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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Validation of the DESI 2024 Lyα forest BAO analysis using synthetic datasets

The first year of data from the Dark Energy Spectroscopic Instrument (DESI) contains the largest set of Lyman-α (Lyα) 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 Lyα forest BAO measurement presented in [1]. 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 Lyα forest. The synthetic data sets span a redshift range 1.8 < z < 3.8, and are analyzed using the same framework and pipeline used for the DESI 2024 Lyα forest BAO measurement. To measure BAO, we use both the Lyα auto-correlation and its cross-correlation with quasar positions. We use the mean of correlation functions from the set of DESI DR1 realizations to show that our model is able to recover unbiased measurements of the BAO position. We also fit each mock individually and study the population of BAO fits in order to validate BAO uncertainties and test our method for estimating the covariance matrix of the Lyα forest correlation functions. Finally, we discuss the implications of our results and identify the needs for the next generation of Lyα forest synthetic data sets, with the top priority being to simulate the effect of BAO broadening due to non-linear evolution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Reconstructing Quasar Spectra and Measuring the Lyα Forest with SpenderQ

Quasar spectra carry the imprint of foreground intergalactic medium (IGM) through absorption features. In particular, absorption caused by neutral hydrogen gas, the "Lyα forest," is a key spectroscopic tracer for cosmological analyses used to measure cosmic expansion and test physics beyond the standard model. Despite their importance, current methods for measuring Lyα absorption cannot directly derive the intrinsic quasar continuum and make strong assumptions on its shape, thus distorting the measured Lyα clustering. We present SpenderQ , a ML-based approach for directly reconstructing the intrinsic quasar spectra and measuring the Lyα forest from observations. SpenderQ uses the Spender spectrum autoencoder to learn a compact and redshift-invariant latent encoding of quasar spectra, combined with an iterative procedure to identify and mask absorption regions. To demonstrate its performance, we apply SpenderQ to 400,000 synthetic quasar spectra created to validate the Dark Energy Spectroscopic Instrument Year 1 Lyα cosmological analyses. SpenderQ accurately reconstructs the true intrinsic quasar spectra, including the broad Lyβ, Lyα, SiIV, CIV, and CIII emission lines. Redward of Lyα, SpenderQ provides percent-level reconstructions of the true quasar spectra. Blueward of Lyα, SpenderQ reconstructs the true spectra to < 5%. SpenderQ reproduces the shapes of individual quasar spectra more robustly than the current state-of-the-art. We, thus, expect it will significantly reduce biases in Lyα clustering measurements and enable studies of quasars and their physical properties. SpenderQ also provides informative latent variable encodings that can be used to, e.g., classify quasars with Broad Absorption Lines. Overall, SpenderQ provides a new data-driven approach for unbiased Lyα forest measurements in cosmological, quasar, and IGM studies.

Hahn, ChangHoon [Arizona U., Astron. Dept. - Stewa↗
DOE OSTI2026

Measurements of Quasar Proximity Zones with the Lyα Forest of DESI Y1 Quasars

Abstract The intergalactic medium (IGM) around a quasar is shaped by its dense environment and by its excess ionizing radiation, which form a “quasar proximity zone” whose size and anisotropy depend on the quasar’s halo mass, luminosity, age, and radiation geometry. Using over 10,000 quasar pairs from the Dark Energy Spectroscopic Instrument (DESI) Year 1 data, with projected comoving separations r ⊥ < 2 h −1 Mpc, we investigate how the proximity zone of foreground quasars at z ∼ 2–3.5 affects Lyα absorption in their background quasars. The large DESI sample enables unprecedented precision in measuring this “transverse proximity” effect, allowing a detailed investigation of the signal’s dependence on the projected separation of quasar pairs and the luminosity of the foreground quasar. We find that enhanced gas clustering near quasars dominates over their ionizing effect, leading to stronger absorption on neighboring sightlines. Under the assumption that quasar ionizing luminosity is isotropic and steady, we infer the IGM overdensity profile in the vicinity of quasars, finding overdensities as high as Δ ∼ 10 at comoving distance ∼1 h −1 Mpc from the most luminous systems. Surprisingly, however, we find no significant dependence of the proximity profile on the luminosity of the foreground quasar. This lack of luminosity dependence could reflect a cancellation between higher ionizing flux and higher gas overdensity, or it could indicate that quasar emission is highly time-variable or anisotropic, so that the observed luminosity does not trace the ionizing flux on nearby sightlines.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Impact of Self-shielding Minihalos on the Lyα Forest at High Redshift

