable biomarkers.

cs.CV↗

arXiv2019

Graph Neural Network for Interpreting Task-fMRI Biomarkers

Finding the biomarkers associated with ASD is helpful for understanding the underlying roots of the disorder and can lead to earlier diagnosis and more targeted treatment. A promising approach to identify biomarkers is using Graph Neural Networks (GNNs), which can be used to analyze graph structured data, i.e. brain networks constructed by fMRI. One way to interpret important features is through looking at how the classification probability changes if the features are occluded or replaced. The major limitation of this approach is that replacing values may change the distribution of the data and lead to serious errors. Therefore, we develop a 2-stage pipeline to eliminate the need to replace features for reliable biomarker interpretation. Specifically, we propose an inductive GNN to embed the graphs containing different properties of task-fMRI for identifying ASD and then discover the brain regions/sub-graphs used as evidence for the GNN classifier. We first show GNN can achieve high accuracy in identifying ASD. Next, we calculate the feature importance scores using GNN and compare the interpretation ability with Random Forest. Finally, we run with different atlases and parameters, proving the robustness of the proposed method. The detected biomarkers reveal their association with social behaviors. We also show the potential of discovering new informative biomarkers. Our pipeline can be generalized to other graph feature importance interpretation problems.

cs.LG↗

arXiv2019

MMDetection: Open MMLab Detection Toolbox and Benchmark

We present MMDetection, an object detection toolbox that contains a rich set of object detection and instance segmentation methods as well as related components and modules. The toolbox started from a codebase of MMDet team who won the detection track of COCO Challenge 2018. It gradually evolves into a unified platform that covers many popular detection methods and contemporary modules. It not only includes training and inference codes, but also provides weights for more than 200 network models. We believe this toolbox is by far the most complete detection toolbox. In this paper, we introduce the various features of this toolbox. In addition, we also conduct a benchmarking study on different methods, components, and their hyper-parameters. We wish that the toolbox and benchmark could serve the growing research community by providing a flexible toolkit to reimplement existing methods and develop their own new detectors. Code and models are available at https://github.com/open-mmlab/mmdetection. The project is under active development and we will keep this document updated.

cs.CV↗

arXiv2019

Deep Flow-Guided Video Inpainting

Video inpainting, which aims at filling in missing regions of a video, remains challenging due to the difficulty of preserving the precise spatial and temporal coherence of video contents. In this work we propose a novel flow-guided video inpainting approach. Rather than filling in the RGB pixels of each frame directly, we consider video inpainting as a pixel propagation problem. We first synthesize a spatially and temporally coherent optical flow field across video frames using a newly designed Deep Flow Completion network. Then the synthesized flow field is used to guide the propagation of pixels to fill up the missing regions in the video. Specifically, the Deep Flow Completion network follows a coarse-to-fine refinement to complete the flow fields, while their quality is further improved by hard flow example mining. Following the guide of the completed flow, the missing video regions can be filled up precisely. Our method is evaluated on DAVIS and YouTube-VOS datasets qualitatively and quantitatively, achieving the state-of-the-art performance in terms of inpainting quality and speed.

cs.CV↗

arXiv2019

Hybrid Task Cascade for Instance Segmentation

Cascade is a classic yet powerful architecture that has boosted performance on various tasks. However, how to introduce cascade to instance segmentation remains an open question. A simple combination of Cascade R-CNN and Mask R-CNN only brings limited gain. In exploring a more effective approach, we find that the key to a successful instance segmentation cascade is to fully leverage the reciprocal relationship between detection and segmentation. In this work, we propose a new framework, Hybrid Task Cascade (HTC), which differs in two important aspects: (1) instead of performing cascaded refinement on these two tasks separately, it interweaves them for a joint multi-stage processing; (2) it adopts a fully convolutional branch to provide spatial context, which can help distinguishing hard foreground from cluttered background. Overall, this framework can learn more discriminative features progressively while integrating complementary features together in each stage. Without bells and whistles, a single HTC obtains 38.4 and 1.5 improvement over a strong Cascade Mask R-CNN baseline on MSCOCO dataset. Moreover, our overall system achieves 48.6 mask AP on the test-challenge split, ranking 1st in the COCO 2018 Challenge Object Detection Task. Code is available at: https://github.com/open-mmlab/mmdetection.

