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Motivated by alignment of correlated sparse random graphs, we introduce a hypothesis testing problem of deciding whether or not two random trees are correlated. We obtain sufficient conditions under which this testing is impossible or…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
The Sackin and Colless indices are two widely-used metrics for measuring the balance of trees and for testing evolutionary models in phylogenetics. This short paper contributes two results about the Sackin and Colless indices of trees. One…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
Species trees represent the historical divergences of populations or species, while gene trees trace the ancestry of individual gene copies sampled within those populations. In cases involving rapid speciation, gene trees with topologies…
Many modern multiclass and multilabel problems are characterized by increasingly large output spaces. For these problems, label embeddings have been shown to be a useful primitive that can improve computational and statistical efficiency.…
Most approaches that tackle the problem of node classification consider nodes to be similar, if they have shared neighbors or are close to each other in the graph. Recent methods for attributed graphs additionally take attributes of…
Weed species classification represents an important step for the development of automated targeting systems that allow the adoption of precision agriculture practices. To reduce costs and yield losses caused by their presence. The…
A rooted tree $T$ with vertex labels $t(v)$ and set-valued edge labels $\lambda(e)$ defines maps $\delta$ and $\varepsilon$ on the pairs of leaves of $T$ by setting $\delta(x,y)=q$ if the last common ancestor $\text{lca}(x,y)$ of $x$ and…
Multi-label classification is a challenging task, particularly in domains where the number of labels to be predicted is large. Deep neural networks are often effective at multi-label classification of images and textual data. When dealing…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
We present an approach to match partially occluded plant leaves with databases of full plant leaves. Although contour based 2D shape matching has been studied extensively in the last couple of decades, matching occluded leaves with full…
Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations:…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
Given a set of leaf-labeled trees with identical leaf sets, the well-known "Maximum Agreement SubTree" problem (MAST) consists of finding a subtree homeomorphically included in all input trees and with the largest number of leaves. Its…
Partial-label learning (PLL) is a multi-class classification problem, where each training example is associated with a set of candidate labels. Even though many practical PLL methods have been proposed in the last two decades, there lacks a…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…
We propose methods that enable efficient hierarchical classification in parallel. Our methods transform a batch of classification scores and labels, corresponding to given nodes in a semantic tree, to scores and labels corresponding to all…
A labeling scheme for nearest common ancestors assigns a distinct binary string, called the label, to every node of a tree, so that given the labels of two nodes (and no further information about the topology of the tree) we can compute the…