Abstract Dense gas in minihalos with masses of 10 6 −10 8 M ⊙ can shield themselves from reionization for ∼100 Myr after being exposed to the UV background. These self-shielded systems, often unresolved in cosmological simulations, can introduce strong absorption in quasar spectra. This paper is the first systematic study on the impact of these systems on the Ly α forest. We first derive the H i column density profile of photoevaporating minihalos by conducting 1D radiation–hydrodynamics simulations. We utilize these results to estimate the Ly α opacity from minihalos in a large-scale simulation that cannot resolve self-shielding. When the ionization rate of the background radiation is 0.03 × 10 −12 s −1 , as expected near the end of reionization at z ∼ 5.5, we find that the incidence rate of damped Ly α absorbers increases by a factor of ∼2−4 compared to at z = 4.5. The Ly α flux is, on average, suppressed by ∼3% of its mean due to minihalos. The absorption features enhance the 1D power spectrum up to ∼5% at k ∼ 0.1 h Mpc −1 (or 10 −3 km −1 s), which is comparable to the enhancement caused by inhomogeneous reionization. The flux is particularly suppressed in the vicinity of large halos along the line-of-sight direction at separations of up to 10 h −1 Mpc at r ⊥ ≲ 2 h −1 Mpc. However, these effects become much smaller for higher ionizing rates (≳0.3 × 10 −12 s −1 ) expected in the post-reionization Universe. Our findings highlight the need to consider minihalo absorption when interpreting the Ly α forest at z ≳ 5.5. Moreover, the sensitivity of these quantities to the ionizing background intensity can be exploited to constrain the intensity itself.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

New Measurements of the Lyα Forest Continuum and Effective Optical Depth with LyCAN and DESI Y1 Data

Abstract We present the Ly α Continuum Analysis Network (LyCAN), a convolutional neural network that predicts the unabsorbed quasar continuum within the rest-frame wavelength range of 1040–1600 Å based on the red side of the Ly α emission line (1216–1600 Å). We developed synthetic spectra based on a Gaussian mixture model representation of nonnegative matrix factorization (NMF) coefficients. These coefficients were derived from high-resolution, low-redshift ( z < 0.2) Hubble Space Telescope/Cosmic Origins Spectrograph (COS) quasar spectra. We supplemented this COS-based synthetic sample with an equal number of DESI Year 5 mock spectra. LyCAN performs extremely well on testing sets, achieving a median error in the forest region of 1.5% on the DESI mock sample, 2.0% on the COS-based synthetic sample, and 4.1% on the original COS spectra. LyCAN outperforms principal component analysis (PCA) and NMF-based prediction methods using the same training set by 40% or more. We predict the intrinsic continua of 83,635 DESI Year 1 spectra in the redshift range of 2.1 ≤ z ≤ 4.2 and perform an absolute measurement of the evolution of the effective optical depth. This is the largest sample employed to measure the optical depth evolution to date. We fit a power law of the form τ ( z ) = τ 0 ( 1 + z ) γ to our measurements and find τ 0 = (2.46 ± 0.14) × 10 −3 and γ = 3.62 ± 0.04. Our results show particular agreement with high-resolution, ground-based observations around z = 2, indicating that LyCAN is able to predict the quasar continuum in the forest region with only spectral information outside the forest.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

The Lyman- α forest from LBGs: First 3D correlation measurement with DESI and prospects for cosmology

