22 research outputs found
String Reconstruction from Substring Compositions
Motivated by mass-spectrometry protein sequencing, we consider a
simply-stated problem of reconstructing a string from the multiset of its
substring compositions. We show that all strings of length 7, one less than a
prime, or one less than twice a prime, can be reconstructed uniquely up to
reversal. For all other lengths we show that reconstruction is not always
possible and provide sometimes-tight bounds on the largest number of strings
with given substring compositions. The lower bounds are derived by
combinatorial arguments and the upper bounds by algebraic considerations that
precisely characterize the set of strings with the same substring compositions
in terms of the factorization of bivariate polynomials. The problem can be
viewed as a combinatorial simplification of the turnpike problem, and its
solution may shed light on this long-standing problem as well. Using well known
results on transience of multi-dimensional random walks, we also provide a
reconstruction algorithm that reconstructs random strings over alphabets of
size in optimal near-quadratic time
A New Algebraic Approach for String Reconstruction from Substring Compositions
We consider the problem of binary string reconstruction from the multiset of
its substring compositions, i.e., referred to as the substring composition
multiset, first introduced and studied by Acharya et al. We introduce a new
algorithm for the problem of string reconstruction from its substring
composition multiset which relies on the algebraic properties of the equivalent
bivariate polynomial formulation of the problem. We then characterize specific
algebraic conditions for the binary string to be reconstructed that guarantee
the algorithm does not require any backtracking through the reconstruction,
and, consequently, the time complexity is bounded polynomially. More
specifically, in the case of no backtracking, our algorithm has a time
complexity of compared to the algorithm by Acharya et al., which has a
time complexity of , where is the length of the binary
string. Furthermore, it is shown that larger sets of binary strings are
uniquely reconstructable by the new algorithm and without the need for
backtracking leading to codebooks of reconstruction codes that are larger, by a
linear factor in size, compared to the previously known construction by
Pattabiraman et al., while having reconstruction complexity
On the Parikh-de-Bruijn grid
We introduce the Parikh-de-Bruijn grid, a graph whose vertices are
fixed-order Parikh vectors, and whose edges are given by a simple shift
operation. This graph gives structural insight into the nature of sets of
Parikh vectors as well as that of the Parikh set of a given string. We show its
utility by proving some results on Parikh-de-Bruijn strings, the abelian analog
of de-Bruijn sequences.Comment: 18 pages, 3 figures, 1 tabl
Reconstruction of Rooted Directed Trees
Let T be a rooted directed tree on n vertices, rooted at v. The rooted subtree frequency vector (RSTF-vector) of T with root v, denoted by rstf(T, v) is a vector of length n whose entry at position k is the number of subtrees of T that contain v and have exactly k vertices. In this paper we present an algorithm for reconstructing rooted directed trees from their rooted subtree frequencies (up to isomorphism). We show that there are examples of nonisomorphic pairs of rooted directed trees that are RSTF-equivalent, that is they share the same rooted subtree frequency vectors. We have found all such pairs (groups) for small sizes by using exhaustive computer search. We show that infinitely many nonisomorphic RSTF-equivalent pairs of trees exist by constructing infinite families of examples
Reconstruction Codes for DNA Sequences with Uniform Tandem-Duplication Errors
DNA as a data storage medium has several advantages, including far greater
data density compared to electronic media. We propose that schemes for data
storage in the DNA of living organisms may benefit from studying the
reconstruction problem, which is applicable whenever multiple reads of noisy
data are available. This strategy is uniquely suited to the medium, which
inherently replicates stored data in multiple distinct ways, caused by
mutations. We consider noise introduced solely by uniform tandem-duplication,
and utilize the relation to constant-weight integer codes in the Manhattan
metric. By bounding the intersection of the cross-polytope with hyperplanes, we
prove the existence of reconstruction codes with greater capacity than known
error-correcting codes, which we can determine analytically for any set of
parameters.Comment: 11 pages, 2 figures, Latex; version accepted for publicatio
Reconstruction of Trees from Jumbled and Weighted Subtrees
Let T be an edge-labeled graph, where the labels are from a finite alphabet Sigma. For a subtree U of T the Parikh vector of U is a vector of length |Sigma| which specifies the multiplicity of each label in U. We ask when T can be reconstructed from the multiset of Parikh vectors of all its subtrees, or all of its paths, or all of its maximal paths. We consider the analogous problems for weighted trees. We show how several well-known reconstruction problems on labeled strings, weighted strings and point sets on a line can be included in this framework. We present reconstruction algorithms and non-reconstructibility results, and extend the polynomial method, previously applied to jumbled strings [Acharya et al., SIAM J. on Discr. Math, 2015] and weighted strings [Bansal et al., CPM 2004], to deal with general trees and special tree classes