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We describe the combinatorics of equilibria and steady states of neurons in threshold-linear networks that satisfy Dale's law. The combinatorial code of a Dale network is characterized in terms of two conditions: (i) a condition on the…
A pedigree is a directed graph in which each vertex (except the founder vertices) has two parents. The main result in this paper is a construction of an infinite family of counter examples to a reconstruction problem on pedigrees, thus…
The class of ranked tree-child networks, tree-child networks arising from an evolution process with a fixed embedding into the plane, has recently been introduced by Bienvenu, Lambert, and Steel. These authors derived counting results for…
The theory of complex trees is introduced as a new approach to study a broad class of self-similar sets. Systems of equations encoded by complex trees tip-to-tip equivalence relations are used to obtain one-parameter families of connected…
In this paper we investigate undirected discrete graphical tree models when all the variables in the system are binary, where leaves represent the observable variables and where all the inner nodes are unobserved. A novel approach based on…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
Describing a complex system is in many ways a problem akin to identifying an object, in that it involves defining boundaries, constituent parts and their relationships by the use of grouping laws. Here we propose a novel method which…
Many classes of phylogenetic networks have been proposed in the literature. A feature of several of these classes is that if one restricts a network in the class to a subset of its leaves, then the resulting network may no longer lie within…
An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…
Tree trace reconstruction aims to learn the binary node labels of a tree, given independent samples of the tree passed through an appropriately defined deletion channel. In recent work, Davies, R\'acz, and Rashtchian used combinatorial…
Syntax connects words to each other in very specific ways. Two words are syntactically connected if they depend directly on each other. Syntactic connections usually happen within a sentence. Gathering all those connection across several…
We present a dataset and experiments on applying recurrent neural networks (RNNs) for guiding clause selection in the connection tableau proof calculus. The RNN encodes a sequence of literals from the current branch of the partial proof…
In this article groups of controlled characters of a combinatorial Hopf algebra are considered from the perspective of infinite-dimensional Lie theory. A character is controlled in our sense if it satisfies certain growth bounds, e.g.\…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
We introduce a novel model-theoretic framework inspired from graph modification and based on the interplay between model theory and algorithmic graph minors. The core of our framework is a new compound logic operating with two types of…
A normal (phylogenetic) network with $k$ reticulations displays $2^k$ phylogenetic trees. In this paper, we establish an analogous result for tree-child (phylogenetic) networks with no underlying $3$-cycles. In particular, we show that a…
Generating trees are a useful technique in the enumeration of various combinatorial objects, particularly restricted permutations. Quite often the generating tree for the set of permutations avoiding a set of patterns requires infinitely…
The use of machine learning algorithms in finance, medicine, and criminal justice can deeply impact human lives. As a consequence, research into interpretable machine learning has rapidly grown in an attempt to better control and fix…
Phylogenetic networks provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…