arXiv subjects

Hao Gao

Publications and source records attributed to Hao Gao.

At least 73 records · Page 4Linked to original sources

arXiv2021

Enhancing Crystal Structure Prediction by decomposition methods based on graph theory

Crystal structure prediction algorithms have become powerful tools for materials discovery in recent years, however, they are usually limited to relatively small systems. The main challenge is that the number of local minima grows exponentially with system size. In this work, we proposed two crossover-mutation schemes based on graph theory to accelerate the evolutionary structure searching. These schemes can detect molecules or clusters inside periodic networks using quotient graphs for crystals and the decomposition can dramatically reduce the searching space. Sufficient examples for the test, including the high pressure phases of methane, ammonia, MgAl2O4, and boron, show that these new evolution schemes can obviously improve the success rate and searching efficiency compared with the standard method in both isolated and extended systems.

cond-mat.mtrl-sci↗

arXiv2021

AHP-Net: adaptive-hyper-parameter deep learning based image reconstruction method for multilevel low-dose CT

Low-dose CT (LDCT) imaging is desirable in many clinical applications to reduce X-ray radiation dose to patients. Inspired by deep learning (DL), a recent promising direction of model-based iterative reconstruction (MBIR) methods for LDCT is via optimization-unrolling DL-regularized image reconstruction, where pre-defined image prior is replaced by learnable data-adaptive prior. However, LDCT is clinically multilevel, since clinical scans have different noise levels that depend of scanning site, patient size, and clinical task. Therefore, this work aims to develop an adaptive-hyper-parameter DL-based image reconstruction method (AHP-Net) that can handle multilevel LDCT of different noise levels. AHP-Net unrolls a half-quadratic splitting scheme with learnable image prior built on framelet filter bank, and learns a network that automatically adjusts the hyper-parameters for various noise levels. As a result, AHP-Net provides a single universal training model that can handle multilevel LDCT. Extensive experimental evaluations using clinical scans suggest that AHP-Net outperformed conventional MBIR techniques and state-of-the-art deep-learning-based methods for multilevel LDCT of different noise levels.

eess.IV↗

arXiv2020

Action potential propagation and block in a model of atrial tissue with myocyte-fibroblast coupling

The electrical coupling between myocytes and fibroblasts and the spacial distribution of fibroblasts within myocardial tissues are significant factors in triggering and sustaining cardiac arrhythmias but their roles are poorly understood. This article describes both direct numerical simulations and an asymptotic theory of propagation and block of electrical excitation in a model of atrial tissue with myocyte-fibroblast coupling. In particular, three idealised fibroblast distributions are introduced: uniform distribution, fibroblast barrier and myocyte strait, all believed to be constituent blocks of realistic fibroblast distributions. Primary action potential biomarkers including conduction velocity, peak potential and triangulation index are estimated from direct simulations in all cases. Propagation block is found to occur at certain critical values of the parameters defining each idealised fibroblast distribution and these critical values are accurately determined. An asymptotic theory proposed earlier is extended and applied to the case of a uniform fibroblast distribution. Biomarker values are obtained from hybrid analytical-numerical solutions of coupled fast-time and slow-time periodic boundary value problems and compare well to direct numerical simulations. The boundary of absolute refractoriness is determined solely by the fast-time problem and is found to depend on the values of the myocyte potential and on the slow inactivation variable of the sodium current ahead of the propagating pulse. In turn, these quantities are estimated from the slow-time problem using a regular perturbation expansion to find the steady state of the coupled myocyte-fibroblast kinetics. The asymptotic theory gives a simple analytical expression that captures with remarkable accuracy the block of propagation in the presence of fibroblasts.

