Related papers: Applied Category Theory for Genomics -- An Initiat…
We introduce and train distributed neural architectures (DNA) in vision and language domains. DNAs are initialized with a proto-architecture that consists of (transformer, MLP, attention, etc.) modules and routers. Any token (or patch) can…
All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…
A community reveals the features and connections of its members that are different from those in other communities in a network. Detecting communities is of great significance in network analysis. Despite the classical spectral clustering…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
Generalized category discovery (GCD) is a recently proposed open-world task. Given a set of images consisting of labeled and unlabeled instances, the goal of GCD is to automatically cluster the unlabeled samples using information…
We outline the global control architecture of genomes. A theory of genomic control information is presented. The concept of a developmental control network called a cene (for control gene) is introduced. We distinguish parts-genes from…
Diversity indices are useful single-number metrics for characterizing a complex distribution of a set of attributes across a population of interest. The utility of these different metrics or sets of metrics depend on the context and…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
Biology is at the precipice of a new era where AI accelerates and amplifies the ability to study how cells operate, organize, and work as systems, revealing why disease happens and how to correct it. Organizations globally are prioritizing…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence,…
Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position…
Humans perceive the world as a series of sequential events, which can be hierarchically organized with different levels of abstraction based on conceptual knowledge. Drawing inspiration from human learning behaviors, this work proposes a…
Classification is an important goal in many branches of mathematics. The idea is to describe the members of some class of mathematical objects, up to isomorphism or other important equivalence in terms of relatively simple invariants. Where…
The article represents a new class of hidden symmetries in long sequences of oligonucleotides of single stranded DNA from their representative set. These symmetries are an addition to symmetries described by the second parity rule of…
This paper uses category theory to develop an entirely new approach to approximate game theory. Game theory is the study of how different agents within a multi-agent system take decisions. At its core, game theory asks what an optimal…
Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the…
This paper concerns open-world classification, where the classifier not only needs to classify test examples into seen classes that have appeared in training but also reject examples from unseen or novel classes that have not appeared in…
For over a century, immunology has masterfully discovered and dissected the components of our immune system, yet its collective behavior remains fundamentally unpredictable. In this perspective, we argue that building on the learnings of…
Some aspects of basic category theory are developed in a finitely complete category $\C$, endowed with two factorization systems which determine the same discrete objects and are linked by a simple reciprocal stability law. Resting on this…