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Engineering a Compact Bit-Sliced Signature Index for Approximate Search on Genomic Data

Florian Gauger
2018
Compact Bit-Sliced Signature Index This chapter gives an in-depth explanation of the Compact Bit-Sliced Signature Index (COBS).  ...  Compact Bit-Sliced Signature Index . Evaluation  ... 
doi:10.5445/ir/1000083201 fatcat:kgsxx22inzh77o3wejx4bds5g4

Improving the Compact Bit-Sliced Signature Index COBS for Large Scale Genomic Data

Daniel Ferizovic
2020
In this thesis we investigate the potential for improving the Compact Bit-Sliced Signature Index (COBS) [BBGI19] for large scale genomic data.  ...  COBS was developed by Bingmann et al. and is an inverted text index based on Bloom filters.  ...  COBS Compaction COBS Compaction The problem that arises with compact COBS lies in how the bit-sliced matrix is constructed.  ... 
doi:10.5445/ir/1000121162 fatcat:h5pdeysypbbwtlos4pzmlwwuiu

Fast Processing and Querying of 170TB of Genomics Data via a Repeated And Merged BloOm Filter (RAMBO) [article]

Gaurav Gupta, Minghao Yan, Benjamin Coleman, Bryce Kille, R. A. Leo Elworth, Tharun Medini, Todd Treangen, Anshumali Shrivastava
2022 arXiv   pre-print
We propose a data structure for search called RAMBO (Repeated And Merged BloOm Filter) which is significantly faster in query time than state-of-the-art genome indexing methods- COBS (Compact bit-sliced  ...  signature index), Sequence Bloom Trees, HowDeSBT, and SSBT.  ...  By removing the hierarchy, BIGSI and its recent follow-up COBS (Compact bit-sliced signature index) [6] obtained substantial memory savings compared to SBTs.  ... 
arXiv:1910.04358v4 fatcat:pff3j76wnbayxgoq7qvdkmx5by

RAMBO: Repeated And Merged BloOm Filter for Ultra-fast Multiple Set Membership Testing (MSMT) on Large-Scale Data [article]

Gaurav Gupta, Minghao Yan, Benjamin Coleman, R. A. Leo Elworth, Tharun Medini, Todd Treangen, Anshumali Shrivastava
2020 arXiv   pre-print
methods: COBS (Compact bit-sliced signature index), Sequence Bloom Trees (a Bloofi based implementation), HowDeSBT, SSBT, and document indexing methods like BitFunnel.  ...  The simplicity of the algorithm and embarrassingly parallel architecture allows us to index a 170 TB genome dataset in a mere 14 hours on a cluster of 100 nodes while competing methods require weeks.  ...  Baselines: We compare our methods with COBS (Compact bit-sliced signature index) [6] (Index based on array of Bloom Filters) and the Bloom Filter tree-based methods, SSBT [20] and HowDeSBT [16] .  ... 
arXiv:1910.02611v2 fatcat:6brzkwe23bhczke3ytm3qgpzy4

Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences

Grace A. Blackwell, Martin Hunt, Kerri M. Malone, Leandro Lima, Gal Horesh, Blaise T. F. Alako, Nicholas R. Thomson, Zamin Iqbal, William P. Hanage
2021 PLoS Biology  
We produced a searchable COmpact Bit-sliced Signature (COBS) index, facilitating the easy interrogation of the entire dataset for a specific sequence (e.g., gene, mutation, or plasmid).  ...  We believe that this combination of uniform processing and variety of search/filter functionalities will make this a resource of very wide utility.  ...  We would also like to thank John Lees for his helpful guidance and support when creating the pp-sketch index of the 661K assemblies.  ... 
doi:10.1371/journal.pbio.3001421 pmid:34752446 pmcid:PMC8577725 fatcat:vv35flueoban7b3uvr4r7gozae

Contributions to Khovanov Homology [article]

Stephan M. Wehrli
2008 arXiv   pre-print
Khovanov homology ist a new link invariant, discovered by M. Khovanov, and used by J. Rasmussen to give a combinatorial proof of the Milnor conjecture.  ...  In this context, we develop a theory of Carter--Saito movie moves for framed link cobordisms.  ...  [Ra, Corollary Obstructions to sliceness A knot K ⊂ R 3 × {0} is called a slice knot if it bounds a smooth disk S ⊂ R 3 × (−∞, The multivariable Levine-Tristram signature defined in [CF] is also an  ... 
arXiv:0810.0778v1 fatcat:bwlpli3hf5gcziwp7jam5eryzm

Stable moduli spaces of hermitian forms [article]

Fabian Hebestreit, Wolfgang Steimle
2021 arXiv   pre-print
The method of proof is abstracted from work of Galatius and Randal-Williams on cobordism categories of manifolds using the identification of the Grothendieck-Witt space of a Poincar\'e category as the  ...  Lemma Let C be a stable category equipped with a weight structure. Then there exists a weight structure on Q n (C) such that an object ϕ : TwAr  ...  We begin by observing that if (D, Ϙ) is a weighted Poincaré category then for every n the Poincaré category Q n (D, Ϙ) inherits a weight structure: A.1. 3.  ... 
arXiv:2103.13911v2 fatcat:vzz3jljo7rfillck6ygh3nj3he

Hermitian K-theory for stable ∞-categories II: Cobordism categories and additivity [article]