q-bio.TO↗

arXiv2020

Dimensionalities and multiplicities determination of crystal nets

Low-dimensional materials have attracted significant attentions over the past decade. To discover new low-dimensional materials, high-throughout screening methods have been applied in different materials databases. For this purpose, the reliability of dimensionality identification is therefore highly important. In this work, we find that the existence of self-penetrating nets may lead to incorrect results by previous methods. In stead of this, we use the quotient graph to analysis the topologies of structures and compute their dimensionalities. Based on the quotient graph, we can calculate not only the dimensionality but also the multiplicity of self-penetrating structures. As a demonstration, we screened the Crystallography Open Database using our method and found hundreds of structures with different dimensionalities and high multiplicities up to eleven.

cond-mat.mtrl-sci↗

arXiv2019

Bas-relief Generation from Point Clouds Based on Normal Space Compression with Real-time Adjustment on CPU

Bas-relief generation based on 3d models is a hot topic in computer graphics. State-of-the-art algorithms take a mesh surface as input, but real-time interaction via CPU cannot be realized. In this paper, a bas-relief generation algorithm that takes a scattered point cloud as input is proposed. The algorithm takes normal vectors as the operation object and the variation of the local surface as the compression criterion. By constructing and solving linear equations of bas-relief vertices, the closed-form solution can be obtained. Since there is no need to compute discrete gradients on a point cloud lacking topology information, it is easier to implement and more intuitive than gradient domain methods. The algorithm provides parameters to adjust the bas-relief height, saturation and detail richness. At the same time, through the solution strategy based on the subspace, it realizes the real-time adjustment of the bas-relief effect based on the computing power of a consumer CPU. In addition, an iterative solution to generate a bas-relief model of a specified height is presented to meet specific application requirements. Experiments show that our algorithm provides a unified solution for various types of bas-relief creation and can generate bas-reliefs with good saturation and rich details.

cs.GR↗

arXiv2019

Point cloud ridge-valley feature enhancement based on position and normal guidance

Ridge-valley features are important elements of point clouds, as they contain rich surface information. To recognize these features from point clouds, this paper introduces an extreme point distance (EPD) criterion with scale independence. Compared with traditional methods, the EPD greatly reduces the number of potential feature points and improves the robustness of multiscale feature point recognition. On this basis, a feature enhancement algorithm based on user priori guidance is proposed that adjusts the coordinates of the feature area by solving an objective equation containing the expected position and normal constraints. Since the expected normal can be expressed as a function of neighborhood point coordinates, the above objective equation can be converted into linear sparse equations with enhanced feature positions as variables, and thus, the closed solution can be obtained. In addition, a parameterization method for scattered point clouds based on feature line guidance is proposed, which reduces the number of unknowns by 2/3 and eliminates lateral sliding in the direction perpendicular to feature lines. Finally, the application of the algorithm in multiscale ridge-valley feature recognition, freeform surface feature enhancement and computer-aided design (CAD) workpiece sharp feature restoration verifies its effectiveness.

cs.GR↗

arXiv2019

A preliminary study on a multi-resolution-level inverse planning algorithm for Gamma Knife radiosurgery

Manual forward planning for GK radiosurgery is complicated and time-consuming, particularly for cases with large or irregularly shaped targets. Inverse planning eases GK planning by solving an optimization problem. However, due to the vast search space, most inverse planning algorithms have to decouple the planning process to isocenter preselection and sector duration optimization. This sequential scheme does not necessarily lead to optimal isocenter locations and hence optimal plans. In this study, we attempt to optimize the isocenter positions, beam shapes and durations simultaneously by proposing a multi-resolution-level (MRL) strategy to handle the large-scale GK optimization problem. In our approach, several rounds of optimizations were performed with a progressively increased spatial resolution for isocenter candidate selection. The isocenters selected from last round and their neighbors on a finer resolution were used as new isocenter candidates for next round of optimization. After plan optimization, shot sequencing was performed to group the optimized sectors to deliverable shots supported by GK treatment units. We have tested our algorithm on 6 GK cases previously treated in our institution (2 meningioma cases, 3 cases with single metastasis and 1 case with 6 metastases). Compared with manual planning, achieving same coverage and similar selectivity, our algorithm improved the gradient index averagely from 3.1 to 2.9 and reduced the maximum dose of brainstem from 8.0Gy to 5.6Gy. The average beam-on time was also reduced by from 103.8 mins to 87.4 mins. Our method was also compared with the inverse planning algorithm provided in Leksell GammaPlan planning system, and outperformed it with better plan quality for all the 6 cases.This preliminary study has demonstrated the effectiveness and feasibility of our MRL inverse planning approach for GK radiosurgery.

