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The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
Recent work has highlighted deep connections between sequence-length requirements for high-probability phylogeny reconstruction and the related problem of the estimation of ancestral sequences. In [Daskalakis et al.'09], building on the…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular,…
Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…
General log-linear models specified by non-negative integer design matrices have a potentially wide range of applications, although using models without the genuine overall effect, that is, ones which cannot be reparameterized to include a…
In this paper, we present a novel data-free method for merging neural networks in weight space. Differently from most existing works, our method optimizes for the permutations of network neurons globally across all layers. This allows us to…
Mechanistic network models specify the mechanisms by which networks grow and change, allowing researchers to investigate complex systems using both simulation and analytical techniques. Unfortunately, it is difficult to write likelihoods…
We investigate the optimization landscape of maximum likelihood estimation (MLE) for the Cavender-Farris-Neyman (CFN) model, a two-state latent tree model fundamental to statistical phylogenetics and the ferromagnetic Ising model. Although…
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy--a rooted, binary, timed tree, with tips corresponding…
In this paper we consider the reconstruction problem on the tree for the hardcore model. We determine new bounds for the non-reconstruction regime on the k-regular tree showing non-reconstruction when lambda < (ln 2-o(1))ln^2(k)/(2 lnln(k))…
The software program BAMM has been widely used to study the dynamics of speciation, extinction, and phenotypic evolution on phylogenetic trees. The program implements a model-based clustering algorithm to identify clades that share common…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
One of the goals of phylogenetic research is to find the species tree describing the evolutionary history of a set of species. But the trees derived from geneti data with the help of tree inference methods are gene trees that need not…
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Tuffley and Steel (1997) proved that Maximum Likelihood and Maximum Parsimony methods in phylogenetics are equivalent for sequences of characters under a simple symmetric model of substitution with no common mechanism. This result has been…
Recent progress in Neural Causal Models (NCMs) showcased how identification and partial identification of causal effects can be automatically carried out via training of neural generative models that respect the constraints encoded in a…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Non-minimal renormalisation schemes such as the momentum subtraction scheme (MOM) have frequently been used for physical computations. The consistency of such a scheme relies on the existence of a coupling redefinition linking it to MSbar.…