arXiv subjects

Chintan Shah

Publications and source records attributed to Chintan Shah.

At least 37 records · Page 2Linked to original sources

arXiv2023

Synthetic DOmain-Targeted Augmentation (S-DOTA) Improves Model Generalization in Digital Pathology

Machine learning algorithms have the potential to improve patient outcomes in digital pathology. However, generalization of these tools is currently limited by sensitivity to variations in tissue preparation, staining procedures and scanning equipment that lead to domain shift in digitized slides. To overcome this limitation and improve model generalization, we studied the effectiveness of two Synthetic DOmain-Targeted Augmentation (S-DOTA) methods, namely CycleGAN-enabled Scanner Transform (ST) and targeted Stain Vector Augmentation (SVA), and compared them against the International Color Consortium (ICC) profile-based color calibration (ICC Cal) method and a baseline method using traditional brightness, color and noise augmentations. We evaluated the ability of these techniques to improve model generalization to various tasks and settings: four models, two model types (tissue segmentation and cell classification), two loss functions, six labs, six scanners, and three indications (hepatocellular carcinoma (HCC), nonalcoholic steatohepatitis (NASH), prostate adenocarcinoma). We compared these methods based on the macro-averaged F1 scores on in-distribution (ID) and out-of-distribution (OOD) test sets across multiple domains, and found that S-DOTA methods (i.e., ST and SVA) led to significant improvements over ICC Cal and baseline on OOD data while maintaining comparable performance on ID data. Thus, we demonstrate that S-DOTA may help address generalization due to domain shift in real world applications.

cs.CV↗

arXiv2023

Charge exchange in X-ray astrophysics

Charge exchange is an atomic process that primarily occurs at interfaces between the neutral and ionized gas. The study of the process has been carried out on three levels: the theoretical calculation of the cross sections, the laboratory measurements of reaction rates and line strengths, and the observational constraints using celestial objects. For a long time in the past, the status of astrophysical observations in the X-ray band lagged behind the other two aspects until the discovery of X-ray from a comet was made in 1996, which changed the research landscape. Recent observational evidence suggests that charge exchange has been seen or can be expected from a surprisingly broad range of locations, from the Earth's exosphere to the large-scale structures of the Universe. The rapid development of high-resolution X-ray spectroscopy, in particular the non-dispersive micro-calorimeters, is paving the way to revolutionary new science possibilities both in the laboratory and astrophysics. This chapter summarizes the current knowledge of charge exchange and its relevance on astrophysics, especially X-ray spectroscopy.

astro-ph.IM↗

arXiv2022

New Measurement Resolves Key Astrophysical Fe XVII Oscillator Strength Problem

One of the most enduring and intensively studied problems of X-ray astronomy is the disagreement of state-of-the art theory and observations for the intensity ratio of two Fe XVII transitions of crucial value for plasma diagnostics, dubbed 3C and 3D. We unravel this conundrum at the PETRA III synchrotron facility by increasing the resolving power two and a half times and the signal-to-noise ratio thousand-fold compared to our previous work. The Lorentzian wings had hitherto been indistinguishable from the background and were thus not modeled, resulting in a biased line-strength estimation. The present experimental oscillator-strength ratio $R_\mathrm{exp}=f_{\mathrm{3C}}/f_{\mathrm{3D}}=3.51(2)_{\mathrm{stat}}(7)_{\mathrm{sys}}$ agrees with our state-of-the-art calculation of $R_\mathrm{th}=3.55(2)$, as well as with some previous theoretical predictions. To further rule out any uncertainties associated with the measured ratio, we also determined the individual natural linewidths and oscillator strengths of 3C and 3D transitions, which also agree well with the theory. This finally resolves the decades-old mystery of Fe XVII oscillator strengths.

physics.atom-ph↗

arXiv2022

Self-training of Machine Learning Models for Liver Histopathology: Generalization under Clinical Shifts

