arXiv subjects

Saul Kohn

Publications and source records attributed to Saul Kohn.

15 recordsLinked to original sources

arXiv2021

A Pathology Deep Learning System Capable of Triage of Melanoma Specimens Utilizing Dermatopathologist Consensus as Ground Truth

Although melanoma occurs more rarely than several other skin cancers, patients' long term survival rate is extremely low if the diagnosis is missed. Diagnosis is complicated by a high discordance rate among pathologists when distinguishing between melanoma and benign melanocytic lesions. A tool that allows pathology labs to sort and prioritize melanoma cases in their workflow could improve turnaround time by prioritizing challenging cases and routing them directly to the appropriate subspecialist. We present a pathology deep learning system (PDLS) that performs hierarchical classification of digitized whole slide image (WSI) specimens into six classes defined by their morphological characteristics, including classification of "Melanocytic Suspect" specimens likely representing melanoma or severe dysplastic nevi. We trained the system on 7,685 images from a single lab (the reference lab), including the the largest set of triple-concordant melanocytic specimens compiled to date, and tested the system on 5,099 images from two distinct validation labs. We achieved Area Underneath the ROC Curve (AUC) values of 0.93 classifying Melanocytic Suspect specimens on the reference lab, 0.95 on the first validation lab, and 0.82 on the second validation lab. We demonstrate that the PDLS is capable of automatically sorting and triaging skin specimens with high sensitivity to Melanocytic Suspect cases and that a pathologist would only need between 30% and 60% of the caseload to address all melanoma specimens.

eess.IV↗

arXiv2021

HERA Phase I Limits on the Cosmic 21-cm Signal: Constraints on Astrophysics and Cosmology During the Epoch of Reionization

Recently, the Hydrogen Epoch of Reionization Array (HERA) collaboration has produced the experiment's first upper limits on the power spectrum of 21-cm fluctuations at z~8 and 10. Here, we use several independent theoretical models to infer constraints on the intergalactic medium (IGM) and galaxies during the epoch of reionization (EoR) from these limits. We find that the IGM must have been heated above the adiabatic cooling threshold by z~8, independent of uncertainties about the IGM ionization state and the nature of the radio background. Combining HERA limits with galaxy and EoR observations constrains the spin temperature of the z~8 neutral IGM to 27 K < T_S < 630 K (2.3 K < T_S < 640 K) at 68% (95%) confidence. They therefore also place a lower bound on X-ray heating, a previously unconstrained aspects of early galaxies. For example, if the CMB dominates the z~8 radio background, the new HERA limits imply that the first galaxies produced X-rays more efficiently than local ones (with soft band X-ray luminosities per star formation rate constrained to L_X/SFR = { 10^40.2, 10^41.9 } erg/s/(M_sun/yr) at 68% confidence), consistent with expectations of X-ray binaries in low-metallicity environments. The z~10 limits require even earlier heating if dark-matter interactions (e.g., through millicharges) cool down the hydrogen gas. Using a model in which an extra radio background is produced by galaxies, we rule out (at 95% confidence) the combination of high radio and low X-ray luminosities of L_{r,\nu}/SFR > 3.9 x 10^24 W/Hz/(M_sun/yr) and L_X/SFR<10^40 erg/s/(M_sun/yr). The new HERA upper limits neither support nor disfavor a cosmological interpretation of the recent EDGES detection. The analysis framework described here provides a foundation for the interpretation of future HERA results.

