Related papers: Incomplete Directed Perfect Phylogeny in Linear Ti…
We consider strongly-connected directed networks of identical synchronous, finite-state processors with in- and out-degree uniformly bounded by a network constant. Via a straightforward extension of Ostrovsky and Wilkerson's Backwards…
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…
Informative data selection is a key requirement for large language models (LLMs) to minimize the amount of data required for fine-tuning, network distillation, and token pruning, enabling fast and efficient deployment, especially under…
Data-efficient image classification is a challenging task that aims to solve image classification using small training data. Neural network-based deep learning methods are effective for image classification, but they typically require…
Depth first search (DFS) tree is a fundamental data structure for solving various problems in graphs. It is well known that it takes $O(m+n)$ time to build a DFS tree for a given undirected graph $G=(V,E)$ on $n$ vertices and $m$ edges. We…
Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. In Maximize Phylogenetic Diversity (MPD) one is asked to find a set of taxa (of bounded size/cost) for…
Mathematical optimization, although often leading to NP-hard models, is now capable of solving even large-scale instances within reasonable time. However, the primary focus is often placed solely on optimality. This implies that while…
Internal Pattern Matching (IPM) queries on a text $T$, given two fragments $X$ and $Y$ of $T$ such that $|Y|<2|X|$, ask to compute all exact occurrences of $X$ within $Y$. IPM queries have been introduced by Kociumaka, Radoszewski, Rytter,…
We present an $\tilde O(m+n^{1.5})$-time randomized algorithm for maximum cardinality bipartite matching and related problems (e.g. transshipment, negative-weight shortest paths, and optimal transport) on $m$-edge, $n$-node graphs. For…
Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in…
Given a simple $n$-vertex, $m$-edge graph $G$ undergoing edge insertions and deletions, we give two new fully dynamic algorithms for exactly maintaining the edge connectivity of $G$ in $\tilde{O}(n)$ worst-case update time and…
The perfect phylogeny mixture (PPM) model is useful due to its simplicity and applicability in scenarios where mutations can be assumed to accumulate monotonically over time. It is the underlying model in many tools that have been used, for…
A maximal matching can be maintained in fully dynamic (supporting both addition and deletion of edges) $n$-vertex graphs using a trivial deterministic algorithm with a worst-case update time of O(n). No deterministic algorithm that…
In the Directed Disjoint Paths problem ($k$-DDP), we are given a digraph $k$ pairs of terminals, and the goal is to find $k$ pairwise vertex-disjoint paths connecting each pair of terminals. Bang-Jensen and Thomassen [SIAM J. Discrete Math.…
In the area of parameterized complexity, to cope with NP-Hard problems, we introduce a parameter k besides the input size n, and we aim to design algorithms (called FPT algorithms) that run in O(f(k)n^d) time for some function f(k) and…
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
Determinantal point processes (DPP) serve as a practicable modeling for many applications of repulsive point processes. A known approach for simulation was proposed in \cite{Hough(2006)}, which generate the desired distribution point wise…
The Densest Subgraph Problem (DSP) is widely used to identify community structures and patterns in networks such as bioinformatics and social networks. While solvable in polynomial time, traditional exact algorithms face computational and…
In this survey we investigate the application of the Adleman-Lipton model on Rural Postman problem, which given an undirected graph $G=(V,E)$ with positive integer lengths on each of its edges and a subset $E^{'}\subseteq E$, asks whether…