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Recently, a new vector encoding, Ordered Leaf Attachment (OLA), was introduced that represents $n$-leaf phylogenetic trees as $n-1$ length integer vectors by recording the placement location of each leaf. Both encoding and decoding of trees…

The well-known Eulerian path problem can be solved in polynomial time (more exactly, there exists a linear time algorithm for this problem). In this paper, we model the problem using a string matching framework, and then initiate an…

Maximum bipartite matching is a fundamental algorithmic problem which can be solved in polynomial time. We consider a natural variant in which there is a separation constraint: the vertices on one side lie on a path or a grid, and two…

We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…

We analyze union-find using potential functions motivated by continuous algorithms, and give alternate proofs of the $O(\log\log{n})$, $O(\log^{*}n)$, $O(\log^{**}n)$, and $O(\alpha(n))$ amortized cost upper bounds. The proof of the…

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…

We give an algorithm that takes as input an $n$-vertex graph $G$ and an integer $k$, runs in time $2^{O(k^2)} n^{O(1)}$, and outputs a tree decomposition of $G$ of width at most $k$, if such a decomposition exists. This resolves the…

We show, for the input vectors $(a_0, a_1, ..., a_{n-1})$ and $(b_0, b_1, ..., b_{n-1})$, where $a_i$'s and $b_j$'s are real numbers, after $O(n\log^4 n)$ time preprocessing for each of them, the vector multiplication $(a_0, a_1, ...,…

The problem of constructing optimal factoring automata arises in the context of unification factoring for the efficient execution of logic programs. Given an ordered set of $n$ strings of length $m$, the problem is to construct a trie-like…

Let $\phi$ be a function that maps any non-empty subset $A$ of $\mathbb{R}^2$ to a non-empty subset $\phi(A)$ of $\mathbb{R}^2$. A $\phi$-cover of a set $T=\{T_1, T_2, \dots, T_m\}$ of pairwise non-crossing trees in the plane is a set of…

For an $m$-edge connected simple graph $G$, finding a spanning tree of $G$ with the maximum number of leaves is MAXSNP-complete. The problem remains NP-complete even if $G$ is planar and the maximal degree of $G$ is at most four. Lu and…

Karloff? and Shirley recently proposed summary trees as a new way to visualize large rooted trees (Eurovis 2013) and gave algorithms for generating a maximum-entropy k-node summary tree of an input n-node rooted tree. However, the algorithm…

In this paper, we are interested in the number of red nodes in red-black trees. We first present an $O(n^2\log n)$ time dynamic programming solution for computing $r(n)$, the largest number of red internal nodes in a red-black tree on $n$…

A factorization $f_1, \ldots, f_m$ of a string $w$ of length $n$ is called a repetition factorization of $w$ if $f_i$ is a repetition, i.e., $f_i$ is a form of $x^kx'$, where $x$ is a non-empty string, $x'$ is a (possibly-empty) proper…

Treedepth is a central parameter to algorithmic graph theory. The current state-of-the-art in computing and approximating treedepth consists of a $2^{O(k^2)} n$-time exact algorithm and a polynomial-time $O(\text{OPT} \log^{3/2}…

We consider the satisfiability problem for the two-variable fragment of the first-order logic extended with modulo counting quantifiers and interpreted over finite words or trees. We prove a small-model property of this logic, which gives a…

Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on…

A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…

We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…

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…