Minimizing Congestion for Balanced Dominators
A primary challenge in metagenomics is reconstructing individual microbial genomes from the mixture of short fragments created by sequencing. Recent work leverages the sparsity of the assembly graph to find \(r\)-dominating sets which enable rapid approximate queries through a dominator-centric grap...
Gespeichert in:
| Veröffentlicht in: | arXiv.org |
|---|---|
| Hauptverfasser: | , , |
| Format: | Paper |
| Sprache: | Englisch |
| Veröffentlicht: |
Ithaca
Cornell University Library, arXiv.org
01.07.2022
|
| Schlagworte: | |
| ISSN: | 2331-8422 |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| Abstract | A primary challenge in metagenomics is reconstructing individual microbial genomes from the mixture of short fragments created by sequencing. Recent work leverages the sparsity of the assembly graph to find \(r\)-dominating sets which enable rapid approximate queries through a dominator-centric graph partition. In this paper, we consider two problems related to reducing uncertainty and improving scalability in this setting. First, we observe that nodes with multiple closest dominators necessitate arbitrary tie-breaking in the existing pipeline. As such, we propose finding \(\textit{sparse}\) dominating sets which minimize this effect via a new \(\textit{congestion}\) parameter. We prove minimizing congestion is NP-hard, and give an \(\mathcal{O}(\sqrt{\Delta^r})\) approximation algorithm, where \(\Delta\) is the max degree. To improve scalability, the graph should be partitioned into uniformly sized pieces, subject to placing vertices with a closest dominator. This leads to \(\textit{balanced neighborhood partitioning}\): given an \(r\)-dominating set, find a partition into connected subgraphs with optimal uniformity so that each vertex is co-assigned with some closest dominator. Using variance of piece sizes to measure uniformity, we show this problem is NP-hard iff \(r\) is greater than \(1\). We design and analyze several algorithms, including a polynomial-time approach which is exact when \(r=1\) (and heuristic otherwise). We complement our theoretical results with computational experiments on a corpus of real-world networks showing sparse dominating sets lead to more balanced neighborhood partitionings. Further, on the metagenome \(\textsf{HuSB1}\), our approach maintains high query containment and similarity while reducing piece size variance. |
|---|---|
| AbstractList | A primary challenge in metagenomics is reconstructing individual microbial genomes from the mixture of short fragments created by sequencing. Recent work leverages the sparsity of the assembly graph to find \(r\)-dominating sets which enable rapid approximate queries through a dominator-centric graph partition. In this paper, we consider two problems related to reducing uncertainty and improving scalability in this setting. First, we observe that nodes with multiple closest dominators necessitate arbitrary tie-breaking in the existing pipeline. As such, we propose finding \(\textit{sparse}\) dominating sets which minimize this effect via a new \(\textit{congestion}\) parameter. We prove minimizing congestion is NP-hard, and give an \(\mathcal{O}(\sqrt{\Delta^r})\) approximation algorithm, where \(\Delta\) is the max degree. To improve scalability, the graph should be partitioned into uniformly sized pieces, subject to placing vertices with