Related papers: Constructing Bio-molecular Databases on a DNA-base…

We model human and animal learning by computing with high-dimensional vectors (H = 10,000 for example). The architecture resembles traditional (von Neumann) computing with numbers, but the instructions refer to vectors and operate on them…

Codes have been used for centuries to convey secret information.To a cryptanalyst, the interception of a code is only the first step in recovering a secret message.Deoxyribonucleic acid (DNA) is a biological and molecular code.Through the…

We apply distributed language embedding methods from Natural Language Processing to assign a vector to each database entity associated token (for example, a token may be a word occurring in a table row, or the name of a column). These…

Many researches demonstrated that the DNA methylation, which occurs in the context of a CpG, has strong correlation with diseases, including cancer. There is a strong interest in analyzing the DNA methylation data to find how to distinguish…

Owing to its immense storage density and durability, DNA has emerged as a promising storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules called data blocks that are stored in an…

A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…

DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…

Topological data analysis (TDA) detects geometric structure in biological data. However, many TDA algorithms are memory intensive and impractical for massive datasets. Here, we introduce a statistical protocol that reduces TDA's memory…

This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…

Bacteriophages, viruses that infect bacteria, store their micron long DNA inside an icosahedral capsid with a typical diameter of 40 nm to 100 nm. Consistent with experimental observations, such confinement conditions induce an arrangement…

DNA-based data storage has been attracting significant attention due to its extremely high data storage density, low power consumption, and long duration compared to conventional data storage media. Despite the recent advancements in DNA…

We propose a novel combination of methods that (i) portrays quantitative characteristics of a DNA sequence as an image, (ii) computes distances between these images, and (iii) uses these distances to output a map wherein each sequence is a…

Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…

Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (rarely accessed data), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…

Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on…

The universally applied Codd's relational model has two constructs: a stored relation, with stored attributes only and a view, only with the inherited ones. In 1992, we have proposed third construct, mixing both types of attributes.…

This tutorial overviews principles behind recent works on training and maintaining machine learning models over relational data, with an emphasis on the exploitation of the relational data structure to improve the runtime performance of the…

This project mathematically models the self-assembly of DNA nanostructures in the shape of select Archimedean graphs using the flexible tile model. Under three different sets of restrictions called scenarios, we employ principles of linear…

The surge in demand for cost-effective, durable long-term archival media, coupled with density limitations of contemporary magnetic media, has resulted in synthetic DNA emerging as a promising new alternative. Despite its benefits, storing…

The problem of reconstructing a string from its error-prone copies, the trace reconstruction problem, was introduced by Vladimir Levenshtein two decades ago. While there has been considerable theoretical work on trace reconstruction,…