The Lyman-α (Lyα) forest is a key tracer of large-scale structure at redshifts z > 2, traditionally studied using the spectra of luminous but relatively rare quasars. In this work, we explore the viability of using the fainter yet significantly more abundant Lyman Break Galaxies (LBGs) as alternative background sources for Lyα forest studies. We analyze 4,151 Lyα forest skewers extracted from LBG spectra obtained in the DESI pilot surveys conducted in the COSMOS and XMM-LSS fields. From this dataset, we present the first measurement of the Lyα forest auto-correlation function derived exclusively from LBG spectra, probing comoving separations up to 48 h -1 Mpc at an effective redshift of z eff = 2.70. The measured LBG Lyα forest auto-correlation is consistent with that derived from DESI DR2 quasar Lyα forest spectra at a comparable redshift, validating the use of LBGs as reliable background sources for Lyα forest analyses. In addition, we measure the cross-correlation between the LBG Lyα forest and the positions of 13,362 galaxies, demonstrating that this observable serves as a sensitive diagnostic for assessing the precision and accuracy of galaxy redshift estimates, and for identifying and correcting systematic offsets. Finally, using both synthetic LBG spectra and Fisher matrix forecasts, we show that a future wide-area survey covering ∼5,000 deg 2 , targeting 1,000 LBGs per square degree at signal-to-noise levels comparable to our sample, could enable LBG-based Lyα forest baryon acoustic oscillation (BAO) measurements with expected uncertainties of σ α ISO = 0.4% (isotropic) and σ α AP = 1.3% (Alcock-Paczynski). This performance is further enhanced when combining the BAO analysis with a Lyα forest Full Shape (FS) approach, yielding a predicted uncertainty of σ α ISO FS = 0.6%. These results open a new avenue for precision cosmology at high redshift using the Lyα forest in dense LBG samples.

Lyman alpha forest↗
DOE OSTI2026

Probing the limits of cosmological information from the Lyman- α forest 2-point correlation functions

The standard cosmological analysis with the Lyα forest relies on a continuum fitting procedure that suppresses information on large scales and distorts the three-dimensional correlation function on all scales. In this work, we present the first cosmological forecasts without continuum fitting distortion in the Lyα forest, focusing on the recovery of large-scale information. Using idealized synthetic data, we compare the constraining power of the full shape of the Lyα forest auto-correlation and its cross-correlation with quasars using the baseline continuum fitting analysis versus the true continuum. We find that knowledge of the true continuum enables a ∼ 10% reduction in uncertainties on the Alcock-Paczyński (AP) parameter and the matter density, Ω m . We also explore the impact of large-scale information by extending the analysis up to separations of 240 h -1 Mpc along and across the line of sight. The combination of these analysis choices can recover significant large-scale information, yielding up to a ∼ 15% improvement in AP constraints. This improvement is analogous to extending the Lyα forest survey area by ∼ 40%.

Lyman alpha forest↗
DOE OSTI2025

Characterization of contaminants in the Lyman-alpha forest auto-correlation with DESI

Baryon Acoustic Oscillations can be measured with sub-percent precision above redshift two with the Lyman-α (Lyα) forest auto-correlation and its cross-correlation with quasar positions. This is one of the key goals of the Dark Energy Spectroscopic Instrument (DESI) which started its main survey in May 2021. We present in this paper a study of the contaminants to the Lyα forest which are mainly caused by correlated signals introduced by the spectroscopic data processing pipeline as well as astrophysical contaminants due to foreground absorption in the intergalactic medium. Notably, an excess signal caused by the sky background subtraction noise is present in the Lyα auto-correlation in the first line-of-sight separation bin. We use synthetic data to isolate this contribution, we also characterize the effect of spectro-photometric calibration noise, and propose a simple model to account for both effects in the analysis of the Lyα forest. We then measure the auto-correlation of the quasar flux transmission fraction of low redshift quasars, where there is no Lyα forest absorption but only its contaminants. We demonstrate that we can interpret the data with a two-component model: data processing noise and triply ionized Silicon and Carbon auto-correlations. This result can be used to improve the modeling of the Lyα auto-correlation function measured with DESI.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Light in the dark forest. Part I. An efficient optimal estimator for 3D Lyman-alpha forest power spectrum

