Related papers: An automaton approach for waiting times in DNA evo…
Suppose that $k$ series, all having the same autocorrelation function, are observed in parallel at $n$ points in time or space. From a single series of moderate length, the autocorrelation parameter $\beta$ can be estimated with limited…
Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and…
We consider the synthesis of deterministic tree transducers from automaton definable specifications, given as binary relations, over finite trees. We consider the case of specifications that are deterministic top-down tree automatic,…
Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events…
Transcription factors regulate gene expression, but how these proteins recognize and specifically bind to their DNA targets is still debated. Machine learning models are effective means to reveal interaction mechanisms. Here we studied the…
The intersection of artificial intelligence and bioinformatics has enabled significant advancements in drug discovery, particularly through the application of machine learning models. In this study, we present a combined approach using…
We explore for the first time the direct construction of string models on quantum annealers, and investigate their efficiency and effectiveness in the model discovery process. Through a thorough comparison with traditional methods such as…
Transcription factor (TF) molecules translocate by facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA). Despite the attention this mechanism received in the last 40 years, only a few studies…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
A knowledge search is a key process for inventions. However, there is inadequate quantitative modeling of dynamic knowledge search processes and associated search costs. In this study, agent-based and complex network methodologies were…
A deep neural network (DNN)-based model has been developed to predict non-parametric distributions of durations of phonemes in specified phonetic contexts and used to explore which factors influence durations most. Major factors in US…
In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…
For genetic algorithms using a bit-string representation of length~$n$, the general recommendation is to take $1/n$ as mutation rate. In this work, we discuss whether this is really justified for multimodal functions. Taking jump functions…
A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
Evolution occurs in populations of reproducing individuals. In stochastic descriptions of evolutionary dynamics, such as the Moran process, individuals are chosen randomly for birth and for death. If the same type is chosen for both steps,…
Inference with transformer-based language models begins with a prompt processing step. In this step, the model generates the first output token and stores the KV cache needed for future generation steps. This prompt processing step can be…
This paper presents a novel hybrid tokenization strategy that enhances the performance of DNA Language Models (DLMs) by combining 6-mer tokenization with Byte Pair Encoding (BPE-600). Traditional k-mer tokenization is effective at capturing…
In genetic systems there is a non-trivial interface between the sequence of symbols which constitutes the chromosome, or ``genotype'', and the products which this sequence encodes --- the ``phenotype''. This interface can be thought of as a…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…