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Inferring Strings from Graphs and Arrays [chapter]

Hideo Bannai, Shunsuke Inenaga, Ayumi Shinohara, Masayuki Takeda
2003 Lecture Notes in Computer Science  
This paper introduces a new problem of inferring strings from graphs, and inferring strings from arrays.  ...  Given a graph G or an array A, we infer a string that suits the graph, or the array, under some condition.  ...  Conclusions and Open Problems In this paper we introduced a new challenging problem named string inference, where we infer strings from given graphs or arrays.  ... 
doi:10.1007/978-3-540-45138-9_15 fatcat:flrqhvyflrhgpexrewi2bag44u

Linear Time Inference of Strings from Cover Arrays using a Binary Alphabet [article]

Tanaeem M. Moosa, Sumaiya Nazeen, M. Sohel Rahman, Rezwana Reaz
2011 arXiv   pre-print
In this paper, we focus on the problem of linear time inference of strings from cover arrays using the least sized alphabet possible.  ...  This algorithm uses several interesting combinatorial properties of cover arrays and an interesting relation between border array and cover array to achieve this. Our algorithm runs in linear time.  ...  Smyth et al. discussed a possible solution of string inference problem from prefix arrays in [10] . Crochemore et al.  ... 
arXiv:1108.5422v1 fatcat:wj6t6so6kjawvd3r3easnjnjym

Subject Index

2004 Journal of Discrete Algorithms  
extraction Adaptive text mining: inferring structure from se- quences, 137 Genome comparison Replacing suffix trees with enhanced suffix arrays, 53 Genome rearrangements Structural properties and  ...  suffix trees with enhanced suffix arrays, 53 Phrase hierarchies Adaptive text mining: inferring structure from se- quences, 137 Phylogenetic tree Parametric multiple sequence alignment and phy- logeny  ... 
doi:10.1016/s1570-8667(04)00076-0 fatcat:3igwdxr5pba53eev4y6a2jzgie

Indeterminate string inference algorithms

Sumaiya Nazeen, M. Sohel Rahman, Rezwana Reaz
2012 Journal of Discrete Algorithms  
We also propose an O (n 2 ) algorithm for reconstructing an indeterminate string from suffix array and LCP array.  ...  We present two efficient algorithms to reconstruct an indeterminate string from a valid border array -one using an unbounded alphabet and the other using minimum sized alphabet.  ...  [4] solved the problem of regular string inference from directed acyclic subsequence graph and directed acyclic word graph, and from suffix array using minimal size alphabet in linear time.  ... 
doi:10.1016/j.jda.2011.08.002 fatcat:kliiisja3fedno3af2o6pmlkny

String Inference from the LCP Array [article]

Juha Kärkkäinen, Marcin Piątkowski, Simon J. Puglisi
2017 arXiv   pre-print
and if it is, reconstructing some string or all strings with that LCP array.  ...  In order to better understand the combinatorics of LCP arrays, we consider the problem of inferring a string from an LCP array, i.e., determining whether a given array of integers is a valid LCP array,  ...  For example, BCSSILA stands for Binary Cyclic String Set Inference from LCP Array.  ... 
arXiv:1606.04573v2 fatcat:jelifxb5drdo5cbjnpnii6g7gq

Inferring an indeterminate string from a prefix graph

Ali Alatabbi, M. Sohel Rahman, W.F. Smyth
2015 Journal of Discrete Algorithms  
It is known from CRSW13 that every feasible array is a prefix table of some indetermintate string.  ...  A prefix graph P = P_y is a labelled simple graph whose structure is determined by a feasible array y.  ...  [19] was the first paper to consider the more general problem of inferring an indeterminate string from a given data structure (specifically, border array, suffix array and LCP array).  ... 
doi:10.1016/j.jda.2014.12.006 fatcat:lcz4xtlvhfcv5bny4rsreqm26a

TypeDevil: Dynamic Type Inconsistency Analysis for JavaScript

Michael Pradel, Parker Schuh, Koushik Sen
2015 2015 IEEE/ACM 37th IEEE International Conference on Software Engineering  
The key idea is to assign a set of observed types to each variable, property, and function, to merge types based in their structure, and to warn developers about variables, properties, and functions that  ...  Applying TypeDevil to widely used benchmark suites and real-world web applications reveals 15 problematic type inconsistencies, including correctness problems, performance problems, and dangerous coding  ...  This research is supported in part by NSF Grants CCF-0747390, CCF-1018729, CCF-1423645, and CCF-1018730, by gifts from Mozilla and Samsung, and by the German Federal Ministry of Education and Research  ... 
doi:10.1109/icse.2015.51 dblp:conf/icse/PradelSS15 fatcat:l6mctuyilndjda5izq3nwbd6iu

A semantic tree algorithm for the generation of sextet polynomials of hexagonal systems

