Related papers: Reconstructing Mixtures of Coded Strings from Pref…
This paper deals with developing techniques for the reconstruction of high-dimensional datasets given each bivariate projection, as would be found in a matrix scatterplot. A graph-based solution is introduced, involving clique-finding,…
Network reconstruction consists in retrieving the hidden interaction structure of a system from observations. Many reconstruction algorithms have been proposed, although less research has been devoted to describe their theoretical…
We study the new problem of Huffman-like codes subject to individual restrictions on the code-word lengths of a subset of the source words. These are prefix codes with minimal expected code-word length for a random source where additionally…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. The common…
Words in some natural languages can have a composite structure. Elements of this structure include the root (that could also be composite), prefixes and suffixes with which various nuances and relations to other words can be expressed.…
We study the fundamental question of how efficiently suffix array entries can be accessed when the array cannot be stored explicitly. The suffix array $SA_T[1..n]$ of a text $T$ of length $n$ encodes the lexicographic order of its suffixes…
In the last two decades about a dozen methods were invented which derive, from a series of composite spectra over the orbit, the spectra of individual components in binary and multiple systems. Reconstructed spectra can then be analyzed…
String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…
In this paper we will describe a new approach on the well-known suffix-array algorithm using Big Table Data Technology. We will demonstrate how it is possible to refactor a well-known algorithm coupled by taking advantage of an…
Motivated by DNA storage in living organisms, and by known biological mutation processes, we study the reverse-complement string-duplication system. We fully classify the conditions under which the system has full expressiveness, for all…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
A \itbf{cover} of a string $x = x[1..n]$ is a proper substring $u$ of $x$ such that $x$ can be constructed from possibly overlapping instances of $u$. A recent paper \cite{FIKPPST13} relaxes this definition --- an \itbf{enhanced cover} $u$…
Trace reconstruction considers the task of recovering an unknown string $x \in \{0,1\}^n$ given a number of independent "traces", i.e., subsequences of $x$ obtained by randomly and independently deleting every symbol of $x$ with some…
It has been shown in the indexing literature that there is an essential difference between prefix/range searches on the one hand, and predecessor/rank searches on the other hand, in that the former provably allows faster query resolution.…
Search is a key service within constraint programming systems, and it demands the restoration of previously accessed states during the exploration of a search tree. Restoration proceeds either bottom-up within the tree to roll back…
Given a set of $k$ strings $I$, their longest common subsequence (LCS) is the string with the maximum length that is a subset of all the strings in $I$. A data-structure for this problem preprocesses $I$ into a data-structure such that the…
A Genome rearrangement problem studies large-scale mutations on a set of DNAs in living organisms. Various rearrangements like reversals, transpositions, translocations, fissions, fusions, and combinations and different variations have been…
We present a construction of subspace codes along with an efficient algorithm for list decoding from both insertions and deletions, handling an information-theoretically maximum fraction of these with polynomially small rate. Our…
Given a Fractional Repetition code, finding the reconstruction and repair degree in a distributed storage system is an important problem. In this work, we present algorithms for computing the reconstruction and repair degree of fractional…
We introduce alphabet-permutation (AP) codes, a new family of error-correcting codes defined by iteratively applying random coordinate-wise permutations to a fixed initial word. A special case recovers random additive codes and random…