Matches in SemOpenAlex for { <https://semopenalex.org/work/W4285709369> ?p ?o ?g. }
Showing items 1 to 62 of
62
with 100 items per page.
- W4285709369 abstract "When analyzing communities of microorganisms from their sequenced DNA, an important task is taxonomic profiling: enumerating the presence and relative abundance of all organisms, or merely of all taxa, contained in the sample. This task can be tackled via compressive-sensing-based approaches, which favor communities featuring the fewest organisms among those consistent with the observed DNA data. Despite their successes, these parsimonious approaches sometimes conflict with biological realism by overlooking organism similarities. Here, we leverage a recently developed notion of biological diversity that simultaneously accounts for organism similarities and retains the optimization strategy underlying compressive-sensing-based approaches. We demonstrate that minimizing biological diversity still produces sparse taxonomic profiles and we experimentally validate superiority to existing compressive-sensing-based approaches. Despite showing that the objective function is almost never convex and often concave, generally yielding NP-hard problems, we exhibit ways of representing organism similarities for which minimizing diversity can be performed via a sequence of linear programs guaranteed to decrease diversity. Better yet, when biological similarity is quantified by $k$-mer co-occurrence (a popular notion in bioinformatics), minimizing diversity actually reduces to one linear program that can utilize multiple $k$-mer sizes to enhance performance. In proof-of-concept experiments, we verify that the latter procedure can lead to significant gains when taxonomically profiling a metagenomic sample, both in terms of reconstruction accuracy and computational performance. Reproducible code is available at https://github.com/dkoslicki/MinimizeBiologicalDiversity." @default.
- W4285709369 created "2022-07-18" @default.
- W4285709369 creator A5002668669 @default.
- W4285709369 creator A5062027901 @default.
- W4285709369 date "2020-01-23" @default.
- W4285709369 modified "2023-09-30" @default.
- W4285709369 title "Finer Metagenomic Reconstruction via Biodiversity Optimization" @default.
- W4285709369 doi "https://doi.org/10.48550/arxiv.2001.08717" @default.
- W4285709369 hasPublicationYear "2020" @default.
- W4285709369 type Work @default.
- W4285709369 citedByCount "0" @default.
- W4285709369 crossrefType "posted-content" @default.
- W4285709369 hasAuthorship W4285709369A5002668669 @default.
- W4285709369 hasAuthorship W4285709369A5062027901 @default.
- W4285709369 hasBestOaLocation W42857093691 @default.
- W4285709369 hasConcept C104317684 @default.
- W4285709369 hasConcept C111919701 @default.
- W4285709369 hasConcept C119857082 @default.
- W4285709369 hasConcept C124101348 @default.
- W4285709369 hasConcept C130217890 @default.
- W4285709369 hasConcept C137858568 @default.
- W4285709369 hasConcept C15151743 @default.
- W4285709369 hasConcept C151730666 @default.
- W4285709369 hasConcept C153083717 @default.
- W4285709369 hasConcept C187191949 @default.
- W4285709369 hasConcept C18903297 @default.
- W4285709369 hasConcept C41008148 @default.
- W4285709369 hasConcept C55493867 @default.
- W4285709369 hasConcept C70721500 @default.
- W4285709369 hasConcept C86803240 @default.
- W4285709369 hasConceptScore W4285709369C104317684 @default.
- W4285709369 hasConceptScore W4285709369C111919701 @default.
- W4285709369 hasConceptScore W4285709369C119857082 @default.
- W4285709369 hasConceptScore W4285709369C124101348 @default.
- W4285709369 hasConceptScore W4285709369C130217890 @default.
- W4285709369 hasConceptScore W4285709369C137858568 @default.
- W4285709369 hasConceptScore W4285709369C15151743 @default.
- W4285709369 hasConceptScore W4285709369C151730666 @default.
- W4285709369 hasConceptScore W4285709369C153083717 @default.
- W4285709369 hasConceptScore W4285709369C187191949 @default.
- W4285709369 hasConceptScore W4285709369C18903297 @default.
- W4285709369 hasConceptScore W4285709369C41008148 @default.
- W4285709369 hasConceptScore W4285709369C55493867 @default.
- W4285709369 hasConceptScore W4285709369C70721500 @default.
- W4285709369 hasConceptScore W4285709369C86803240 @default.
- W4285709369 hasLocation W42857093691 @default.
- W4285709369 hasLocation W42857093692 @default.
- W4285709369 hasOpenAccess W4285709369 @default.
- W4285709369 hasPrimaryLocation W42857093691 @default.
- W4285709369 hasRelatedWork W1979856858 @default.
- W4285709369 hasRelatedWork W2073909558 @default.
- W4285709369 hasRelatedWork W2155652097 @default.
- W4285709369 hasRelatedWork W2203727450 @default.
- W4285709369 hasRelatedWork W2335964703 @default.
- W4285709369 hasRelatedWork W2786547608 @default.
- W4285709369 hasRelatedWork W2950883119 @default.
- W4285709369 hasRelatedWork W2953154619 @default.
- W4285709369 hasRelatedWork W2958564218 @default.
- W4285709369 hasRelatedWork W4307291644 @default.
- W4285709369 isParatext "false" @default.
- W4285709369 isRetracted "false" @default.
- W4285709369 workType "article" @default.