physics.med-ph↗

arXiv2019

ADASS: Adaptive Sample Selection for Training Acceleration

Stochastic gradient decent~(SGD) and its variants, including some accelerated variants, have become popular for training in machine learning. However, in all existing SGD and its variants, the sample size in each iteration~(epoch) of training is the same as the size of the full training set. In this paper, we propose a new method, called \underline{ada}ptive \underline{s}ample \underline{s}election~(ADASS), for training acceleration. During different epoches of training, ADASS only need to visit different training subsets which are adaptively selected from the full training set according to the Lipschitz constants of the loss functions on samples. It means that in ADASS the sample size in each epoch of training can be smaller than the size of the full training set, by discarding some samples. ADASS can be seamlessly integrated with existing optimization methods, such as SGD and momentum SGD, for training acceleration. Theoretical results show that the learning accuracy of ADASS is comparable to that of counterparts with full training set. Furthermore, empirical results on both shallow models and deep models also show that ADASS can accelerate the training process of existing methods without sacrificing accuracy.

stat.ML↗

arXiv2019

On the Convergence of Memory-Based Distributed SGD

Distributed stochastic gradient descent~(DSGD) has been widely used for optimizing large-scale machine learning models, including both convex and non-convex models. With the rapid growth of model size, huge communication cost has been the bottleneck of traditional DSGD. Recently, many communication compression methods have been proposed. Memory-based distributed stochastic gradient descent~(M-DSGD) is one of the efficient methods since each worker communicates a sparse vector in each iteration so that the communication cost is small. Recent works propose the convergence rate of M-DSGD when it adopts vanilla SGD. However, there is still a lack of convergence theory for M-DSGD when it adopts momentum SGD. In this paper, we propose a universal convergence analysis for M-DSGD by introducing \emph{transformation equation}. The transformation equation describes the relation between traditional DSGD and M-DSGD so that we can transform M-DSGD to its corresponding DSGD. Hence we get the convergence rate of M-DSGD with momentum for both convex and non-convex problems. Furthermore, we combine M-DSGD and stagewise learning that the learning rate of M-DSGD in each stage is a constant and is decreased by stage, instead of iteration. Using the transformation equation, we propose the convergence rate of stagewise M-DSGD which bridges the gap between theory and practice.

stat.ML↗

arXiv2019

Fast Parameter Inference in a Biomechanical Model of the Left Ventricle using Statistical Emulation

A central problem in biomechanical studies of personalised human left ventricular (LV) modelling is estimating the material properties and biophysical parameters from in-vivo clinical measurements in a time frame suitable for use within a clinic. Understanding these properties can provide insight into heart function or dysfunction and help inform personalised medicine. However, finding a solution to the differential equations which mathematically describe the kinematics and dynamics of the myocardium through numerical integration can be computationally expensive. To circumvent this issue, we use the concept of emulation to infer the myocardial properties of a healthy volunteer in a viable clinical time frame using in-vivo magnetic resonance image (MRI) data. Emulation methods avoid computationally expensive simulations from the LV model by replacing the biomechanical model, which is defined in terms of explicit partial differential equations, with a surrogate model inferred from simulations generated before the arrival of a patient, vastly improving computational efficiency at the clinic. We compare and contrast two emulation strategies: (i) emulation of the computational model outputs and (ii) emulation of the loss between the observed patient data and the computational model outputs. These strategies are tested with two different interpolation methods, as well as two different loss functions...

