In mass spectrometry (MS) experiments, more than thousands of peaks are detected in the space of mass-to-charge ratio and chromatographic retention time, each associated with an abundance measurement. However, a large proportion of the peaks consists of experimental noise and low abundance compounds are typically masked by noise peaks, compromising the quality of the data. In this paper, we propose a new measure of similarity between a pair of MS experiments, called truncated rank correlation (TRC). To provide a robust metric of similarity in noisy high-dimensional data, TRC uses truncated top ranks (or top m-ranks) for calculating correlation. A comprehensive numerical study suggests that TRC outperforms traditional sample correlation and Kendall's τ. We apply TRC to measuring test-retest reliability of two MS experiments, including biological replicate analysis of the metabolome in HEK293 cells and metabolomic profiling of benign prostate hyperplasia (BPH) patients. An R package trc of the proposed TRC and related functions is available at https://sites.google.com/site/dhyeonyu/software.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1515/sagmb-2018-0056 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
GPU-Accelerated Solution of the Bethe-Salpeter Equation for Large and Heterogeneous Systems.
J Chem Theory Comput
December 2024
Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, United States.
We present a massively parallel GPU-accelerated implementation of the Bethe-Salpeter equation (BSE) for the calculation of the vertical excitation energies (VEEs) and optical absorption spectra of condensed and molecular systems, starting from single-particle eigenvalues and eigenvectors obtained with density functional theory. The algorithms adopted here circumvent the slowly converging sums over empty and occupied states and the inversion of large dielectric matrices through a density matrix perturbation theory approach and a low-rank decomposition of the screened Coulomb interaction, respectively. Further computational savings are achieved by exploiting the nearsightedness of the density matrix of semiconductors and insulators to reduce the number of screened Coulomb integrals.
View Article and Find Full Text PDFEfficient and scalable wave function compression using corner hierarchical matrices.
J Chem Phys
November 2024
Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA.
Article Synopsis
- Current methods like complete active space and full configuration interaction limit quantum chemists' ability to analyze strongly correlated electronic structures due to exponential scaling issues.
- The introduction of corner hierarchically approximated CI (CHACI) improves wave function compression using a new type of hierarchical matrix that benefits from low-rank decomposition techniques.
- Tests on the molecule dodecacene show that CHACI achieves better compression rates than traditional methods, with advantages from specific strategies like focusing on the upper-left corner of the CI vector, sorting the vector before compression, and optimizing block ranks for higher information density.
: Ultrafast Spectroscopy beyond the Fourier Limit Using Bayesian Inference.
J Phys Chem A
October 2024
Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan 48824, United States.
The discrete Fourier transform (dFT) plays a central role in many ultrafast experiments, allowing the recovery of spectroscopic observables from time-domain measurements. In resonant experiments when population relaxation and coherence components of the signal coexist, the dFT is usually preceded by multiexponential fitting to remove the large population term. However, this procedure results in errors in both the recovered decay rates and the line shapes of the coherence spectral components.
View Article and Find Full Text PDFOptimal survival analyses with prevalent and incident patients.
Lifetime Data Anal
October 2024
Department of Biostatistics, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
Period-prevalent cohorts are often used for their cost-saving potential in epidemiological studies of survival outcomes. Under this design, prevalent patients allow for evaluations of long-term survival outcomes without the need for long follow-up, whereas incident patients allow for evaluations of short-term survival outcomes without the issue of left-truncation. In most period-prevalent survival analyses from the existing literature, patients have been recruited to achieve an overall sample size, with little attention given to the relative frequencies of prevalent and incident patients and their statistical implications.
View Article and Find Full Text PDFSynthesis of higher-B CEST Z-spectra from lower-B data via deep learning and singular value decomposition.
NMR Biomed
December 2024
Center for Biomedical Imaging Research, Tsinghua University, Beijing, China.
Chemical exchange saturation transfer (CEST) MRI at 3 T suffers from low specificity due to overlapping CEST effects from multiple metabolites, while higher field strengths (B) allow for better separation of Z-spectral "peaks," aiding signal interpretation and quantification. However, data acquisition at higher B is restricted by equipment access, field inhomogeneity and safety issues. Herein, we aim to synthesize higher-B Z-spectra from readily available data acquired with 3 T clinical scanners using a deep learning framework.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!