cs.CV↗

arXiv2019

Efficient Interpretation of Deep Learning Models Using Graph Structure and Cooperative Game Theory: Application to ASD Biomarker Discovery

Discovering imaging biomarkers for autism spectrum disorder (ASD) is critical to help explain ASD and predict or monitor treatment outcomes. Toward this end, deep learning classifiers have recently been used for identifying ASD from functional magnetic resonance imaging (fMRI) with higher accuracy than traditional learning strategies. However, a key challenge with deep learning models is understanding just what image features the network is using, which can in turn be used to define the biomarkers. Current methods extract biomarkers, i.e., important features, by looking at how the prediction changes if "ignoring" one feature at a time. In this work, we go beyond looking at only individual features by using Shapley value explanation (SVE) from cooperative game theory. Cooperative game theory is advantageous here because it directly considers the interaction between features and can be applied to any machine learning method, making it a novel, more accurate way of determining instance-wise biomarker importance from deep learning models. A barrier to using SVE is its computational complexity: $2^N$ given $N$ features. We explicitly reduce the complexity of SVE computation by two approaches based on the underlying graph structure of the input data: 1) only consider the centralized coalition of each feature; 2) a hierarchical pipeline which first clusters features into small communities, then applies SVE in each community. Monte Carlo approximation can be used for large permutation sets. We first validate our methods on the MNIST dataset and compare to human perception. Next, to insure plausibility of our biomarker results, we train a Random Forest (RF) to classify ASD/control subjects from fMRI and compare SVE results to standard RF-based feature importance. Finally, we show initial results on ranked fMRI biomarkers using SVE on a deep learning classifier for the ASD/control dataset.

cs.CV↗

arXiv2019

Prediction of treatment outcome for autism from structure of the brain based on sure independence screening

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder, and behavioral treatment interventions have shown promise for young children with ASD. However, there is limited progress in understanding the effect of each type of treatment. In this project, we aim to detect structural changes in the brain after treatment and select structural features associated with treatment outcomes. The difficulty in building large databases of patients who have received specific treatments and the high dimensionality of medical image analysis problems are the challenges in this work. To select predictive features and build accurate models, we use the sure independence screening (SIS) method. SIS is a theoretically and empirically validated method for ultra-high dimensional general linear models, and it achieves both predictive accuracy and correct feature selection by iterative feature selection. Compared with step-wise feature selection methods, SIS removes multiple features in each iteration and is computationally efficient. Compared with other linear models such as elastic-net regression, support vector regression (SVR) and partial least squares regression (PSLR), SIS achieves higher accuracy. We validated the superior performance of SIS in various experiments: First, we extract brain structural features from FreeSurfer, including cortical thickness, surface area, mean curvature and cortical volume. Next, we predict different measures of treatment outcomes based on structural features. We show that SIS achieves the highest correlation between prediction and measurements in all tasks. Furthermore, we report regions selected by SIS as biomarkers for ASD.

q-bio.NC↗

arXiv2019

What evidence does deep learning model use to classify Skin Lesions?

Melanoma is a type of skin cancer with the most rapidly increasing incidence. Early detection of melanoma using dermoscopy images significantly increases patients' survival rate. However, accurately classifying skin lesions by eye, especially in the early stage of melanoma, is extremely challenging for the dermatologists. Hence, the discovery of reliable biomarkers will be meaningful for melanoma diagnosis. Recent years, the value of deep learning empowered computer-assisted diagnose has been shown in biomedical imaging based decision making. However, much research focuses on improving disease detection accuracy but not exploring the evidence of pathology. In this paper, we propose a method to interpret the deep learning classification findings. Firstly, we propose an accurate neural network architecture to classify skin lesions. Secondly, we utilize a prediction difference analysis method that examines each patch on the image through patch-wised corrupting to detect the biomarkers. Lastly, we validate that our biomarker findings are corresponding to the patterns in the literature. The findings can be significant and useful to guide clinical diagnosis.

cs.CV↗

arXiv2018

How many weights can a cyclic code have ?

