Related papers: Comparing DNA sequence collections by direct compa…
Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive…
Transformer architectures have facilitated the development of large-scale and general-purpose sequence models for prediction tasks in natural language processing and computer vision, e.g., GPT-3 and Swin Transformer. Although originally…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string $S$, it produces a dictionary $D$ and a parse $P$ of…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
The Lempel-Ziv factorization (LZ77) and the Run-Length encoded Burrows-Wheeler Transform (RLBWT) are two important tools in text compression and indexing, being their sizes $z$ and $r$ closely related to the amount of text…
Inverted indexes are vital in providing fast key-word-based search. For every term in the document collection, a list of identifiers of documents in which the term appears is stored, along with auxiliary information such as term frequency,…
Computing the similarity between two DNA sequences is of vital importance in bioscience, yet it can be computationally expensive on classical hardware. For example, the edit distance with move operations (EDM), a DNA similarity measure of…
Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters.…
We propose an external memory algorithm for the computation of the BWT and LCP array for a collection of sequences. Our algorithm takes the amount of available memory as an input parameter, and tries to make the best use of it by splitting…
Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…
Traditional supervised bearing fault diagnosis methods rely on massive labelled data, yet annotations may be very time-consuming or infeasible. The fault diagnosis approach that utilizes limited labelled data is becoming increasingly…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine…
A new array based data structure named black-white array (BWA) is introduced as an effective and efficient alternative to the list or tree based data structures for dynamic data set. It consists of two sub-arrays, one white and one black of…
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…
Recent developments in next generation sequencing technology have led to the creation of extensive, open-source protein databases consisting of hundreds of millions of sequences. To render these sequences applicable in biomedical…
Query-by-example search often uses dynamic time warping (DTW) for comparing queries and proposed matching segments. Recent work has shown that comparing speech segments by representing them as fixed-dimensional vectors --- acoustic word…
With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…
Biological sequence comparison is a key step in inferring the relatedness of various organisms and the functional similarity of their components. Thanks to the Next Generation Sequencing efforts, an abundance of sequence data is now…