astro-ph.CO↗

arXiv2020

The 21 cm-kSZ-kSZ Bispectrum during the Epoch of Reionization

The high-redshift 21 cm signal from the Epoch of Reionization (EoR) is a promising observational probe of the early universe. Current- and next-generation radio interferometers such as the Hydrogen Epoch of Reionization Array (HERA) and Square Kilometre Array (SKA) are projected to measure the 21 cm auto power spectrum from the EoR. Another observational signal of this era is the kinetic Sunyaev-Zel'dovich (kSZ) signal in the cosmic microwave background (CMB), which will be observed by the upcoming Simons Observatory (SO) and CMB-S4 experiments. The 21 cm signal and the contribution to the kSZ from the EoR are expected to be anti-correlated, the former coming from regions of neutral gas in the intergalactic medium and the latter coming from ionized regions. However, the naive cross-correlation between the kSZ and 21 cm maps suffers from a cancellation that occurs because ionized regions are equally likely to be moving toward or away from the observer and so there is no net correlation with the 21 cm signal. We present here an investigation of the 21 cm-kSZ-kSZ bispectrum, which should not suffer the same cancellation as the simple two-point cross-correlation. We show that there is a significant and non-vanishing signal that is sensitive to the reionization history, suggesting the statistic may be used to confirm or infer the ionization fraction as a function of redshift. In the absence of foreground contamination, we forecast that this signal is detectable at high statistical significance with HERA and SO. The bispectrum we study suffers from the fact that the kSZ signal is sensitive only to Fourier modes with long-wavelength line-of-sight components, which are generally lost in the 21 cm data sets owing to foreground contamination. We discuss possible strategies for alleviating this contamination, including an alternative four-point statistic that may help circumvent this issue.

astro-ph.CO↗

arXiv2019

Astro2020 Science White Paper: Insights Into the Epoch of Reionization with the Highly-Redshifted 21-cm Line

The epoch of reionization, when photons from early galaxies ionized the intergalactic medium about a billion years after the Big Bang, is the last major phase transition in the Universe's history. Measuring the characteristics of the transition is important for understanding early galaxies and the cosmic web and for modeling dwarf galaxies in the later Universe. But such measurements require probes of the intergalactic medium itself. Here we describe how the 21-cm line of neutral hydrogen provides a powerful probe of the reionization process and therefore important constraints on both the galaxies and intergalactic absorbers at that time. While existing experiments will make precise statistical measurements over the next decade, we argue that improved 21-cm analysis techniques - allowing imaging of the neutral gas itself - as well as improved theoretical models, are crucial for testing our understanding of this important era.

astro-ph.CO↗

arXiv2019

Astro 2020 Science White Paper: Fundamental Cosmology in the Dark Ages with 21-cm Line Fluctuations

The Dark Ages are the period between the last scattering of the cosmic microwave background and the appearance of the first luminous sources, spanning approximately 1100 < z < 30. The only known way to measure fluctuations in this era is through the 21-cm line of neutral hydrogen. Such observations have enormous potential for cosmology, because they span a large volume while the fluctuations remain linear even on small scales. Observations of 21-cm fluctuations during this era can therefore constrain fundamental aspects of our Universe, including inflation and any exotic physics of dark matter. While the observational challenges to these low-frequency 21-cm observations are enormous, especially from the terrestrial environment, they represent an important goal for cosmology.

astro-ph.CO↗

arXiv2019

Astro2020 Science White Paper: First Stars and Black Holes at Cosmic Dawn with Redshifted 21-cm Observations

The "cosmic dawn" refers to the period of the Universe's history when stars and black holes first formed and began heating and ionizing hydrogen in the intergalactic medium (IGM). Though exceedingly difficult to detect directly, the first stars and black holes can be constrained indirectly through measurements of the cosmic 21-cm background, which traces the ionization state and temperature of intergalactic hydrogen gas. In this white paper, we focus on the science case for such observations, in particular those targeting redshifts z $\gtrsim$ 10 when the IGM is expected to be mostly neutral. 21-cm observations provide a unique window into this epoch and are thus critical to advancing first star and black hole science in the next decade.

astro-ph.CO↗

arXiv2019

Cosmology with the Highly Redshifted 21cm Line

In addition to being a probe of Cosmic Dawn and Epoch of Reionization astrophysics, the 21cm line at $z>6$ is also a powerful way to constrain cosmology. Its power derives from several unique capabilities. First, the 21cm line is sensitive to energy injections into the intergalactic medium at high redshifts. It also increases the number of measurable modes compared to existing cosmological probes by orders of magnitude. Many of these modes are on smaller scales than are accessible via the CMB, and moreover have the advantage of being firmly in the linear regime (making them easy to model theoretically). Finally, the 21cm line provides access to redshifts prior to the formation of luminous objects. Together, these features of 21cm cosmology at $z>6$ provide multiple pathways toward precise cosmological constraints. These include the "marginalizing out" of astrophysical effects, the utilization of redshift space distortions, the breaking of CMB degeneracies, the identification of signatures of relative velocities between baryons and dark matter, and the discovery of unexpected signs of physics beyond the $\Lambda$CDM paradigm at high redshifts.

