Related papers: Fast low-level pattern matching algorithm
Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an…
Pattern matching of streaming time series with lower latency under limited computing resource comes to a critical problem, especially as the growth of Industry 4.0 and Industry Internet of Things. However, against traditional single pattern…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…
Recently, Transformer-based encoder-decoder models have demonstrated strong performance in multilingual speech recognition. However, the decoder's autoregressive nature and large size introduce significant bottlenecks during inference.…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
Sequence segmentation is a well-studied problem, where given a sequence of elements, an integer K, and some measure of homogeneity, the task is to split the sequence into K contiguous segments that are maximally homogeneous. A classic…
Matching pursuit algorithms are an important class of algorithms in signal processing and machine learning. We present a blended matching pursuit algorithm, combining coordinate descent-like steps with stronger gradient descent steps, for…
Template matching is widely used for many applications in image and signal processing and usually is time-critical. Traditional methods usually focus on how to reduce the search locations by coarse-to-fine strategy or full search combined…
This article introduces a new DNA sequence compression algorithm which is based on LUT and LZ77 algorithm. Combined a LUT-based pre-coding routine and LZ77 compression routine,this algorithm can approach a compression ratio of 1.9bits…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
RNA design, the task of finding a sequence that folds into a target secondary structure, has broad biological and biomedical impact but remains computationally challenging due to the exponentially large sequence space and exponentially many…
We present a very fast algorithm for general matrix factorization of a data matrix for use in the statistical analysis of high-dimensional data via latent factors. Such data are prevalent across many application areas and generate an…
Many machine learning tasks require finding per-part correspondences between objects. In this work we focus on low-level correspondences - a highly ambiguous matching problem. We propose to use a hierarchical semantic representation of the…
Efficient pattern matching is fundamental for practical term rewrite engines. By preprocessing the given patterns into a finite deterministic automaton the matching patterns can be decided in a single traversal of the relevant parts of the…
Inducing latent tree structures from sequential data is an emerging trend in the NLP research landscape today, largely popularized by recent methods such as Gumbel LSTM and Ordered Neurons (ON-LSTM). This paper proposes FASTTREES, a new…
Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an…
Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…