  In the central regions of active galaxies, dense molecular medium are exposed
to various types of radiation and energy injections, such as UV, X-ray, cosmic
ray, and shock dissipation. With the rapid progress of chemical models and
implementation of new-generation mm/submm interferometry, we are now able to
use molecules as powerful diagnostics of the physical and chemical processes in
galaxies. Here we give a brief overview on the recent ALMA results to
demonstrate how molecules can reveal underlying physical and chemical processes
in galaxies. First, new detections of Galactic molecular absorption systems
with elevated HCO/H$^{13}$CO$^+$ column density ratios are reported, indicating
that these molecular media are irradiated by intense UV fields. Second, we
discuss the spatial distributions of various types of shock tracers including
HNCO, CH$_3$OH and SiO in NGC 253 and NGC 1068. Lastly, we provide an overview
of proposed diagnostic methods of nuclear energy sources using ALMA, with an
emphasis on the synergy with sensitive mid-infrared spectroscopy, which will be
implemented by JWST and SPICA to disentangle the complex nature of heavily
obscured galaxies across the cosmic time.
