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We show how to efficiently sample the joint posterior of two non-covariant experiments with a large set of nuisance parameters. Specifically, we train an ensemble of normalizing flows to learn the posterior distribution of both experiments. Once trained, we can use the flows to reweight $\mathcal{O} (10^9)$ samples from both measurements to compute the joint posterior in seconds -- saving up to $\mathcal{O}(1)$ ton of $\text{CO}_2$ per Monte Carlo run. Using this new technique we find joint constraints between the Dark Energy Survey $3 \times 2$ point measurement, South Pole Telescope and Planck CMB lensing and a BOSS direct fit full shape analyses, for the first time. We find $\Omega_{\rm m} = 0.32^{+0.01}_{-0.01}$ and $S_8 = 0.79 ^ {+0.01}_ {-0.01}$. We release a public package called {\tt CombineHarvesterFlow} (https://github.com/pltaylor16/CombineHarvesterFlow) which performs these calculations., Comment: 10 pages, 6 figures. Accepted to The Open Journal Of Astrophysics

The first year of data from the Dark Energy Spectroscopic Instrument (DESI) contains the largest set of Lyman-$\alpha$ (Ly$\alpha$) forest spectra ever observed. This data, collected in the DESI Data Release 1 (DR1) sample, has been used to measure the Baryon Acoustic Oscillation (BAO) feature at redshift $z=2.33$. In this work, we use a set of 150 synthetic realizations of DESI DR1 to validate the DESI 2024 Ly$\alpha$ forest BAO measurement. The synthetic data sets are based on Gaussian random fields using the log-normal approximation. We produce realistic synthetic DESI spectra that include all major contaminants affecting the Ly$\alpha$ forest. The synthetic data sets span a redshift range $1.8

We present a publicly-available code to generate sets of mock Lyman-$\alpha$ (\lya) forest data that have realistic large-scale correlations including those due to the Baryonic Acoustic Oscillations (BAO). The primary purpose of these mocks is to test the analysis procedures of the Extended Baryon Oscillation Survey (eBOSS) and the Dark Energy Spectroscopy Instrument (DESI) surveys. The transmitted flux fraction, $F(\lambda)$, of background quasars due to \lya\ absorption in the intergalactic medium (IGM) is simulated using the Fluctuating Gunn-Petterson Approximation (FGPA) applied to Gaussian random fields produced through the use of fast Fourier transforms (FFT). The output includes the IGM-\lya\ transmitted flux fraction along quasar lines of sight and a catalog of high-column-density systems appropriately placed at high-density regions of the IGM. This output serves as input to additional code that superimposes the IGM tranmission on realistic quasar spectra, adds absorption by high-column-density systems and metals, and simulates instrumental transmission and noise. Redshift space distortions (RSD) of the flux correlations are implemented by including the large-scale velocity-gradient field in the FGPA resulting in a correlation function of $F(\lambda)$ that can be accurately predicted. One hundred realizations have been produced over the 14,000 deg$^2$ DESI survey footprint with 100 quasars per deg$^{2}$. The analysis of these realizations shows that the correlations of $F(\lambda)$ follows the prediction within the accuracy of eBOSS survey. The most time-consuming part of the mock production occurs before application of the FGPA, and the existing pre-FGPA forests can be used to easily produce new mock sets with modified redshift-dependent bias parameters or observational conditions, Comment: accepted by JCAP

The Lyman-$\alpha$ (Ly$\alpha$) three-dimensional correlation functions have been widely used to perform cosmological inference using the baryon acoustic oscillation (BAO) scale. While the traditional inference approach employs a data vector with several thousand data points, we apply near-maximal score compression down to tens of compressed data elements. We show that carefully constructed additional data beyond those linked to each inferred model parameter are required to preserve meaningful goodness-of-fit tests that guard against unknown systematics, and to avoid information loss due to non-linear parameter dependencies. We demonstrate, on suites of realistic mocks and DR16 data from the Extended Baryon Oscillation Spectroscopic Survey, that our compression approach is lossless and unbiased, yielding a posterior that is indistinguishable from that of the traditional analysis. As an early application, we investigate the impact of a covariance matrix estimated from a limited number of mocks, which is only well-conditioned in compressed space., Comment: Matches version published in MNRAS

