Related papers: How to build a DNA search engine like Google?
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Many search systems work with large amounts of natural language data, e.g., search queries, user profiles and documents, where deep learning based natural language processing techniques (deep NLP) can be of great help. In this paper, we…
Finding patterns in data and being able to retrieve information from those patterns is an important task in Information retrieval. Complex search requirements which are not fulfilled by simple string matching and require exploring certain…
With the recent explosion in the size and complexity of source codebases and software projects, the need for efficient source code search engines has increased dramatically. Unfortunately, existing information retrieval-based methods fail…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
There are many research works on the designing of architectures for the deep neural networks (DNN), which are named neural architecture search (NAS) methods. Although there are many automatic and manual techniques for NAS problems, there is…
Document retrieval is a key stage of standard Web search engines. Existing dual-encoder dense retrievers obtain representations for questions and documents independently, allowing for only shallow interactions between them. To overcome this…
This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…
In web search, typically a candidate generation step selects a small set of documents---from collections containing as many as billions of web pages---that are subsequently ranked and pruned before being presented to the user. In Bing, the…
The World Wide Web (WWW) allows the people to share the information (data) from the large database repositories globally. The amount of information grows billions of databases. We need to search the information will specialize tools known…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
The immense amounts of source code provide ample challenges and opportunities during software development. To handle the size of code bases, developers commonly search for code, e.g., when trying to find where a particular feature is…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…
DNA sequencing to identify genetic variants is becoming increasingly valuable in clinical settings. Assessment of variants in such sequencing data is commonly implemented through Bayesian heuristic algorithms. Machine learning has shown…
Genetic algorithms are considered as one of the most efficient search techniques. Although they do not offer an optimal solution, their ability to reach a suitable solution in considerably short time gives them their respectable role in…
Neural Networks sequentially build high-level features through their successive layers. We propose here a new neural network model where each layer is associated with a set of candidate mappings. When an input is processed, at each layer,…
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…