Related papers: Constructing a Minimum-Level Phylogenetic Network …
Phylogenetic networks are rooted acyclic directed graphs in which the leaves are identified with members of a set X of species. The cluster of a vertex is the set of leaves that are descendants of the vertex. A network is "distinct-cluster"…
We consider the problem of detecting a planted clique of size $k$ in a random graph on $n$ vertices. When the size of the clique exceeds $\Theta(\sqrt{n})$, polynomial-time algorithms for detection proliferate. We study faster -- namely,…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
Inferring the phylogenetic relationships among a sample of organisms is a fundamental problem in modern biology. While distance-based hierarchical clustering algorithms achieved early success on this task, these have been supplanted by…
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…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display graphs are created by identifying common leaf labels in two or more phylogenetic trees or networks. The treewidth of such graphs is bounded as a…
Despite recent theoretical progress on the non-convex optimization of two-layer neural networks, it is still an open question whether gradient descent on neural networks without unnatural modifications can achieve better sample complexity…
Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe…
The heterogeneous structure implies that a very few nodes may play the critical role in maintaining structural and functional properties of a large-scale network. Identifying these vital nodes is one of the most important tasks in network…
Ranked tree-child networks are a recently introduced class of rooted phylogenetic networks in which the evolutionary events represented by the network are ordered so as to respect the flow of time. This class includes the well-studied…
Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary `Tree of Life'. This approach recognises that extinction not only removes species but…
Let $L$ be a set of $n$ lines in the plane, not necessarily in general position. We present an efficient algorithm for finding all the vertices of the arrangement $A(L)$ of maximum level, where the level of a vertex $v$ is the number of…
For an arbitrary undirected simple graph G with m edges, we give an algorithm with running time O(m^4 |L|^2) to generate the set L of all minimal edge dominating sets of G. For bipartite graphs we obtain a better result; we show that their…
Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…
Kloks, Kratsch, and Spinrad showed how treewidth and minimum-fill, NP-hard combinatorial optimization problems related to minimal triangulations, are broken into subproblems by block subgraphs defined by minimal separators. These ideas were…