astro-ph.CO↗

arXiv2019

Optimizing Sparse RFI Prediction using Deep Learning

Radio Frequency Interference (RFI) is an ever-present limiting factor among radio telescopes even in the most remote observing locations. When looking to retain the maximum amount of sensitivity and reduce contamination for Epoch of Reionization studies, the identification and removal of RFI is especially important. In addition to improved RFI identification, we must also take into account computational efficiency of the RFI-Identification algorithm as radio interferometer arrays such as the Hydrogen Epoch of Reionization Array grow larger in number of receivers. To address this, we present a Deep Fully Convolutional Neural Network (DFCN) that is comprehensive in its use of interferometric data, where both amplitude and phase information are used jointly for identifying RFI. We train the network using simulated HERA visibilities containing mock RFI, yielding a known "ground truth" dataset for evaluating the accuracy of various RFI algorithms. Evaluation of the DFCN model is performed on observations from the 67 dish build-out, HERA-67, and achieves a data throughput of 1.6$\times 10^{5}$ HERA time-ordered 1024 channeled visibilities per hour per GPU. We determine that relative to an amplitude only network including visibility phase adds important adjacent time-frequency context which increases discrimination between RFI and Non-RFI. The inclusion of phase when predicting achieves a Recall of 0.81, Precision of 0.58, and $F_{2}$ score of 0.75 as applied to our HERA-67 observations.

astro-ph.IM↗

arXiv2018

Identifying Reionization Sources from 21cm Maps using Convolutional Neural Networks

Active Galactic Nuclei (AGN) and star-forming galaxies are leading candidates for being the luminous sources that reionized our Universe. Next-generation 21cm surveys are promising to break degeneracies between a broad range of reionization models, hence revealing the nature of the source population. While many current efforts are focused on a measurement of the 21cm power spectrum, some surveys will also image the 21cm field during reionization. This provides further information with which to determine the nature of reionizing sources. We create a Convolutional Neural Network (CNN) that is efficiently able to distinguish between 21cm maps that are produced by AGN versus galaxies scenarios with an accuracy of 92-100%, depending on redshift and neutral fraction range. An exception to this is when our Universe is highly ionized, since the source models give near-identical 21cm maps in that case. When adding thermal noise from typical 21cm experiments, the classification accuracy depends strongly on the effectiveness of foreground removal. Our results show that if foregrounds can be removed reasonably well, SKA, HERA and LOFAR should be able to discriminate between source models with greater accuracy at a fixed redshift. Only future SKA 21cm surveys are promising to break the degeneracies in the power spectral analysis.

astro-ph.CO↗

arXiv2018

Reionization Models Classifier using 21cm Map Deep Learning

Next-generation 21cm observations will enable imaging of reionization on very large scales. These images will contain more astrophysical and cosmological information than the power spectrum, and hence providing an alternative way to constrain the contribution of different reionizing sources populations to cosmic reionization. Using Convolutional Neural Networks, we present a simple network architecture that is sufficient to discriminate between Galaxy-dominated versus AGN-dominated models, even in the presence of simulated noise from different experiments such as the HERA and SKA.

astro-ph.CO↗

arXiv2018

Improved 21 cm Epoch Of Reionization Power Spectrum Measurements with a Hybrid Foreground Subtraction and Avoidance Technique

Observations of the 21cm Epoch of Reionization (EoR) signal are dominated by Galactic and extragalactic foregrounds. The need for foreground removal has led to the development of two main techniques, often referred to as "foreground avoidance" and "foreground subtraction." Avoidance is associated with filtering foregrounds in Fourier space, while subtraction uses an explicit foreground model that is removed. Using 1088 hours of data from the 64-element PAPER array, we demonstrate that subtraction of a foreground model prior to delay-space foreground filtering results in a modest but measurable improvement of the performance of the filter. This proof-of-concept result shows that improvement stems from the reduced dynamic range requirements needed for the foreground filter: subtraction of a foreground model reduces the total foreground power, so for a fixed dynamic range, the filter can push towards fainter limits. We also find that the choice of window function used in the foreground filter can have an appreciable affect on the performance near the edges of the observing band. We demonstrate these effects using a smaller 3 hour sampling of data from the MWA, and find that the hybrid filtering and subtraction removal approach provides similar improvements across the band as seen in the case with PAPER-64.

