arXiv subjects

Yuan Zhao

Publications and source records attributed to Yuan Zhao.

At least 55 records · Page 3Linked to original sources

arXiv2022

Program Repair: Automated vs. Manual

Various automated program repair (APR) techniques have been proposed to fix bugs automatically in the last decade. Although recent researches have made significant progress on the effectiveness and efficiency, it is still unclear how APR techniques perform with human intervention in a real debugging scenario. To bridge this gap, we conduct an extensive study to compare three state-of-the-art APR tools with manual program repair, and further investigate whether the assistance of APR tools (i.e., repair reports) can improve manual program repair. To that end, we recruit 20 participants for a controlled experiment, resulting in a total of 160 manual repair tasks and a questionnaire survey. The experiment reveals several notable observations that (1) manual program repair may be influenced by the frequency of repair actions sometimes; (2) APR tools are more efficient in terms of debugging time, while manual program repair tends to generate a correct patch with fewer attempts; (3) APR tools can further improve manual program repair regarding the number of correctly-fixed bugs, while there exists a negative impact on the patch correctness; (4) participants are used to consuming more time to identify incorrect patches, while they are still misguided easily; (5) participants are positive about the tools' repair performance, while they generally lack confidence about the usability in practice. Besides, we provide some guidelines for improving the usability of APR tools (e.g., the misleading information in reports and the observation of feedback).

cs.SE↗

arXiv2021

Streaming Variational Monte Carlo

Nonlinear state-space models are powerful tools to describe dynamical structures in complex time series. In a streaming setting where data are processed one sample at a time, simultaneous inference of the state and its nonlinear dynamics has posed significant challenges in practice. We develop a novel online learning framework, leveraging variational inference and sequential Monte Carlo, which enables flexible and accurate Bayesian joint filtering. Our method provides an approximation of the filtering posterior which can be made arbitrarily close to the true filtering distribution for a wide class of dynamics models and observation models. Specifically, the proposed framework can efficiently approximate a posterior over the dynamics using sparse Gaussian processes, allowing for an interpretable model of the latent dynamics. Constant time complexity per sample makes our approach amenable to online learning scenarios and suitable for real-time applications.

stat.ML↗

arXiv2021

One-bit Spectrum Sensing with the Eigenvalue Moment Ratio Approach

One-bit analog-to-digital converter (ADC), performing signal sampling as an extreme simple comparator, is an overwhelming technology for spectrum sensing due to its low-cost, low-power consumptions and high sampling rate. In this letter, we propose a novel one-bit sensing approach based on the eigenvalue moment ratio (EMR), which has been proved to be highly efficient for conventional multi-antenna spectrum sensing in $\infty$-bit situation. Particularly, we determine the asymptotic distribution of one-bit EMR under null hypothesis via the central limited theorem (CLT), allowing us to perform spectrum sensing with one-bit samples directly. Theoretical and simulation analysis show the new approach can provide reasonably good sensing performance at a low hardware cost.

cs.IT↗

arXiv2021

COSINE: A Web Server for Clonal and Subclonal Structure Inference and Evolution in Cancer Genomics

Cancers evolve from mutation of a single cell with sequential clonal and subclonal expansion of somatic mutation acquisition. Inferring clonal and subclonal structures from bulk or single cell tumor genomic sequencing data has a huge impact on cancer evolution studies. Clonal state and mutational order can provide detailed insight into tumor origin and its future development. In the past decade, a variety of methods have been developed for subclonal reconstruction using bulk tumor sequencing data. As these methods have been developed in different programming languages and using different input data formats, their use and comparison can be problematic. Therefore, we established a web server for clonal and subclonal structure inference and evolution of cancer genomic data (COSINE), which included 12 popular subclonal reconstruction methods. We decomposed each method via a detailed workflow of single processing steps with a user-friendly interface. To the best of our knowledge, this is the first web server providing online subclonal inference, including the most popular subclonal reconstruction methods. COSINE is freely accessible at www.clab-cosine.net or http://bio.rj.run:48996/cun-web.

q-bio.GN↗

arXiv2021

Segmentation of common and internal carotid arteries from 3D ultrasound images using adaptive triple U-Net