The highly anisotropic nature of the Lyman-alpha (Lyα) forest data introduces a complex survey window function that complicates the measurement of the three-dimensional power spectrum ( P 3D ). In this paper, we present the first fully optimal estimator for P 3D , which exactly deconvolves the survey window function and marginalizes contaminated modes that distort the power spectrum. Our approach adapts optimal estimator techniques developed for the 2D cosmic microwave background data to the 3D case. To achieve computational feasibility, we employ the conjugate gradient method and implement the P 3 M formalism to handle large-scale and small-scale operations separately and efficiently. We validate our estimator using Monte Carlo mocks and Gaussian simulations, demonstrating its accuracy and computational efficiency. We confirm that mode marginalization eliminates distortions arising from quasar continuum errors and delivers robust power spectrum estimation, though it also inflates errors at large scales. This first implementation works in the flat-sky case; we discuss the remaining steps needed to generalize it to the curved-sky case. This formalism offers a foundation for the Lyα forest P 3D measurements and a new path toward cosmological constraints from the Lyα forest data.

Lyman alpha forest↗
DOE OSTI2025

Weighted FFT estimators for 1D and 3D correlations of the Lyman- α forest

Correlations in the Lyman-α (Lyα) forest, both as a function of line of sight separation (1D) and 3D separation, provide a unique window to the distribution of matter at redshifts not accessible by current galaxy surveys. While optimal quadratic estimators have been used to measure 1D correlations, they are computationally expensive and difficult to extend to 3D analyses. On the other hand, estimators based on the Fast Fourier Transform (FFT) are significantly faster, but are affected by missing data in the spectra (masked pixels) and so far have not used pixel weights to reduce the uncertainties in the measurement. In this publication we describe how to compute the window matrix that enables forward-modelling the impact of masked pixels and weights on the FFT-based estimators. Here, we use Gaussian and hydrodynamical simulations with artificially masked pixels to validate the method on the measurement of 1D correlations. Finally, we show that the formalism can be extended to model the impact on 3D correlations, in particular on the cross-spectrum, the correlation of 1D Fourier modes as a function of transverse separation. This work will enable more precise clustering measurements with the Lyα forest dataset recently collected by the Dark Energy Spectroscopic Instrument (DESI).

Lokken, Martine [Univ. Autonoma de Barcelona (Spai↗
DOE OSTI2025

Validation of the DESI 2024 Lyman alpha forest BAL masking strategy

Broad absorption line quasars (BALs) exhibit blueshifted absorption relative to a number of their prominent broad emission features. These absorption features can contribute to quasar redshift errors and add absorption to the Lyman-α (Lyα) forest that is unrelated to large-scale structure. We present a detailed analysis of the impact of BALs on the Baryon Acoustic Oscillation (BAO) results with the Lyα forest from the first year of data from the Dark Energy Spectroscopic Instrument (DESI). The baseline strategy for the first year analysis is to mask all pixels associated with all BAL absorption features that fall within the wavelength region used to measure the forest. We explore a range of alternate masking strategies and demonstrate that these changes have minimal impact on the BAO measurements with both DESI data and synthetic data. This includes when we mask the BAL features associated with emission lines outside of the forest region to minimize their contribution to redshift errors. We identify differences in the properties of BALs in the synthetic datasets relative to the observational data, as well as use the synthetic observations to characterize the completeness of the BAL identification algorithm, and demonstrate that incompleteness and differences in the BALs between real and synthetic data also do not impact the BAO results for the Lyα forest.

