arXiv subjects

Jiawei Yang

Publications and source records attributed to Jiawei Yang.

At least 91 records · Page 5Linked to original sources

arXiv2021

TumorCP: A Simple but Effective Object-Level Data Augmentation for Tumor Segmentation

Deep learning models are notoriously data-hungry. Thus, there is an urging need for data-efficient techniques in medical image analysis, where well-annotated data are costly and time consuming to collect. Motivated by the recently revived "Copy-Paste" augmentation, we propose TumorCP, a simple but effective object-level data augmentation method tailored for tumor segmentation. TumorCP is online and stochastic, providing unlimited augmentation possibilities for tumors' subjects, locations, appearances, as well as morphologies. Experiments on kidney tumor segmentation task demonstrate that TumorCP surpasses the strong baseline by a remarkable margin of 7.12% on tumor Dice. Moreover, together with image-level data augmentation, it beats the current state-of-the-art by 2.32% on tumor Dice. Comprehensive ablation studies are performed to validate the effectiveness of TumorCP. Meanwhile, we show that TumorCP can lead to striking improvements in extremely low-data regimes. Evaluated with only 10% labeled data, TumorCP significantly boosts tumor Dice by 21.87%. To the best of our knowledge, this is the very first work exploring and extending the "Copy-Paste" design in medical imaging domain. Code is available at: https://github.com/YaoZhang93/TumorCP.

cs.CV↗

arXiv2021

Insight-HXMT observations of jet-like corona in a black hole X-ray binary MAXI J1820+070

A black hole X-ray binary produces hard X-ray radiation from its corona and disk when the accreting matter heats up. During an outburst, the disk and corona co-evolves with each other. However, such an evolution is still unclear in both its geometry and dynamics. Here we report the unusual decrease of the reflection fraction in MAXI J1820+070, which is the ratio of the coronal intensity illuminating the disk to the coronal intensity reaching the observer, as the corona is observed to contrast during the decay phase. We postulate a jet-like corona model, in which the corona can be understood as a standing shock where the material flowing through. In this dynamical scenario, the decrease of the reflection fraction is a signature of the corona's bulk velocity. Our findings suggest that as the corona is observed to get closer to the black hole, the coronal material might be outflowing faster.

astro-ph.HE↗

arXiv2021

Exploring Instance-Level Uncertainty for Medical Detection

The ability of deep learning to predict with uncertainty is recognized as key for its adoption in clinical routines. Moreover, performance gain has been enabled by modelling uncertainty according to empirical evidence. While previous work has widely discussed the uncertainty estimation in segmentation and classification tasks, its application on bounding-box-based detection has been limited, mainly due to the challenge of bounding box aligning. In this work, we explore to augment a 2.5D detection CNN with two different bounding-box-level (or instance-level) uncertainty estimates, i.e., predictive variance and Monte Carlo (MC) sample variance. Experiments are conducted for lung nodule detection on LUNA16 dataset, a task where significant semantic ambiguities can exist between nodules and non-nodules. Results show that our method improves the evaluating score from 84.57% to 88.86% by utilizing a combination of both types of variances. Moreover, we show the generated uncertainty enables superior operating points compared to using the probability threshold only, and can further boost the performance to 89.52%. Example nodule detections are visualized to further illustrate the advantages of our method.

