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Word embedding models offer continuous vector representations that can capture rich contextual semantics based on their word co-occurrence patterns. While these word vectors can provide very effective features used in many NLP tasks such as…
We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in…
We generalize the problem of reconstructing strings from their substring compositions first introduced by Acharya et al. in 2015 motivated by polymer-based advanced data storage systems utilizing mass spectrometry. Namely, we see strings as…
In this paper, we consider a new low-quality label learning problem: learning time series detection models from temporally imprecise labels. In this problem, the data consist of a set of input time series, and supervision is provided by a…
Epistemic logic programs (ELPs) are a popular generalization of standard Answer Set Programming (ASP) providing means for reasoning over answer sets within the language. This richer formalism comes at the price of higher computational…
A suitable choice of the representation of candidate solutions is crucial for the efficiency of evolutionary algorithms and related metaheuristics. We focus on problems in permutation spaces, which are at the core of numerous practical…
In this paper we study lower bounds for the fundamental problem of text indexing with mismatches and differences. In this problem we are given a long string of length $n$, the "text", and the task is to preprocess it into a data structure…
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…
Broadband infrastructure owners do not always know how their customers are connected in the local networks, which are structured as rooted trees. A recent study is able to infer the topology of a local network using discrete time series…
Word and graph embeddings are widely used in deep learning applications. We present a data structure that captures inherent hierarchical properties from an unordered flat embedding space, particularly a sense of direction between pairs of…
We present a set of integer programs (IPs) for the Steiner tree problem with the property that the best solution obtained by solving all, provides an optimal Steiner tree. Each IP is polynomial in the size of the underlying graph and our…
LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an…
The interval graph for a set of intervals on a line consists of one vertex for each interval, and an edge for each intersecting pair of intervals. A probe interval graph is a variant that is motivated by an application to genomics, where…
Sliding suffix trees (Fiala & Greene, 1989) for an input text $T$ over an alphabet of size $\sigma$ and a sliding window $W$ of $T$ can be maintained in $O(|T| \log \sigma)$ time and $O(|W|)$ space. The two previous approaches that achieve…
Computing time is becoming a key issue for tracking algorithms both online and off-line. Programming using adequate data structures can largely improve the efficiency of the reconstruction in terms of time response. We propose using one…
A suffix tree is able to efficiently locate a pattern in an indexed string, but not in general the most recent copy of the pattern in an online stream, which is desirable in some applications. We study the most general version of the…
Based on the Breslauer-Italiano online suffix tree construction algorithm (2013) with double logarithmic worst-case guarantees on the update time per letter, we develop near-real-time algorithms for several classical problems on strings,…
Suppose that we are given two independent sets $I_b$ and $I_r$ of a graph such that $|I_b|=|I_r|$, and imagine that a token is placed on each vertex in $I_b$. Then, the sliding token problem is to determine whether there exists a sequence…