With the advent of ALMA, complete surveys of gas and dust in protoplanetary disks are being carried out in different star forming regions. In particular, continuum emission is used to trace the large (mm-sized) dust grains and CO isotopologues are observed in order to trace the bulk of the gas. The attempt is to simultaneously constrain the gas and dust disk mass as well as the gas/dust mass ratio. In this work the observations from the Lupus disk survey have been analyzed with thermo-chemical disk models, including radiative transfer, CO isotope-selective processes and freeze-out. We find that CO-based gas masses are very low, often smaller than 1MJ. Moreover, gas/dust mass ratios are much lower than value of 100 found in the ISM, being mainly between 1 and 10. This result can be interpreted either as rapid loss of gas, or as a chemical effect removing carbon from CO and locking it into more complex molecules or in larger bodies. Current data cannot distinguish between the two scenarios (except for sources with detected HD lines), but future observations of e.g. [CI] and hydrocarbon lines will help to calibrate CO-based gas masses and to constrain disk gas masses.