We present the first measurements of Lyman-$\alpha$ (Ly$\alpha$) forest correlations using early data from the Dark Energy Spectroscopic Instrument (DESI). We measure the auto-correlation of Ly$\alpha$ absorption using 88,509 quasars at $z>2$, and its cross-correlation with quasars using a further 147,899 tracer quasars at $z\gtrsim1.77$. Then, we fit these correlations using a 13-parameter model based on linear perturbation theory and find that it provides a good description of the data across a broad range of scales. We detect the BAO peak with a signal-to-noise ratio of $3.8\sigma$, and show that our measurements of the auto- and cross-correlations are fully-consistent with previous measurements by the Extended Baryon Oscillation Spectroscopic Survey (eBOSS). Even though we only use here a small fraction of the final DESI dataset, our uncertainties are only a factor of 1.7 larger than those from the final eBOSS measurement. We validate the existing analysis methods of Ly$\alpha$ correlations in preparation for making a robust measurement of the BAO scale with the first year of DESI data.

The full-shape correlations of the Lyman alpha (Ly$\alpha$) forest contain a wealth of cosmological information through the Alcock-Paczy\'{n}ski effect. However, these measurements are challenging to model without robustly testing and verifying the theoretical framework used for analyzing them. Here, we leverage the accuracy and volume of the $N$-body simulation suite \textsc{AbacusSummit} to generate high-resolution Ly$\alpha$ skewers and quasi-stellar object (QSO) catalogs. One of the main goals of our mocks is to aid in the full-shape Ly$\alpha$ analysis planned by the Dark Energy Spectroscopic Instrument (DESI) team. We provide optical depth skewers for six of the fiducial cosmology base-resolution simulations ($L_{\rm box} = 2\,h^{-1}{\rm Gpc}$, $N = 6912^3$) at $z = 2.5$. We adopt a simple recipe based on the Fluctuating Gunn-Peterson Approximation (FGPA) for constructing these skewers from the matter density in an $N$-body simulation and calibrate it against the 1D and 3D Ly$\alpha$ power spectra extracted from the hydrodynamical simulation IllustrisTNG (TNG; $L_{\rm box} = 205\,h^{-1}{\rm Mpc}$, $N = 2500^3$). As an important application, we study the non-linear broadening of the baryon acoustic oscillation (BAO) peak and show the cross-correlation between DESI-like QSOs and our Ly$\alpha$ forest skewers. We find differences on small scales between the Kaiser approximation prediction and our mock measurements of the Ly$\alpha$$\times$QSO cross-correlation, which would be important to account for in upcoming analyses. The \textsc{AbacusSummit} Ly$\alpha$ forest mocks open up the possibility for improved modelling of cross correlations between Ly$\alpha$ and cosmic microwave background (CMB) lensing and Ly$\alpha$ and QSOs, and for forecasts of the 3-point Ly$\alpha$ correlation function. Our catalogues and skewers are publicly available on Globus., Comment: 17 pages, 8 figures, Globus link: https://app.globus.org/file-manager?origin_id=9ce29982-eed1-11ed-9bb4-c9bb788c490e&path=%2F

We present the first clustering measurement of Strong Blended Lyman $\alpha$ (SBLA) absorption systems by measuring their cross-correlation with the Lyman $\alpha$ forest. SBLAs are a new population of absorbers detected within the Lyman $\alpha$ forest. We find a bias of $2.329\pm0.057$, consistent with that of Damped Lyman $\alpha$ absorbers (DLAs). For DLAs, we recover a bias of $2.331\pm0.057$ larger than previously reported (P\'erez-R\`afols et al. 2018b). We also find a redshift space distortion parameter $\beta=0.417\pm0.010$, also consistent with the recovered value for DLAs ($\beta=0.416\pm0.010$). This is consistent with SBLA and DLA systems tracing different portions of the circumgalactic medium of a broadly common population of galaxies. Given these common clustering properties, we combined them to perform a cross-correlation of galaxies in absorption with the Ly$\alpha$ forest. We find that the BAO scale uncertainty of this new measurement is $1.75\times$ that of Ly$\alpha$ auto-correlation and $1.6\times$ that of the quasar cross-correlation with the Ly$\alpha$ forest. We note that the current preferred metal contamination model for fitting the correlation functions with respect to the Ly$\alpha$ forest is not realistic enough for SBLA systems, likely due to their status as high redshift precision sites of high metal enrichment. Mock spectra including SBLA systems and their associated metal absorption are required to understand this sample fully. We conclude that SBLAs have the potential to complement the standard Ly$\alpha$ cosmological analyses in future surveys., Comment: accepted in MNRAS; 15 pages, 6 figures, 3 tables

