Related papers: Chaining with overlaps revisited
Longest common extension queries (often called longest common prefix queries) constitute a fundamental building block in multiple string algorithms, for example computing runs and approximate pattern matching. We show that a sequence of $q$…
Spike sorting is a class of algorithms used in neuroscience to attribute the time occurences of particular electric signals, called action potential or spike, to neurons. We rephrase this problem as a particular optimization problem : Lasso…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
The longest common subsequence (LCS) problem is a central problem in stringology that finds the longest common subsequence of given two strings $A$ and $B$. More recently, a set of four constrained LCS problems (called generalized…
Suppose we want to seek the longest common subsequences (LCSs) of two strings as informative patterns that explain the relationship between the strings. The dynamic programming algorithm gives us a table from which all LCSs can be extracted…
The Longest Common Increasing Subsequence problem (LCIS) is a natural variant of the celebrated Longest Common Subsequence (LCS) problem. For LCIS, as well as for LCS, there is an $O(n^2)$-time algorithm and a SETH-based conditional lower…
We consider the classic problem of computing the Longest Common Subsequence (LCS) of two strings of length $n$. While a simple quadratic algorithm has been known for the problem for more than 40 years, no faster algorithm has been found…
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…
Confidence calibration - the process to calibrate the output probability distribution of neural networks - is essential for safety-critical applications of such networks. Recent works verify the link between mis-calibration and overfitting.…
The goal of co-clustering is to simultaneously identify a clustering of rows as well as columns of a two dimensional data matrix. A number of co-clustering techniques have been proposed including information-theoretic co-clustering and the…
We give subquadratic algorithms that, given two necklaces each with n beads at arbitrary positions, compute the optimal rotation of the necklaces to best align the beads. Here alignment is measured according to the p norm of the vector of…
A simple-triangle graph is the intersection graph of triangles that are defined by a point on a horizontal line and an interval on another horizontal line. The time complexity of the recognition problem for simple-triangle graphs was a…
Reconfigurable optical topologies are emerging as a promising technology to improve the efficiency of datacenter networks. This paper considers the problem of scheduling opportunistic links in such reconfigurable datacenters. We study the…
The {\it matrix-chain multiplication} problem is a classic problem that is widely taught to illustrate dynamic programming. The textbook solution runs in $\theta(n^3)$ time. However, there is a complex $O(n \log n)$-time method \cite{HU82},…
Genome assembly is a prominent problem studied in bioinformatics, which computes the source string using a set of its overlapping substrings. Classically, genome assembly uses assembly graphs built using this set of substrings to compute…
This paper studies the lattice agreement problem and the generalized lattice agreement problem in distributed message passing systems. In the lattice agreement problem, given input values from a lattice, processes have to non-trivially…
This paper considers the problem of scheduling jobs on single and parallel machines where all the jobs possess different processing times but a common due date. There is a penalty involved with each job if it is processed earlier or later…
Auctions are widely used in exchanges to match buy and sell requests. Once the buyers and sellers place their requests, the exchange determines how these requests are to be matched. The two most popular objectives used while determining the…
In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using…
Consider words of length $n$. The set of all periods of a word of length $n$ is a subset of $\{0,1,2,\ldots,n-1\}$. However, any subset of $\{0,1,2,\ldots,n-1\}$ is not necessarily a valid set of periods. In a seminal paper in 1981, Guibas…