Density peaks clustering algorithm (DPC) relies on local-density and relative-distance of dataset to find cluster centers. However, the calculation of these attributes is based on Euclidean distance simply, and DPC is not satisfactory when dataset's density is uneven or dimension is higher. In ...
Section 4 describes how mass-based clustering can be obtained by simply replacing distance measure with mass-based dissimilarity in an existing density-based clustering algorithm. It also provides the analyses on the condition under which mass-based clustering performs better than density-based ...
Fast mass spectrometry search and clustering of untargeted metabolomics data Article 02 January 2024 Introduction Molecular networking (MN)1 within the GNPS web platform (http://gnps.ucsd.edu)2 has been used for the analysis of nontargeted mass spectrometry data in various fields3,4. MN relies ...
aPeakDecoder algorithm. Step-1: data is processed in untargeted mode (UFD, MS-DIAL) to extract all precursor ion features (MS1) and their respective deconvoluted fragment ions (pseudo MS2) based on co-elution and co-mobility. Step-2: a preliminary training set is generated by using the dete...
The present work provides an automatic data analysis workflow (AntDAS2) by developing three novel algorithms, as follows: (i) a density-based ion clustering algorithm is designed for extracted-ion chromatogram extraction from high-resolution mass spectrometry; (ii) a new maximal value-based peak ...
Violin shapes show the kernel density estimation of the data distribution and the median as white dot. Thick black bars denote the interquartile range. d, Specific nucleotide sequence motifs in 5′ UTRs of mRNAs contribute to the prediction of protein levels in a subset of tissues. Clustering ...
Therefore, in this paper, a combination of kernel density estimation (KDE) and the density-based spatial clustering of applications with noise (DBSCAN) algorithm was used to complete the rock discontinuity clustering. First, the KDE algorithm was used to identify the peaks representing the direction...
biomarker signatures by taking the most differential features (by statistical significance, biological plausibility, or both) via supervised or unsupervised clustering methods, and test if their relative expression can separate healthy and disease samples. For HCM, this was demonstrated in a recent ...
such that only interactions above this score were included in the predicted networks. Networks were clustered by the Markov clustering (MCL) algorithm with inflation parameter set as 3 (indirectly related to the precision of the clustering, i.e., the higher the inflation, the more abundant the ...