Objective: Vessel-wall-volume (VWV) and localized vessel-wall-thickness (VWT) measured from 3D ultrasound (US) carotid images are sensitive to anti-atherosclerotic effects of medical/dietary treatments. VWV and VWT measurements require the lumen-intima (LIB) and media-adventitia boundaries (MAB) at the common and internal carotid arteries (CCA and ICA). However, most existing segmentation techniques were capable of automating only CCA segmentation. An approach capable of segmenting the MAB and LIB from the CCA and ICA was required to accelerate VWV and VWT quantification. Methods: Segmentation for CCA and ICA were performed independently using the proposed two-channel U-Net, which was driven by a novel loss function known as the adaptive triple Dice loss (ADTL). A test-time augmentation (TTA) approach is used, in which segmentation was performed three times based on axial images and its flipped versions; the final segmentation was generated by pixel-wise majority voting. Results: Experiments involving 224 3DUS volumes produce a Dice-similarity-coefficient (DSC) of 95.1%$\pm$4.1% and 91.6%$\pm$6.6% for the MAB and LIB, in the CCA, respectively, and 94.2%$\pm$3.3% and 89.0%$\pm$8.1% for the MAB and LIB, in the ICA, respectively. TTA and ATDL independently contributed to a statistically significant improvement to all boundaries except the LIB in ICA. The total time required to segment the entire 3DUS volume (CCA+ICA) is 1.4s. Conclusion: The proposed two-channel U-Net with ADTL and TTA can segment the CCA and ICA accurately and efficiently from the 3DUS volume. Significance: Our approach has the potential to accelerate the transition of 3DUS measurements of carotid atherosclerosis to clinical research.

eess.IV↗

arXiv2020

Incorporating Gas Pipeline Leakage Failure Modes in Risk Evaluation of Electricity-Gas Integrated Energy Systems

In the existing literatures for the risk evaluation of electricity-gas integrated energy system (EGIES), the impacts of gas leakage in pipelines are ignored. This paper presents a method to incorporate the failure modes of gas pipeline leakage in EGIES risk evaluation. A Markov state transition model of gas pipeline with multi-state and multi-mode transition process, and a bi-level Monte Carlo sampling method for this model are developed. A stochastic topology change based network model of EGIES considering the pipeline leakage failure modes is presented. The risk indices for EGIES based on the load shedding, including those specifically for gas leakage risks, are also proposed. An EGIES with a modified RBTS and a 7-node gas system was used to demonstrate an application of the proposed method and models. The results indicate that pipeline leakage failures have significant impacts on the risk of EGIES. Ignoring pipeline leakage failures in the risk evaluation of EGIES will result in an overly underestimation of system risk and most likely a misleading conclusion in system planning.

eess.SY↗

arXiv2020

$P^2$ Net: Augmented Parallel-Pyramid Net for Attention Guided Pose Estimation

We propose an augmented Parallel-Pyramid Net ($P^2~Net$) with feature refinement by dilated bottleneck and attention module. During data preprocessing, we proposed a differentiable auto data augmentation ($DA^2$) method. We formulate the problem of searching data augmentaion policy in a differentiable form, so that the optimal policy setting can be easily updated by back propagation during training. $DA^2$ improves the training efficiency. A parallel-pyramid structure is followed to compensate the information loss introduced by the network. We innovate two fusion structures, i.e. Parallel Fusion and Progressive Fusion, to process pyramid features from backbone network. Both fusion structures leverage the advantages of spatial information affluence at high resolution and semantic comprehension at low resolution effectively. We propose a refinement stage for the pyramid features to further boost the accuracy of our network. By introducing dilated bottleneck and attention module, we increase the receptive field for the features with limited complexity and tune the importance to different feature channels. To further refine the feature maps after completion of feature extraction stage, an Attention Module ($AM$) is defined to extract weighted features from different scale feature maps generated by the parallel-pyramid structure. Compared with the traditional up-sampling refining, $AM$ can better capture the relationship between channels. Experiments corroborate the effectiveness of our proposed method. Notably, our method achieves the best performance on the challenging MSCOCO and MPII datasets.

cs.CV↗

arXiv2020

Rescuing neural spike train models from bad MLE

The standard approach to fitting an autoregressive spike train model is to maximize the likelihood for one-step prediction. This maximum likelihood estimation (MLE) often leads to models that perform poorly when generating samples recursively for more than one time step. Moreover, the generated spike trains can fail to capture important features of the data and even show diverging firing rates. To alleviate this, we propose to directly minimize the divergence between neural recorded and model generated spike trains using spike train kernels. We develop a method that stochastically optimizes the maximum mean discrepancy induced by the kernel. Experiments performed on both real and synthetic neural data validate the proposed approach, showing that it leads to well-behaving models. Using different combinations of spike train kernels, we show that we can control the trade-off between different features which is critical for dealing with model-mismatch.

