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Bayesian phylogenetic inference is often conducted via local or sequential search over topologies and branch lengths using algorithms such as random-walk Markov chain Monte Carlo (MCMC) or Combinatorial Sequential Monte Carlo (CSMC).…
Bayesian inference for phylogenetics is a gold standard for computing distributions of phylogenies. It faces the challenging problem of. moving throughout the high-dimensional space of trees. However, hyperbolic space offers a low…
Many high-dimensional and large-volume data sets of practical relevance have hierarchical structures induced by trees, graphs or time series. Such data sets are hard to process in Euclidean spaces and one often seeks low-dimensional…
Many high-dimensional practical data sets have hierarchical structures induced by graphs or time series. Such data sets are hard to process in Euclidean spaces and one often seeks low-dimensional embeddings in other space forms to perform…
Learning good image representations that are beneficial to downstream tasks is a challenging task in computer vision. As such, a wide variety of self-supervised learning approaches have been proposed. Among them, contrastive learning has…
Hyperbolic spaces, which have the capacity to embed tree structures without distortion owing to their exponential volume growth, have recently been applied to machine learning to better capture the hierarchical nature of data. In this…
Hyperbolic spaces have recently gained momentum in the context of machine learning due to their high capacity and tree-likeliness properties. However, the representational power of hyperbolic geometry is not yet on par with Euclidean…
Taxonomic classification in biodiversity research involves organizing biological specimens into structured hierarchies based on evidence, which can come from multiple modalities such as images and genetic information. We investigate whether…
This paper introduces methodology for performing Bayesian inference sequentially on a sequence of posteriors on spaces of different dimensions. We show how this may be achieved through the use of sequential Monte Carlo (SMC) samplers (Del…
Traditionally, the field of computational Bayesian statistics has been divided into two main subfields: variational methods and Markov chain Monte Carlo (MCMC). In recent years, however, several methods have been proposed based on combining…
Foundation models pre-trained on massive datasets, including large language models (LLMs), vision-language models (VLMs), and large multimodal models, have demonstrated remarkable success in diverse downstream tasks. However, recent studies…
Phylogenetics, the inference of evolutionary trees from molecular sequence data such as DNA, is an enterprise that yields valuable evolutionary understanding of many biological systems. Bayesian phylogenetic algorithms, which approximate a…
Clustering, as an unsupervised technique, plays a pivotal role in various data analysis applications. Among clustering algorithms, Spectral Clustering on Euclidean Spaces has been extensively studied. However, with the rapid evolution of…
Representing data in hyperbolic space can effectively capture latent hierarchical relationships. With the goal of enabling accurate classification of points in hyperbolic space while respecting their hyperbolic geometry, we introduce…
Geometric representation learning has recently shown great promise in several machine learning settings, ranging from relational learning to language processing and generative models. In this work, we consider the problem of performing…
Learning the representation of data with hierarchical structures in the hyperbolic space attracts increasing attention in recent years. Due to the constant negative curvature, the hyperbolic space resembles tree metrics and captures the…
Hyperbolic models are known to produce networks with properties observed empirically in most network datasets, including heavy-tailed degree distribution, high clustering, and hierarchical structures. As a result, several embeddings…
Hamiltonian Monte Carlo (HMC) is an efficient and effective means of sampling posterior distributions on Euclidean space, which has been extended to manifolds with boundary. However, some applications require an extension to more general…
This paper investigates the self-similar solutions of the Einstein-axion-dilaton configuration from type IIB string theory and the global SL(2,R) symmetry. We consider the Continuous Self Similarity (CSS), where the scale transformation is…
Sequential Monte Carlo (SMC) methods comprise one of the most successful approaches to approximate Bayesian filtering. However, SMC without good proposal distributions struggle in high dimensions. We propose nested sequential Monte Carlo…