arXiv subjects

Heng Li

Publications and source records attributed to Heng Li.

At least 181 records · Page 10Linked to original sources

arXiv2022

SOFFLFM: Super-resolution optical fluctuation Fourier light-field microscopy

Fourier light-field microscopy (FLFM) uses a micro-lens array (MLA) to segment the Fourier Plane of the microscopic objective lens to generate multiple two-dimensional perspective views, thereby reconstructing the three-dimensional(3D) structure of the sample using 3D deconvolution calculation without scanning. However, the resolution of FLFM is still limited by diffraction, and furthermore, dependent on the aperture division. In order to improve its resolution, a Super-resolution optical fluctuation Fourier light field microscopy (SOFFLFM) was proposed here, in which the Sofi method with ability of super-resolution was introduced into FLFM. SOFFLFM uses higher-order cumulants statistical analysis on an image sequence collected by FLFM, and then carries out 3D deconvolution calculation to reconstruct the 3D structure of the sample. Theoretical basis of SOFFLFM on improving resolution was explained and then verified with simulations. Simulation results demonstrated that SOFFLFM improved lateral and axial resolution by more than sqrt(2) and 2 times in the 2nd and 4th order accumulations, compared with that of FLFM.

physics.optics↗

arXiv2022

Generating non-jumps from a known one

Let $r\ge 2$ be an integer. The real number $α\in [0,1]$ is a jump for $r$ if there exists a constant $c > 0$ such that for any $ε>0$ and any integer $m \geq r$, there exists an integer $n_0(ε, m)$ satisfying any $r$-uniform graph with $n\ge n_0(ε, m)$ vertices and density at least $α+ε$ contains a subgraph with $m$ vertices and density at least $α+c$. A result of Erdős, Stone and Simonovits implies that every $α\in [0,1)$ is a jump for $r=2$. Erdős asked whether the same is true for $r\ge 3$. Frankl and Rödl gave a negative answer by showing that $1-\frac{1}{l^{r-1}}$ is not a jump for $r$ if $r\ge 3$ and $l>2r$. After that, more non-jumps are found using a method of Frankl and Rödl. In this note, we show a method to construct maps $f \colon [0,1] \to [0,1]$ that preserve non-jumps, if $α$ is a non-jump for $r$ given by the method of Frankl and Rödl, then $f(α)$ is also a non-jump for $r$. We use these maps to study hypergraph Turán densities and answer a question posed by Grosu.

math.CO↗

arXiv2022

Fast sequence to graph alignment using the graph wavefront algorithm

Motivation: A pan-genome graph represents a collection of genomes and encodes sequence variations between them. It is a powerful data structure for studying multiple similar genomes. Sequence-to-graph alignment is an essential step for the construction and the analysis of pan-genome graphs. However, existing algorithms incur runtime proportional to the product of sequence length and graph size, making them inefficient for aligning long sequences against large graphs. Results: We propose the graph wavefront alignment algorithm (Gwfa), a new method for aligning a sequence to a sequence graph. Although the worst-case time complexity of Gwfa is the same as the existing algorithms, it is designed to run faster for closely matching sequences, and its runtime in practice often increases only moderately with the edit distance of the optimal alignment. On four real datasets, Gwfa is up to four orders of magnitude faster than other exact sequence-to-graph alignment algorithms. We also propose a graph pruning heuristic on top of Gwfa, which can achieve an additional $\sim$10-fold speedup on large graphs. Availability: Gwfa code is accessible at https://github.com/lh3/gwfa.

q-bio.GN↗

arXiv2022

Singularity-Avoidance Prescribed Performance Attitude Tracking of Spacecraft

The attitude tracking problem with preassigned performance requirements has earned tremendous interest in recent years, and the Prescribed Performance Control (PPC) scheme is often adopted to tackle this problem. Nevertheless, traditional PPC schemes have inherent problems, which the solution still lacks, such as the singularity problem when the state constraint is violated and the potential over-control problem when the state trajectory approaches the constraint boundary. This paper proposes a Singularity-Avoidance Prescribed Performance Control scheme (SAPPC) to deal with these problems. A novel shear mapping-based error transformation is proposed to provide a globally non-singular error transformation procedure, while a time-varying constraint boundary is employed to exert appropriate constraint strength at different control stages, alleviating the potential instability caused by the over-control problem. Besides, a novel piece-wise reference performance function (RPF) is constructed to provide a relevant reference trajectory for the state responding signals, allowing precise control of the system's responding behavior. Based on the proposed SAPPC scheme, a backstepping controller is developed, with the predefined-time stability technique and the dynamic surface control technique employed to enhance the controller's robustness and performance. Finally, theoretical analysis and numerical simulation results are presented to validate the proposed control scheme's effectiveness and robustness.

