Related papers: Ultrametrics in the genetic code and the genome
We propose a general framework for converting global and local similarities between biological sequences to quasi-metrics. In contrast to previous works, our formulation allows asymmetric distances, originating from uneven weighting of…
Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their…
We derive theoretical upper and lower bounds on the maximum size of DNA codes of length n with constant GC-content w and minimum Hamming distance d, both with and without the additional constraint that the minimum Hamming distance between…
Deciphering cell type heterogeneity is crucial for systematically understanding tissue homeostasis and its dysregulation in diseases. Computational deconvolution is an efficient approach estimating cell type abundances from a variety of…
It is possible to formulate 2d field theory on the ultrametric space with the free correlators identical to 2d correlators and the same potential. Such model should carry some features of original model for scale invariant theories. For the…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
Reconstructing who infected whom is a central challenge in analysing epidemiological data. Recently, advances in sequencing technology have led to increasing interest in Bayesian approaches to inferring who infected whom using genetic data…
We study the locally recoverable codes on algebraic curves. In the first part of this article, we provide a bound of generalized Hamming weight of these codes. Whereas in the second part, we propose a new family of algebraic geometric LRC…
A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…
In this paper, we investigate compact ultrametric measure spaces which form a subset $\mathcal{U}^w$ of the collection of all metric measure spaces $\mathcal{M}^w$. Similar as for the ultrametric Gromov-Hausdorff distance on the collection…
Surrogate models are a well established approach to reduce the number of expensive function evaluations in continuous optimization. In the context of genetic programming, surrogate modeling still poses a challenge, due to the complex…
Motivation: mtDNA distance matrices are standard inputs for distance-based phylogeny, but computing all pairwise alignments is costly. Missing entries can degrade inferred topology and branch lengths, and generic matrix-completion methods…
The arrangement of network nodes in hyperbolic spaces has become a widely studied problem, motivated by numerous results suggesting the existence of hidden metric spaces behind the structure of complex networks. Although several methods…
A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
Genetic Algorithms (GAs) are explored as a tool for probing new physics with high dimensionality. We study the 19-dimensional pMSSM, including experimental constraints from all sources and assessing the consistency of potential signals of…
The GC-content is very variable in different genome regions and species but although many hypothesis we still do not know the reason why. Here we show that a relationship exists with the mutation rate, in particular we noticed a new…
A new set of DNA base-nucleic acid codes and their hypercomplex number representation have been introduced for taking the probability of each nucleotide into full account. A new scoring system has been proposed to suit the hypercomplex…
The advances in WDM technology lead to the great interest in traffic grooming problems. As traffic often changes from time to time, the problem of grooming dynamic traffic is of great practical value. In this paper, we discuss dynamic…