Related papers: Motif matching using gapped patterns
We consider the problem of detecting a noisy induced multiplex template network in a larger multiplex background network. Our approach, which extends the framework of Sussman et al. (2019) to the multiplex setting, leverages a multiplex…
This paper addresses the challenging problem of retrieval and matching of graph structured objects, and makes two key contributions. First, we demonstrate how Graph Neural Networks (GNN), which have emerged as an effective model for various…
Protein motifs are conserved fragments occurred frequently in protein sequences. They have significant functions, such as active site of an enzyme. Search and clustering protein sequence motifs are computational intensive. Most existing…
We introduce the \textit{multi-view pattern matching} problem, where a text can have multiple views. Each view is a string of the same size and drawn from disjoint alphabets. The pattern is drawn from the union of all alphabets. The…
Dependent pattern matching is a key feature in dependently typed programming. However, there is a theory-practice disconnect: while many proof assistants implement pattern matching as primitive, theoretical presentations give semantics to…
Maximum weight matching is one of the most fundamental combinatorial optimization problems with a wide range of applications in data mining and bioinformatics. Developing distributed weighted matching algorithms is challenging due to the…
We revisit a fundamental problem in string matching: given a pattern of length m and a text of length n, both over an alphabet of size $\sigma$, compute the Hamming distance between the pattern and the text at every location. Several…
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…
We propose a new method for shape recognition and retrieval based on dynamic programming. Our approach uses the dynamic programming algorithm to compute the optimal score and to find the optimal alignment between two strings. First, each…
This paper addresses the problem of fixed motion and measurement models for multi-target filtering using an adaptive learning framework. This is performed by defining target tuples with random finite set terminology and utilisation of…
Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…
Filtering point targets in highly cluttered and noisy data frames can be very challenging, especially for complex target motions. Fixed motion models can fail to provide accurate predictions, while learning based algorithm can be difficult…
Network motif provides a way to uncover the basic building blocks of most complex networks. This task usually demands high computer processing, specially for motif with 5 or more vertices. This paper presents an extended methodology with…
Network motif algorithms have been a topic of research mainly after the 2002-seminal paper from Milo \emph{et al}, that provided motifs as a way to uncover the basic building blocks of most networks. In Bioinformatics, motifs have been…
We study the problem of response selection for multi-turn conversation in retrieval-based chatbots. The task requires matching a response candidate with a conversation context, whose challenges include how to recognize important parts of…
Real-time analysis of graphs containing temporal information, such as social media streams, Q&A networks, and cyber data sources, plays an important role in various applications. Among them, detecting patterns is one of the fundamental…
Motif searching is an important step in the detection of rare events occurring in a set of DNA or protein sequences. One formulation of the problem is known as (l,d)-motif search or Planted Motif Search (PMS). In PMS we are given two…
We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…
Semantic matching is of central importance to many natural language tasks \cite{bordes2014semantic,RetrievalQA}. A successful matching algorithm needs to adequately model the internal structures of language objects and the interaction…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…