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TraitLab is a software package for simulating, fitting and analysing tree-like binary data under a stochastic Dollo model of evolution. The model also allows for rate heterogeneity through catastrophes, evolutionary events where many traits…
Random Forests (RF) is a popular machine learning method for classification and regression problems. It involves a bagging application to decision tree models. One of the primary advantages of the Random Forests model is the reduction in…
Accurate estimation of plant skeletal structure (e.g., branching structure) from images is essential for smart agriculture and plant science. Unlike human skeletons with fixed topology, plant skeleton estimation presents a unique challenge,…
Humans recognize object structure from both their appearance and motion; often, motion helps to resolve ambiguities in object structure that arise when we observe object appearance only. There are particular scenarios, however, where…
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
A popular testbed for deep learning has been multimodal recognition of human activity or gesture involving diverse inputs such as video, audio, skeletal pose and depth images. Deep learning architectures have excelled on such problems due…
This paper focuses on unsupervised modeling of morphological families, collectively comprising a forest over the language vocabulary. This formulation enables us to capture edgewise properties reflecting single-step morphological…
Machine and deep learning have grown in popularity and use in biological research over the last decade but still present challenges in interpretability of the fitted model. The development and use of metrics to determine features driving…
In this paper, we propose DeepTree, a novel method for modeling trees based on learning developmental rules for branching structures instead of manually defining them. We call our deep neural model situated latent because its behavior is…
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…
Reachability analysis is a powerful tool when it comes to capturing the behaviour, thus verifying the safety, of autonomous systems. However, general-purpose methods, such as Hamilton-Jacobi approaches, suffer from the curse of…
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
Measuring the complexity of tree structures can be beneficial in areas that use tree data structures for storage, communication, and processing purposes. This complexity can then be used to compress tree data structures to their…
We tackle the challenging problem of creating full and accurate three dimensional reconstructions of botanical trees with the topological and geometric accuracy required for subsequent physical simulation, e.g. in response to wind forces.…
We present Collaborative Trees, a novel tree model designed for regression prediction, along with its bagging version, which aims to analyze complex statistical associations between features and uncover potential patterns inherent in the…
Three-way dissimilarities are a generalization of (two-way) dissimilarities which can be used to indicate the lack of homogeneity or resemblance between any three objects. Such maps have applications in cluster analysis, and have been used…
A Profile Mixture Model is a model of protein evolution, describing sequence data in which sites are assumed to follow many related substitution processes on a single evolutionary tree. The processes depend in part on different amino acid…
Metabolic modelling has entered a mature phase with dozens of methods and software implementations available to the practitioner and the theoretician. It is not easy for a modeller to be able to see the wood (or the forest) for the trees.…
In this paper, we address the problem of identifying protein functionality using the information contained in its aminoacid sequence. We propose a method to define sequence similarity relationships that can be used as input for…