Related papers: How to build a DNA search engine like Google?
One of the important factors that make a search engine fast and accurate is a concise and duplicate free index. In order to remove duplicate and near-duplicate documents from the index, a search engine needs a swift and reliable duplicate…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
We present a simple web search engine for indexing and searching html documents using python programming language. Because python is well known for its simple syntax and strong support for main operating systems, we hope it will be…
Traditional query processing relies on engines that are carefully optimized and engineered by many experts. However, new techniques and user requirements evolve rapidly, and existing systems often cannot keep pace. At the same time, these…
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…
Statistical analysis of DNA mixtures is known to pose computational challenges due to the enormous state space of possible DNA profiles. We propose a Bayesian network representation for genotypes, allowing computations to be performed…
In this paper we propose a novel network adaption method called Differentiable Network Adaption (DNA), which can adapt an existing network to a specific computation budget by adjusting the width and depth in a differentiable manner. The…
As data retrieval demands become increasingly complex, traditional search methods often fall short in addressing nuanced and conceptual queries. Vector similarity search has emerged as a promising technique for finding semantically similar…
The exponential growth of information source on the web and in turn continuing technological progress of searching the information by using tools like Search Engines gives rise to many problems for the user to know which tool is best for…
For DNA sequences of various species we construct the Google matrix G of Markov transitions between nearby words composed of several letters. The statistical distribution of matrix elements of this matrix is shown to be described by a power…
In todays era with the rapid growth of information on the web, makes users turn to search engines as a replacement of traditional media. This makes sorting of particular information through billions of webpages and displaying the relevant…
This paper surveys foundation models for AI-enabled biological design, focusing on recent developments in applying large-scale, self-supervised models to tasks such as protein engineering, small molecule design, and genomic sequence design.…
This article presents results of experimental studies the effectiveness of the genetic algorithm that was applied to effective queries creation and relevant document selection. Studies were carried out to the comparative analysis of the…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
Powerful yet complex deep neural networks (DNNs) have fueled a booming demand for efficient DNN solutions to bring DNN-powered intelligence into numerous applications. Jointly optimizing the networks and their accelerators are promising in…
The DNA cryptography is a new and very promising direction in cryptography research. DNA can be used in cryptography for storing and transmitting the information, as well as for computation. Although in its primitive stage, DNA cryptography…
When it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be…
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that…
The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical…
Taking inspiration from biological evolution, we explore the idea of "Can deep neural networks evolve naturally over successive generations into highly efficient deep neural networks?" by introducing the notion of synthesizing new highly…