arXiv subjects

Chun Li

Publications and source records attributed to Chun Li.

At least 55 records · Page 3Linked to original sources

arXiv2024

A versatile framework for attitude tuning of beamlines at advanced light sources

Aside from regular beamline experiments at light sources, the preparation steps before these experiments are also worth systematic consideration in terms of automation; a representative category in these steps is attitude tuning, which typically appears in names like beam focusing, sample alignment etc. With the goal of saving time and manpower in both writing and using in mind, a Mamba-based attitude-tuning framework is created. It supports flexible input/output ports, easy integration of diverse evaluation functions, and free selection of optimisation algorithms; with the help from Mamba's infrastructure, machine learning (ML) and artificial intelligence (AI) technologies can also be readily integrated. The tuning of a polycapillary lens and of an X-ray emission spectrometer are given as examples for the general use of this framework, featuring powerful command-line interfaces (CLIs) and friendly graphical user interfaces (GUIs) that allow comfortable human-in-the-loop control. The tuning of a Raman spectrometer demonstrates more specialised use of the framework with customised optimisation algorithms. With similar applications in mind, our framework is estimated to be capable of fulfilling a majority of attitude-tuning needs. Also reported is a virtual-beamline mechanism based on easily customisable simulated detectors and motors, which facilitates both testing for developers and training for users.

physics.ins-det↗

arXiv2024

The Stellar Abundances and Galactic Evolution Survey (SAGES) III -- The g/r/i-band Data Release

The Stellar Abundances and Galactic Evolution Survey (SAGES) is a multi-band survey that covers the northern sky area of ~12000 deg2. Nanshan One-meter Wide-field Telescope (NOWT) of Xinjiang Astronomical Observatory (XAO) carried out observations on g/r/i bands. We present here the survey strategy, data processing, catalog construction, and database schema. The observations of NOWT started in 2016 August and was completed in 2018 January, total 17827 frames were obtained and ~4600 deg2 sky areas were covered. In this paper, we released the catalog of the data in the g/r/i bands observed with NOWT. In total, there are 109,197,578 items of the source records. The catalog is the supplement for the SDSS for the bright end, and the combination of our catalog and these catalogs could be helpful for source selections for other surveys and the Milky Way sciences, e.g., white dwarf candidates and stellar flares.

astro-ph.GA↗

arXiv2024

Probability-scale residuals for event-time data

The probability-scale residual (PSR) is defined as $E\{sign(y, Y^*)\}$, where $y$ is the observed outcome and $Y^*$ is a random variable from the fitted distribution. The PSR is particularly useful for ordinal and censored outcomes for which fitted values are not available without additional assumptions. Previous work has defined the PSR for continuous, binary, ordinal, right-censored, and current status outcomes; however, development of the PSR has not yet been considered for data subject to general interval censoring. We develop extensions of the PSR, first to mixed-case interval-censored data, and then to data subject to several types of common censoring schemes. We derive the statistical properties of the PSR and show that our more general PSR encompasses several previously defined PSR for continuous and censored outcomes as special cases. The performance of the residual is illustrated in real data from the Caribbean, Central, and South American Network for HIV Epidemiology.

stat.ME↗

arXiv2024

An open-source, adaptive solver for particle-resolved simulations with both subcycling and non-subcycling methods

We present the IAMReX, an adaptive and parallel solver for particle-resolved simulations on the multi-level grid. The fluid equations are solved using a finite-volume scheme on the block-structured semi-staggered grids with both subcycling and non-subcycling methods. The particle-fluid interaction is resolved using the multidirect forcing immersed boundary method. The associated Lagrangian markers used to resolve fluid-particle interface only exist on the finest-level grid, which greatly reduces memory usage. The volume integrals are numerically calculated to capture the free motion of particles accurately, and the repulsive potential model is also included to account for the particle-particle collision. We demonstrate the versatility, accuracy, and efficiency of the present multi-level framework by simulating fluid-particle interaction problems with various types of kinematic constraints. The cluster of monodisperse particles case is presented at the end to show the capability of the current solver in handing with multiple particles. The source code and testing cases used in this work can be accessed at https://github.com/ruohai0925/IAMR/tree/development. Input scripts and raw postprocessing data are also available for reproducing all results.

