Related papers: Algorithms for the Constrained Perfect Phylogeny w…
Despite strong performance on a variety of tasks, neural sequence models trained with maximum likelihood have been shown to exhibit issues such as length bias and degenerate repetition. We study the related issue of receiving…
In this paper, we resolve the computational complexity of a number of outstanding open problems with practical applications. Here is the list of problems we show to be PPAD-complete, along with the domains of practical significance:…
Pattern learning in an important problem in Natural Language Processing (NLP). Some exhaustive pattern learning (EPL) methods (Bod, 1992) were proved to be flawed (Johnson, 2002), while similar algorithms (Och and Ney, 2004) showed great…
The graph coloring problem (GCP) is one of the most studied NP-HARD problems in computer science. Given a graph , the task is to assign a color to all vertices such that no vertices sharing an edge receive the same color and that the number…
In the NP-hard Optimizing PD with Dependencies (PDD) problem, the input consists of a phylogenetic tree $T$ over a set of taxa $X$, a food-web that describes the prey-predator relationships in $X$, and integers $k$ and $D$. The task is to…
We consider the selective graph coloring problem, which is a generalization of the classical graph coloring problem. Given a graph together with a partition of its vertex set into clusters, we want to choose exactly one vertex per cluster…
This paper focuses on the problem of generating human face pictures from specific attributes. The existing CNN-based face generation models, however, either ignore the identity of the generated face or fail to preserve the identity of the…
The Stable Matching Problem with Couples (SMP-C) is a ubiquitous real-world extension of the stable matching problem (SMP) involving complementarities. Although SMP can be solved in polynomial time, SMP-C is NP-Complete. Hence, it is not…
Crossover is the process of recombining the genetic features of two parents. For many applications where crossover is applied to permutations, relevant genetic features are pairs of adjacent elements, also called edges in the permutation…
Correctly identifying neuronal subsets is critical to multiple downstream methods in several areas of neuroscience research. The hippocampal interneuron characterization technology has achieved rapid development in recent years. However,…
The maximum clique problem is a well known NP-Hard problem with applications in data mining, network analysis, informatics, and many other areas. Although there exist several algorithms with acceptable runtimes for certain classes of…
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…
Given a simple polygon $\cal P$, in the Art Gallery problem the goal is to find the minimum number of guards needed to cover the entire $\cal P$, where a guard is a point and can see another point $q$ when $\overline{pq}$ does not cross the…
Many practical problems in almost all scientific and technological disciplines have been classified as computationally hard (NP-hard or even NP-complete). In life sciences, combinatorial optimization problems frequently arise in molecular…
We introduce a new and broader formulation of the stable marriage problem (SMP), called the stable polygamy problem (SPP), where multiple individuals from a larger group $L$ of $|L|$ individuals can be matched with a single individual from…
Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one…
Permutation Pattern Matching (or PPM) is a decision problem whose input is a pair of permutations $\pi$ and $\tau$, represented as sequences of integers, and the task is to determine whether $\tau$ contains a subsequence order-isomorphic to…
A hamiltonian sequence is a path walk $P$ that can be a hamiltonian path or hamiltonian circuit. Determining whether such hamiltonian sequence exists in a given graph \G is a NP-Complete problem. In this paper, a novel algorithm for…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…