eess.SY↗

arXiv2022

Structure-consistent Restoration Network for Cataract Fundus Image Enhancement

Fundus photography is a routine examination in clinics to diagnose and monitor ocular diseases. However, for cataract patients, the fundus image always suffers quality degradation caused by the clouding lens. The degradation prevents reliable diagnosis by ophthalmologists or computer-aided systems. To improve the certainty in clinical diagnosis, restoration algorithms have been proposed to enhance the quality of fundus images. Unfortunately, challenges remain in the deployment of these algorithms, such as collecting sufficient training data and preserving retinal structures. In this paper, to circumvent the strict deployment requirement, a structure-consistent restoration network (SCR-Net) for cataract fundus images is developed from synthesized data that shares an identical structure. A cataract simulation model is firstly designed to collect synthesized cataract sets (SCS) formed by cataract fundus images sharing identical structures. Then high-frequency components (HFCs) are extracted from the SCS to constrain structure consistency such that the structure preservation in SCR-Net is enforced. The experiments demonstrate the effectiveness of SCR-Net in the comparison with state-of-the-art methods and the follow-up clinical applications. The code is available at https://github.com/liamheng/ArcNet-Medical-Image-Enhancement.

eess.IV↗

arXiv2022

Studying the Practices of Deploying Machine Learning Projects on Docker

Docker is a containerization service that allows for convenient deployment of websites, databases, applications' APIs, and machine learning (ML) models with a few lines of code. Studies have recently explored the use of Docker for deploying general software projects with no specific focus on how Docker is used to deploy ML-based projects. In this study, we conducted an exploratory study to understand how Docker is being used to deploy ML-based projects. As the initial step, we examined the categories of ML-based projects that use Docker. We then examined why and how these projects use Docker, and the characteristics of the resulting Docker images. Our results indicate that six categories of ML-based projects use Docker for deployment, including ML Applications, MLOps/ AIOps, Toolkits, DL Frameworks, Models, and Documentation. We derived the taxonomy of 21 major categories representing the purposes of using Docker, including those specific to models such as model management tasks (e.g., testing, training). We then showed that ML engineers use Docker images mostly to help with the platform portability, such as transferring the software across the operating systems, runtimes such as GPU, and language constraints. However, we also found that more resources may be required to run the Docker images for building ML-based software projects due to the large number of files contained in the image layers with deeply nested directories. We hope to shed light on the emerging practices of deploying ML software projects using containers and highlight aspects that should be improved.

cs.SE↗

arXiv2022

A comparative study of non-deep learning, deep learning, and ensemble learning methods for sunspot number prediction

Solar activity has significant impacts on human activities and health. One most commonly used measure of solar activity is the sunspot number. This paper compares three important non-deep learning models, four popular deep learning models, and their five ensemble models in forecasting sunspot numbers. In particular, we propose an ensemble model called XGBoost-DL, which uses XGBoost as a two-level nonlinear ensemble method to combine the deep learning models. Our XGBoost-DL achieves the best forecasting performance (RMSE = 25.70 and MAE = 19.82) in the comparison, outperforming the best non-deep learning model SARIMA (RMSE = 54.11 and MAE = 45.51), the best deep learning model Informer (RMSE = 29.90 and MAE = 22.35) and the NASA's forecast (RMSE = 48.38 and MAE = 38.45). Our XGBoost-DL forecasts a peak sunspot number of 133.47 in May 2025 for Solar Cycle 25 and 164.62 in November 2035 for Solar Cycle 26, similar to but later than the NASA's at 137.7 in October 2024 and 161.2 in December 2034. An open-source Python package of our XGBoost-DL for the sunspot number prediction is available at https://github.com/yd1008/ts_ensemble_sunspot.

astro-ph.SR↗

arXiv2022

Understanding Quantum Software Engineering Challenges An Empirical Study on Stack Exchange Forums and GitHub Issues

With the advance in quantum computing, quantum software becomes critical for exploring the full potential of quantum computing systems. Recently, quantum software engineering (QSE) becomes an emerging area attracting more and more attention. However, it is not clear what are the challenges and opportunities of quantum computing facing the software engineering community. This work aims to understand the QSE-related challenges perceived by developers. We perform an empirical study on Stack Exchange forums where developers post-QSE-related questions & answers and Github issue reports where developers raise QSE-related issues in practical quantum computing projects. Based on an existing taxonomy of question types on Stack Overflow, we first perform a qualitative analysis of the types of QSE-related questions asked on Stack Exchange forums. We then use automated topic modeling to uncover the topics in QSE-related Stack Exchange posts and GitHub issue reports. Our study highlights some particularly challenging areas of QSE that are different from that of traditional software engineering, such as explaining the theory behind quantum computing code, interpreting quantum program outputs, and bridging the knowledge gap between quantum computing and classical computing, as well as their associated opportunities.

