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A deep learning strategy is developed for fast and accurate gas property measurements using flame emission spectroscopy (FES). Particularly, the short-gated fast FES is essential to resolve fast-evolving combustion behaviors. However, as the exposure time for capturing the flame emission spectrum gets shorter, the signal-to-noise ratio (SNR) decreases, and characteristic spectral features indicating the gas properties become relatively weaker. Then, the property estimation based on the short-gated spectrum is difficult and inaccurate. Denoising convolutional neural networks (CNN) can enhance the SNR of the short-gated spectrum. A new CNN architecture including a reversible down- and up-sampling (DU) operator and a loss function based on proper orthogonal decomposition (POD) coefficients is proposed. For training and testing the CNN, flame chemiluminescence spectra were captured from a stable methane-air flat flame using a portable spectrometer (spectral range: 250 - 850 nm, resolution: 0.5 nm) with varied equivalence ratio (0.8 - 1.2), pressure (1 - 10 bar), and exposure time (0.05, 0.2, 0.4, and 2 s). The long exposure (2 s) spectra were used as the ground truth when training the denoising CNN. A kriging model with POD is trained by the long-gated spectra for calibration, and then the prediction of the gas properties taking the denoised short-gated spectrum as the input: The property prediction errors of pressure and equivalence ratio were remarkably lowered in spite of the low SNR attendant with reduced exposure.