As architecture, systems, and data management communities pay greater attention to innovative big data systems and architecture, the pressure of benchmarking and evaluating these systems rises. However, the complexity, diversity, frequently changed workloads, and rapid evolution of parison with the traditional benchmarks: including PAR-SEC, HPCC, and SPECCPU, big data applications have very low operation intensity, which measures the ratio of the total number of instructions divided by the total byte number of memory accesses; Second, the volume of data input has non-negligible impact on micro-architecture characteristics, which may impose challenges for simulation-based big data architecture research; Last but not least, corroborating the observations in CloudSuite and DCBench (which use smaller data inputs), we find that the numbers of L1 instruction cache (L1I) misses per 1000 instructions (in short, MPKI) of the big data applications are higher than in the traditional benchmarks; also, we find that L3 caches are effective for the big data applications, corroborating the observation in DCBench.
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.
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