cs.CV↗

arXiv2021

Atlas-aware ConvNetfor Accurate yet Robust Anatomical Segmentation

Convolutional networks (ConvNets) have achieved promising accuracy for various anatomical segmentation tasks. Despite the success, these methods can be sensitive to data appearance variations. Considering the large variability of scans caused by artifacts, pathologies, and scanning setups, robust ConvNets are vital for clinical applications, while have not been fully explored. In this paper, we propose to mitigate the challenge by enabling ConvNets' awareness of the underlying anatomical invariances among imaging scans. Specifically, we introduce a fully convolutional Constraint Adoption Module (CAM) that incorporates probabilistic atlas priors as explicit constraints for predictions over a locally connected Conditional Random Field (CFR), which effectively reinforces the anatomical consistency of the labeling outputs. We design the CAM to be flexible for boosting various ConvNet, and compact for co-optimizing with ConvNets for fusion parameters that leads to the optimal performance. We show the advantage of such atlas priors fusion is two-fold with two brain parcellation tasks. First, our models achieve state-of-the-art accuracy among ConvNet-based methods on both datasets, by significantly reducing structural abnormalities of predictions. Second, we can largely boost the robustness of existing ConvNets, proved by: (i) testing on scans with synthetic pathologies, and (ii) training and evaluation on scans of different scanning setups across datasets. Our method is proposing to be easily adopted to existing ConvNets by fine-tuning with CAM plugged in for accuracy and robustness boosts.

cs.CV↗

arXiv2021

T-Net: Learning Feature Representation with Task-specific Supervision for Biomedical Image Analysis

The encoder-decoder network is widely used to learn deep feature representations from pixel-wise annotations in biomedical image analysis. Under this structure, the performance profoundly relies on the effectiveness of feature extraction achieved by the encoding network. However, few models have considered adapting the attention of the feature extractor even in different kinds of tasks. In this paper, we propose a novel training strategy by adapting the attention of the feature extractor according to different tasks for effective representation learning. Specifically, the framework, named T-Net, consists of an encoding network supervised by task-specific attention maps and a posterior network that takes in the learned features to predict the corresponding results. The attention map is obtained by the transformation from pixel-wise annotations according to the specific task, which is used as the supervision to regularize the feature extractor to focus on different locations of the recognition object. To show the effectiveness of our method, we evaluate T-Net on two different tasks, i.e. , segmentation and localization. Extensive results on three public datasets (BraTS-17, MoNuSeg and IDRiD) have indicated the effectiveness and efficiency of our proposed supervision method, especially over the conventional encoding-decoding network.

eess.IV↗

arXiv2021

Oral-3D: Reconstructing the 3D Bone Structure of Oral Cavity from 2D Panoramic X-ray

Panoramic X-ray (PX) provides a 2D picture of the patient's mouth in a panoramic view to help dentists observe the invisible disease inside the gum. However, it provides limited 2D information compared with cone-beam computed tomography (CBCT), another dental imaging method that generates a 3D picture of the oral cavity but with more radiation dose and a higher price. Consequently, it is of great interest to reconstruct the 3D structure from a 2D X-ray image, which can greatly explore the application of X-ray imaging in dental surgeries. In this paper, we propose a framework, named Oral-3D, to reconstruct the 3D oral cavity from a single PX image and prior information of the dental arch. Specifically, we first train a generative model to learn the cross-dimension transformation from 2D to 3D. Then we restore the shape of the oral cavity with a deformation module with the dental arch curve, which can be obtained simply by taking a photo of the patient's mouth. To be noted, Oral-3D can restore both the density of bony tissues and the curved mandible surface. Experimental results show that Oral-3D can efficiently and effectively reconstruct the 3D oral structure and show critical information in clinical applications, e.g., tooth pulling and dental implants. To the best of our knowledge, we are the first to explore this domain transformation problem between these two imaging methods.

eess.IV↗

arXiv2020

OralViewer: 3D Demonstration of Dental Surgeries for Patient Education with Oral Cavity Reconstruction from a 2D Panoramic X-ray

Patient's understanding on forthcoming dental surgeries is required by patient-centered care and helps reduce fear and anxiety. Due to the gap of expertise between patients and dentists, conventional techniques of patient education are usually not effective for explaining surgical steps. In this paper, we present \textit{OralViewer} -- the first interactive application that enables dentist's demonstration of dental surgeries in 3D to promote patients' understanding. \textit{OralViewer} takes a single 2D panoramic dental X-ray to reconstruct patient-specific 3D teeth structures, which are then assembled with registered gum and jaw bone models for complete oral cavity modeling. During the demonstration, \textit{OralViewer} enables dentists to show surgery steps with virtual dental instruments that can animate effects on a 3D model in real-time. A technical evaluation shows our deep learning based model achieves a mean Intersection over Union (IoU) of 0.771 for 3D teeth reconstruction. A patient study with 12 participants shows \textit{OralViewer} can improve patients' understanding of surgeries. An expert study with 3 board-certified dentists further verifies the clinical validity of our system.

