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Abstract For submillimeter spectroscopy with ground-based single-dish telescopes, removing the noise contribution from the Earth’s atmosphere and the instrument is essential. For this purpose, here we propose a new method based on a data-scientific approach. The key technique is statistical matrix decomposition that automatically separates the signals of astronomical emission lines from the drift noise components in the fast-sampled (1–10 Hz) time-series spectra obtained by a position-switching (PSW) observation. Because the proposed method does not apply subtraction between two sets of noisy data (i.e., on-source and off-source spectra), it improves the observation sensitivity by a factor of $\sqrt{2}$. It also reduces artificial signals such as baseline ripples on a spectrum, which may also help to improve the effective sensitivity. We demonstrate this improvement by using the spectroscopic data of emission lines toward a high-redshift galaxy observed with a 2 mm receiver on the 50 m Large Millimeter Telescope. Since the proposed method is carried out offline and no additional measurements are required, it offers an instant improvement on the spectra reduced so far with the conventional method. It also enables efficient deep spectroscopy driven by the future 50 m class large submillimeter single-dish telescopes, where fast PSW observations by mechanical antenna or mirror drive are difficult to achieve.