physics.flu-dyn↗

arXiv2024

Candidate Members of the VMP/EMP Disk System of the Galaxy from the SkyMapper and SAGES Surveys

Photometric stellar surveys now cover a large fraction of the sky, probe to fainter magnitudes than large-scale spectroscopic surveys, and are relatively free from the target-selection biases often associated with such studies. Photometric-metallicity estimates that include narrow/medium-band filters can achieve comparable accuracy and precision to existing low-resolution spectroscopic surveys such as SDSS/SEGUE and LAMOST. Here we report on an effort to identify likely members of the Galactic disk system among the very metal-poor (VMP; [Fe/H] $\leq$ --2) and extremely metal-poor (EMP; [Fe/H] $\leq$ --3) stars. Our analysis is based on an initial sample of $\sim11.5$ million stars with full space motions selected from the SkyMapper Southern Survey (SMSS) and Stellar Abundance and Galactic Evolution Survey (SAGES). After applying a number of quality cuts to obtain the best available metallicity and dynamical estimates, we analyze a total of $\sim$5.86 million stars in the combined SMSS/SAGES sample. We employ two techniques that, depending on the method, identify between 876 and 1,476 VMP stars (6.9%-11.7% of all VMP stars) and between 40 and 59 EMP stars (12.4%-18.3% of all EMP stars) that appear to be members of the Galactic disk system on highly prograde orbits (v$_ϕ > 150$ km/s). The total number of candidate VMP/EMP disk-like stars is 1,496, the majority of which have low orbital eccentricities, ecc $\le 0.4$; many have ecc $\le 0.2$. The large fractions of VMP/EMP stars associated with the Milky Way disk system strongly suggest the presence of an early forming ``primordial" disk.

astro-ph.GA↗

arXiv2024

Unveiling Incomplete Modality Brain Tumor Segmentation: Leveraging Masked Predicted Auto-Encoder and Divergence Learning

Brain tumor segmentation remains a significant challenge, particularly in the context of multi-modal magnetic resonance imaging (MRI) where missing modality images are common in clinical settings, leading to reduced segmentation accuracy. To address this issue, we propose a novel strategy, which is called masked predicted pre-training, enabling robust feature learning from incomplete modality data. Additionally, in the fine-tuning phase, we utilize a knowledge distillation technique to align features between complete and missing modality data, simultaneously enhancing model robustness. Notably, we leverage the Holder pseudo-divergence instead of the KLD for distillation loss, offering improve mathematical interpretability and properties. Extensive experiments on the BRATS2018 and BRATS2020 datasets demonstrate significant performance enhancements compared to existing state-of-the-art methods.

eess.IV↗

arXiv2024

Semi-Supervised Disease Classification based on Limited Medical Image Data

In recent years, significant progress has been made in the field of learning from positive and unlabeled examples (PU learning), particularly in the context of advancing image and text classification tasks. However, applying PU learning to semi-supervised disease classification remains a formidable challenge, primarily due to the limited availability of labeled medical images. In the realm of medical image-aided diagnosis algorithms, numerous theoretical and practical obstacles persist. The research on PU learning for medical image-assisted diagnosis holds substantial importance, as it aims to reduce the time spent by professional experts in classifying images. Unlike natural images, medical images are typically accompanied by a scarcity of annotated data, while an abundance of unlabeled cases exists. Addressing these challenges, this paper introduces a novel generative model inspired by Hölder divergence, specifically designed for semi-supervised disease classification using positive and unlabeled medical image data. In this paper, we present a comprehensive formulation of the problem and establish its theoretical feasibility through rigorous mathematical analysis. To evaluate the effectiveness of our proposed approach, we conduct extensive experiments on five benchmark datasets commonly used in PU medical learning: BreastMNIST, PneumoniaMNIST, BloodMNIST, OCTMNIST, and AMD. The experimental results clearly demonstrate the superiority of our method over existing approaches based on KL divergence. Notably, our approach achieves state-of-the-art performance on all five disease classification benchmarks. By addressing the limitations imposed by limited labeled data and harnessing the untapped potential of unlabeled medical images, our novel generative model presents a promising direction for enhancing semi-supervised disease classification in the field of medical image analysis.