Upper and lower bounds on the largest number of weights in a cyclic code of given length, dimension and alphabet are given. An application to irreducible cyclic codes is considered. Sharper upper bounds are given for the special cyclic codes (called here strongly cyclic), {whose nonzero codewords have period equal to the length of the code}. Asymptotics are derived on the function $Γ(k,q),$ {that is defined as} the largest number of nonzero weights a cyclic code of dimension $k$ over $\F_q$ can have, and an algorithm to compute it is sketched. The nonzero weights in some infinite families of Reed-Muller codes, either binary or $q$-ary, as well as in the $q$-ary Hamming code are determined, two difficult results of independent interest.

cs.IT↗

arXiv2018

Repetitive Motion Estimation Network: Recover cardiac and respiratory signal from thoracic imaging

Tracking organ motion is important in image-guided interventions, but motion annotations are not always easily available. Thus, we propose Repetitive Motion Estimation Network (RMEN) to recover cardiac and respiratory signals. It learns the spatio-temporal repetition patterns, embedding high dimensional motion manifolds to 1D vectors with partial motion phase boundary annotations. Compared with the best alternative models, our proposed RMEN significantly decreased the QRS peaks detection offsets by 59.3%. Results showed that RMEN could handle the irregular cardiac and respiratory motion cases. Repetitive motion patterns learned by RMEN were visualized and indicated in the feature maps.

cs.CV↗

arXiv2018

Prediction of severity and treatment outcome for ASD from fMRI

Autism spectrum disorder (ASD) is a complex neurodevelopmental syndrome. Early diagnosis and precise treatment are essential for ASD patients. Although researchers have built many analytical models, there has been limited progress in accurate predictive models for early diagnosis. In this project, we aim to build an accurate model to predict treatment outcome and ASD severity from early stage functional magnetic resonance imaging (fMRI) scans. The difficulty in building large databases of patients who have received specific treatments and the high dimensionality of medical image analysis problems are challenges in this work. We propose a generic and accurate two-level approach for high-dimensional regression problems in medical image analysis. First, we perform region-level feature selection using a predefined brain parcellation. Based on the assumption that voxels within one region in the brain have similar values, for each region we use the bootstrapped mean of voxels within it as a feature. In this way, the dimension of data is reduced from number of voxels to number of regions. Then we detect predictive regions by various feature selection methods. Second, we extract voxels within selected regions, and perform voxel-level feature selection. To use this model in both linear and non-linear cases with limited training examples, we apply two-level elastic net regression and random forest (RF) models respectively. To validate accuracy and robustness of this approach, we perform experiments on both task-fMRI and resting state fMRI datasets. Furthermore, we visualize the influence of each region, and show that the results match well with other findings.

q-bio.NC↗

arXiv2018

Brain Biomarker Interpretation in ASD Using Deep Learning and fMRI

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder. Finding the biomarkers associated with ASD is extremely helpful to understand the underlying roots of the disorder and can lead to earlier diagnosis and more targeted treatment. Although Deep Neural Networks (DNNs) have been applied in functional magnetic resonance imaging (fMRI) to identify ASD, understanding the data-driven computational decision making procedure has not been previously explored. Therefore, in this work, we address the problem of interpreting reliable biomarkers associated with identifying ASD; specifically, we propose a 2-stage method that classifies ASD and control subjects using fMRI images and interprets the saliency features activated by the classifier. First, we trained an accurate DNN classifier. Then, for detecting the biomarkers, different from the DNN visualization works in computer vision, we take advantage of the anatomical structure of brain fMRI and develop a frequency-normalized sampling method to corrupt images. Furthermore, in the ASD vs. control subjects classification scenario, we provide a new approach to detect and characterize important brain features into three categories. The biomarkers we found by the proposed method are robust and consistent with previous findings in the literature. We also validate the detected biomarkers by neurological function decoding and comparing with the DNN activation maps.

cs.CV↗