cs.HC↗

arXiv2020

Loss-analysis via Attention-scale for Physiologic Time Series

Physiologic signals have properties across multiple spatial and temporal scales, which can be shown by the complexity-analysis of the coarse-grained physiologic signals by scaling techniques such as the multiscale. Unfortunately, the results obtained from the coarse-grained signals by the multiscale may not fully reflect the properties of the original signals because there is a loss caused by scaling techniques and the same scaling technique may bring different losses to different signals. Another problem is that multiscale does not consider the key observations inherent in the signal. Here, we show a new analysis method for time series called the loss-analysis via attention-scale. We show that multiscale is a special case of attention-scale. The loss-analysis can complement to the complexity-analysis to capture aspects of the signals that are not captured using previously developed measures. This can be used to study ageing, diseases, and other physiologic phenomenon.

cs.LG↗

arXiv2020

The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge

There is a large body of literature linking anatomic and geometric characteristics of kidney tumors to perioperative and oncologic outcomes. Semantic segmentation of these tumors and their host kidneys is a promising tool for quantitatively characterizing these lesions, but its adoption is limited due to the manual effort required to produce high-quality 3D segmentations of these structures. Recently, methods based on deep learning have shown excellent results in automatic 3D segmentation, but they require large datasets for training, and there remains little consensus on which methods perform best. The 2019 Kidney and Kidney Tumor Segmentation challenge (KiTS19) was a competition held in conjunction with the 2019 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) which sought to address these issues and stimulate progress on this automatic segmentation problem. A training set of 210 cross sectional CT images with kidney tumors was publicly released with corresponding semantic segmentation masks. 106 teams from five continents used this data to develop automated systems to predict the true segmentation masks on a test set of 90 CT images for which the corresponding ground truth segmentations were kept private. These predictions were scored and ranked according to their average So rensen-Dice coefficient between the kidney and tumor across all 90 cases. The winning team achieved a Dice of 0.974 for kidney and 0.851 for tumor, approaching the inter-annotator performance on kidney (0.983) but falling short on tumor (0.923). This challenge has now entered an "open leaderboard" phase where it serves as a challenging benchmark in 3D semantic segmentation.

eess.IV↗

arXiv2020

Helical Edge States and Quantum Phase Transitions in Tetralayer Graphene

Helical conductors with spin-momentum locking are promising platforms for Majorana fermions. Here we report observation of two topologically distinct phases supporting helical edge states in charge neutral Bernal-stacked tetralayer graphene in Hall bar and Corbino geometries. As the magnetic field B and out-of-plane displacement field D are varied, we observe a phase diagram consisting of an insulating phase and two metallic phases, with 0, 1 and 2 helical edge states, respectively. These phases are accounted for by a theoretical model that relates their conductance to spin-polarization plateaus. Transitions between them arise from a competition among inter-layer hopping, electrostatic and exchange interaction energies. Our work highlights the complex competing symmetries and the rich quantum phases in few-layer graphene.

cond-mat.mes-hall↗

arXiv2020

Cascaded Volumetric Convolutional Network for Kidney Tumor Segmentation from CT volumes

Automated segmentation of kidney and tumor from 3D CT scans is necessary for the diagnosis, monitoring, and treatment planning of the disease. In this paper, we describe a two-stage framework for kidney and tumor segmentation based on 3D fully convolutional network (FCN). The first stage preliminarily locate the kidney and cut off the irrelevant background to reduce class imbalance and computation cost. Then the second stage precisely segment the kidney and tumor on the cropped patch. The proposed method ranks the 4th place out of 105 competitive teams in MICCAI 2019 KiTS Challenge with a Composite Dice of 90.24%.