stat.AP↗

arXiv2019

Prediction of pressure-induced stabilization of noble-gas-atom compounds with alkali oxides and alkali sulfides

The cubic antifluorite structure comprises a face-centered cubic sublattice of anions with cations on the tetrahedral sites. The voids in the antifluorite structure that are crucial for superionicity in Li2O might also act as atomic traps. Trapping of guest atoms and small molecules within voids of a host structure leads to the formation of what are known as clathrate compounds. Here we investigate the possibility of trapping helium or larger neon guest atoms under pressure within alkali metal oxide and sulfide structures. We find stable helium and neon-bearing compounds at very low pressures. These structures are stabilized by a reduction in volume from incorporation of helium or neon atoms within the antifluorite structure. We predict that NeCs2S could be stable at ambient pressure. Our study suggests a novel class of alkali oxide and sulfide materials incorporating noble gas atoms that might potentially be useful for gas storage.

cond-mat.mtrl-sci↗

arXiv2019

Quantized Epoch-SGD for Communication-Efficient Distributed Learning

Due to its efficiency and ease to implement, stochastic gradient descent (SGD) has been widely used in machine learning. In particular, SGD is one of the most popular optimization methods for distributed learning. Recently, quantized SGD (QSGD), which adopts quantization to reduce the communication cost in SGD-based distributed learning, has attracted much attention. Although several QSGD methods have been proposed, some of them are heuristic without theoretical guarantee, and others have high quantization variance which makes the convergence become slow. In this paper, we propose a new method, called Quantized Epoch-SGD (QESGD), for communication-efficient distributed learning. QESGD compresses (quantizes) the parameter with variance reduction, so that it can get almost the same performance as that of SGD with less communication cost. QESGD is implemented on the Parameter Server framework, and empirical results on distributed deep learning show that QESGD can outperform other state-of-the-art quantization methods to achieve the best performance.

cs.LG↗

arXiv2018

A novel superhard tungsten nitride predicted by machine-learning accelerated crystal structure searching

Transition metal nitrides have been suggested to have both high hardness and good thermal stability with large potential application value, but so far stable superhard transition metal nitrides have not been synthesized. Here, with our newly developed machine-learning accelerated crystal structure searching method, we designed a superhard tungsten nitride, h-WN6, which can be synthesized at pressure around 65 GPa and quenchable to ambient pressure. This h-WN6 is constructed with single-bonded N6 rings and presents ionic-like features, which can be formulated as W2.4+N62.4-. It has a band gap of 1.6 eV at 0 GPa and exhibits an abnormal gap broadening behavior under pressure. Excitingly, this h-WN6 is found to be the hardest among transition metal nitrides known so far (Vickers hardness around 57 GPa) and also has a very high melting temperature (around 1900 K). These predictions support the designing rules and may stimulate future experiments to synthesize superhard material.

cond-mat.mtrl-sci↗

arXiv2018

Feature-Distributed SVRG for High-Dimensional Linear Classification

Linear classification has been widely used in many high-dimensional applications like text classification. To perform linear classification for large-scale tasks, we often need to design distributed learning methods on a cluster of multiple machines. In this paper, we propose a new distributed learning method, called feature-distributed stochastic variance reduced gradient (FD-SVRG) for high-dimensional linear classification. Unlike most existing distributed learning methods which are instance-distributed, FD-SVRG is feature-distributed. FD-SVRG has lower communication cost than other instance-distributed methods when the data dimensionality is larger than the number of data instances. Experimental results on real data demonstrate that FD-SVRG can outperform other state-of-the-art distributed methods for high-dimensional linear classification in terms of both communication cost and wall-clock time, when the dimensionality is larger than the number of instances in training data.