astro-ph.IM↗

arXiv2017

Galactic wind X-ray heating of the intergalactic medium during the Epoch of Reionization

The diffuse soft X-ray emissivity from galactic winds is computed during the Epoch of Reionization (EoR). We consider two analytic models, a pressure-driven wind and a superbubble model, and a 3D cosmological simulation including gas dynamics from the First Billion Years (FiBY) project. The analytic models are normalized to match the diffuse X-ray emissivity of star-forming galaxies in the nearby Universe. The cosmological simulation uses physically motivated star formation and wind prescriptions, and includes radiative transfer corrections. The models and the simulation all are found to produce sufficient heating of the Intergalactic Medium to be detectable by current and planned radio facilities through 21 cm measurements during the EoR. While the analytic models predict a 21 cm emission signal relative to the Cosmic Microwave Background sets in by $z_{\rm trans} \simeq 8 - 10$, the predicted signal in the FiBY simulation remains in absorption until reionization completes. The 21 cm absorption differential brightness temperature reaches a minimum of $\Delta T \simeq -130$ to $-200$ mK, depending on model. Allowing for additional heat from high mass X-ray binaries pushes the transition to emission to $z_{\rm trans} \simeq 10 - 12$, with shallower absorption signatures having a minimum of $\Delta T \simeq -110$ to $-140$ mK. The 21 cm signal may be a means of distinguishing between the wind models, with the superbubble model favouring earlier reheating. While an early transition to emission may indicate X-ray binaries dominate the reheating, a transition to emission as early as $z_{\rm trans} > 12$ would suggest the presence of additional heat sources.

astro-ph.CO↗

arXiv2016

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software.

astro-ph.IM↗

arXiv2016

The Hydrogen Epoch of Reionization Array Dish II: Characterization of Spectral Structure with Electromagnetic Simulations and its science Implications

We use time-domain electromagnetic simulations to determine the spectral characteristics of the Hydrogen Epoch of Reionization Arrays (HERA) antenna. These simulations are part of a multi-faceted campaign to determine the effectiveness of the dish's design for obtaining a detection of redshifted 21 cm emission from the epoch of reionization. Our simulations show the existence of reflections between HERA's suspended feed and its parabolic dish reflector that fall below -40 dB at 150 ns and, for reasonable impedance matches, have a negligible impact on HERA's ability to constrain EoR parameters. It follows that despite the reflections they introduce, dishes are effective for increasing the sensitivity of EoR experiments at relatively low cost. We find that electromagnetic resonances in the HERA feed's cylindrical skirt, which is intended to reduce cross coupling and beam ellipticity, introduces significant power at large delays ($-40$ dB at 200 ns) which can lead to some loss of measurable Fourier modes and a modest reduction in sensitivity. Even in the presence of this structure, we find that the spectral response of the antenna is sufficiently smooth for delay filtering to contain foreground emission at line-of-sight wave numbers below $k_\parallel \lesssim 0.2$ $h$Mpc$^{-1}$, in the region where the current PAPER experiment operates. Incorporating these results into a Fisher Matrix analysis, we find that the spectral structure observed in our simulations has only a small effect on the tight constraints HERA can achieve on parameters associated with the astrophysics of reionization.

astro-ph.CO↗

arXiv2015

New Limits on Polarized Power Spectra at 126 and 164 MHz: Relevance to Epoch of Reionization Measurements

Polarized foreground emission is a potential contaminant of attempts to measure the fluctuation power spectrum of highly redshifted 21 cm HI emission from the epoch of reionization. Using the Donald C. Backer Precision Array for Probing the Epoch of Reionization (PAPER), we present limits on the observed power spectra of all four Stokes parameters in two frequency bands, centered at 126 MHz ($z=10.3$) and 164 MHz ($z=7.66$) for a three-month observing campaign of a 32-antenna deployment, for which unpolarized power spectrum results have been reported at $z=7.7$ (Parsons et al 2014) and $7.5 < z < 10.5$ (Jacobs et al 2014). The power spectra in this paper are processed in the same way as in those works, and show no definitive detection of polarized power. This non-detection appears to be largely due to the suppression of polarized power by ionospheric rotation measure fluctuations, which strongly affect Stokes Q and U. We are able to show that the net effect of polarized leakage is a negligible contribution at the levels of of the limits reported in Parsons et al 2014 and Jacobs et al 2014.

astro-ph.CO↗