eess.IV↗

arXiv2019

Resource Allocation Using Gradient Boosting Aided Deep Q-Network for IoT in C-RANs

In this paper, we investigate dynamic resource allocation (DRA) problems for Internet of Things (IoT) in real-time cloud radio access networks (C-RANs), by combining gradient boosting approximation and deep reinforcement learning to solve the following two major problems. Firstly, in C-RANs, the decision making process of resource allocation is time-consuming and computational-expensive, motivating us to use an approximation method, i.e. the gradient boosting decision tree (GBDT) to approximate the solutions of second order cone programming (SOCP) problem. Moreover, considering the innumerable states in real-time C-RAN systems, we employ a deep reinforcement learning framework, i.e., deep Q-network (DQN) to generate a robust policy that controls the status of remote radio heads (RRHs). We propose a GBDT-based DQN framework for the DRA problem, where the heavy computation to solve SOCP problems is cut down and great power consumption is saved in the whole C-RAN system. We demonstrate that the generated policy is error-tolerant even the gradient boosting regression may not be strictly subject to the constraints of the original problem. Comparisons between the proposed method and existing baseline methods confirm the advantages of our method.

cs.IT↗

arXiv2019

The Medium Energy (ME) X-ray telescope onboard the Insight-HXMT astronomy satellite

The Medium Energy X-ray telescope (ME) is one of the three main telescopes on board the Insight Hard X-ray Modulation Telescope (Insight-HXMT) astronomy satellite. ME contains 1728 pixels of Si-PIN detectors sensitive in 5-30 keV with a total geometrical area of 952 cm2. Application Specific Integrated Circuit (ASIC) chips, VA32TA6, is used to achieve low power consumption and low readout noise. The collimators define three kinds of field of views (FOVs) for the telescope, 1°{\times}4°, 4°{\times}4°, and blocked ones. Combination of such FOVs can be used to estimate the in-orbit X-ray and particle background components. The energy resolution of ME is ~3 keV at 17.8 keV (FWHM) and the time resolution is 255 μs. In this paper, we introduce the design and performance of ME.

astro-ph.IM↗

arXiv2019

Insight-HXMT observations of Swift J0243.6+6124 during its 2017-2018 outburst

The recently discovered neutron star transient Swift J0243.6+6124 has been monitored by {\it the Hard X-ray Modulation Telescope} ({\it Insight-\rm HXMT). Based on the obtained data, we investigate the broadband spectrum of the source throughout the outburst. We estimate the broadband flux of the source and search for possible cyclotron line in the broadband spectrum. No evidence of line-like features is, however, found up to $\rm 150~keV$. In the absence of any cyclotron line in its energy spectrum, we estimate the magnetic field of the source based on the observed spin evolution of the neutron star by applying two accretion torque models. In both cases, we get consistent results with $B\rm \sim 10^{13}~G$, $D\rm \sim 6~kpc$ and peak luminosity of $\rm >10^{39}~erg~s^{-1}$ which makes the source the first Galactic ultraluminous X-ray source hosting a neutron star.

astro-ph.HE↗

arXiv2018

Integer and Fractional Quantum Hall effect in Ultra-high Quality Few-layer Black Phosphorus Transistors

As a high mobility two-dimensional semiconductor with strong structural and electronic anisotropy, atomically thin black phosphorus (BP) provides a new playground for investigating the quantum Hall (QH) effect, including outstanding questions such as the functional dependence of Landau level (LL) gaps on magnetic field B, and possible anisotropic fractional QH states. Using encapsulating few-layer BP transistors with mobility up to 55,000 cm2/Vs, we extract LL gaps over an exceptionally wide range of B for QH states at filling factors ν=-1 to -4, which are determined to be linear in B, thus resolving a controversy raised by its anisotropy. Furthermore, a fractional QH state at ν~ -4/3 and an additional feature at -0.56+/- 0.1 are observed, underscoring BP as a tunable 2D platform for exploring electron interactions.

