Related papers: Revisiting an equivalence between maximum parsimon…

Multivariate clustering in astrophysics is a recent development justified by the bigger and bigger surveys of the sky. The phylogenetic approach is probably the most unexpected technique that has appeared for the unsupervised classification…

The effort to understand network systems in increasing detail has resulted in a diversity of methods designed to extract their large-scale structure from data. Unfortunately, many of these methods yield diverging descriptions of the same…

Inference is typically intractable in high-treewidth undirected graphical models, making maximum likelihood learning a challenge. One way to overcome this is to restrict parameters to a tractable set, most typically the set of…

We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…

Associative memories are structures that store data in such a way that it can later be retrieved given only a part of its content -- a sort-of error/erasure-resilience property. They are used in applications ranging from caches and memory…

We present new results for consistency of maximum likelihood estimators with a focus on multivariate mixed models. Our theory builds on the idea of using subsets of the full data to establish consistency of estimators based on the full…

In this paper we investigate an extremal problem on binary phylogenetic trees. Given two such trees $T_1$ and $T_2$, both with leaf-set ${1,2,...,n}$, we are interested in the size of the largest subset $S \subseteq {1,2,...,n}$ of leaves…

Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…

Palindromes are popular and important objects in textual data processing, bioinformatics, and combinatorics on words. Let $S = XaY$ be a string where $X$ and $Y$ are of the same length, and $a$ is either a single character or the empty…

Relational models for contingency tables are generalizations of log-linear models, allowing effects associated with arbitrary subsets of cells in a possibly incomplete table, and not necessarily containing the overall effect. In this…

We propose an efficient algorithm for approximate computation of the profile maximum likelihood (PML), a variant of maximum likelihood maximizing the probability of observing a sufficient statistic rather than the empirical sample. The PML…

It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…

Ranking problems based on pairwise comparisons, such as those arising in online gaming, often involve a large pool of items to order. In these situations, the gap in performance between any two items can be significant, and the smallest and…

We study the consistency and optimality of the maximum marginal likelihood estimate (MMLE) in the hyperparameter inference for large-degree-of-freedom models. We perform main analyses within the exponential family, where the natural…

It is common in phylogenetics to have some, perhaps partial, information about the overall evolutionary tree of a group of organisms and wish to find an evolutionary tree of a specific gene for those organisms. There may not be enough…

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…

If predictions for species extinctions hold, then the `tree of life' today may be quite different to that in (say) 100 years. We describe a technique to quantify how much each species is likely to contribute to future biodiversity, as…

Traditional Quartet Puzzling algorithms use maximum likelihood methods to reconstruct quartet trees, and a puzzling algorithm to combine these quartets into a tree for the full collection of $n$ taxa. We propose a variation of Quartet…

Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…

Statistical inference using pairwise comparison data is an effective approach to analyzing large-scale sparse networks. In this paper, we propose a general framework to model the mutual interactions in a network, which enjoys ample…