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We use the Ly-$\alpha$ Mass Association Scheme (LyMAS; Peirani et al. 2014)to predict cross-correlations at $z=2.5$ between dark matter halos andtransmitted flux in the Ly-$\alpha$ forest, and compare to cross-correlationsmeasured for quasars and damped Ly-$\alpha$ systems (DLAs) from the BaryonOscillation Spectroscopic Survey (BOSS) by Font-Ribera et al. (2012, 2013). Wecalibrate LyMAS using Horizon-AGN hydrodynamical cosmological simulations of a$(100\ h^{-1}\ \mathrm{Mpc})^3$ comoving volume. We apply this calibration to a$(1\ h^{-1}\ \mathrm{Gpc})^3$ simulation realized with $2048^3$ dark matterparticles. In the 100 $h^{-1}$ Mpc box, LyMAS reproduces the halo-fluxcorrelations computed from the full hydrodynamic gas distribution very well. Inthe 1 $h^{-1}$ Gpc box, the amplitude of the large scale cross-correlationtracks the halo bias $b_h$ as expected. We provide empirical fitting functionsthat describe our numerical results. In the transverse separation bins used forthe BOSS analyses, LyMAS cross-correlation predictions follow linear theoryaccurately down to small scales. Fitting the BOSS measurements requiresinclusion of random velocity errors; we find best-fit RMS velocity errors of399 km s$^{-1}$ and 252 km s$^{-1}$ for quasars and DLAs, respectively. Weinfer bias-weighted mean halo masses of $M_h/10^{12}\h^{-1}M_\odot=2.19^{+0.16}_{-0.15}$ and $0.69^{+0.16}_{-0.14}$ for the hosthalos of quasars and DLAs, with $\sim 0.2$ dex systematic uncertaintyassociated with redshift evolution, IGM parameters, and selection of datafitting range.

Modeling Lyman-\alpha\ Forest Cross-Correlations with LyMAS