Lyman alpha forest↗
DOE OSTI2025

DESI 2024 IV: Baryon Acoustic Oscillations from the Lyman alpha forest

We present the measurement of Baryon Acoustic Oscillations (BAO) from the Lyman-α(Lyα) forest of high-redshift quasars with the first-year dataset of the Dark Energy Spectroscopic Instrument (DESI). Our analysis uses over 420 000 Lyα forest spectra and their correlation with the spatial distribution of more than 700 000 quasars. An essential facet of this work is the development of a new analysis methodology on a blinded dataset. We conducted rigorous tests using synthetic data to ensure the reliability of our methodology and findings before unblinding. Additionally, we conducted multiple data splits to assess the consistency of the results and scrutinized various analysis approaches to confirm their robustness. For a given value of the sound horizon (r d ), we measure the expansion at z eff = 2.33 with 2% precision, H(z eff ) = (239.2 ± 4.8) (147.09 Mpc /r d ) km/s/Mpc. Similarly, we present a 2.4% measurement of the transverse comoving distance to the same redshift, DM(z eff ) = (5.84 ± 0.14) (r d /147.09 Mpc) Gpc. Together with other DESI BAO measurements at lower redshifts, these results are used in a companion paper to constrain cosmological parameters.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Modelling the impact of quasar redshift errors on the full-shape analysis of correlations in the Lyman-α forest.

In preparation for the first cosmological measurements from the full shape of the Lyman-α (Lyα) forest from DESI, we must carefully model all relevant systematics that might bias our analysis. It was shown in Youles et al. (2022) that random quasar redshift errors produce a smoothing effect on the mean quasar continuum in the Lyα forest region. This, in turn, gives rise to spurious features in the Lyα autocorrelation and its cross-correlation with quasars. Using synthetic data sets based on the DESI survey, we confirm that the impact on BAO measurements is small, but that a bias is introduced to parameters which depend on the full shape of our correlations. We combine a model of this contamination in the cross-correlation (Youles et al. 2022) with a new model we introduce here for the auto-correlation. These are parametrised by 3 parameters, which, when included in a joint fit to both correlation functions, successfully eliminate any impact of redshift errors on our full-shape constraints. We also present a strategy for removing this contamination from real data, by removing ∼0.3% of correlating pairs.

cosmology↗
DOE OSTI2026

DESI DR1 Ly α 1D power spectrum: Validation of estimators

The Data Release 1 (DR1) of the Dark Energy Spectroscopic Instrument (DESI) is the largest sample to date for small-scale Lyα forest cosmology, accessed through its one-dimensional power spectrum (P 1D ). The Lyα forest P 1D is extracted from quasar spectra that are highly inhomogeneous (both in wavelength and between quasars) in noise properties due to intrinsic properties of the quasar, atmospheric and astrophysical contamination, and also sensitive to low-level details of the spectral extraction pipeline. We employ two estimators in DR1 analysis to measure P 1D : the optimal estimator and the fast Fourier transform (FFT) estimator. To ensure robustness of our DR1 measurements, we validate these two power spectrum and covariance matrix estimation methodologies against the challenging aspects of the data. First, using a set of 20 synthetic 1D realizations of DR1, we derive the masking bias corrections needed for the FFT estimator and the continuum fitting bias needed for both estimators. We demonstrate that both estimators, including their covariances, are unbiased with these corrections using the Kolmogorov-Smirnov test. Second, we substantially extend our previous suite of CCD image simulations to include 675,000 quasars, allowing us to accurately quantify the pipeline's performance. This set of simulations reveals biases at the highest k values, corresponding to a resolution error of a few percent. We base the resolution systematics error budget of DR1 P 1D on these values, but do not derive corrections from them since the simulation fidelity is insufficient for precise corrections.

Lyman alpha forest↗
DOE OSTI2025

DESI DR1 Lyα 1D power spectrum: the optimal estimator measurement

The one-dimensional power spectrum P 1D of Lyα forest offers rich insights into cosmological and astrophysical parameters, including constraints on the sum of neutrino masses, warm dark matter models, and the thermal state of the intergalactic medium. We present the measurement of P 1D using the optimal quadratic maximum likelihood estimator applied to over 300,000 Lyα quasars from Data Release 1 (DR1) of the Dark Energy Spectroscopic Instrument (DESI) survey. This sample represents the largest to date for P 1D measurements and is larger than the Extended Baryon Oscillation Spectroscopic Survey (eBOSS) by a factor of 1.7. We conduct a meticulous investigation of instrumental and analysis systematics and quantify their impact on P 1D . This includes the development of a cross-exposure estimator that eliminates the need to model the pipeline noise and has strong potential for future P 1D measurements. We also present new insights into metal contamination through the 1D correlation function. Using a fitting function we measure the evolution of the Lyα forest bias with high precision: b F (z) = (-0.218 ± 0.002) × ((1 + z)/4) 2.96±0.06 . In a companion validation paper, we substantially extend our previous suite of CCD image simulations to quantify the pipeline's exquisite performance accurately. In another companion paper, we present DR1 P 1D measurements using the Fast Fourier Transform (FFT) approach to power spectrum estimation. These two measurements produce a forest bias parameter that differs by 2.2 sigma. However, our model is simplistic, so this disagreement will be investigated in future work.