eess.IV↗

arXiv2023

Progress and outlook on advanced fly scans based on Mamba

Development related to PandABox-based fly scans is an important part of the active work on Mamba, the software framework for beamline experiments at the High Energy Photon Source (HEPS); presented in this paper is the progress of our development, and some outlook for advanced fly scans based on knowledge learned during the process. By treating fly scans as a collaboration between a few loosely coupled subsystems - motors / mechanics, detectors / data processing, sequencer devices like PandABox - systematic analyses of issues in fly scans are conducted. Interesting products of these analyses include a general-purpose software-based fly-scan mechanism, a general way to design undulator-monochromator fly scans, a sketch of how to practically implement online tuning of fly-scan behaviours based on processing of the data acquired, and many more. Based on the results above, an architectural discussion on >=10kHz fly scans is given.

physics.ins-det↗

arXiv2023

PandA(Box) flies on Bluesky: maintainable and user-friendly fly scans with Mamba at HEPS

Purpose: Fly scans are indispensible in many experiments at the High Energy Photon Source (HEPS). PandABox, the main platform to implement fly scans at HEPS, needs to be integrated into Mamba, the experiment control system developed at HEPS based on Bluesky. Methods: In less than 600 lines of easily customisable and extensible backend code, provided are full control of PandABox's TCP server in native ophyd, automated configuration (also including wiring) of "PandA blocks" for constant-speed mapping experiments of various dimensions, as well as generation of scans deliberately fragmented to deal with hardware limits in numbers of exposure frames or sequencer table entries. Results: The upper-level control system for PandABox has been ported to Bluesky, enabling the combination of both components' flexibility in fly-scan applications. Based on this backend, a user-friendly Mamba frontend is developed for X-ray fluorescence (XRF) mapping experiments, which provides fully online visual feedback.

physics.ins-det↗

arXiv2023

Rank Intraclass Correlation for Clustered Data

Clustered data are common in biomedical research. Observations in the same cluster are often more similar to each other than to observations from other clusters. The intraclass correlation coefficient (ICC), first introduced by R. A. Fisher, is frequently used to measure this degree of similarity. However, the ICC is sensitive to extreme values and skewed distributions, and depends on the scale of the data. It is also not applicable to ordered categorical data. We define the rank ICC as a natural extension of Fisher's ICC to the rank scale, and describe its corresponding population parameter. The rank ICC is simply interpreted as the rank correlation between a random pair of observations from the same cluster. We also extend the definition when the underlying distribution has more than two hierarchies. We describe estimation and inference procedures, show the asymptotic properties of our estimator, conduct simulations to evaluate its performance, and illustrate our method in three real data examples with skewed data, count data, and three-level ordered categorical data.

stat.ME↗

arXiv2023

Photometric calibration of the Stellar Abundance and Galactic Evolution Survey (SAGES): Nanshan One-meter Wide-field Telescope g, r, and i band imaging data

In this paper, a total of approximately 2.6 million dwarfs were constructed as standard stars, with an accuracy of about 0.01-0.02 mag for each band, by combining spectroscopic data from the Large Sky Area Multi-Object Fiber Spectroscopic Telescope Data Release 7, photometric data from the corrected Gaia Early Data Release 3, and photometric metallicities. Using the spectroscopy based stellar color regression method (SCR method) and the photometric-based SCR method (SCR' method), we performed the relative calibration of the Nanshan One-meter Wide-field Telescope imaging data. Based on the corrected Pan-STARRS DR1 photometry, the absolute calibration was also performed. In the photometric calibration process, we analyzed the dependence of the calibration zero points on different images (observation time), different gates of the CCD detector, and different CCD positions. We found that the stellar flat and the relative gain between different gates depend on time. The amplitude of gain variation in three channels is approximately 0.5%-0.7% relative to the other channel, with a maximum value of 4%. In addition, significant spatial variations of the stellar flat fitting residual are found and corrected. Using repeated sources in the adjacent images, we checked and discovered internal consistency of about 1-2 mmag in all the filters. Using the PS1 magnitudes synthesized by Gaia DR3 BP/RP spectra by the synthetic photometry method, we found that the photometric calibration uniformity is about 1-2 mmag for all the bands, at a spatial resolution of 1.3 degree. A detailed comparison between the spectroscopy-based SCR and photometric-based SCR method magnitude offsets was performed, and we achieved an internal consistency precision of about 2 mmag or better with resolutions of 1.3 degree for all the filters. Which is mainly from the position-dependent errors of the E(B-V) used in SCR' method.

