Related papers: Fast Circular Pattern Matching
Keypoint matching can be slow and unreliable in challenging conditions such as repetitive textures or wide-baseline views. In such cases, known geometric relations (e.g., the fundamental matrix) can be used to restrict potential…
The most fundamental problem considered in algorithms for text processing is pattern matching: given a pattern $p$ of length $m$ and a text $t$ of length $n$, does $p$ occur in $t$? Multiple versions of this basic question have been…
Kernel approximation via nonlinear random feature maps is widely used in speeding up kernel machines. There are two main challenges for the conventional kernel approximation methods. First, before performing kernel approximation, a good…
Introduction: The extracellular matrix (ECM) is a networkof proteins and carbohydrates that has a structural and bio-chemical function. The ECM plays an important role in dif-ferentiation, migration and signaling. Several studies…
Consensus problems for strings and sequences appear in numerous application contexts, ranging from bioinformatics over data mining to machine learning. Closing some gaps in the literature, we show that several fundamental problems in this…
In 1982, Papadimitriou and Yannakakis introduced the Exact Matching (EM) problem where given an edge colored graph, with colors red and blue, and an integer $k$, the goal is to decide whether or not the graph contains a perfect matching…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
The circular dictionary matching problem is an extension of the classical dictionary matching problem where every string in the dictionary is interpreted as a circular string: after reading the last character of a string, we can move back…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
In this work, we consider pattern matching variants in small space, that is, in the read-only setting, where we want to bound the space usage on top of storing the strings. Our main contribution is a space-time trade-off for the Internal…
Extracellular matrix (ECM) remodeling is central to a wide variety of healthy and diseased tissue processes. Unfortunately, predicting ECM remodeling under various chemical and mechanical conditions has proven to be excessively challenging,…
Normalized cross-correlation is the reference approach to carry out template matching on images. When it is computed in Fourier space, it can handle efficiently template translations but it cannot do so with template rotations. Including…
Temporal graph learning is pivotal for deciphering dynamic systems, where the core challenge lies in explicitly modeling the underlying evolving patterns that govern network transformation. However, prevailing methods are predominantly…
Extreme Learning Machines (ELM) provide a fast alternative to traditional gradient-based learning in neural networks, offering rapid training and robust generalization capabilities. Its theoretical basis shows its universal approximation…
Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…
Quantum computations are typically compiled into a circuit of basic quantum gates. Just like for classical circuits, a quantum compiler should optimize the quantum circuit, e.g. by minimizing the number of required gates. Optimizing quantum…
Contrast pattern mining (CPM) is an important and popular subfield of data mining. Traditional sequential patterns cannot describe the contrast information between different classes of data, while contrast patterns involving the concept of…
Reconstructing the evolutionary history of a set of species is a central task in computational biology. In real data, it is often the case that some information is missing: the Incomplete Directed Perfect Phylogeny (IDPP) problem asks,…
We consider the problem of computing the Maximal Exact Matches (MEMs) of a given pattern $P[1 .. m]$ on a large repetitive text collection $T[1 .. n]$, which is represented as a (hopefully much smaller) run-length context-free grammar of…
The paper investigates the problem of fitting protein complexes into electron density maps. They are represented by high-resolution cryoEM density maps converted into overlapping matrices and partly show a structure of a complex. The…