Related papers: Novel Distances for Dollo Data
In many applications, a large number of features are collected with the goal to identify a few important ones. Sometimes, these features lie in a metric space with a known distance matrix, which partially reflects their co-importance…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences…
Recent works have shown that deep metric learning algorithms can benefit from weak supervision from another input modality. This additional modality can be incorporated directly into the popular triplet-based loss function as distances.…
The problem of similarity search is one of the main problems in computer science. This problem has many applications in text-retrieval, web search, computational biology, bioinformatics and others. Similarity between two data objects can be…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
Distance metric learning (DML) approaches learn a transformation to a representation space where distance is in correspondence with a predefined notion of similarity. While such models offer a number of compelling benefits, it has been…
The ratio of two densities provides a direct characterization of their differences. We consider the two-sample comparison problem by estimating this ratio given i.i.d. observations from two distributions. To this end, we propose additive…
The composition of pretraining data is a key determinant of foundation models' performance, but there is no standard guideline for allocating a limited computational budget across different data sources. Most current approaches either rely…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the "hybridization potential" of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a…
Many network applications are based on binary-state networks, where each component has one of two states: success or failure. Efficient algorithms to evaluate binary-state network reliability are continually being developed. Reliability…
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI)…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Although several RDF knowledge bases are available through the LOD initiative, the ontology schema of such linked datasets is not very rich. In particular, they lack object properties. The problem of finding new object properties (and their…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…
As a variant of standard convolution, a dilated convolution can control effective receptive fields and handle large scale variance of objects without introducing additional computational costs. To fully explore the potential of dilated…
Recent studies on plant disease diagnosis using machine learning (ML) have highlighted concerns about the overestimated diagnostic performance due to inappropriate data partitioning, where training and test datasets are derived from the…