Related papers: On Injective Embeddings of Tree Patterns
Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates…
Rooted bifurcating trees are mathematical objects used to model evolutionary relationships and arise naturally in both coalescent theory and phylogenetics. Recent numerical representations of tree topologies, known as F-matrices, allow for…
The problem of inferring an inductive invariant for verifying program safety can be formulated in terms of binary classification. This is a standard problem in machine learning: given a sample of good and bad points, one is asked to find a…
One can often make inferences about a growing network from its current state alone. For example, it is generally possible to determine how a network changed over time or pick among plausible mechanisms explaining its growth. In practice,…
Suppose we have two trees on the same set of leaves, in which nodes are weighted such that children are heavier than their parents. We say a node from the first tree and a node from the second tree are induced together if they have a common…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
We study a class of combinatorial objects that we call "decorated trees". These consist of vertices, arrows and edges, where each edge is decorated by two integers (one near each of its endpoints), each arrow is decorated by an integer, and…
In analogy to other concepts of a similar nature, we define the inducibility of a rooted binary tree. Given a fixed rooted binary tree $B$ with $k$ leaves, we let $\gamma(B,T)$ be the proportion of all subsets of $k$ leaves in $T$ that…
Tree embedding has been a fundamental method in algorithm design with wide applications. We focus on the efficiency of building tree embedding in various computational settings under high-dimensional Euclidean $\mathbb{R}^d$. We devise a…
We provide decidability and undecidability results on the model-checking problem for infinite tree structures. These tree structures are built from sequences of elements of infinite relational structures. More precisely, we deal with the…
There is a deep connection between permutations and trees. Certain sub-structures of permutations, called sub-permutations, bijectively map to sub-trees of binary increasing trees. This opens a powerful tool set to study enumerative and…
The input to the agreement problem is a collection $P = \{T_1, T_2, \dots , T_k\}$ of phylogenetic trees, called input trees, over partially overlapping sets of taxa. The question is whether there exists a tree $T$, called an agreement…
The idea of "vertex at the infinity" naturally appears when studying indecomposable injective representations of tree quivers. In this paper we formalize this behavior and find the structure of all the indecomposable injective…
Efficient embedding virtual clusters in physical network is a challenging problem. In this paper we consider a scenario where physical network has a structure of a balanced tree. This assumption is justified by many real- world…
We provide time- and sample-efficient algorithms for learning and testing latent-tree Ising models, i.e. Ising models that may only be observed at their leaf nodes. On the learning side, we obtain efficient algorithms for learning a…
Networks are one of the most powerful structures for modeling problems in the real world. Downstream machine learning tasks defined on networks have the potential to solve a variety of problems. With link prediction, for instance, one can…
Inference of species networks from genomic data under the Network Multispecies Coalescent Model is currently severely limited by heavy computational demands. It also remains unclear how complicated networks can be for consistent inference…
The relative importance of the intrinsic and extrinsic factors determining the variety of geometric shapes exhibited by dendritic trees remains unclear. This question was addressed by developing a model of the growth of dendritic trees…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
We identify the complexity of the classification problem for automorphisms of a given countable regularly branching tree up to conjugacy. We consider both the rooted and unrooted cases. Additionally, we calculate the complexity of the…