stat.ML↗

arXiv2020

Non-parametric generalized linear model

A fundamental problem in statistical neuroscience is to model how neurons encode information by analyzing electrophysiological recordings. A popular and widely-used approach is to fit the spike trains with an autoregressive point process model. These models are characterized by a set of convolutional temporal filters, whose subsequent analysis can help reveal how neurons encode stimuli, interact with each other, and process information. In practice a sufficiently rich but small ensemble of temporal basis functions needs to be chosen to parameterize the filters. However, obtaining a satisfactory fit often requires burdensome model selection and fine tuning the form of the basis functions and their temporal span. In this paper we propose a nonparametric approach for jointly inferring the filters and hyperparameters using the Gaussian process framework. Our method is computationally efficient taking advantage of the sparse variational approximation while being flexible and rich enough to characterize arbitrary filters in continuous time lag. Moreover, our method automatically learns the temporal span of the filter. For the particular application in neuroscience, we designed priors for stimulus and history filters useful for the spike trains. We compare and validate our method on simulated and real neural spike train data.

stat.ML↗

arXiv2020

Machine Learning in Population and Public Health

Research in population and public health focuses on the mechanisms between different cultural, social, and environmental factors and their effect on the health, of not just individuals, but communities as a whole. We present here a very brief introduction into research in these fields, as well as connections to existing machine learning work to help activate the machine learning community on such topics and highlight specific opportunities where machine learning, public and population health may synergize to better achieve health equity.

cs.CY↗

arXiv2020

Variational online learning of neural dynamics

New technologies for recording the activity of large neural populations during complex behavior provide exciting opportunities for investigating the neural computations that underlie perception, cognition, and decision-making. Nonlinear state space models provide an interpretable signal processing framework by combining an intuitive dynamical system with a probabilistic observation model, which can provide insights into neural dynamics, neural computation, and development of neural prosthetics and treatment through feedback control. It brings the challenge of learning both latent neural state and the underlying dynamical system because neither is known for neural systems a priori. We developed a flexible online learning framework for latent nonlinear state dynamics and filtered latent states. Using the stochastic gradient variational Bayes approach, our method jointly optimizes the parameters of the nonlinear dynamical system, the observation model, and the black-box recognition model. Unlike previous approaches, our framework can incorporate non-trivial distributions of observation noise and has constant time and space complexity. These features make our approach amenable to real-time applications and the potential to automate analysis and experimental design in ways that testably track and modify behavior using stimuli designed to influence learning.

stat.ML↗

arXiv2020

Augmented Parallel-Pyramid Net for Attention Guided Pose-Estimation

The target of human pose estimation is to determine body part or joint locations of each person from an image. This is a challenging problems with wide applications. To address this issue, this paper proposes an augmented parallel-pyramid net with attention partial module and differentiable auto-data augmentation. Technically, a parallel pyramid structure is proposed to compensate the loss of information. We take the design of parallel structure for reverse compensation. Meanwhile, the overall computational complexity does not increase. We further define an Attention Partial Module (APM) operator to extract weighted features from different scale feature maps generated by the parallel pyramid structure. Compared with refining through upsampling operator, APM can better capture the relationship between channels. At last, we proposed a differentiable auto data augmentation method to further improve estimation accuracy. We define a new pose search space where the sequences of data augmentations are formulated as a trainable and operational CNN component. Experiments corroborate the effectiveness of our proposed method. Notably, our method achieves the top-1 accuracy on the challenging COCO keypoint benchmark and the state-of-the-art results on the MPII datasets.

cs.CV↗

arXiv2020

On the Role of Dataset Quality and Heterogeneity in Model Confidence

Safety-critical applications require machine learning models that output accurate and calibrated probabilities. While uncalibrated deep networks are known to make over-confident predictions, it is unclear how model confidence is impacted by the variations in the data, such as label noise or class size. In this paper, we investigate the role of the dataset quality by studying the impact of dataset size and the label noise on the model confidence. We theoretically explain and experimentally demonstrate that, surprisingly, label noise in the training data leads to under-confident networks, while reduced dataset size leads to over-confident models. We then study the impact of dataset heterogeneity, where data quality varies across classes, on model confidence. We demonstrate that this leads to heterogenous confidence/accuracy behavior in the test data and is poorly handled by the standard calibration algorithms. To overcome this, we propose an intuitive heterogenous calibration technique and show that the proposed approach leads to improved calibration metrics (both average and worst-case errors) on the CIFAR datasets.

