In tandem mass spectrometry (MS/MS)-based proteomics, search engines rely on comparison between an experimental MS/MS spectrum and the theoretical spectra of the candidate peptides. Hence, accurate prediction of the theoretical spectra of peptides appears to be particularly important. Here, we present pDeep, a deep neural network-based model for the spectrum prediction of peptides. Using the bidirectional long short-term memory (BiLSTM), pDeep can predict higher-energy collisional dissociation, electron-transfer dissociation, and electron-transfer and higher-energy collision dissociation MS/MS spectra of peptides with >0.9 median Pearson correlation coefficients. Further, we showed that intermediate layer of the neural network could reveal physicochemical properties of amino acids, for example the similarities of fragmentation behaviors between amino acids. We also showed the potential of pDeep to distinguish extremely similar peptides (peptides that contain isobaric amino acids, for example, GG = N, AG = Q, or even I = L), which were very difficult to distinguish using traditional search engines.

Depth sensing is crucial for 3D reconstruction and scene understanding. Active depth sensors provide dense metric measurements, but often suffer from limitations such as restricted operating ranges, low spatial resolution, sensor interference, and high power consumption. In this paper, we propose a deep learning (DL) method to estimate per-pixel depth and its uncertainty continuously from a monocular video stream, with the goal of effectively turning an RGB camera into an RGB-D camera. Unlike prior DL-based methods, we estimate a depth probability distribution for each pixel rather than a single depth value, leading to an estimate of a 3D depth probability volume for each input frame. These depth probability volumes are accumulated over time under a Bayesian filtering framework as more incoming frames are processed sequentially, which effectively reduces depth uncertainty and improves accuracy, robustness, and temporal stability. Compared to prior work, the proposed approach achieves more accurate and stable results, and generalizes better to new datasets. Experimental results also show the output of our approach can be directly fed into classical RGB-D based 3D scanning methods for 3D scene reconstruction.

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