Lyman alpha forest↗
DOE OSTI2026

ODIN: Confirmation and 3D Reconstruction of Six Massive Protoclusters at Cosmic Noon

Protoclusters represent sites of accelerated galaxy formation and extreme astrophysical activity characteristic of dense environments. Identifying massive protoclusters and mapping their spatial structures are therefore crucial for understanding how large-scale environment influences galaxy evolution. We combine wide-field Lyα imaging from the One-hundred-deg$^{2}$ DECam Imaging in Narrowbands survey with extensive Dark Energy Spectroscopic Instrument and ancillary spectroscopy across the extended COSMOS and XMM Large Scale Structure (LSS) fields (≈14 deg$^{2}$) to search for massive protoclusters. We confirm six systems at z ≈ 2.4 and ≈ 3.1, including three newly identified structures and three which overlap with previously known structures and/or systems detected using other tracers. We reconstruct their three-dimensional structures, estimate descendant halo masses, and for one structure at z ≈ 3.12, demonstrate that overlapping narrowband filters (NB497 and N501) provide accurate redshift tomography for emission-line galaxies. One protocluster at z ≈ 2.45 overlaps with one of the LATIS tomographic fields, enabling direct comparison between galaxy and H i overdensities traced by Lyα forest absorption. Another at z ≈ 3.12 hosts a massive quiescent galaxy (M$_{*}$ ≈ 1.2 × 10$^{11}$M$_{⊙}$), suggesting that overdense environments may play a role in accelerating galaxy assembly and quenching. Comparing Lyα emission properties across environments, we find that protocluster galaxies exhibit higher median line fluxes and a deficit of faint emitters relative to the field. The effect is strongest when combining 2D and 3D density information, indicating that galaxies in the densest protocluster cores are most affected by environmental processes. This effect is stronger at z ≈ 3.1 than at z ≈ 2.4, suggesting possible redshift evolution.

Ortiz, Ashley [Purdue U.] (ORCID:000900083184304X)↗
DOE OSTI2025

Identifying Missing Quasars from the DESI Bright Galaxy Survey

The Dark Energy Spectroscopic Instrument (DESI) cosmology survey includes a Bright Galaxy Survey (BGS), which will yield spectra for over 10 million bright galaxies (r < 20.2 AB mag). The resulting sample will be valuable for both cosmological and astrophysical studies. However, the star/galaxy separation criterion implemented in the nominal BGS target selection algorithm excludes quasar host galaxies in addition to bona fide stars. While this excluded population is comparatively rare (∼3–4 per square degrees), it may hold interesting clues regarding galaxy and quasar physics. Therefore, we present a target selection strategy that was implemented to recover these missing active galactic nuclei (AGN) from the BGS sample. The design of the selection criteria was both motivated and confirmed using spectroscopy. The resulting BGS-AGN sample is uniformly distributed over the entire DESI footprint. According to DESI survey validation data, the sample comprises 93% quasi-stellar objects (QSOs), 3% narrow-line AGN or blazars with a galaxy contamination rate of 2%, and a stellar contamination rate of 2%. Peaking around redshift z = 0.5, the BGS-AGN sample is intermediary between quasars from the rest of the BGS and those from the DESI QSO sample in terms of redshifts and AGN luminosities. The stacked spectrum is nearly identical to that of the DESI QSO targets, confirming that the sample is dominated by quasars. We highlight interesting small populations reaching z > 2, which are either faint quasars with nearby projected companions or very bright quasars with strong absorption features including the Lyα forest, metal absorbers, and/or broad absorption lines.

79 ASTRONOMY AND ASTROPHYSICS↗