© The Authors 2025.Context. Physical and chemical properties, such as kinetic temperature, volume density, and molecular composition of interstellar clouds are inherent in their line spectra at submillimeter wavelengths. Therefore, the spectral line profiles could be used to estimate the physical conditions of a given source. Aims. We present a new bottom-up approach, based on machine learning (ML) algorithms, to extract the physical conditions in a straightforward way from the line profiles without using radiative transfer equations. Methods. We simulated, for the typical physical conditions of dense molecular clouds and star-forming regions, the emission in spectral lines of the two isomers HCN and HNC, from J = 1 0 to J = 5 4 between 30 and 500 GHz, which are commonly observed in dense molecular clouds and star forming regions. The generated data cloud distribution has been parametrised using the line intensities and widths to enable a new way to analyse the spectral line profiles and to infer the physical conditions of the region. The line profile parameters have been charted to the HNC/HCN ratio and the excitation temperature of the molecule(s). Three ML algorithms have been trained, tested, and compared aiming to unravel the excitation conditions of HCN and HNC and their abundance ratio. Results. Machine learning results obtained with two spectral lines, one for each isomer HCN and HNC, have been compared with the local thermodynamic equilibrium (LTE) analysis for the cold source R CrA IRS 7B. The estimate of the excitation temperature and of the abundance ratio, in this case considering the two spectral lines, is in agreement with our LTE analysis. The complete optimisation procedure of the algorithms (training, testing, and prediction of the target quantities) have the potential to predict interstellar cloud properties from line profile inputs at lower computational cost than before. Conclusions. It is the first time that the spectral line profiles are m...