Histopathology images are gigapixel-sized and include features and information at different resolutions. Collecting annotations in histopathology requires highly specialized pathologists, making it expensive and time-consuming. Self-training can alleviate annotation constraints by learning from both labeled and unlabeled data, reducing the amount of annotations required from pathologists. We study the design of teacher-student self-training systems for Non-alcoholic Steatohepatitis (NASH) using clinical histopathology datasets with limited annotations. We evaluate the models on in-distribution and out-of-distribution test data under clinical data shifts. We demonstrate that through self-training, the best student model statistically outperforms the teacher with a $3\%$ absolute difference on the macro F1 score. The best student model also approaches the performance of a fully supervised model trained with twice as many annotations.

cs.CV↗

arXiv2022

X-ray spectra of the Fe-L complex III: systematic uncertainties in the atomic data

There has been a growing request from the X-ray astronomy community for a quantitative estimate of systematic uncertainties originating from the atomic data used in plasma codes. Though there have been several studies looking into atomic data uncertainties using theoretical calculations, in general, there is no commonly accepted solution for this task. We present a new approach for estimating uncertainties in the line emissivities for the current models of collisional plasma, mainly based upon dedicated analysis of observed high resolution spectra of stellar coronae and galaxy clusters. We find that the systematic uncertainties of the observed lines consistently show anti-correlation with the model line fluxes, after properly accounting for the additional uncertainties from the ion concentration calculation. The strong lines in the spectra are in general better reproduced, indicating that the atomic data and modeling of the main transitions are more accurate than those for the minor ones. This underlying anti-correlation is found to be roughly independent on source properties, line positions, ion species, and the line formation processes. We further apply our method to the simulated XRISM and Athena observations of collisional plasma sources and discuss the impact of uncertainties on the interpretation of these spectra. The typical uncertainties are 1-2% on temperature and 3-20% on abundances of O, Ne, Fe, Mg, and Ni.

astro-ph.HE↗

arXiv2022

Uncertainties in Atomic Data for Modeling Astrophysical Charge Exchange Plasmas

Relevant uncertainties on theoretical atomic data are vital to determine the accuracy of plasma diagnostics in a number of areas including in particular the astrophysical study. We present a new calculation of the uncertainties on the present theoretical ion-impact charge exchange atomic data and X-ray spectra based on a set of comparisons with the existing laboratory data obtained in historical merged-beam, cold-target recoil-ion momentum spectroscopy, and electron beam ion traps experiments. The average systematic uncertainties are found to be 35-88% on the total cross sections, and 57-75% on the characteristic line ratios. The model deviation increases as the collision energy decreases. The errors on total cross sections further induce a significant uncertainty to the calculation of ionization balance for low temperature collisional plasmas. Substantial improvements of the atomic database and dedicated laboratory measurements are needed to get the current models ready for the X-ray spectra from the next X-ray spectroscopic mission.

astro-ph.HE↗

arXiv2021

The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification

The BraTS 2021 challenge celebrates its 10th anniversary and is jointly organized by the Radiological Society of North America (RSNA), the American Society of Neuroradiology (ASNR), and the Medical Image Computing and Computer Assisted Interventions (MICCAI) society. Since its inception, BraTS has been focusing on being a common benchmarking venue for brain glioma segmentation algorithms, with well-curated multi-institutional multi-parametric magnetic resonance imaging (mpMRI) data. Gliomas are the most common primary malignancies of the central nervous system, with varying degrees of aggressiveness and prognosis. The RSNA-ASNR-MICCAI BraTS 2021 challenge targets the evaluation of computational algorithms assessing the same tumor compartmentalization, as well as the underlying tumor's molecular characterization, in pre-operative baseline mpMRI data from 2,040 patients. Specifically, the two tasks that BraTS 2021 focuses on are: a) the segmentation of the histologically distinct brain tumor sub-regions, and b) the classification of the tumor's O[6]-methylguanine-DNA methyltransferase (MGMT) promoter methylation status. The performance evaluation of all participating algorithms in BraTS 2021 will be conducted through the Sage Bionetworks Synapse platform (Task 1) and Kaggle (Task 2), concluding in distributing to the top ranked participants monetary awards of $60,000 collectively.

