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Reconstruction techniques for intrinsic quasar continua are crucial for the precision study of Lyman-$alpha$ (Ly-$alpha$) and Lyman-$beta$ (Ly-$beta$) transmission at $z>5.0$, where the $lambda<1215 A$ emission of quasars is nearly completely absorbed. While the number and quality of spectroscopic observations has become theoretically sufficient to quantify Ly-$alpha$ transmission at $5.0<z<6.0$ to better than $1%$, the biases and uncertainties arising from predicting the unabsorbed continuum are not known to the same level. In this paper, we systematically evaluate eight reconstruction techniques on a unified testing sample of $2.7<z<3.5$ quasars drawn from eBOSS. The methods include power-law extrapolation, stacking of neighbours, and six variants of Principal Component Analysis (PCA) using direct projection, fitting of components, or neural networks to perform weight mapping. We find that power-law reconstructions and the PCA with fewest components and smallest training sample display the largest biases in the Ly-$alpha$ forest ($-9.58%/+8.22%$ respectively). Power-law extrapolations have larger scatters than previously assumed of $+13.1%/-13.2%$ over Ly-$alpha$ and $+19.9%/-20.1%$ over Ly-$beta$. We present two new PCAs which achieve the best current accuracies of $9%$ for Ly-$alpha$ and $17%$ for Ly-$beta$. We apply the eight techniques after accounting for wavelength-dependent biases and scatter to a sample $19$ quasars at $z>5.7$ with IR X-Shooter spectroscopy, obtaining well-characterised measurements for the mean flux transmission at $4.7<z<6.3$. Our results demonstrate the importance of testing and, when relevant, training, continuum reconstruction techniques in a systematic way.
In an effort to search for Ly$alpha$ emission from circum- and intergalactic gas on scales of hundreds of kpc around $zsim3$ quasars, and thus characterise the physical properties of the gas in emission, we have initiated an extensive fast-survey wit
Distant luminous quasars provide important information on the growth of the first supermassive black holes, their host galaxies and the epoch of reionization. The identification of quasars is usually performed through detection of their Lyman-$alpha$
The imprint of Baryonic Acoustic Oscillations (BAO) on the matter power spectrum can be constrained using the neutral hydrogen density in the intergalactic medium as a tracer of the matter density. One of the goals of the Baryon Oscillation Spectrosc
We report on a search for ultraluminous Lyman alpha emitting galaxies (LAEs) at z=6.6 using the NB921 filter on Hyper Suprime-Cam on the Subaru telescope. We searched a 30 degree squared area around the North Ecliptic Pole, which we observed in broad
We present a study of ~100 high redshift (z~2-4) extremely strong damped Lyman-alpha systems (ESDLA, with N(HI)>0.5x10^22 cm^-2) detected in quasar spectra from the Baryon Oscillation Spectroscopic Survey SDSS-III DR11. We study the neutral hydrogen,