cs.LG↗

arXiv2020

Classical Inputs and Measurements Enable Phase Sensitivity beyond the Shot-Noise Limit

Coherent-state-based phase estimation is a fruitful testbed for the field of precision measurements since coherent states are robust to decoherence when compared with exotic quantum states. The seminal work done by Caves (https://doi.org/10.1103/PhysRevD.23.1693 , Phys. Rev. D 23, 1693 (1981)) stated that the phase sensitivity of a U(2) interferometer fed with a coherent state is limited by the shot-noise limit (SNL). In this Letter, we demonstrate that this bound is not conclusive sensitivity limit and can be broken when the measurement includes an external phase reference. The SNL can be surpassed by a factor of $\sqrt{2}$ and the validity is supported through the calculation of quantum Fisher information. Additionally, we discuss other single-mode Gaussian inputs of which sensitivities are beyond the SNL. Our work shows potential applications for many metological scenarios, particularly when the measured samples immersed in great lossy environments or can withstand bright illumination.

quant-ph↗

arXiv2019

Single-shot Precise Ranging using Twisted Light

Over the past decade, optical orbital angular momentum (OAM) modes were shown to offer advantages in optical information acquisition. Here, we introduce a new scheme for optical ranging in which depth is estimated through the angular rotation of petal-like patterns produced by superposition of OAM modes. Uncertainty of depth estimation in our strategy depends on how fast the petal-like pattern rotates and how precisely the rotation angle can be estimated. The impact of these two factors on ranging accuracy are analyzed in presence of noise. We show that focusing the probe beam provides a quadratic enhancement on ranging accuracy because rotation speed of the beam is inversely proportional to the square of beam radius. Uncertainty of depth estimation is also proportional to uncertainty of rotation estimation, which can be optimized by picking proper OAM superposition. Finally, we unveil the possibility of optical ranging for scattering surface with uncertainties of few micrometers under noise. Unlike existing methods which rely on continuous detection for a period of time to achieve such ranging accuracy, our scheme needs only single-shot measurement.

physics.optics↗

arXiv2019

Control of Structured Light Enables Nearly Perfect Noise-filtering

The performance of laser-based active sensing has been severely limited by two types of noise: electrical noise, stemming from elements; optical noise, laser jamming from an eavesdropper and background from environment. Conventional methods to filter optical noise take advantage of the differences between signal and noise in time, wavelength, and polarization. However, they may be limited when the noise and signal share the same information on these degrees of freedoms (DoFs). In order to overcome this drawback, we experimentally demonstrate a groundbreaking noise-filtering method by controlling orbital angular momentum (OAM) to distinguish signal from noise. We provide a proof-of-principle experiment and discuss the dependence of azimuthal index of OAM and detection aperture on signal-to-noise ratio (SNR). Our results suggest that using OAM against noise is an efficient method, offering a new route to optical sensing immersed in high-level noise.

physics.optics↗

arXiv2019

Conclusive nonlinear phase sensitivity limit for a Mach-Zehnder interferometer with single-mode non-vacuum inputs

Many works have stated that nonlinear interactions can improve phase sensitivity beyond the Heisenberg limit scaling of $1/N$ with $N$ being the mean photon number. This raises some open questions---among them the conclusive sensitivity limits with respect to single-mode inputs. Namely, when one of two inputs is vacuum, is there a shot-noise-style sensitivity bound on a nonlinear Mach-Zehnder interferometer? Within the reach of second-order nonlinear phase shifts, we make an attempt to provide an answer to this question. Based upon phase-averaging approach, this puzzle is partially resolved with careful calculations of the quantum Fisher information regarding three kinds of common inputs: Gaussian states, squeezed number states, and Schrödinger cat states. The results suggest that shot-noise-style sensitivity limit is no longer available, and the ideal candidate is squeezed vacuum.

quant-ph↗

arXiv2019

A nearly optimal and robust protocol for nonlinear phase estimation using coherent states

We propose a protocol for the second-order nonlinear phase estimation with a coherent state as input and balanced homodyne detection as measurement strategy. The sensitivity is sub-Heisenberg limit, which scales as $N^{-3/2}$ for $N$ photons on average. By ruling out hidden resources in quantum Fisher information, the fundamental sensitivity limit is recalculated and compared to the optimal sensitivity of our protocol. In addition, we investigate the effect of photon loss on sensitivity, and discuss the robustness of measurement strategy. The results indicate that our protocol is nearly optimal and robust.

quant-ph↗