We determine the product of the expansion rate and angular-diameter distance at redshift $z=2.3$ from the anisotropy of Lyman-$\alpha$ (Ly$\alpha$) forest correlations measured by the Sloan Digital Sky Survey (SDSS). Our result is the most precise from large-scale structure at $z>1$. In flat $\Lambda$CDM we determine the matter density to be $\Omega_\mathrm{m}=0.36^{+0.03}_{-0.04}$ from Ly$\alpha$ alone. This is a factor of two tighter than baryon acoustic oscillation results from the same data due to our use of a wide range of scales ($25

The three-dimensional distribution of the Ly$\alpha$ forest has been extensively used to constrain cosmology through measurements of the baryon acoustic oscillations (BAO) scale. However, more cosmological information could be extracted from the full shapes of the Ly$\alpha$ forest correlations through the Alcock-Paczy\'nski (AP) effect. In this work, we prepare for a cosmological analysis of the full shape of the Ly$\alpha$ forest correlations by studying synthetic data of the extended Baryon Oscillation Spectroscopic Survey (eBOSS). We use a set of one hundred eBOSS synthetic data sets in order to validate such an analysis. These mocks undergo the same analysis process as the real data. We perform a full-shape analysis on the mean of the correlation functions measured from the one hundred eBOSS realizations, and find that our model of the Ly$\alpha$ correlations performs well on current data sets. We show that we are able to obtain an unbiased full-shape measurement of $D_M/D_H(z_\mathrm{eff})$, where $D_M$ is the transverse comoving distance, $D_H$ is the Hubble distance, and $z_\mathrm{eff}$ is the effective redshift of the measurement. We test the fit over a range of scales, and decide to use a minimum separation of $r_\mathrm{min}=25\ h^{-1}\text{Mpc}$. We also study and discuss the impact of the main contaminants affecting Ly$\alpha$ forest correlations, and give recommendations on how to perform such analysis with real data. While the final eBOSS Ly$\alpha$ BAO analysis measured $D_M/D_H(z_\mathrm{eff}=2.33)$ with $4\%$ statistical precision, a full-shape fit of the same correlations could provide a $\sim2\%$ measurement.

When performing cosmological inference, standard analyses of the Lyman-$\alpha$ (Ly$\alpha$) three-dimensional correlation functions only consider the information carried by the distinct peak produced by baryon acoustic oscillations (BAO). In this work, we address whether this compression is sufficient to capture all the relevant cosmological information carried by these functions. We do this by performing a direct fit to the full shape, including all physical scales without compression, of synthetic Ly$\alpha$ auto-correlation functions and cross-correlations with quasars at effective redshift $z_{\rm{eff}}=2.3$, assuming a DESI-like survey, and providing a comparison to the classic method applied to the same dataset. Our approach leads to a $3.5\%$ constraint on the matter density $\Omega_{\rm{M}}$, which is about three to four times better than what BAO alone can probe. The growth term $f \sigma_{8} (z_{\rm{eff}})$ is constrained to the $10\%$ level, and the spectral index $n_{\rm{s}}$ to $\sim 3-4\%$. We demonstrate that the extra information resulting from our `direct fit' approach, except for the $n_{\rm{s}}$ constraint, can be traced back to the Alcock-Paczy\'nski effect and redshift space distortion information., Comment: Matches version published in MNRAS

We propose a new method for fitting the full-shape of the Lyman-$\alpha$ (Ly$\alpha$) forest three-dimensional (3D) correlation function in order to measure the Alcock-Paczynski (AP) effect. Our method preserves the robustness of baryon acoustic oscillations (BAO) analyses, while also providing extra cosmological information from a broader range of scales. We compute idealized forecasts for the Dark Energy Spectroscopic Instrument (DESI) using the Ly$\alpha$ auto-correlation and its cross-correlation with quasars, and show how this type of analysis improves cosmological constraints. The DESI Ly$\alpha$ BAO analysis is expected to measure $H(z_\mathrm{eff})r_\mathrm{d}$ and $D_\mathrm{M}(z_\mathrm{eff})/r_\mathrm{d}$ with a precision of $\sim0.9\%$ each, where $H$ is the Hubble parameter, $r_\mathrm{d}$ is the comoving BAO scale, $D_\mathrm{M}$ is the comoving angular diameter distance and the effective redshift of the measurement is $z_\mathrm{eff}\simeq2.3$. By fitting the AP parameter from the full shape of the two correlations, we show that we can obtain a precision of $\sim0.5-0.6\%$ on each of $H(z_\mathrm{eff})r_\mathrm{d}$ and $D_\mathrm{M}(z_\mathrm{eff})/r_\mathrm{d}$. Furthermore, we show that a joint full-shape analysis of the Ly$\alpha$ auto-correlation and its cross-correlation with quasars can measure the linear growth rate times the amplitude of matter fluctuations in spheres of $8\;h^{-1}$Mpc, $f\sigma_8(z_\mathrm{eff})$. Such an analysis could provide the first ever measurement of $f\sigma_8(z_\mathrm{eff})$ at redshift $z_\mathrm{eff}>2$. By combining this with the quasar auto-correlation in a joint analysis of the three high-redshift two-point correlation functions, we show that DESI could be able to measure $f\sigma_8(z_\mathrm{eff}\simeq2.3)$ with a precision of $5-12\%$, depending on the smallest scale fitted.

