Related papers: Approximate word matches between two random sequen…
We consider the classical problem of discrete distribution estimation using i.i.d. samples in a novel scenario where additional side information is available on the distribution. In large alphabet datasets such as text corpora, such side…
There are two methods for counting the number of occurrences of a string in another large string. One is to count the number of places where the string is found. The other is to determine how many pieces of string can be extracted without…
Considering the optimal alignment of two i.i.d. random sequences of length $n$, we show that when the scoring function is chosen randomly, almost surely the empirical distribution of aligned letter pairs in all optimal alignments converges…
We introduce a novel definition of approximate palindromes in strings, and provide an algorithm to find all maximal approximate palindromes in a string with up to $k$ errors. Our definition is based on the usual edit operations of…
Written language is a complex communication signal capable of conveying information encoded in the form of ordered sequences of words. Beyond the local order ruled by grammar, semantic and thematic structures affect long-range patterns in…
A pattern p (i.e., a string of variables and terminals) matches a word w, if w can be obtained by uniformly replacing the variables of p by terminal words. The respective matching problem, i.e., deciding whether or not a given pattern…
We introduce data structures answering queries concerning the occurrences of patterns from a given dictionary $\mathcal{D}$ in fragments of a given string $T$ of length $n$. The dictionary is internal in the sense that each pattern in…
How do two distributions of texts differ? Humans are slow at answering this, since discovering patterns might require tediously reading through hundreds of samples. We propose to automatically summarize the differences by "learning a…
Word $W$ is said to encounter word $V$ provided there is a homomorphism $\phi$ mapping letters to nonempty words so that $\phi(V)$ is a substring of $W$. For example, taking $\phi$ such that $\phi(h)=c$ and $\phi(u)=ien$, we see that…
We consider the problem of estimating the probability of an observed string drawn i.i.d. from an unknown distribution. The key feature of our study is that the length of the observed string is assumed to be of the same order as the size of…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
Nearest neighbor (NN) matching as a tool to align data sampled from different groups is both conceptually natural and practically well-used. In a landmark paper, Abadie and Imbens (2006) provided the first large-sample analysis of NN…
The $d$-dimensional pattern matching problem is to find an occurrence of a pattern of length $m \times \dots \times m$ within a text of length $n \times \dots \times n$, with $n \ge m$. This task models various problems in text and image…
The combined universal probability $\mathbf{m}(D)$ of strings $x$ in sets $D$ is close to max $\mathbf{m}(x)$ over $x$ in $D$: their logs differ by at most $D$'s information $\mathbf{I}(D:\mathcal{H})$ about the halting sequence…
This paper extends the problem of 2-dimensional palindrome search into the area of approximate matching. Using the Hamming distance as the measure, we search for 2D palindromes that allow up to $k$ mismatches. We consider two different…
What advantage do \emph{sequential} procedures provide over batch algorithms for testing properties of unknown distributions? Focusing on the problem of testing whether two distributions $\mathcal{D}_1$ and $\mathcal{D}_2$ on $\{1,\dots,…
We consider the classical sequential binary hypothesis testing problem in which there are two hypotheses governed respectively by distributions $P_0$ and $P_1$ and we would like to decide which hypothesis is true using a sequential test. It…
The syntactic structure of a sentence is often represented using syntactic dependency trees. The sum of the distances between syntactically related words has been in the limelight for the past decades. Research on dependency distances led…
Dynamic Time Warping (DTW) is a widely used similarity measure for comparing strings that encode time series data, with applications to areas including bioinformatics, signature verification, and speech recognition. The standard…
We introduce the natural notion of a matching frame in a $2$-dimensional string. A matching frame in a $2$-dimensional $n\times m$ string $M$, is a rectangle such that the strings written on the horizontal sides of the rectangle are…