cs.SE↗

arXiv2022

Bug Characteristics in Quantum Software Ecosystem

With the advance in quantum computing in recent years, quantum software becomes vital for exploring the full potential of quantum computing systems. Quantum programming is different from classical programming, for example, the state of a quantum program is probabilistic in nature, and a quantum computer is error-prone due to the instability of quantum mechanisms. Therefore, the characteristics of bugs in quantum software projects may be very different from that of classical software projects. This work aims to understand the characteristics of bugs in quantum software projects, in order to provide insights to help devise effective testing and debugging mechanisms. To achieve this goal, we conduct an empirical study on the bug reports of 125 quantum software projects. We observe that quantum software projects are more buggy than classical software projects and that quantum project bugs are more costly to fix than classical project bugs. We also identify the types of the bugs and the quantum programming components where they occurred. Our study shows that the bugs are spread across different components, but quantum-specific bugs particularly appear in the compiler, gate operation, and state preparation components. The three most occurring types of bugs are Program anomaly bugs, Configuration bugs, and Data type and structure bugs. Our study highlights some particularly challenging areas in quantum software development, such as the lack of scientific quantum computation libraries that implement comprehensive mathematical functions for quantum computing. Quantum developers also seek specialized data manipulation libraries for quantum software engineering like Numpy for quantum computing. Our findings also provide insights for future work to advance the quantum program development, testing, and debugging of quantum software, such as providing tooling support for debugging low-level circuits.

cs.SE↗

arXiv2022

On the Importance of Performing App Analysis Within Peer Groups

The competing nature of the app market motivates us to shift our focus on apps that provide similar functionalities and directly compete with each other (i.e., peer apps). In this work, we study the ratings and the review text of 100 Android apps across 10 peer app groups. We highlight the importance of performing peer-app analysis by showing that it can provide a unique perspective over performing a global analysis of apps (i.e., mixing apps from multiple categories). First, we observe that comparing user ratings within peer groups can provide very different results from comparing user ratings from a global perspective. Then, we show that peer-app analysis provides a different perspective to spot the dominant topics in the user reviews, and to understand the impact of the topics on user ratings. Our findings suggest that future efforts may pay more attention to performing and supporting app analysis from a peer group context. For example, app store owners may consider an additional rating mechanism that normalizes app ratings within peer groups, and future research may help developers understand the characteristics of specific peer groups and prioritize their efforts.

cs.SE↗

arXiv2022

FB-MSTCN: A Full-Band Single-Channel Speech Enhancement Method Based on Multi-Scale Temporal Convolutional Network

In recent years, deep learning-based approaches have significantly improved the performance of single-channel speech enhancement. However, due to the limitation of training data and computational complexity, real-time enhancement of full-band (48 kHz) speech signals is still very challenging. Because of the low energy of spectral information in the high-frequency part, it is more difficult to directly model and enhance the full-band spectrum using neural networks. To solve this problem, this paper proposes a two-stage real-time speech enhancement model with extraction-interpolation mechanism for a full-band signal. The 48 kHz full-band time-domain signal is divided into three sub-channels by extracting, and a two-stage processing scheme of `masking + compensation' is proposed to enhance the signal in the complex domain. After the two-stage enhancement, the enhanced full-band speech signal is restored by interval interpolation. In the subjective listening and word accuracy test, our proposed model achieves superior performance and outperforms the baseline model overall by 0.59 MOS and 4.0% WAcc for the non-personalized speech denoising task.

eess.AS↗

arXiv2022

An Annotation-free Restoration Network for Cataractous Fundus Images

Cataracts are the leading cause of vision loss worldwide. Restoration algorithms are developed to improve the readability of cataract fundus images in order to increase the certainty in diagnosis and treatment for cataract patients. Unfortunately, the requirement of annotation limits the application of these algorithms in clinics. This paper proposes a network to annotation-freely restore cataractous fundus images (ArcNet) so as to boost the clinical practicability of restoration. Annotations are unnecessary in ArcNet, where the high-frequency component is extracted from fundus images to replace segmentation in the preservation of retinal structures. The restoration model is learned from the synthesized images and adapted to real cataract images. Extensive experiments are implemented to verify the performance and effectiveness of ArcNet. Favorable performance is achieved using ArcNet against state-of-the-art algorithms, and the diagnosis of ocular fundus diseases in cataract patients is promoted by ArcNet. The capability of properly restoring cataractous images in the absence of annotated data promises the proposed algorithm outstanding clinical practicability.

