Related papers: High fidelity epigenetic inheritance: Information …
We develop a latent variable model and an efficient spectral algorithm motivated by the recent emergence of very large data sets of chromatin marks from multiple human cell types. A natural model for chromatin data in one cell type is a…
Computational biology and bioinformatics provide vast data gold-mines from protein sequences, ideal for Language Models taken from NLP. These LMs reach for new prediction frontiers at low inference costs. Here, we trained two…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Time-delay embedding is a powerful technique for reconstructing the state space of nonlinear time series. However, the fidelity of reconstruction relies on the assumption that the time-delay map is an embedding, which is implicitly…
We experimentally demonstrate that information replication by templated ligation of DNA strands inherits a kinetic proofreading mechanism and achieves significant error suppression through cascade replication. A simple simulation model…
A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis…
Erwin Schrodinger famously and presciently ascribed the vehicle transmitting the hereditary information underlying life to an `aperiodic crystal'. We compare and contrast this, only later discovered to be stored in the linear biomolecule…
Hypercycles are information integration systems which are thought to overcome the information crisis of prebiotic evolution by ensuring the coexistence of several short templates. For imperfect template replication, we derive a simple…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
We introduce the notion of trace-norm isometric encoding and explore its implications for passive and active methods to protect quantum information against errors. Beside providing an operational foundations to the "subsystems principle"…
A good feature representation is a determinant factor to achieve high performance for many machine learning algorithms in terms of classification. This is especially true for techniques that do not build complex internal representations of…
A system is offered for imitation resistant transmitting of encrypted information in wireless communication networks on the basis of redundant residue polynomial codes. The particular feature of this solution is complexing of methods for…
Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of…
Achieving human-like memory recall in artificial systems remains a challenging frontier in computer vision. Humans demonstrate remarkable ability to recall images after a single exposure, even after being shown thousands of images. However,…
Post-translational modifications (PTMs) form a combinatorial "code" that regulates protein function, yet deciphering this code - linking modified sites to their catalytic enzymes - remains a central unsolved problem in understanding…
Gene activation in eukaryotes involves the concerted action of histone tail modifiers, chromatin remodellers and transcription factors, whose precise coordination is currently unknown. We demonstrate that the experimentally observed…
As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our…
This paper presents the computational methods of information cohomology applied to genetic expression in and in the companion paper and proposes its interpretations in terms of statistical physics and machine learning. In order to further…
Specialised transformers-based models (such as BioBERT and BioMegatron) are adapted for the biomedical domain based on publicly available biomedical corpora. As such, they have the potential to encode large-scale biological knowledge. We…