We present a measurement of baryonic acoustic oscillations (BAO) from Lyman-$\alpha$ (Ly$\alpha$) absorption and quasars at an effective redshift $z=2.33$ using the complete extended Baryonic Oscillation Spectroscopic Survey (eBOSS). The sixteenth and final eBOSS data release (SDSS DR16) contains all data from eBOSS and its predecessor, the Baryonic Oscillation Spectroscopic Survey (BOSS), providing $210,005$ quasars with $z_{q}>2.10$ that are used to measure Ly$\alpha$ absorption. We measure the BAO scale both in the auto-correlation of Ly$\alpha$ absorption and in its cross correlation with $341,468$ quasars with redshift $z_{q}>1.77$. Apart from the statistical gain from new quasars and deeper observations, the main improvements over previous work come from more accurate modeling of physical and instrumental correlations and the use of new sets of mock data. Combining the BAO measurement from the auto- and cross-correlation yields the constraints of the two ratios $D_{H}(z=2.33)/r_{d} = 8.99 \pm 0.19$ and $D_{M}(z=2.33)/r_{d} = 37.5 \pm 1.1$, where the error bars are statistical. These results are within $1.5\sigma$ of the prediction of the flat-$\Lambda$CDM cosmology of Planck~(2016). The analysis code, \texttt{picca}, the catalog of the flux-transmission field measurements, and the $\Delta \chi^{2}$ surfaces are publicly available., Comment: 37 pages, 23 figures, Matches the published version by ApJ

We present the cosmological implications from final measurements of clustering using galaxies, quasars, and Ly$\alpha$ forests from the completed Sloan Digital Sky Survey (SDSS) lineage of experiments in large-scale structure. These experiments, composed of data from SDSS, SDSS-II, BOSS, and eBOSS, offer independent measurements of baryon acoustic oscillation (BAO) measurements of angular-diameter distances and Hubble distances relative to the sound horizon, $r_d$, from eight different samples and six measurements of the growth rate parameter, $f\sigma_8$, from redshift-space distortions (RSD). This composite sample is the most constraining of its kind and allows us to perform a comprehensive assessment of the cosmological model after two decades of dedicated spectroscopic observation. We show that the BAO data alone are able to rule out dark-energy-free models at more than eight standard deviations in an extension to the flat, $\Lambda$CDM model that allows for curvature. When combined with Planck Cosmic Microwave Background (CMB) measurements of temperature and polarization the BAO data provide nearly an order of magnitude improvement on curvature constraints. The RSD measurements indicate a growth rate that is consistent with predictions from Planck primary data and with General Relativity. When combining the results of SDSS BAO and RSD with external data, all multiple-parameter extensions remain consistent with a $\Lambda$CDM model. Regardless of cosmological model, the precision on $\Omega_\Lambda$, $H_0$, and $\sigma_8$, remains at roughly 1\%, showing changes of less than 0.6\% in the central values between models. The inverse distance ladder measurement under a o$w_0w_a$CDM yields $H_0= 68.20 \pm 0.81 \, \rm km\, s^{-1} Mpc^{-1}$, remaining in tension with several direct determination methods. (abridged), Comment: A summary of all SDSS BAO and RSD measurements with accompanying legacy figures can be found here: https://www.sdss.org/science/final-bao-and-rsd-measurements/ . The full cosmological interpretation of these measurements can be found here: https://www.sdss.org/science/cosmology-results-from-eboss/

