Related papers: Applied Category Theory for Genomics -- An Initiat…
Understanding how genes interact and relate to each other is a fundamental question in biology. However, current practices for describing these relationships, such as drawing diagrams or graphs in a somewhat arbitrary manner, limit our…
Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures.…
There are many books designed to introduce category theory to either a mathematical audience or a computer science audience. In this book, our audience is the broader scientific community. We attempt to show that category theory can be…
Over the past several years, DNA sequencing has emerged as one of the driving forces in life-sciences, paving the way for affordable and accurate whole genome sequencing. As genomes represent the entirety of an organism's hereditary…
A taxonomy is a standardized framework to classify and organize items into categories. Hierarchical taxonomies are ubiquitous, ranging from the classification of organisms to the file system on a computer. Characterizing the typical…
Category theory has foundational importance because it provides conceptual lenses to characterize what is important and universal in mathematics---with adjunctions being the primary lense. If adjunctions are so important in mathematics,…
The purpose of this paper is to give an introduction to the field of Schema Theory written by a mathematician and for mathematicians. In particular, we endeavor to to highlight areas of the field which might be of interest to a…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
Recent advances in DNA sequencing technologies have put ubiquitous availability of fully sequenced human genomes within reach. It is no longer hard to imagine the day when everyone will have the means to obtain and store one's own DNA…
Over the past two decades machine learning has permeated almost every realm of technology. At the same time, many researchers have begun using category theory as a unifying language, facilitating communication between different scientific…
The unprecedented pace of machine learning research has lead to incredible advances, but also poses hard challenges. At present, the field lacks strong theoretical underpinnings, and many important achievements stem from ad hoc design…
While artificial intelligence (AI) has become widespread, many commercial AI systems are not yet accessible to individual researchers nor the general public due to the deep knowledge of the systems required to use them. We believe that AI…
Generalized Category Discovery (GCD) is a pragmatic and challenging open-world task, which endeavors to cluster unlabeled samples from both novel and old classes, leveraging some labeled data of old classes. Given that knowledge learned…
In recent years, Whole Genome Sequencing (WGS) evolved from a futuristic-sounding research project to an increasingly affordable technology for determining complete genome sequences of complex organisms, including humans. This prompts a…
In the quest for unveiling novel categories at test time, we confront the inherent limitations of traditional supervised recognition models that are restricted by a predefined category set. While strides have been made in the realms of…
This short introductory category theory textbook is for readers with relatively little mathematical background (e.g. the first half of an undergraduate mathematics degree). At its heart is the concept of a universal property, important…
How information is encoded in bio-molecular sequences is difficult to quantify since such an analysis usually requires sampling an exponentially large genetic space. Here we show how information theory reveals both robust and compressed…
A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early…