cs.CV↗

arXiv2021

Fe XVII $2p$-$3s$ line ratio diagnostic of shock formation radius in O stars

The $2p$-$3s$ lines of Fe XVII in the X-ray spectrum of the O-type star $ζ$ Puppis exhibit an anomalous (3G + M2)/(3F) line ratio of $\sim$1.4, in comparison with $\sim$2.4 for almost all other collisionally excited astrophysical spectra. Based on the work of Mauche et al. (2001), we conjectured that the strong UV field of $ζ$ Puppis produces the observed ratio by depopulation of metastable $3s$ excited states, and that the ratio can potentially be used as an independent diagnostic of plasma formation radius. We used the Flexible Atomic Code (FAC) collisional-radiative model to model the effect of UV photoexcitation from O stars on the Fe XVII lines. We compared our model calculations to archival spectra of coronal and hot stars from the Chandra HETGS and XMM-Newton RGS to benchmark our calculations for various electron densities and UV field intensities. Our calculations show that UV photoexcitation does not produce a sufficiently large dynamic range in the 3F/(3F + 3G + M2) fraction to explain the difference in the observed ratio between coronal stars and $ζ$ Pup. Thus, this effect likely cannot explain the observed line ratio of $ζ$ Pup, and its origin is still unexplained.

astro-ph.HE↗

arXiv2021

High-resolution Laboratory Measurements of K-shell X-ray Line Polarization and Excitation Cross Sections in Heliumlike S XV Ions

We report measurements of electron-impact excitation cross sections for the strong K-shell n=2-1 transitions in S XV using the LLNL EBIT-I electron beam ion trap, two crystal spectrometers, and the EBIT Calorimeter Spectrometer. The cross sections are determined by direct normalization to the well known cross sections of radiative electron capture, measured simultaneously. Using contemporaneous polarization measurements with the two crystal spectrometers, whose dispersion planes are oriented parallel and perpendicular to the electron beam direction, the polarization of the direct excitation line emission is determined, and in turn the isotropic total cross sections are extracted. We further experimentally investigate various line-formation mechanisms, finding that radiative cascades and collisional inner-shell ionization dominate the degree of linear polarization and total line-emission cross sections of the forbidden line $z$.

physics.atom-ph↗

arXiv2021

Comprehensive Laboratory Measurements Resolving the LMM Dielectronic Recombination Satellite Lines in Ne-like Fe XVII Ions

We investigated experimentally and theoretically dielectronic recombination (DR) populating doubly excited configurations $3l3l'$ (LMM) in Fe XVII, the strongest channel for soft X-ray line formation in this ubiquitous species. We used two different electron beam ion traps and two complementary measurement schemes for preparing the Fe XVII samples and evaluating their purity, observing negligible contamination effects. This allowed us to diagnose the electron density in both EBITs. We compared our experimental resonant energies and strengths with those of previous independent work at a storage ring as well as those of configuration interaction, multiconfiguration Dirac-Fock calculations, and many-body perturbation theory. This last approach showed outstanding predictive power in the comparison with the combined independent experimental results. From these we also inferred DR rate coefficients, unveiling discrepancies from those compiled in the OPEN-ADAS and AtomDB databases.

physics.atom-ph↗

arXiv2020

Observation of strong two-electron--one-photon transitions in few-electron ion

We resonantly excite the $K$ series of O$^{5+}$ and O$^{6+}$ up to principal quantum number $n=11$ with monochromatic x rays, producing $K$-shell holes, and observe their relaxation by soft-x-ray emission. Some photoabsorption resonances of O$^{5+}$ reveal strong two-electron--one-photon (TEOP) transitions. We find that for the $[(1s\,2s)_1\,5p_{3/2}]_{3/2;1/2}$ states, TEOP relaxation is by far stronger than the radiative decay and competes with the usually much faster Auger decay path. This enhanced TEOP decay arises from a strong correlation with the near-degenerate upper states $[(1s\,2p_{3/2})_1\,4s]_{3/2;1/2}$ of a Li-like satellite blend of the He-like $Kα$ transition. Even in three-electron systems, TEOP transitions can play a dominant role, and the present results should guide further research on the ubiquitous and abundant many-electron ions where electronic energy degeneracies are far more common and configuration mixing is stronger.

