Related papers: Can we 'future-proof' consensus trees?
This paper presents two new deterministic algorithms for constructing consensus trees. Given an input of k phylogenetic trees with identical leaf label sets and n leaves each, the first algorithm constructs the majority rule (+) consensus…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
Community detection methods attempt to divide a network into groups of nodes that share similar properties, thus revealing its large-scale structure. A major challenge when employing such methods is that they are often degenerate, typically…
The inference of new information on the relatedness of species by phylogenetic trees based on DNA data is one of the main challenges of modern biology. But despite all technological advances, DNA sequencing is still a time-consuming and…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…
The Bayesian method is noted to produce spuriously high posterior probabilities for phylogenetic trees in analysis of large datasets, but the precise reasons for this over-confidence are unknown. In general, the performance of Bayesian…
Monte Carlo Tree Search (MCTS) is a sampling best-first method to search for optimal decisions. The success of MCTS depends heavily on how the MCTS statistical tree is built and the selection policy plays a fundamental role in this. A…
The theory of belief functions is widely used for data from multiple sources. Different evidence combination rules have been proposed in this framework according to the properties of the sources to combine. However, most of these…
Phylogenetic mixture models, in which the sites in sequences undergo different substitution processes along the same or different trees, allow the description of heterogeneous evolutionary processes. As data sets consisting of longer…
Social consensus is important for society. Sometimes the success of society depends on a consensus (e.g. the decision to pay taxes or to commit to the constitution). Examples for continuous opinion dynamics are discussions about tax rates…
This paper derives a unifying theorem establishing consistency results for a broad class of tree-based algorithms. It improves current results in two aspects. First of all, it can be applied to algorithms that vary from traditional Random…
Background: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of trait through time,…
Towards a future where machine learning systems will integrate into every aspect of people's lives, researching methods to interpret such systems is necessary, instead of focusing exclusively on enhancing their performance. Enriching the…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
We study distributed plurality consensus among $n$ nodes, each of which initially holds one of $k$ opinions. The goal is to eventually agree on the initially dominant opinion. We consider an asynchronous communication model in which each…
Using Machine Learning systems in the real world can often be problematic, with inexplicable black-box models, the assumed certainty of imperfect measurements, or providing a single classification instead of a probability distribution. This…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
In the field of chemistry, there have been many attempts to predict the properties of unknown compounds from statistical models constructed using machine learning. In an area where many known compounds are present (the interpolation area),…
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…