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/H13CO+ 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, CH3OH 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.