a closest dominator. This leads to \(\textit{balanced neighborhood partitioning}\): given an \(r\)-dominating set, find a partition into connected subgraphs with optimal uniformity so that each vertex is co-assigned with some closest dominator. Using variance of piece sizes to measure uniformity, we show this problem is NP-hard iff \(r\) is greater than \(1\). We design and analyze several algorithms, including a polynomial-time approach which is exact when \(r=1\) (and heuristic otherwise). We complement our theoretical results with computational experiments on a corpus of real-world networks showing sparse dominating sets lead to more balanced neighborhood partitionings. Further, on the metagenome \(\textsf{HuSB1}\), our approach maintains high query containment and similarity while reducing piece size variance. |
| Author | Mizutani, Yosuke Sullivan, Blair D Staker, Annie |
| Author_xml | – sequence: 1 givenname: Yosuke surname: Mizutani fullname: Mizutani, Yosuke – sequence: 2 givenname: Annie surname: Staker fullname: Staker, Annie – sequence: 3 givenname: Blair surname: Sullivan middlename: D fullname: Sullivan, Blair D |
| BookMark | eNotjk1PAjEUABujiYj8AG-beO76-vq5R11FTSBcuJPu7ispgVa7YIy_XhI9zW1mbthlyokYuxNQK6c1PPjyHb9qFAJrAY2VF2yCUgruFOI1m43jDgDQWNRaThhfxhQP8SembdXmtKXxGHOqQi7Vk9_71NNQPedDTP6Yy3jLroLfjzT755St5y_r9o0vVq_v7eOCe42Wk1N-aJyxgaALZEihCR1ZLRR1DnrtXSM6wGA6K0AqKcEi9iSGxhupnZyy-z_tR8mfp_PSZpdPJZ2LGzQCtXFOW_kL5UdFRA |
| ContentType | Paper |
| Copyright | 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
| Copyright_xml | – notice: 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
| DBID | 8FE 8FG ABJCF ABUWG AFKRA AZQEC BENPR BGLVJ CCPQU DWQXO HCIFZ L6V M7S PHGZM PHGZT PIMPY PKEHL PQEST PQGLB PQQKQ PQUKI PRINS PTHSS |
| DOI | 10.48550/arxiv.2112.10973 |
| DatabaseName | ProQuest SciTech Collection ProQuest Technology Collection Materials Science & Engineering Collection ProQuest Central (Alumni) ProQuest Central UK/Ireland ProQuest Central Essentials - QC ProQuest Central Technology collection ProQuest One Community College ProQuest Central SciTech Premium Collection ProQuest Engineering Collection Engineering Database Proquest Central Premium ProQuest One Academic ProQuest Publicly Available Content Database ProQuest One Academic Middle East (New) ProQuest One Academic Eastern Edition (DO NOT USE) ProQuest One Applied & Life Sciences ProQuest One Academic (retired) ProQuest One Academic UKI Edition ProQuest Central China Engineering Collection |
| DatabaseTitle | Publicly Available Content Database Engineering Database Technology Collection ProQuest One Academic Middle East (New) ProQuest Central Essentials ProQuest One Academic Eastern Edition ProQuest Central (Alumni Edition) SciTech Premium Collection ProQuest One Community College ProQuest Technology Collection ProQuest SciTech Collection ProQuest Central China ProQuest Central ProQuest One Applied & Life Sciences ProQuest Engineering Collection ProQuest One Academic UKI Edition ProQuest Central Korea Materials Science & Engineering Collection ProQuest Central (New) ProQuest One Academic ProQuest One Academic (New) Engineering Collection |
| DatabaseTitleList | Publicly Available Content Database |
| Database_xml | – sequence: 1 dbid: PIMPY name: Publicly Available Content Database url: http://search.proquest.com/publiccontent sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Physics |
