Unsupervised Physics Informed Decomposition of Incomplete Time-Resolved Spectroscopy

Raman spectroscopy is often hindered by strong autofluorescence backgrounds, which are typically handled by waiting for fluorescence to bleach before recording the Raman spectrum. Here, we instead show that short, incomplete recordings of the bleaching process already contain enough information to recover the underlying Raman signal. We present the first unsupervised model that operates on short, incomplete, variable-length sequences of time-resolved spectra, decomposing them into Raman spectra and autofluorescence components while simultaneously removing measurement noise. Our VAE-based method simultaneously learns (i) a bank of fluorophore spectra comprising the baseline, (ii) a model of the measurement noise, and (iii) the distribution of Raman spectra and decay behavior. We evaluate our method on spectral reconstruction and downstream peak detection, where it outperforms state-of-the-art approaches on multiple simulated benchmarks as well as on a newly collected real-world dataset of spectral time series. We further show that fluorescence decay dynamics themselves contain discriminative information that may be exploited in future work.