Related papers: Orienting Ordered Scaffolds: Complexity and Algori…
One of the important problems in multiprocessor systems is Task Graph Scheduling. Task Graph Scheduling is an NP-Hard problem. Both learning automata and genetic algorithms are search tools which are used for solving many NP-Hard problems.…
Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…
In the Upper Degree-Constrained Partial Orientation problem we are given an undirected graph $G=(V,E)$, together with two degree constraint functions $d^-,d^+ : V \to \mathbb{N}$. The goal is to orient as many edges as possible, in such a…
Orienting the edges of an undirected graph such that the resulting digraph satisfies some given constraints is a classical problem in graph theory, with multiple algorithmic applications. In particular, an $st$-orientation orients each edge…
The paper focuses on two problems: (i) how to orient the edges of an undirected graph in order to maximize the number of ordered vertex pairs (x,y) such that there is a directed path from x to y, and (ii) how to orient the edges so as to…
The Ordered Covering Problem (OCP) arises in the context of the Discretizable Molecular Distance Geometry Problem (DMDGP), where the ordering of pruning edges significantly impacts the performance of the SBBU algorithm for protein structure…
It is required to find an optimal order of constructing the edges of a network so as to minimize the sum of the weighted connection times of relevant pairs of vertices. Construction can be performed anytime anywhere in the network, with a…
Optimal power flow (OPF) is an important problem for power generation and it is in general non-convex. With the employment of renewable energy, it will be desirable if OPF can be solved very efficiently so its solution can be used in real…
Neural network algorithms have been recently applied to construct Parton Distribution Function (PDF) parametrizations which provide an alternative to standard global fitting procedures. We propose a technique based on an interactive neural…
In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and…
There are many classical problems in P whose time complexities have not been improved over the past decades. Recent studies of "Hardness in P" have revealed that, for several of such problems, the current fastest algorithm is the best…
Phylogenies depicting the evolutionary history of genetically heterogeneous subpopulations of cells from the same cancer, i.e., cancer phylogenies, offer valuable insights about cancer development and guide treatment strategies. Many…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Genetic and comparative genomic studies indicate that extant genomes are more properly considered to be a fusion product of random mutations over generations and genomic material transfers between individuals of different lineages. This has…
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…
In the framework of convolutional neural networks that lie at the heart of deep learning, downsampling is often performed with a max-pooling operation that only retains the element with maximum activation, while completely discarding the…
We consider the Shortest Odd Path problem, where given an undirected graph $G$, a weight function on its edges, and two vertices $s$ and $t$ in $G$, the aim is to find an $(s,t)$-path with odd length and, among all such paths, of minimum…
The linear ordering problem (LOP), which consists in ordering M objects from their pairwise comparisons, is commonly applied in many areas of research. While efforts have been made to devise efficient LOP algorithms, verification of whether…
Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…