Related papers: Applied Category Theory for Genomics -- An Initiat…
Significant fraction (98.5% in humans) of most animal genomes is non- coding dark matter. Its largely unknown function (1-5) is related to programming (rather than to spontaneous mutations) of accurate adaptation to rapidly changing…
Generalized Category Discovery (GCD) utilizes labeled samples of known classes to discover novel classes in unlabeled samples. Existing methods show effective performance on artificial datasets with balanced distributions. However,…
Category, or property generalization is a central function in the human cognition. It plays a crucial role in a variety of domains, such as learning, everyday reasoning, specialized reasoning, and decision making. Judging the content of a…
The study of complex systems through the lens of category theory consistently proves to be a powerful approach. We propose that cognition deserves the same category-theoretic treatment. We show that by considering a highly-compact cognitive…
Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…
``The purpose of life is to obtain knowledge, use it to live with as much satisfaction as possible, and pass it on with improvements and modifications to the next generation.'' This may sound philosophical, and the interpretation of words…
Categories such as animal or furniture are acquired at an early age and play an important role in processing, organizing, and communicating world knowledge. Categories exist across cultures: they allow to efficiently represent the…
Research done using model organisms has been fundamental to the biological understanding of human genes, diseases and phenotypes. Model organisms provide tractable systems for experiments to enhance understanding of biological mechanisms…
Grids - the collection of heterogeneous computers spread across the globe - present a new paradigm for the large scale problems in variety of fields. We discuss two representative cases in the area of condensed matter physics outlining the…
The data revolution holds significant promise for the health sector. Vast amounts of data collected from individuals will be transformed into knowledge, AI models, predictive systems, and best practices. One area of health that stands to…
Category theory has foundational importance because it provides conceptual lenses to characterize what is important in mathematics. Originally the main lenses were universal mapping properties and natural transformations. In recent decades,…
The idea that all life on earth traces back to a common beginning dates back at least to Charles Darwin's {\em Origin of Species}. Ever since, biologists have tried to piece together parts of this `tree of life' based on what we can observe…
In this paper, we generalize the construction method of schemes to other algebraic categories, and show that the category of coherent schemes can be characterized by a universal property, if we fix the class of Grothendieck topology. Also,…
Significant fraction (about 98.5% in humans, 24% in microbe Rickettsia prowazekii) of most animal genomes is non-coding DNA. Although recent studies established functions of its certain portions, it remains genomic dark matter. The paper…
Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing…
Neural networks have become an increasingly popular tool for solving many real-world problems. They are a general framework for differentiable optimization which includes many other machine learning approaches as special cases. In this…
The information contained in the genome is insufficient for the control of organism development. Thus, the whereabouts of actual operational directives and workings of the genome remain obscure. In this work, it is suggested that the genome…
Higher category theory is an exceedingly active area of research, whose rapid growth has been driven by its penetration into a diverse range of scientific fields. Its influence extends through key mathematical disciplines, notably homotopy…
Category theory is a branch of mathematics that provides a formal framework for understanding the relationship between mathematical structures. To this end, a category not only incorporates the data of the desired objects, but also…
To comprehend the hierarchical organization of large integrated systems, we introduce the hierarchical map equation, which reveals multilevel structures in networks. In this information-theoretic approach, we exploit the duality between…