astro-ph.SR↗

arXiv2023

Beyond spectroscopy. II. Stellar parameters for over twenty million stars in the northern sky from SAGES DR1 and Gaia DR3

We present precise photometric estimates of stellar parameters, including effective temperature, metallicity, luminosity classification, distance, and stellar age, for nearly 26 million stars using the methodology developed in the first paper of this series, based on the stellar colors from the Stellar Abundances and Galactic Evolution Survey (SAGES) DR1 and Gaia EDR3. The optimal design of stellar-parameter sensitive $uv$ filters by SAGES has enabled us to determine photometric-metallicity estimates down to $-3.5$, similar to our previous results with the SkyMapper Southern Survey (SMSS), yielding a large sample of over five million metal-poor (MP; [Fe/H]$\le -1.0$) stars and nearly one million very metal-poor (VMP; [Fe/H]$\le -2.0$) stars. The typical precision is around $0.1$ dex for both dwarf and giant stars with [Fe/H]$>-1.0$, and 0.15-0.25/0.3-0.4 dex for dwarf/giant stars with [Fe/H]$<-1.0$. Using the precise parallax measurements and stellar colors from Gaia, effective temperature, luminosity classification, distance and stellar age are further derived for our sample stars. This huge data set in the Northern sky from SAGES, together with similar data in the Southern sky from SMSS, will greatly advance our understanding of the Milky Way, in particular its formation and evolution.

astro-ph.GA↗

arXiv2023

The Stellar Abundances and Galactic Evolution Survey (SAGES) -- -- I. General Description and the First Data Release (DR1)

The Stellar Abundances and Galactic Evolution Survey (SAGES) of the northern sky is a specifically-designed multi-band photometric survey aiming to provide reliable stellar parameters with accuracy comparable to those from low-resolution optical spectra. It was carried out with the 2.3-m Bok telescope of Steward Observatory and three other telescopes. The observations in the $u_s$ and $v_s$ passband produced over 36,092 frames of images in total, covering a sky area of $\sim9960$ degree$^2$. The median survey completeness of all observing fields for the two bands are of $u_{\rm s}=20.4$ mag and $v_s=20.3$ mag, respectively, while the limiting magnitudes with signal-to-noise ratio (S/N) of 100 are $u_s\sim17$ mag and $v_s\sim18$ mag, correspondingly. We combined our catalog with the data release 1 (DR1) of the first of Panoramic Survey Telescope And Rapid Response System (Pan-STARRS1, PS1) catalog, and obtained a total of 48,553,987 sources which have at least one photometric measurement in each of the SAGES $u_s$ and $v_s$ and PS1 $grizy$ passbands, which is the DR1 of SAGES and it will be released in our paper. We compare our $gri$ point-source photometry with those of PS1 and found an RMS scatter of $\sim2$% in difference of PS1 and SAGES for the same band. We estimated an internal photometric precision of SAGES to be on the order of $\sim1$%. Astrometric precision is better than $0^{\prime\prime}.2$ based on comparison with the DR1 of Gaia mission. In this paper, we also describe the final end-user database, and provide some science applications.

astro-ph.GA↗

arXiv2023

Asymptotic Properties for Cumulative Probability Models for Continuous Outcomes

Regression models for continuous outcomes often require a transformation of the outcome, which the user either specify {\it a priori} or estimate from a parametric family. Cumulative probability models (CPMs) nonparametrically estimate the transformation and are thus a flexible analysis approach for continuous outcomes. However, it is difficult to establish asymptotic properties for CPMs due to the potentially unbounded range of the transformation. Here we show asymptotic properties for CPMs when applied to slightly modified data where the outcomes are censored at the ends. We prove uniform consistency of the estimated regression coefficients and the estimated transformation function over the non-censored region, and describe their joint asymptotic distribution. We show with simulations that results from this censored approach and those from the CPM on the original data are similar when a small fraction of data are censored. We reanalyze a dataset of HIV-positive patients with CPMs to illustrate and compare the approaches.

stat.ME↗

arXiv2023

Exploring Functional Photonic Devices made from a Chiral Metal-Organic Framework Material by a Multiscale Computational Method

