Related papers: Likelihood-Based Root State Reconstruction on a Tr…
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…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
In this paper, we propose a probabilistic parsing model, which defines a proper conditional probability distribution over non-projective dependency trees for a given sentence, using neural representations as inputs. The neural network…
Generative, temporal network models play an important role in analyzing the dependence structure and evolution patterns of complex networks. Due to the complicated nature of real network data, it is often naive to assume that the underlying…
Our work introduces an approach for estimating the contribution of attachment mechanisms to the formation of growing networks. We present a generic model in which growth is driven by the continuous attachment of new nodes according to…
This short communication uses a simple experiment to show that fitting to a power law distribution by using graphical methods based on linear fit on the log-log scale is biased and inaccurate. It shows that using maximum likelihood…
In this paper we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
Much evidence from biological theory and empirical data indicates that, gene tree, phylogenetic trees reconstructed from different genes (loci), do not have to have exactly the same tree topologies. Such incongruence between gene trees…
The Lyman-$\alpha$ forest is a highly non-linear field with a lot of information available in the data beyond the power spectrum. The flux probability distribution function (PDF) has been used as a successful probe of small-scale physics.…
We study downlink channel estimation in a frequency-division duplex (FDD) massive MIMO system from PMI-only feedback under a 5G NR-type limited-feedback architecture. In this architecture, the user selects a preferred codeword from a shared…
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 'no common mechanism' (NCM) models of character evolution, each character can evolve on a phylogenetic tree under a partially or totally separate process (e.g. with its own branch lengths). In such cases, the usual conditions that…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…
The standard paradigm of neural language generation adopts maximum likelihood estimation (MLE) as the optimizing method. From a distributional view, MLE in fact minimizes the Kullback-Leibler divergence (KLD) between the distribution of the…
We study maximal clades in random phylogenetic trees with the Yule-Harding model or, equivalently, in binary search trees. We use probabilistic methods to reprove and extend earlier results on moment asymptotics and asymptotic normality. In…
In this work, we revisit the estimation of the model parameters of a Weibull distribution based on iid observations, using the maximum likelihood estimation (MLE) method which does not yield closed expressions of the estimators. Among other…
Consider a collection of random variables attached to the vertices of a graph. The reconstruction problem requires to estimate one of them given `far away' observations. Several theoretical results (and simple algorithms) are available when…
The tree-metric theorem provides a necessary and sufficient condition for a dissimilarity matrix to be a tree metric, and has served as the foundation for numerous distance-based reconstruction methods in phylogenetics. Our main result is…
We study the maximum likelihood estimation (MLE) in the multivariate deviated model where the data are generated from the density function $(1-\lambda^{\ast})h_{0}(x)+\lambda^{\ast}f(x|\mu^{\ast}, \Sigma^{\ast})$ in which $h_{0}$ is a known…