physics.atom-ph↗

arXiv2020

X-ray spectra of the Fe-L complex II: atomic data constraints from EBIT experiment and X-ray grating observations of Capella

The Hitomi results for the Perseus cluster have shown that accurate atomic models are essential to the success of X-ray spectroscopic missions, and just as important as knowledge on instrumental calibration and astrophysical modeling. Preparing the models requires a multifaceted approach, including theoretical calculations, laboratory measurements, and calibration using real observations. In a previous paper, we presented a calculation of the electron impact cross sections on the transitions forming the Fe-L complex. In the present work, we systematically test the calculation against cross sections of ions measured in an electron beam ion trap experiment. A two-dimensional analysis in the electron beam energies and X-ray photon energies is utilized to disentangle radiative channels following dielectronic recombination, direct electron-impact excitation, and resonant excitation processes in the experimental data. The data calibrated through laboratory measurements are further fed into global modeling of the Chandra grating spectrum of Capella. We investigate and compare the fit quality, as well as sensitivity of the derived physical parameters to the underlying atomic data and the astrophysical plasma modeling. We further list the potential areas of disagreement between the observation and the present calculations, which in turn calls for renewed efforts in theoretical calculations and targeted laboratory measurements.

astro-ph.HE↗

arXiv2020

Finding Patient Zero: Learning Contagion Source with Graph Neural Networks

Locating the source of an epidemic, or patient zero (P0), can provide critical insights into the infection's transmission course and allow efficient resource allocation. Existing methods use graph-theoretic centrality measures and expensive message-passing algorithms, requiring knowledge of the underlying dynamics and its parameters. In this paper, we revisit this problem using graph neural networks (GNNs) to learn P0. We establish a theoretical limit for the identification of P0 in a class of epidemic models. We evaluate our method against different epidemic models on both synthetic and a real-world contact network considering a disease with history and characteristics of COVID-19. % We observe that GNNs can identify P0 close to the theoretical bound on accuracy, without explicit input of dynamics or its parameters. In addition, GNN is over 100 times faster than classic methods for inference on arbitrary graph topologies. Our theoretical bound also shows that the epidemic is like a ticking clock, emphasizing the importance of early contact-tracing. We find a maximum time after which accurate recovery of the source becomes impossible, regardless of the algorithm used.

cs.SI↗

arXiv2020

High Resolution Photoexcitation Measurements Exacerbate the Long-Standing Fe XVII Oscillator Strength Problem

For more than 40 years, most astrophysical observations and laboratory studies of two key soft x-ray diagnostic $2p-3d$ transitions, $3C$ and $3D$, in Fe XVII ions found oscillator strength ratios $f(3C)/f(3D)$ disagreeing with theory, but uncertainties had precluded definitive statements on this much studied conundrum. Here, we resonantly excite these lines using synchrotron radiation at PETRA III, and reach, at a millionfold lower photon intensities, a 10 times higher spectral resolution, and 3 times smaller uncertainty than earlier work. Our final result of $f(3C)/f(3D) = 3.09(8)(6)$ supports many of the earlier clean astrophysical and laboratory observations, while departing by five sigmas from our own newest large-scale ab initio calculations, and excluding all proposed explanations, including those invoking nonlinear effects and population transfers.

physics.atom-ph↗

arXiv2019

Revisiting the Fe XVII line emission problem: laboratory measurements of the 3s-2p and 3d-2p line-formation channels

