Related papers: Three phases in the evolution of the standard gene…
It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but…
Gene Regulatory Networks (GRNs) consisting of combinations of transcription factors (TFs) and their cis promoters are assumed to be sufficient to direct the development of organisms. Mutations in GRNs are assumed to be the primary drivers…
A method for automatically finding a program (bytecode) realizing the given algorithm is developed. The algorithm is specified as a set of tests (input\_data) $ \rightarrow $ (output\_data). Genetic methods made it possible to find the…
Compact Genetic Algorithms (cGAs) are condensed variants of classical Genetic Algorithms (GAs) that use a probability vector representation of the population instead of the complete population. cGAs have been shown to significantly reduce…
We formulate code concatenation as the action of a unitary quantum circuit on an expanding tree geometry and find that for certain classes of gates, applied identically at each node, a binary tree circuit encodes a single logical qubit with…
Neural codes appear efficient. Naturally, neuroscientists contend that an efficient process is responsible for generating efficient codes. They argue that natural selection is the efficient process that generates those codes. Although…
Text-conditioned molecular generation aims to translate natural-language descriptions into chemical structures, enabling scientists to specify functional groups, scaffolds, and physicochemical constraints without handcrafted rules.…
We calculate the optimality of a doublet precursor to the canonical genetic code with respect to mitigating the effects of point mutations and compare our results to corresponding ones for the canonical genetic code. We find that the…
We consider controllable DNA sequence design, where sequences are generated by conditioning on specific biological properties. While language models (LMs) such as GPT and BERT have achieved remarkable success in natural language generation,…
Code generation maps a program description to executable source code in a programming language. Existing approaches mainly rely on a recurrent neural network (RNN) as the decoder. However, we find that a program contains significantly more…
Molecular codes translate information written in one type of molecules into another molecular language. We introduce a simple model that treats molecular codes as noisy information channels. An optimal code is a channel that conveys…
The Gene Ontology aims to define the universe of functions known for gene products, at the molecular, cellular and organism levels. While the ontology is designed to cover all aspects of biology in a "species independent manner", the fact…
Oscillatory gene circuits are ubiquitous to biology and are involved in fundamental processes of cell cycle, circadian rhythms and developmental systems. The synthesis of small, non-natural oscillatory genetic circuits have been…
The primary aim of automated performance improvement is to reduce the running time of programs while maintaining (or improving on) functionality. In this paper, Genetic Programming is used to find performance improvements in regular…
Genome modeling conventionally treats gene sequence as a language, reflecting its structured motifs and long-range dependencies analogous to linguistic units and organization principles such as words and syntax. Recent studies utilize…
Stars with initial mass above roughly 8 solar masses will evolve to form a core made of iron group elements at which point no further exothermic nuclear reactions between charged nuclei may prevent the core collapse. Electron captures,…
This paper presents a procedure to add broader diversity at the beginning of the evolutionary process. It consists of creating two initial populations with different parameter settings, evolving them for a small number of generations,…
In recent years the field of genetic programming has made significant advances towards automatic programming. Research and development of contemporary program synthesis methods, such as PushGP and Grammar Guided Genetic Programming, can…
Recently, researchers have applied genetic algorithms (GAs) to address some problems in quantum computation. Also, there has been some works in the designing of genetic algorithms based on quantum theoretical concepts and techniques. The so…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…