| EISSN | 2331-8422 |
| Genre | Working Paper/Pre-Print |
| GroupedDBID | 8FE 8FG ABJCF ABUWG AFKRA ALMA_UNASSIGNED_HOLDINGS AZQEC BENPR BGLVJ CCPQU DWQXO FRJ HCIFZ L6V M7S M~E PHGZM PHGZT PIMPY PKEHL PQEST PQGLB PQQKQ PQUKI PRINS PTHSS |
| ID | FETCH-LOGICAL-a527-e84ad9867fe0bfe6e426fbe7514eb80c5a891b02f6b71034330722ce1d9a63583 |
| IEDL.DBID | BENPR |
| IngestDate | Mon Jun 30 09:18:10 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | false |
| IsScholarly | false |
| Language | English |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-a527-e84ad9867fe0bfe6e426fbe7514eb80c5a891b02f6b71034330722ce1d9a63583 |
| Notes | SourceType-Working Papers-1 ObjectType-Working Paper/Pre-Print-1 content type line 50 |
| OpenAccessLink | https://www.proquest.com/docview/2612568857?pq-origsite=%requestingapplication% |
| PQID | 2612568857 |
| PQPubID | 2050157 |
| ParticipantIDs | proquest_journals_2612568857 |
| PublicationCentury | 2000 |
| PublicationDate | 20220701 |
| PublicationDateYYYYMMDD | 2022-07-01 |
| PublicationDate_xml | – month: 07 year: 2022 text: 20220701 day: 01 |
| PublicationDecade | 2020 |
| PublicationPlace | Ithaca |
| PublicationPlace_xml | – name: Ithaca |
| PublicationTitle | arXiv.org |
| PublicationYear | 2022 |
| Publisher | Cornell University Library, arXiv.org |
| Publisher_xml | – name: Cornell University Library, arXiv.org |
| SSID | ssj0002672553 |
| Score | 1.799344 |
| SecondaryResourceType | preprint |
| Snippet | A primary challenge in metagenomics is reconstructing individual microbial genomes from the mixture of short fragments created by sequencing. Recent work... |
| SourceID | proquest |
| SourceType | Aggregation Database |
| SubjectTerms | Algorithms Apexes Congestion Neighborhoods Parameter identification Partitioning Polynomials |
| Title | Minimizing Congestion for Balanced Dominators |
| URI | https://www.proquest.com/docview/2612568857 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV09T8MwED1BCxIT3-KjVBlYQ1Pnw86E1NIKhlYRdChTZTsXKQNJSUqF-PX4TAoDEgtjlAyxHd893728B3At-9rLNHIXZZaaA4pQbhxLokCZZMBILSZV1myCT6diPo-TpuBWN7TKTUy0gTotNdXIeyR1FUZChPx2-eqSaxR1VxsLjW1ok1JZ0IL2YDRNHr-rLCziBjP7X-1MK97Vk9V7vr4xjzMr3-j_CsI2s4z3__tOB9BO5BKrQ9jC4gh2LaNT18fgTvIif8k_TGpyhmVBbSSzBI7BqM6A6IwaU-euJCIM-e2cwGw8mg3v3cYbwZUhMzMrApnGIuIZeirDCE2izRRyA39QCU-HUsR95bEsUgZC-IFvtjJjGvtpLA3EEP4ptIqywDNwQrvPSQeQpOS1p1Sg-6HmIZeISqbn0NkMftF83_XiZ-QXf9--hD1GPwxYgmsHWqvqDa9gR69XeV11m-XqEuPyyVwlD5Pk-RPru6HX |
| linkProvider | ProQuest |
| linkToHtml | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMw1V07T8MwED6VFgQTb_EokAHG0MR52BkQEi1Vqz5UiQ7dKtu5SBlISlPK4z_xH7HdFgYkNgbmSJZ1vtx35_v8HcAld6WTSKQ28iRWBQoTdhRxTYFSYEC0WkwszLAJ2u-z0SgalOBj9RZG0ypXMdEE6jiX-o68pqWugpCxgN5Onmw9NUp3V1cjNBZu0cG3F1WyFTfthjrfK0Ka98N6y15OFbB5QNSemM_jiIU0QUckGKKCqEQgVYkDCubIgLPIFQ5JQqHA1_NVvU8JkejGEVfgzDy17BpUfB38DVPw4etKh4RUJejeondqlMJqfPqazq9VkUWMVqT3I-IbGGtu_zMD7EBlwCc43YUSZnuwYdiqstgHu5dm6WP6rmDXqueZbpEp97JU_m3daaqmxNhq5Jrko2cJHcDwLzZ4COUsz_AIrMDEMK1xqGXypSOEL91A0oByRMHjY6iubD1e_rvF-NvQJ79_voDN1rDXHXfb_c4pbBH9MMIQeatQnk2f8QzW5XyWFtNz4ycWjP_4WD4Boqb4nQ |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Minimizing+Congestion+for+Balanced+Dominators&rft.jtitle=arXiv.org&rft.au=Mizutani%2C+Yosuke&rft.au=Staker%2C+Annie&rft.au=Sullivan%2C+Blair+D&rft.date=2022-07-01&rft.pub=Cornell+University+Library%2C+arXiv.org&rft.eissn=2331-8422&rft_id=info:doi/10.48550%2Farxiv.2112.10973 |