Related papers: Comparing reverse complementary genomic words base…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
Propensity Score Matching (PSM) stands as a widely embraced method in comparative effectiveness research. PSM crafts matched datasets, mimicking some attributes of randomized designs, from observational data. In a valid PSM design where all…
When an individual's DNA is sequenced, sensitive medical information becomes available to the sequencing laboratory. A recently proposed way to hide an individual's genetic information is to mix in DNA samples of other individuals. We…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
Next-generation sequencing technologies now constitute a method of choice to measure gene expression. Data to analyze are read counts, commonly modeled using Negative Binomial distributions. A relevant issue associated with this…
A fundamental method of reconstructing networks, e.g. in the context of gene regulation, relies on the precision matrix (the inverse of the variance-covariance matrix) as an indicator which variables are associated with each other. The…
A growing number of RNA sequences are now known to have distributions of multiple stable sequences. Recent algorithms use the list of nucleotides in a sequence and auxiliary experimental data to predict such distributions. Although the…
Language models (LMs) are increasingly being studied as models of human language learners. Due to the nascency of the field, it is not well-established whether LMs exhibit similar learning dynamics to humans, and there are few direct…
Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate…
Kernel embeddings of distributions and the Maximum Mean Discrepancy (MMD), the resulting distance between distributions, are useful tools for fully nonparametric two-sample testing and learning on distributions. However, it is rarely that…
In this paper we quantify the consistency of word usage in written texts represented by complex networks, where words were taken as nodes, by measuring the degree of preservation of the node neighborhood.} Words were considered highly…
We hereby present a solution to a semantic textual similarity (STS) problem in which it is necessary to match two sentences containing, as the only distinguishing factor, highly specific information (such as names, addresses, identification…
Languages are grouped into families that share common linguistic traits. While this approach has been successful in understanding genetic relations between diverse languages, more analyses are needed to accurately quantify their…
The frequencies at which individual words occur across languages follow power law distributions, a pattern of findings known as Zipf's law. A vast literature argues over whether this serves to optimize the efficiency of human communication,…
Distribution matching is the process of invertibly mapping a uniformly distributed input sequence onto sequences that approximate the output of a desired discrete memoryless source. The special case of a binary output alphabet and…
Factor complexity $\mathcal{C}$ and palindromic complexity $\mathcal{P}$ of infinite words with language closed under reversal are known to be related by the inequality $\mathcal{P}(n) + \mathcal{P}(n+1) \leq 2 +…
The goal of this paper is to study the similarity between sequences using a distance between the \emph{context} trees associated to the sequences. These trees are defined in the framework of \emph{Sparse Probabilistic Suffix Trees} (SPST),…
We consider the problem of metric learning subject to a set of constraints on relative-distance comparisons between the data items. Such constraints are meant to reflect side-information that is not expressed directly in the feature vectors…
Compositional spectra (CS) analysis based on k-mer scoring of DNA sequences was employed in this study for dot-plot comparison of human and primate genomes. The detection of extended conserved synteny regions was based on continuous fuzzy…