Evidence map›Paper›PMID 36649383›Full record

ArticleResearch in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- )2022

A Fast, Provably Accurate Approximation Algorithm for Sparse Principal Component Analysis Reveals Human Genetic Variation Across the World.

Agniva Chowdhury, Aritra Bose, Samson Zhou, David P Woodruff, Petros Drineas

Abstract read
In one paragraph

Article in Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Agniva ChowdhuryComputer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN.
Aritra BoseComputational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY.ORCID 0000-0002-8665-056X
Samson ZhouSchool of Computer Science, Carnegie Mellon University, Pittsburgh, PA.
David P WoodruffSchool of Computer Science, Carnegie Mellon University, Pittsburgh, PA.
Petros DrineasDepartment of Computer Science, Purdue University, West Lafayette, IN.ORCID 0000-0003-1994-8670

Funding

Secure and Privacy-preserving Genome-wide and Phenome-wide Association Studies via Intel Software Guard Extensions (SGX)R01HG010798 · NHGRI · TRUSTEES OF INDIANA UNIVERSITY · PI TANG, HAIXU, WANG, XIAOFENG · 2019 to 2022
$1.4M
NHGRI NIH HHS R01 HG010798
6 · The paper itself

Abstract

Principal component analysis (PCA) is a widely used dimensionality reduction technique in machine learning and multivariate statistics. To improve the interpretability of PCA, various approaches to obtain sparse principal direction loadings have been proposed, which are termed Sparse Principal Component Analysis (SPCA). In this paper, we present ThreSPCA, a provably accurate algorithm based on thresholding the Singular Value Decomposition for the SPCA problem, without imposing any restrictive assumptions on the input covariance matrix. Our thresholding algorithm is conceptually simple; much faster than current state-of-the-art; and performs well in practice. When applied to genotype data from the 1000 Genomes Project, ThreSPCA is faster than previous benchmarks, at least as accurate, and leads to a set of interpretable biomarkers, revealing genetic diversity across the world.

Indexed as

Population StratificationPopulation StructurePrincipal Component AnalysisSparse PCA

Identifiers

PMID36649383
PMCPMC9836035

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.