We determined relative X-ray photon emission cross sections in Fe XVII ions that were mono-energetically excited in an electron beam ion trap. Line formation for the 3s (3s-2p) and 3d (3d-2p) transitions of interest proceeds through dielectronic recombination (DR), direct electron-impact excitation (DE), resonant excitation (RE), and radiative cascades. By reducing the electron-energy spread to a sixth of that of previous works and increasing counting statistics by three orders of magnitude, we account for hitherto unresolved contributions from DR and the little-studied RE process to the 3d transitions, and also for cascade population of the 3s line manifold through forbidden states. We found good agreement with state-of-the-art many-body perturbation theory (MBPT) and distorted-wave (DW) method for the 3s transition, while in the 3d transitions known discrepancies were confirmed. Our results show that DW calculations overestimate the 3d line emission due to DE by ~20%. Inclusion of electron-electron correlation effects through the MBPT method in the DE cross section calculations reduces this disagreement by ~11%. The remaining ~9% in 3d and ~11% in 3s/3d discrepancies are consistent with those found in previous laboratory measurements, solar, and astrophysical observations. Meanwhile, spectral models of opacity, temperature, and turbulence velocity should be adjusted to these experimental cross sections to optimize the accuracy of plasma diagnostics based on these bright soft X-ray lines of Fe XVII.

astro-ph.HE↗

arXiv2019

X-ray spectra of the Fe-L complex

The Hitomi results on the Perseus cluster lead to improvements in our knowledge of atomic physics which are crucial for the precise diagnostic of hot astrophysical plasma observed with high-resolution X-ray spectrometers. However, modeling uncertainties remain, both within but especially beyond Hitomi's spectral window. A major challenge in spectral modeling is the Fe-L spectrum, which is basically a complex assembly of n>2 to n=2 transitions of Fe ions in different ionization states, affected by a range of atomic processes such as collisional excitation, resonant excitation, radiative recombination, dielectronic recombination, and innershell ionization. In this paper we perform a large-scale theoretical calculation on each of the processes with the flexible atomic code (FAC), focusing on ions of Fe XVII to Fe XXIV that form the main body of the Fe-L complex. The new data are found to be consistent within 20% with the recent individual R-matrix calculations for the main Fe-L lines. By further testing the new FAC calculations with the high-quality RGS data from 15 elliptical galaxies and galaxy clusters, we note that the new model gives systematically better fits than the current SPEX v3.04 code, and the mean Fe abundance decreases by 12%, while the O/Fe ratio increases by 16% compared with the results from the current code. Comparing the FAC fit results to those with the R-matrix calculations, we find a temperature-dependent discrepancy of up to ~10% on the Fe abundance between the two theoretical models. Further dedicated tests with both observed spectra and targeted laboratory measurements are needed to resolve the discrepancies, and ultimately, to get the atomic data ready for the next high-resolution X-ray spectroscopy mission.

astro-ph.HE↗

arXiv2019

Unlocking the Capabilities of Future High-Resolution X-ray Spectroscopy Missions Through Laboratory Astrophysics

Thanks to high-resolution and non-dispersive spectrometers onboard future X-ray missions such as XRISM and Athena, we are finally poised to answer important questions about the formation and evolution of galaxies and large-scale structure. However, we currently lack an adequate understanding of many atomic processes behind the spectral features we will soon observe. Large error bars on parameters as critical as transition energies and atomic cross sections can lead to unacceptable uncertainties in the calculations of e.g., elemental abundance, velocity, and temperature. Unless we address these issues, we risk limiting the full scientific potential of these missions. Laboratory astrophysics, which comprises theoretical and experimental studies of the underlying physics behind observable astrophysical processes, is therefore central to the success of these missions.

astro-ph.HE↗

arXiv2018

Resonance strengths for KLL dielectronic recombination of highly charged mercury ions and improved empirical $\boldsymbol{Z}$-scaling law

Theoretical and experimental resonance strengths for KLL dielectronic recombination (DR) into He-, Li-, Be-, and B-like mercury ions are presented, based on state-resolved DR x-ray spectra recorded at the Heidelberg electron beam ion trap. The DR resonance strengths were experimentally extracted by normalizing them to simultaneously recorded radiative recombination signals. The results are compared to state-of-the-art atomic calculations that include relativistic electron-electron correlation and configuration mixing effects. Combining the present data with other existing ones, we derive an improved semi-empirical $Z$-scaling law for DR resonance strength as a function of the atomic number, taking into account higher-order relativistic corrections, which are especially relevant for heavy highly charged ions.

physics.atom-ph↗