Electronic circular dichroism is an important optical phenomenon offering insights into chiral molecular materials. On the other hand, metal-organic frameworks (MOFs) are a novel group of crystalline porous thin-film materials that provide tailor-made chemical and physical properties by carefully selecting their building units. Combining these two aspects of contemporary material research and integrating chiral molecules into MOFs promises devices with unprecedented functionality. However, considering the nearly unlimited degrees of freedom concerning the choice of materials and the geometrical details of the possibly structured films, we urgently need to complement advanced experimental methods with equally strong modeling techniques. Most notably, these modeling techniques must cope with the challenge that the material and devices thereof cover size scales from Ångströms to mm. In response to that need, we outline a computational workflow that seamlessly combines quantum chemical methods to capture the properties of individual molecules with optical simulations to capture the properties of functional devices made from these molecular materials. We concentrate on chiral properties and apply our work to UiO-67-BINOL MOFs, for which experimental results are available to benchmark the results of our simulations and explore the optical properties of cavities and metasurfaces made from that chiral material.

cond-mat.mtrl-sci↗

arXiv2022

Analyzing Clustered Continuous Response Variables with Ordinal Regression Models

Continuous response variables often need to be transformed to meet regression modeling assumptions; however, finding the optimal transformation is challenging and results may vary with the choice of transformation. When a continuous response variable is measured repeatedly for a subject or the continuous responses arise from clusters, it is more challenging to model the continuous response data due to correlation within clusters. We extend a widely used ordinal regression model, the cumulative probability model (CPM), to fit clustered continuous response variables based on generalized estimating equation (GEE) methods for ordinal responses. With our approach, estimates of marginal parameters, cumulative distribution functions (CDFs), expectations, and quantiles conditional on covariates can be obtained without pre-transformation of the potentially skewed continuous response data. Computational challenges arise with large numbers of distinct values of the continuous response variable, and we propose two feasible and computationally efficient approaches to fit CPMs for clustered continuous response variables with different working correlation structures. We study finite sample operating characteristics of the estimators via simulation, and illustrate their implementation with two data examples. One studies predictors of CD4:CD8 ratios in an HIV study. The other uses data from The Lung Health Study to investigate the contribution of a single nucleotide polymorphism to lung function decline.

stat.ME↗

arXiv2022

Fitting Semiparametric Cumulative Probability Models for Big Data

Cumulative probability models (CPMs) are a robust alternative to linear models for continuous outcomes. However, they are not feasible for very large datasets due to elevated running time and memory usage, which depend on the sample size, the number of predictors, and the number of distinct outcomes. We describe three approaches to address this problem. In the divide-and-combine approach, we divide the data into subsets, fit a CPM to each subset, and then aggregate the information. In the binning and rounding approaches, the outcome variable is redefined to have a greatly reduced number of distinct values. We consider rounding to a decimal place and rounding to significant digits, both with a refinement step to help achieve the desired number of distinct outcomes. We show with simulations that these approaches perform well and their parameter estimates are consistent. We investigate how running time and peak memory usage are influenced by the sample size, the number of distinct outcomes, and the number of predictors. As an illustration, we apply the approaches to a large publicly available dataset investigating matrix multiplication runtime with nearly one million observations.

stat.CO↗

arXiv2022

Addressing Detection Limits with Semiparametric Cumulative Probability Models

Detection limits (DLs), where a variable is unable to be measured outside of a certain range, are common in research. Most approaches to handle DLs in the response variable implicitly make parametric assumptions on the distribution of data outside DLs. We propose a new approach to deal with DLs based on a widely used ordinal regression model, the cumulative probability model (CPM). The CPM is a type of semiparametric linear transformation model. CPMs are rank-based and can handle mixed distributions of continuous and discrete outcome variables. These features are key for analyzing data with DLs because while observations inside DLs are typically continuous, those outside DLs are censored and generally put into discrete categories. With a single lower DL, the CPM assigns values below the DL as having the lowest rank. When there are multiple DLs, the CPM likelihood can be modified to appropriately distribute probability mass. We demonstrate the use of CPMs with simulations and two HIV data examples. The first example models a biomarker in which 15% of observations are below a DL. The second uses multi-cohort data to model viral load, where approximately 55% of observations are outside DLs which vary across sites and over time.

stat.ME↗