Related papers: A family of fast exact pattern matching algorithms
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
Finding the most similar subsequences between two multidimensional time series has many applications: e.g. capturing dependency in stock market or discovering coordinated movement of baboons. Considering one pattern occurring in one time…
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,…
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…
The simplex algorithm for linear programming is based on the fact that any local optimum with respect to the polyhedral neighborhood is also a global optimum. We show that a similar result carries over to submodular maximization. In…
The maximum clique problem is a well known NP-Hard problem with applications in data mining, network analysis, information retrieval and many other areas related to the World Wide Web. There exist several algorithms for the problem with…
Cartesian tree matching is the problem of finding all substrings in a given text which have the same Cartesian trees as that of a given pattern. In this paper, we deal with Cartesian tree matching for the case of multiple patterns. We…
Many computational problems admit fast algorithms on special inputs, however, the required properties might be quite restrictive. E.g., many graph problems can be solved much faster on interval or cographs, or on graphs of small…
Associative memories are data structures addressed using part of the content rather than an index. They offer good fault reliability and biological plausibility. Among different families of associative memories, sparse ones are known to…
Deep learning has recently demonstrated its ability to rival the human brain for visual object recognition. As datasets get larger, a natural question to ask is if existing deep learning architectures can be extended to handle the 50+K…
Finding approximate occurrences of a pattern in a text using a full-text index is a central problem in bioinformatics and has been extensively researched. Bidirectional indices have opened new possibilities in this regard allowing the…
Weighted Hamming distance, as a similarity measure between binary codes and binary queries, provides superior accuracy in search tasks than Hamming distance. However, how to efficiently and accurately find $K$ binary codes that have the…
Matching algorithms are used routinely to match donors to recipients for solid organs transplantation, for the assignment of medical residents to hospitals, record linkage in databases, scheduling jobs on machines, network switching, online…
Approximate dictionary matching is a classic string matching problem (checking if a query string occurs in a collection of strings) with applications in, e.g., spellchecking, online catalogs, geolocation, and web searchers. We present a…
When a human matches two images, the viewer has a natural tendency to view the wide area around the target pixel to obtain clues of right correspondence. However, designing a matching cost function that works on a large window in the same…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…
We resolve a long-standing open question, about the existence of a constant-factor approximation algorithm for the average-case \textsc{Decision Tree} problem with uniform probability distribution over the hypotheses. We answer the question…
With the aggressive scaling of VLSI technology, the explosion of layout patterns creates a critical bottleneck for DFM applications like OPC. Pattern clustering is essential to reduce data complexity, yet existing methods struggle with…
Matrix multiplication is a fundamental computation in many scientific disciplines. In this paper, we show that novel fast matrix multiplication algorithms can significantly outperform vendor implementations of the classical algorithm and…
We present a new algorithm which detects the maximal possible number of matched disjoint pairs satisfying a given caliper when a bipartite matching is done with respect to a scalar index (e.g., propensity score), and constructs a…