cs.LG↗

arXiv2017

Superhard and Superconducting B6C

Crystal structure searching and ab initio calculations have been used here to explore low-energy structures of boron carbides under high pressure. Under pressures of 85-110 GPa, a metastable B6C with R-3m symmetry is found to be energetically more stable than the mixture of previous B4C and elemental boron. This B6C is a rhombohedral structure and contains mooncake-like B24 clusters with stuffing of C2 pairs. The mechanical and dynamical stabilities of this structure at ambient pressure are confirmed by its elastic constants and phonon dispersions. The bulk modulus and shear modulus of this newly predicted B6C at ambient pressure reach high values of 291 GPa and 272 GPa, respectively. The Vickers hardness is calculated to be around 48 GPa, and its melting temperature at ambient pressure is estimated to be around 2500 K, indicating that this metastable B6C is a potential superhard material with very good thermal stability. Interestingly, this superhard B6C structure is also found to be superconducting and its superconducting critical temperature (Tc) is evaluated to be around 12.5 K at ambient pressure by electron-phonon coupling.

cond-mat.mtrl-sci↗

arXiv2017

Silicon clathrates for photovoltaics predicted by a two-step crystal structure search

Silicon in a cubic diamond structure currently plays a significant role in the photovoltaic industry. However, the intrinsic band structures of crystalline silicon restrict its sunlight conversion efficiency. Recently, a clathrate-like Si-24 has been successfully synthesized, which has a quasi-direct bandgap and sheds light on silicon-based photovoltaics. Here, we proposed a two-step crystal structure search method based on first-principles calculations and explored silicon clathrate structures extensively. First, the guest-host compounds were searched at high pressure, and then, the porous guest-free silicon clathrates were obtained by removing the guest atoms. Using potassium as the guest atom, we identified four metastable silicon clathrate structures, and some of them have bandgaps close to the optimal range of the Shockley-Queisser limit and have a better absorption rate than the cubic diamond silicon. These silicon clathrates may have promising value in photovoltaic applications.

cond-mat.mtrl-sci↗

arXiv2017

Depth Assisted Full Resolution Network for Single Image-based View Synthesis

Researches in novel viewpoint synthesis majorly focus on interpolation from multi-view input images. In this paper, we focus on a more challenging and ill-posed problem that is to synthesize novel viewpoints from one single input image. To achieve this goal, we propose a novel deep learning-based technique. We design a full resolution network that extracts local image features with the same resolution of the input, which contributes to derive high resolution and prevent blurry artifacts in the final synthesized images. We also involve a pre-trained depth estimation network into our system, and thus 3D information is able to be utilized to infer the flow field between the input and the target image. Since the depth network is trained by depth order information between arbitrary pairs of points in the scene, global image features are also involved into our system. Finally, a synthesis layer is used to not only warp the observed pixels to the desired positions but also hallucinate the missing pixels with recorded pixels. Experiments show that our technique performs well on images of various scenes, and outperforms the state-of-the-art techniques.

cs.CV↗

arXiv2017

A coupled mitral valve -- left ventricle model with fluid-structure interaction

Understanding the interaction between the valves and walls of the heart is important in assessing and subsequently treating heart dysfunction. With advancements in cardiac imaging, nonlinear mechanics and computational techniques, it is now possible to explore the mechanics of valve-heart interactions using anatomically and physiologically realistic models. This study presents an integrated model of the mitral valve (MV) coupled to the left ventricle (LV), with the geometry derived from in vivo clinical magnetic resonance images. Numerical simulations using this coupled MV-LV model are developed using an immersed boundary/finite element method. The model incorporates detailed valvular features, left ventricular contraction, nonlinear soft tissue mechanics, and fluid-mediated interactions between the MV and LV wall. We use the model to simulate the cardiac function from diastole to systole, and investigate how myocardial active relaxation function affects the LV pump function. The results of the new model agree with in vivo measurements, and demonstrate that the diastolic filling pressure increases significantly with impaired myocardial active relaxation to maintain the normal cardiac output. The coupled model has the potential to advance fundamental knowledge of mechanisms underlying MV-LV interaction, and help in risk stratification and optimization of therapies for heart diseases.

physics.med-ph↗