cond-mat.mes-hall↗

arXiv2018

Long-Distance Spin Transport Through a Graphene Quantum Hall Antiferromagnet

Antiferromagnetic insulators (AFMI) are robust against stray fields, and their intrinsic dynamics could enable ultrafast magneto-optics and ultrascaled magnetic information processing. Low dissipation, long distance spin transport and electrical manipulation of antiferromagnetic order are much sought-after goals of spintronics research. Here, we report the first experimental evidence of robust long-distance spin transport through an AFMI, in our case the gate-controlled, canted antiferromagnetic (CAF) state that appears at the charge neutrality point of graphene in the presence of an external magnetic field. Utilizing gate-controlled quantum Hall (QH) edge states as spin-dependent injectors and detectors, we observe large, non-local electrical signals across a 5 micron-long, insulating channel only when it is biased into the nu=0 CAF state. Among possible transport mechanisms, spin superfluidity in an antiferromagnetic state gives the most consistent interpretation of the non-local signal's dependence on magnetic field, temperature and filling factors. This work also demonstrates that graphene in the QH regime is a powerful model system for fundamental studies of antiferromagnetic, and in the case of a large in-plane field, ferromagnetic spintronics.

cond-mat.mes-hall↗

arXiv2017

A Generalised Seizure Prediction with Convolutional Neural Networks for Intracranial and Scalp Electroencephalogram Data Analysis

Seizure prediction has attracted a growing attention as one of the most challenging predictive data analysis efforts in order to improve the life of patients living with drug-resistant epilepsy and tonic seizures. Many outstanding works have been reporting great results in providing a sensible indirect (warning systems) or direct (interactive neural-stimulation) control over refractory seizures, some of which achieved high performance. However, many works put heavily handcraft feature extraction and/or carefully tailored feature engineering to each patient to achieve very high sensitivity and low false prediction rate for a particular dataset. This limits the benefit of their approaches if a different dataset is used. In this paper we apply Convolutional Neural Networks (CNNs) on different intracranial and scalp electroencephalogram (EEG) datasets and proposed a generalized retrospective and patient-specific seizure prediction method. We use Short-Time Fourier Transform (STFT) on 30-second EEG windows with 50% overlapping to extract information in both frequency and time domains. A standardization step is then applied on STFT components across the whole frequency range to prevent high frequencies features being influenced by those at lower frequencies. A convolutional neural network model is used for both feature extraction and classification to separate preictal segments from interictal ones. The proposed approach achieves sensitivity of 81.4%, 81.2%, 82.3% and false prediction rate (FPR) of 0.06/h, 0.16/h, 0.22/h on Freiburg Hospital intracranial EEG (iEEG) dataset, Children's Hospital of Boston-MIT scalp EEG (sEEG) dataset, and Kaggle American Epilepsy Society Seizure Prediction Challenge's dataset, respectively. Our prediction method is also statistically better than an unspecific random predictor for most of patients in all three datasets.

cs.CV↗

arXiv2017

Surface Transport and Quantum Hall Effect in Ambipolar Black Phosphorus Double Quantum Wells

Quantum wells constitute one of the most important classes of devices in the study of 2D systems. In a double layer QW, the additional "which-layer" degree of freedom gives rise to celebrated phenomena such as Coulomb drag, Hall drag and exciton condensation. Here we demonstrate facile formation of wide QWs in few-layer black phosphorus devices that host double layers of charge carriers. In contrast to tradition QWs, each 2D layer is ambipolar, and can be tuned into n-doped, p-doped or intrinsic regimes. Fully spin-polarized quantum Hall states are observed on each layer, with enhanced Lande g-factor that is attributed to exchange interactions. Our work opens the door for using 2D semiconductors as ambipolar single, double or wide QWs with unusual properties such as high anisotropy.

cond-mat.mes-hall↗