Related papers: Recognizing Union-Find trees is NP-complete
Algorithms for learning decision trees often include heuristic local-search operations such as (1) adjusting the threshold of a cut or (2) also exchanging the feature of that cut. We study minimizing the number of classification errors by…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
A multilabeled tree (or MUL-tree) is a rooted tree in which every leaf is labelled by an element from some set, but in which more than one leaf may be labelled by the same element of that set. In phylogenetics, such trees are used in…
This paper solves a long standing open problem of whether NP-complete problems could be solved in polynomial time on a deterministic Turing machine by showing that the indistinguishable binomial decision tree can be formed in a 3-SAT…
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…
Estimating a joint Highest Posterior Density credible set for a multivariate posterior density is challenging as dimension gets larger. Credible intervals for univariate marginals are usually presented for ease of computation and…
Despite the latest prevailing success of deep neural networks (DNNs), several concerns have been raised against their usage, including the lack of intepretability the gap between DNNs and other well-established machine learning models, and…
Succinct data structures give space-efficient representations of large amounts of data without sacrificing performance. They rely one cleverly designed data representations and algorithms. We present here the formalization in Coq/SSReflect…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
Dynamic regression trees are an attractive option for automatic regression and classification with complicated response surfaces in on-line application settings. We create a sequential tree model whose state changes in time with the…
A dynamic forest data structure maintains a forest (and associated data like edge weights) under edge insertions and deletions. Dynamic forests are widely used to solve online and offline graph problems. Well-known examples of dynamic…
We define an algorithm k which takes a connected graph G on a totally ordered vertex set and returns an increasing tree R (which is not necessarily a subtree of G). We characterize the set of graphs G such that k(G)=R. Because this set has…
A suffix tree is a data structure used mainly for pattern matching. It is known that the space complexity of simple suffix trees is quadratic in the length of the string. By a slight modification of the simple suffix trees one gets the…
Additive models, such as produced by gradient boosting, and full interaction models, such as classification and regression trees (CART), are widely used algorithms that have been investigated largely in isolation. We show that these models…
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.…
Daily internet communication relies heavily on tree-structured graphs, embodied by popular data formats such as XML and JSON. However, many recent generative (probabilistic) models utilize neural networks to learn a probability distribution…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…
We characterize those countable rooted trees whose full automorphism group has uncountable strong cofinality or contains an open subgroup with ample generics.
An $\alpha$-thin tree $T$ of a graph $G$ is a spanning tree such that every cut of $G$ has at most an $\alpha$ proportion of its edges in $T$. The Thin Tree Conjecture proposes that there exists a function $f$ such that for any $\alpha >…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…