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Partial Label Learning (PLL) aims to learn from the data where each training example is associated with a set of candidate labels, among which only one is correct. The key to deal with such problem is to disambiguate the candidate label…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
Forward-time models of diversification (i.e., speciation and extinction) produce phylogenetic trees that grow "vertically" as time goes by. Pruning the extinct lineages out of such trees leads to natural models for reconstructed trees…
The maximum clique problem is a classical NP-complete problem in graph theory and has important applications in many domains. In this paper we show, in a partially non-constructive way, the existence of an exact polynomial-time algorithm…
The ancestral sequence reconstruction problem is the inference, back in time, of the properties of common sequence ancestors from measured properties of contemporary populations. Standard algorithms for this problem assume independent…
Nowadays hybrid evolutionary algorithms, i.e, heuristic search algorithms combining several mutation operators some of which are meant to implement stochastically a well known technique designed for the specific problem in question while…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
Many complex questions in biology, physics, and mathematics can be mapped to the graph isomorphism problem and the closely related graph automorphism problem. In particular, these problems appear in the context of network visualization,…
Constraint programming (CP) is a powerful tool for modeling mathematical concepts and objects and finding both solutions or counter examples. One of the major strengths of CP is that problems can easily be combined or expanded. In this…
In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using…
Storyline drawings are a popular visualization of interactions of a set of characters over time, e.g., to show participants of scenes in a book or movie. Characters are represented as $x$-monotone curves that converge vertically for…
Recent progress has been made on developing a unified framework for joint text detection and recognition in natural images, but existing joint models were mostly built on two-stage framework by involving ROI pooling, which can degrade the…
Given an integer $k$ and a graph where every edge is colored either red or blue, the goal of the exact matching problem is to find a perfect matching with the property that exactly $k$ of its edges are red. Soon after Papadimitriou and…
We show that for any two values $\alpha, \beta >0 $ for which $\alpha+\beta>1$ then there is a value $N$ so that for all $n \geq N$ the following holds. For any binary phylogenetic tree $T$ on $n$ leaves there is a set of $\lfloor n^\alpha…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
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…
This note presents a simple and effective variation of genetic algorithm (GA) for solving RCPSP, denoted as 2-Phase Genetic Algorithm (2PGA). The 2PGA implements GA parent selection in two phases: Phase-1 includes the best current solutions…
The NP-complete graph problem Cluster Editing seeks to transform a static graph into a disjoint union of cliques by making the fewest possible edits to the edges. We introduce a natural interpretation of this problem in temporal graphs,…
The 0-1 Multidimensional Knapsack Problem (MKP) is a classical NP-hard combinatorial optimization problem with many engineering applications. In this paper, we propose a novel algorithm combining evolutionary computation with the exact…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…