The principle possibility of extraction of fluorescence of nanoparticles in the presence of background autofluorescence of a biological environment using neural network algorithms is demonstrated. It is shown that the methods used allow detection of carbon nanoparticles fluorescence against the background of the autofluorescence of egg white with a sufficiently low concentration detection threshold (not more than 2 μg/ml for carbon dots 3 μg/ml and for nanodiamonds). It was also shown that the use of the input data compression can further improve the accuracy of solving the inverse problem by 1.5 times.