eess.IV↗

arXiv2022

Intrinsic spin-momentum dynamics of surface electromagnetic waves in complex dispersive system

Spin-momentum locking is an intrinsic property of surface electromagnetic fields and its study has led to the discovery of photonic spin lattices and diverse applications. Previously, dispersion was ignored in the spin-momentum locking, giving rise to abnormal phenomena contradictory to the physical realities. Here, we formulate four dispersive spin-momentum equations for surface waves, revealing universally that the transverse spin vector is locked with the momentum. The locking property obeys the right-hand rule in the dielectric but the left-hand rule in the dispersive metal/magnetic materials. In addition to the dispersion, the structural features can affect the spin-momentum locking significantly. Remarkably, an extraordinary longitudinal spin originating from the coupling polarization ellipticity is uncovered even for the purely polarized state. We further demonstrate the spin-momentum locking properties with diverse photonic topological lattices by engineering the rotating symmetry. The findings open up opportunities for designing robust nanodevices with practical importance in chiral quantum optics.

physics.optics↗

arXiv2021

Metagenome assembly of high-fidelity long reads with hifiasm-meta

Current metagenome assemblers developed for short sequence reads or noisy long readswere not optimized for accurate long reads. Here we describe hifiasm-meta, a new metagenome assembler that exploits the high accuracy of recent data. Evaluated on seven empirical datasets, hifiasm-meta reconstructed tens to hundreds of complete circular bacterial genomes per dataset, consistently outperforming other metagenome assemblers.

q-bio.GN↗

arXiv2021

Constructing Sub-scale Surrogate Model for Proppant Settling in Inclined Fractures from Simulation Data with Multi-fidelity Neural Network

Particle settling in inclined channels is an important phenomenon that occurs during hydraulic fracturing of shale gas production. Generally, in order to accurately simulate the large-scale (field-scale) proppant transport process, constructing a fast and accurate sub-scale proppant settling model, or surrogate model, becomes a critical issue, since mapping between physical parameters and proppant settling velocity is complex. Previously, particle settling has usually been investigated via high-fidelity experiments and meso-scale numerical simulations, both of which are time-consuming. In this work, a new method is proposed and utilized, i.e., the multi-fidelity neural network (MFNN), to construct a settling surrogate model, which could utilize both high-fidelity and low-fidelity (thus, less expensive) data. The results demonstrate that constructing the settling surrogate with the MFNN can reduce the need for high-fidelity data and thus computational cost by 80%, while the accuracy lost is less than 5% compared to a high-fidelity surrogate. Moreover, the investigated particle settling surrogate is applied in macro-scale proppant transport simulation, which shows that the settling model is significant to proppant transport and yields accurate results. This opens novel pathways for rapidly predicting proppant settling velocity in reservoir applications.

physics.flu-dyn↗

arXiv2021

Robust haplotype-resolved assembly of diploid individuals without parental data

Routine single-sample haplotype-resolved assembly remains an unresolved problem. Here we describe a new algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to produce a haplotype-resolved assembly without the sequencing of parents. Applied to human and other vertebrate samples, our algorithm consistently outperforms existing single-sample assembly pipelines and generates assemblies of comparable quality to the best pedigree-based assemblies.

q-bio.GN↗

arXiv2021

New strategies to improve minimap2 alignment accuracy

Summary: We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly repetitive regions and align through insertions or deletions up to 100kb by default, addressing major weakness in minimap2 v2.18 or earlier. Availability and implementation: https://github.com/lh3/minimap2

q-bio.GN↗

arXiv2021

Two-Grid Domain Decomposition Methods for the Coupled Stokes-Darcy System

In this paper, we propose two novel Robin-type domain decomposition methods based on the two-grid techniques for the coupled Stokes-Darcy system. Our schemes firstly adopt the existing Robin-type domain decomposition algorithm to obtain the coarse grid approximate solutions. Then two modified domain decomposition methods are further constructed on the fine grid by utilizing the framework of two-grid methods to enhance computational efficiency, via replacing some interface terms by the coarse grid information. The natural idea of using the two-grid frame to optimize the domain decomposition method inherits the best features of both methods and can overcome some of the domain decomposition deficits. The resulting schemes can be implemented easily using many existing mature solvers or codes in a flexible way, which are much effective under smaller mesh sizes or some realistic physical parameters. Moreover, several error estimates are carried out to show the stability and convergence of the schemes. Finally, three numerical experiments are performed and compared with the classical two-grid method, which verifies the validation and efficiency of the proposed algorithms.

math.NA↗