5,968 research outputs found
On the Complexity of Exact Pattern Matching in Graphs: Binary Strings and Bounded Degree
Exact pattern matching in labeled graphs is the problem of searching paths of
a graph that spell the same string as the pattern . This
basic problem can be found at the heart of more complex operations on variation
graphs in computational biology, of query operations in graph databases, and of
analysis operations in heterogeneous networks, where the nodes of some paths
must match a sequence of labels or types. We describe a simple conditional
lower bound that, for any constant , an -time or an -time algorithm for exact pattern
matching on graphs, with node labels and patterns drawn from a binary alphabet,
cannot be achieved unless the Strong Exponential Time Hypothesis (SETH) is
false. The result holds even if restricted to undirected graphs of maximum
degree three or directed acyclic graphs of maximum sum of indegree and
outdegree three. Although a conditional lower bound of this kind can be somehow
derived from previous results (Backurs and Indyk, FOCS'16), we give a direct
reduction from SETH for dissemination purposes, as the result might interest
researchers from several areas, such as computational biology, graph database,
and graph mining, as mentioned before. Indeed, as approximate pattern matching
on graphs can be solved in time, exact and approximate matching are
thus equally hard (quadratic time) on graphs under the SETH assumption. In
comparison, the same problems restricted to strings have linear time vs
quadratic time solutions, respectively, where the latter ones have a matching
SETH lower bound on computing the edit distance of two strings (Backurs and
Indyk, STOC'15).Comment: Using Lemma 12 and Lemma 13 might to be enough to prove Lemma 14.
However, the proof of Lemma 14 is correct if you assume that the graph used
in the reduction is a DAG. Hence, since the problem is already quadratic for
a DAG and a binary alphabet, it has to be quadratic also for a general graph
and a binary alphabe
Improved Algorithms for Approximate String Matching (Extended Abstract)
The problem of approximate string matching is important in many different
areas such as computational biology, text processing and pattern recognition. A
great effort has been made to design efficient algorithms addressing several
variants of the problem, including comparison of two strings, approximate
pattern identification in a string or calculation of the longest common
subsequence that two strings share.
We designed an output sensitive algorithm solving the edit distance problem
between two strings of lengths n and m respectively in time
O((s-|n-m|)min(m,n,s)+m+n) and linear space, where s is the edit distance
between the two strings. This worst-case time bound sets the quadratic factor
of the algorithm independent of the longest string length and improves existing
theoretical bounds for this problem. The implementation of our algorithm excels
also in practice, especially in cases where the two strings compared differ
significantly in length. Source code of our algorithm is available at
http://www.cs.miami.edu/\~dimitris/edit_distanceComment: 10 page
Near-Linear Time Insertion-Deletion Codes and (1+)-Approximating Edit Distance via Indexing
We introduce fast-decodable indexing schemes for edit distance which can be
used to speed up edit distance computations to near-linear time if one of the
strings is indexed by an indexing string . In particular, for every length
and every , one can in near linear time construct a string
with , such that, indexing
any string , symbol-by-symbol, with results in a string where for which edit
distance computations are easy, i.e., one can compute a
-approximation of the edit distance between and any other
string in time.
Our indexing schemes can be used to improve the decoding complexity of
state-of-the-art error correcting codes for insertions and deletions. In
particular, they lead to near-linear time decoding algorithms for the
insertion-deletion codes of [Haeupler, Shahrasbi; STOC `17] and faster decoding
algorithms for list-decodable insertion-deletion codes of [Haeupler, Shahrasbi,
Sudan; ICALP `18]. Interestingly, the latter codes are a crucial ingredient in
the construction of fast-decodable indexing schemes
Constant-factor approximation of near-linear edit distance in near-linear time
We show that the edit distance between two strings of length can be
computed within a factor of in time as long as
the edit distance is at least for some .Comment: 40 pages, 4 figure
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