Baptiste Calmès, Emanuele Dotto, Yonatan Harpaz, Fabian Hebestreit, Markus Land, Kristian Moi, Denis Nardin, Thomas Nikolaus, Wolfgang Steimle
2021 arXiv   pre-print
Our Grothendieck-Witt spectra are defined via a version of the hermitian Q-construction, and a novel feature of our approach is to interpret the latter as a cobordism category.  ...  This perspective also allows us to give a hermitian version – along with a concise proof – of the theorem of Blumberg, Gepner and Tabuada, and provides a cobordism theoretic description of the aforementioned  ...  with a new proof of the index theorems of Weiss and Williams.  ... 
arXiv:2009.07224v3 fatcat:ttfnvahhd5dpjfuvezdnqeviu4

Geometric transversality in higher genus Gromov-Witten theory [article]

Andreas Gerstenberger
2014 arXiv   pre-print
The construction of manifold structures and fundamental classes on the (compactified) moduli spaces appearing in Gromov-Witten theory is a long-standing problem.  ...  This article aims to generalise this from the case of surfaces of genus 0 dealt with in [CM07] to the general case, also using some of the methods from [IP03] and symplectic field theory, namely the compactness  ...  To present these problems and their solutions in a bit more detail, assume for simplicity that Σ a neighbourhood of b in the stratum of the stratification by signature on M that contains b and s. t.  ... 
arXiv:1309.1426v3 fatcat:imbs2vnifzgave725c7fs3t2z4

Khovanov homology and rational unknotting [article]

Damian Iltgen, Lukas Lewark, Laura Marino
2021 arXiv   pre-print
necessary to relate a knot to the unknot).  ...  While λ is a lower bound for the unknotting number, in fact more is true: λ is a lower bound for the proper rational unknotting number (the minimal number of rational tangle replacements preserving connectivity  ...  bound for the slice genus [Ras10] .  ... 
arXiv:2110.15107v1 fatcat:dvqgyu775vaoxlezifkcsyb3pq

Five Lectures on Khovanov Homology [article]

Paul Turner
2006 arXiv   pre-print
The lectures cover the basic definitions, important properties, a number of variants and some applications.  ...  vector space over Q), together with a module homomorphism, the counit, ǫ : V → R such that the bilinear form −, − : Recall that a 1+1-dimensional TQFT is a monoidal functor Cob 1+1 → Mod R where Cob 1  ...  If you want to prove existence of exotic smooth structure on R 4 you can do this if you are in possession of a knot which is topologically slice but not smoothly slice (slice means zero slice genus).  ... 
arXiv:math/0606464v1 fatcat:afy7xfev65hpter4biy6e7ntzy

The Classification of Two-Dimensional Extended Topological Field Theories [article]

Christopher J. Schommer-Pries
2014 arXiv   pre-print
The first develops a variant of higher Morse theory and uses it to obtain a combinatorial description of surfaces suitable for the higher categorical language used later.  ...  As an immediate corollary we obtain a concrete classification when the target is the symmetric monoidal bicategory of algebras, bimodules, and intertwiners over a fixed commutative ground ring.  ...  A signature is a collection Σ = (Σ f ) f ∈F of 2-dimensional globular sets indexed by (representatives of) the compact globular sets F .  ... 
arXiv:1112.1000v2 fatcat:umfh5fxfybc4thzs7j75fatipm

Life on Jackson Creek, Smith County, Texas: Archeological Investigations of a 14th Century Caddo Domicile at the Leaning Rock Site (41SM325)

Mark Walters, Leslie G. Cecil, Linda S. Cummings, J. Phil Dering, Jeffer R. Ferguson, Michael D. Glascock, Timothy K. Perttula, LeeAnna Schniebs, Harry J. Schafer, Jesse Todd, Chester P. Walker
2008 Index of Texas Archaeology Open Access Grey Literature from the Lone Star State  
It is common practice to also gin: sites informal names and after recording several hundred sites, selecting a name becomes a challenge.  ...  This was not a formal survey with transect lines. nor one using regularly spaced shovel tests. but was rather more of a "windshield"' type survey, consisting of driving across pasture lands looking at  ...  Perttula, who not only contributed the sections on decorated sherds and plain rims, but also edited the rest of the article, and donated an AMS date on a charred maize cob.  ... 
doi:10.21112/.ita.2008.1.24 fatcat:o6lfof55inf3ff7xiagt3crgkm

Software quality analysis with the use of computational intelligence

Marek Reformat, Witold Pedrycz, Nicolino J Pizzi
2003 Information and Software Technology  
There is a need to find a way to support quality related activities using data gathered during quality assurance processes, which involve humans.  ...  In particular, self-organizing maps and evolutionary-based developed decision trees are used to gain a better insight into the software data and to support a process of classification of software objects  ...  ), or multi-slice (4D data) images.  ... 
doi:10.1016/s0950-5849(03)00012-0 fatcat:diuzfrtrjrea7ldrennzileluy

Technical Design Report for PANDA Electromagnetic Calorimeter (EMC) [article]

PANDA Collaboration: W. Erni, B. Krusche, O. Wang, T. Held, M. Steinke, M. Bragadireanu, F. Giacoppo, E. Bialkowski, A. Kozela, A. Szczurek, E. Lisowski , B. Kamys, A. Magiera (+92 others)
2008 arXiv   pre-print
After a start signature the first eight bits are used as an address to select a readout chip.  ...  The next two bits are used to select one of four internal data registers into which the following 10 data bits are written.  ... 
arXiv:0810.1216v1 fatcat:ol2l5bflubarjaeqbhzd3pezhm
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