Related papers: Applied Category Theory for Genomics -- An Initiat…
Conscious experience permeates our daily lives, yet general consensus on a theory of consciousness remains elusive. In the face of such difficulty, an alternative strategy is to address a more general (meta-level) version of the problem for…
The classification of life should be based upon the fundamental mechanism in the evolution of life. We found that the global relationships among species should be circular phylogeny, which is quite different from the common sense based upon…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
Quantum computing holds significant potential for applications in biology and medicine, spanning from the simulation of biomolecules to machine learning approaches for subtyping cancers on the basis of clinical features. This potential is…
The conception of multi-alphabetical genetics is represented. Matrix forms of the representation of the multi-level system of molecular-genetic alphabets have revealed algebraic properties of this system. These properties are connected with…
It is widely acknowledged that there is a diversity problem in genomics stemming from the vast underrepresentation of non-European genetic ancestry populations. While many challenges exist to address this gap, a major complicating factor is…
Random matrices now play a role in many parts of computational mathematics. To advance these applications, it is desirable to have tools that are flexible, easy to use, and powerful. Over the last 25 years, researchers have developed a…
We give a self-contained introduction to accessible categories and how they shed light on both model- and set-theoretic questions. We survey for example recent developments on the study of presentability ranks, a notion of cardinality…
Category discovery (CD) is an emerging open-world learning task, which aims at automatically categorizing unlabelled data containing instances from unseen classes, given some labelled data from seen classes. This task has attracted…
Category theory provides a means through which many far-ranging fields of mathematics can be related by their similar structure. In a paper by Robinson [2], this interconnectivity afforded by categorical perspectives allowed for the…
In the near future, all the human genes will be identified. But understanding the functions coded in the genes is a much harder problem. For example, by using block entropy, one has that the DNA code is closer to a random code then written…
The concept of category from mathematics happens to be useful to computer programmers in many ways. Unfortunately, all "good" explanations of categories so far have been designed by mathematicians, or at least theoreticians with a strong…
We present our position on the elusive quest for a general-purpose framework for specifying and studying deep learning architectures. Our opinion is that the key attempts made so far lack a coherent bridge between specifying constraints…
In a Systems Engineering setting, various models are produced using a variety of methods and tools. Focusing on a type of models -- called descriptive models -- which we shall describe, we argue that, while the clarity and precision of…
Throughout the evolution of biological species on Earth, cells and organs have developed many complex structures and processes to ensure their interactions with individual chemical molecules (small and macromolecular) and nanoscale objects…
The rapid advances in the field of optimization methods in many pure and applied science pose the difficulty of keeping track of the developments as well as selecting an appropriate technique that best suits the problem in-hand. From a…
Despite the promising results of disentangled representation learning in discovering latent patterns in graph-structured data, few studies have explored disentanglement for hypergraph-structured data. Integrating hyperedge disentanglement…
Genomic approaches have revolutionized medical research, providing valuable insights into human physiology and disease. Despite major benefits from large collections of genomes, the lack of diversity in genomic data represents a significant…
With infinitely many high-quality data points, infinite computational power, an infinitely large foundation model with a perfect training algorithm and guaranteed zero generalization error on the pretext task, can the model be used for…
Using a large database (~ 215 000 records) of relevant articles, we empirically study the "complex systems" field and its claims to find universal principles applying to systems in general. The study of references shared by the papers…