We study and compare fitting methods for the Lyman-$\alpha$ (Ly$\alpha$) forest 3D correlation function. We use the nested sampler PolyChord and the community code picca to perform a Bayesian analysis which we compare with previous frequentist analyses. By studying synthetic correlation functions, we find that the frequentist profile likelihood produces results in good agreement with a full Bayesian analysis. On the other hand, Maximum Likelihood Estimation with the Gaussian approximation for the uncertainties is inadequate for current data sets. We compute for the first time the full posterior distribution from the Ly$\alpha$ forest correlation functions measured by the extended Baryon Oscillation Spectroscopic Survey (eBOSS). We highlight the benefits of sampling the full posterior distribution by expanding the baseline analysis to better understand the contamination by Damped Ly$\alpha$ systems (DLAs). We make our improvements and results publicly available as part of the picca package., Comment: 18 pages, 4 figures

We investigate constraints on the Hubble constant ($H_0$) using Baryon Acoustic Oscillations (BAO) and baryon density measurements from Big Bang Nucleosynthesis (BBN). We start by investigating the tension between galaxy BAO measurements and those using the Lyman-$\alpha$ forest, within a Bayesian framework. Using the latest results from eBOSS DR14 we find that the probability of this tension being statistical is $\simeq6.3\%$ assuming flat $\Lambda$CDM. We measure $H_0 = 67.6\pm1.1$ km s$^{-1}$ Mpc$^{-1}$, with a weak dependence on the BBN prior used, in agreement with results from Planck Cosmic Microwave Background (CMB) results and in strong tension with distance ladder results. Finally, we forecast the future of BAO $+$ BBN measurements of $H_0$, using the Dark Energy Spectroscopic Instrument (DESI). We find that the choice of BBN prior will have a significant impact when considering future BAO measurements from DESI., Comment: 14 pages, 3 figures

We investigate the impact of prior models on the upper bound of the sum of neutrino masses, $\sum m_{\nu}$. We use data from Large Scale Structure of galaxies, Cosmic Microwave Background, Type Ia SuperNovae, and Big Bang Nucleosynthesis. We probe physically motivated neutrino mass models (respecting oscillation experiment constraints) and compare them to constraints using standard cosmological approximations. The former give a consistent upper bound of $\sum m_{\nu} \lesssim 0.26$ eV ($95\%$ CI) and yields a strong competitive upper bound for the lightest neutrino mass species, $m_0^{\nu} < 0.086$ eV ($95\%$ CI). By contrast one of the approximations, which is somewhat inconsistent with oscillation experiments, yields an upper bound of $\sum m_{\nu} \lesssim 0.15$ eV ($95\%$ CI), which differs substantially from the former upper bound. We, therefore, argue that cosmological neutrino mass and hierarchy determination should be pursued using physically motivated models since approximations might lead to incorrect and nonphysical upper bounds., Comment: 5 pages, 2 figures

We constrain cosmological parameters by analysing the angular power spectra of the Baryon Oscillation Spectroscopic Survey DR12 galaxies, a spectroscopic follow-up of around 1.3 million SDSS galaxies over 9,376 deg$^2$ with an effective volume of $\sim 6.5$ (Gpc $h^{-1}$)$^3$ in the redshift range $0.15 \leq z < 0.80$. We split this sample into 13 tomographic bins ($\Delta z = 0.05$); angular power spectra were calculated using a Pseudo-$C_{\ell}$ estimator, and covariance matrices were estimated using log-normal simulated maps. Cosmological constraints obtained from these data were combined with constraints from Planck CMB experiment as well as the JLA supernovae compilation. Considering a $w$CDM cosmological model measured on scales up to $k_{max} = 0.07h$ Mpc$^{-1}$, we constrain a constant dark energy equation-of-state with a $\sim 4\%$ error at the 1-$\sigma$ level: $w_0 = -0.993^{+0.046}_{-0.043}$, together with $\Omega_m = 0.330\pm 0.012$, $\Omega_b = 0.0505 \pm 0.002$, $S_8 \equiv \sigma_8 \sqrt{\Omega_m/0.3} = 0.863 \pm 0.016$, and $h = 0.661 \pm 0.012$. For the same combination of datasets, but now considering a $\Lambda$CDM model with massive neutrinos and the same scale cut, we find: $\Omega_m = 0.328 \pm 0.009$, $\Omega_b = 0.05017^{+0.0009}_{-0.0008}$, $S_8 = 0.862 \pm 0.017$, and $h = 0.663^{+0.006}_{-0.007}$ and a 95\% credible interval (CI) upper limit of $\sum m_{\nu} < 0.14$ eV for a normal hierarchy. These results are competitive if not better than standard analyses with the same dataset, and demonstrate this should be a method of choice for future surveys, opening the door for their full exploitation in cross-correlations probes., Comment: 28 pages, 28 figures, 3 appendices