M.M. Balakrishnarajan, P. Venuvanalingam
1999 Computers and Mathematics with Applications  
Hexagons of the graph are defined as symbols and each node of the tree is defined as a set of mutually disjoint hexagon patterns of the graph.  ...  This is a #P Complete combinatorial enumeration problem, and artificial intelligence (AI) is employed for efficient enumeration.  ...  Adjacency table of Remnant graph List of hexagons Depth of the node Array of S(H;x) coefficients set of sextets and pendant edges Procedure TRAVERSE ( GRAPH VAR VAR DEPTH : VAR RESULT : VAR NODE  ... 
doi:10.1016/s0898-1221(99)00050-4 fatcat:yteyqjtonrezznqjjzavq6ufre

Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees [article]

Chris Whidden, Frederick A. Matsen IV
2017 arXiv   pre-print
Such graphs are used to better understand the behaviour of phylogenetic methods and recommend parameter choices and diagnostic criteria.  ...  We also develop the first efficient algorithms for constructing the nearest-neighbor interchange (NNI) and tree bisection-and-reconnection (TBR) graphs  ...  This is possible if the edge lists are stored as an array of expandable sorted arrays and each of the graph vertices are indexed by tree IDs.  ... 
arXiv:1606.08893v3 fatcat:6djums2tjjbn7fssrh6zsc6jke

Page 2948 of Mathematical Reviews Vol. , Issue 83h [page]

1983 Mathematical Reviews  
G.; Siromoney, Rani 83g:68112 On the generative capacity of compound string and array grammars. Inform. Sci. % (1982), no. 3, 231-241.  ...  As usual, the language generated is the set of terminal strings generated from the start symbol S.  ... 

Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees [chapter]

Chris Whidden, Frederick A. Matsen
2018 2018 Proceedings of the Fifteenth Workshop on Analytic Algorithmics and Combinatorics (ANALCO)  
Such graphs are used to better understand the behaviour of phylogenetic methods and recommend parameter choices and diagnostic criteria.  ...  stores tree adjacencies using such strings.  ...  This is possible if the edge lists are stored as an array of expandable sorted arrays and each of the graph vertices are indexed by tree IDs.  ... 
doi:10.1137/1.9781611975062.8 dblp:conf/analco/WhiddenM18 fatcat:qz4u7biu6vhtliqjwgbmq47hqa

Inferring a tree from walks

Osamu Maruyama, Satoru Miyano
1996 Theoretical Computer Science  
The tree inference from a walk is, given a string x of colors, finding the smallest tree that realizes a walk whose sequence of edge-colors coincides with x.  ...  It is also shown that the problem of inferring a linear chain from partial walks is NP-complete, while the linear chain inference from a single walk is known to be solvable in polynomial time.  ...  The first author's research is partly supported by Grants-in-Aid for JSPS research fellows from the Ministry of Education, Science and Culture, Japan.  ... 
doi:10.1016/0304-3975(95)00156-5 fatcat:neddyx3ljre3bnxsq72sisivsy

Wheeler graphs: A framework for BWT-based data structures

Travis Gagie, Giovanni Manzini, Jouni Sirén
2017 Theoretical Computer Science  
We show that if the state diagram of a finite-state automaton is a Wheeler graph then, by its path coherence, we can order the nodes such that, for any string, the nodes reachable from the initial state  ...  We first define Wheeler graphs and show they have a property we call path coherence.  ...  Hence, we can infer the position from the range and store just the character a in the succinct representation (Lemma 4). A generalization [44] of PBWT relaxes the requirements.  ... 
doi:10.1016/j.tcs.2017.06.016 pmid:29276331 pmcid:PMC5727778 fatcat:lon5o2wmwravdnyifdf3uvuate

Mathematics of Digital Hyperspace [article]

Jeremy Kepner, Timothy Davis, Vijay Gadepally, Hayden Jananthan, Lauren Milechin
2021 arXiv   pre-print
With the addition of key based indices (such as pointers to strings) and semilinks, GraphBLAS can become a richer associative array algebra and be a plug-in replacement for spreadsheets, database tables  ...  The GraphBLAS standard currently supports hypergraphs, hypersparse matrices, the mathematics required for semilinks, and seamlessly performs graph, network, and matrix operations.  ...  Construction of an adjacency array of a graph from its incidence arrays via array multiply.  ... 
arXiv:2103.15203v1 fatcat:zq767tvhlzftzgomzsdxj3p2zq

Efficient construction of an assembly string graph using the FM-index

J. T. Simpson, R. Durbin
2010 Bioinformatics  
Here, we show how to use suffix array-based methods that have formed the basis of recent very fast sequence mapping algorithms to find overlaps and generate assembly string graphs asymptotically faster  ...  As well as an approach that finds all overlaps then implements transitive reduction to produce a string graph, we show how to output directly only the irreducible overlaps, significantly shrinking memory  ...  ACKNOWLEDGEMENTS We thank Veli Mäkinen and members of the Durbin group for discussions related to string matching and sequence assembly. Conflict of interest: none declared.  ... 
doi:10.1093/bioinformatics/btq217 pmid:20529929 pmcid:PMC2881401 fatcat:jyzibj7ec5ahxgzktbm725yesa
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