Related papers: Position Heaps for Parameterized Strings
We show how to determine whether a given pattern p of length m occurs in a given text t of length n in ${\tilde O}(\sqrt{n}+\sqrt{m})$\footnote{${\tilde O}$ allows for logarithmic factors in m and $n/m$} time, with inverse polynomial…
In this paper we present a new problem, the fast set intersection problem, which is to preprocess a collection of sets in order to efficiently report the intersection of any two sets in the collection. In addition we suggest new solutions…
In this contribution a practical approach to determine and store position dependent parameters is presented. These parameters can be obtained, among others, using experimental results or expert knowledge and are stored in 'Information…
Superposition of sigmoid function over a finite time interval is shown to be equivalent to the linear combination of the solutions of a linearly parameterized system of logistic differential equations. Due to the linearity with respect to…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
Pattern matching is the most central task for text indices. Most recent indices leverage compression techniques to make pattern matching feasible for massive but highly-compressible datasets. Within this kind of indices, we propose a new…
The hierarchical overlap graph (HOG) is a graph that encodes overlaps from a given set P of n strings, as the overlap graph does. A best known algorithm constructs HOG in O(||P|| log n) time and O(||P||) space, where ||P|| is the sum of…
With the advent of large-scale heterogeneous search engines comes the problem of unified search control resulting in mismatches that could have otherwise avoided. A mechanism is needed to determine exact patterns in web mining and…
Conformal prediction has recently emerged as a promising strategy for quantifying the uncertainty of a predictive model; these algorithms modify the model to output sets of labels that are guaranteed to contain the true label with high…
In the String Matching in Labeled Graphs (SMLG) problem, we need to determine whether a pattern string appears on a given labeled graph or a given automaton. Under the Orthogonal Vectors hypothesis, the SMLG problem cannot be solved in…
Localized patterns are coherent structures embedded in a quiescent state and occur in both discrete and continuous media across a wide range of applications. While it is well-understood how domain covering patterns (for example stripes and…
In this paper we consider several variants of the pattern matching problem. In particular, we investigate the following problems: 1) Pattern matching with k mismatches; 2) Approximate counting of mismatches; and 3) Pattern matching with…
In this paper, we present structured message passing (SMP), a unifying framework for approximate inference algorithms that take advantage of structured representations such as algebraic decision diagrams and sparse hash tables. These…
Graph rewriting is a popular tool for the optimisation and modification of graph expressions in domains such as compilers, machine learning and quantum computing. The underlying data structures are often port graphs - graphs with labels at…
Pattern tree are based on integrated rules which are equal to a combination of some points connected to each other in a hierarchical structure, called Enquiry Hierarchical (EH). The main operation in pattern enquiry seeking is to locate the…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
Deciding feasibility of large systems of linear equations and inequalities is one of the most fundamental algorithmic tasks. However, due to data inaccuracies or modeling errors, in practical applications one often faces linear systems that…
Network alignment generalizes and unifies several approaches for forming a matching or alignment between the vertices of two graphs. We study a mathematical programming framework for network alignment problem and a sparse variation of it…
Let $S_1, S_2 \in \Sigma^*$ strings, we say that $S_1$ {\em jumble match} $S_2$ if they are permutations of each other. Given a text $T$ of size $N$ and a string $S \in \Sigma^*$, the problem of \emph{Jumbled Pattern Matching} (JPM) is to…
We successfully combine Expectation-Maximization algorithm and variational approaches for parameter learning and computing inference on Markov random felds. This is a general method that can be applied to many computer vision tasks. In this…