Related papers: Applied Category Theory for Genomics -- An Initiat…
The last twenty years have witnessed molecular data emerge as a primary research instrument in most branches of mycology. Fungal systematics, taxonomy, and ecology have all seen tremendous progress and have undergone rapid, far-reaching…
The extent to which the benefits of science can be fully realized depends critically upon the quality of the connection between researchers themselves and between researchers and members of the public. We believe that it is now possible to…
In this paper, we consider the problem of answering count queries for genomic data subject to perfect privacy constraints. Count queries are often used in applications that collect aggregate (population-wide) information from biomedical…
High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…
The present article is the first of a series whose goal is to define a logical formalism in which it is possible to reason about genetics. In this paper, we introduce the main concepts of our language whose domain of discourse consists of a…
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…
In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology, Nevertheless, I argue that Shannon's concept…
Compact categories have lately seen renewed interest via applications to quantum physics. Being essentially finite-dimensional, they cannot accomodate (co)limit-based constructions. For example, they cannot capture protocols such as quantum…
Death has long been overlooked in evolutionary algorithms. Recent research has shown that death (when applied properly) can benefit the overall fitness of a population and can outperform sub-sections of a population that are "immortal" when…
Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…
These notes were originally developed as lecture notes for a category theory course. They should be well-suited to anyone that wants to learn category theory from scratch and has a scientific mind. There is no need to know advanced…
Artificial intelligence has provided us with an exploration of a whole new research era. As more data and better computational power become available, the approach is being implemented in various fields. The demand for it in health…
Engineering the entire genome of an organism enables large-scale changes in organization, function, and external interactions, with significant implications for industry, medicine, and the environment. Improvements to DNA synthesis and…
This paper makes a number of connections between life and various facets of genetic and evolutionary algorithms research. Specifically, it addresses the topics of adaptation, multiobjective optimization, decision making, deception, and…
We propose a novel definition of life in terms of which its emergence in the universe is expected, and its ever-creative open-ended evolution is entailed by no law. Living organisms are Kantian Wholes that achieve Catalytic Closure,…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
Category theory has been successfully applied in various domains of science, shedding light on universal principles unifying diverse phenomena and thereby enabling knowledge transfer between them. Applications to machine learning have been…
Mutual information is one of the essential building blocks of information theory. Yet, it is only finitely defined for distributions with fast decaying tails on a countable joint alphabet of two random elements. The unboundedness of mutual…