A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
Paper proposes learnable topological features for efficient phylogenetic inference.
Improved phylogenetic inference with normalizing flows.
New method embeds phylogenetic trees for clustering, recovering evolutionary relationships.
PhyloGFN uses GFlowNets to infer phylogenetic trees from sequence data.
PhyloVAE learns tree topologies without supervision.
GeoPhy uses geometric gradients to efficiently infer phylogenetic trees from molecular data.
A new variational method speeds up Bayesian phylogenetic inference.
Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special features, including "sampled ancestors" in which we sequence a genotype along wit…
We report the results of fifteen sets of portfolio selection simulations using stocks in the ASX200 index for the period May 2000 to December 2013. We investigated five portfolio selection methods, randomly and from within industrial groups, and three based on neighbor-Net phylogenetic networks. We report that using ra…
Improved phylogenetic inference using VBPI-Mixtures for tree topology and branch length.
Develops a variational method for ultrametric phylogenetic trees.
Paper improves tree probability estimation using stochastic optimization and variance reduction.
ARTree uses deep learning to infer tree topologies efficiently.
Improved phylogenetic tree reconstruction using flexible branch length distributions.
New method uses hyperbolic space for faster phylogenetic tree inference.
Bayesian supertrees method uses variational Bayes for overlapping taxon subsets.
VCSMC improves efficiency in Bayesian phylogenetic inference.
Mathematical foundation for phylogenetic tree uncertainty quantification.
Most data in genome-wide phylogenetic analysis (phylogenomics) is essentially multidimensional, posing a major challenge to human comprehension and computational analysis. Also, we can not directly apply statistical learning models in data science to a set of phylogenetic trees since the space of phylogenetic trees is …
Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated due to phylogenetic relationships. In this paper we give a flexible statistical model for such data, by combining assumptions from phylogenetics with Gaussian pro…
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 of galaxies, stellar populations or globular clusters. On one side, this is a s…
By expressing prior distributions as general stochastic processes, nonparametric Bayesian methods provide a flexible way to incorporate prior knowledge and constrain the latent structure in statistical inference. The Indian buffet process (IBP) is such an example that can be used to define a prior distribution on infin…
Proposes a new phylogenetic tree space with biologically principled geometry.
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 from each other and from the underlying species tree, possibly confounding phyloge…
Nonparametric Bayesian models are often based on the assumption that the objects being modeled are exchangeable. While appropriate in some applications (e.g., bag-of-words models for documents), exchangeability is sometimes assumed simply for computational reasons; non-exchangeable models might be a better choice for a…
Latent tree models are graphical models defined on trees, in which only a subset of variables is observed. They were first discussed by Judea Pearl as tree-decomposable distributions to generalise star-decomposable distributions such as the latent class model. Latent tree models, or their submodels, are widely used in:…
Researchers improve tree model recovery from noisy data.
Unified framework for inference in complex nonlinear processes.
Phylogeny is the field of modelling the temporal discrete dynamics of speciation. Complex models can nowadays be studied using the Approximate Bayesian Computation approach which avoids likelihood calculations. The field's progression is hampered by the lack of robust software to estimate the numerous parameters of the…
Develops kernels for matchings, overcoming computational challenges.
New model addresses instability in hierarchical clustering of social networks.
Phylogenetic approaches are finding more and more applications outside the field of biology. Astrophysics is no exception since an overwhelming amount of multivariate data has appeared in the last twenty years or so. In particular, the diversification of galaxies throughout the evolution of the Universe quite naturally…
Many biological characteristics of evolutionary interest are not scalar variables but continuous functions. Here we use phylogenetic Gaussian process regression to model the evolution of simulated function-valued traits. Given function-valued data only from the tips of an evolutionary tree and utilising independent pri…
A toric cube is a subset of the standard cube defined by binomial inequalities. These basic semialgebraic sets are precisely the images of standard cubes under monomial maps. We study toric cubes from the perspective of topological combinatorics. Explicit decompositions as CW-complexes are constructed. Their open cells…
This paper presents a novel application of a clustering algorithm developed for constructing a phylogenetic network to the correlation matrix for 126 stocks listed on the Shanghai A Stock Market. We show that by visualizing the correlation matrix using a Neighbor-Net network and using the circular ordering produced dur…
We study the problem of distinguishing between two distributions on a metric space; i.e., given metric measure spaces and , we are interested in the problem of determining from finite data whether or not is . The key is to use pairwise distances between observat…
We consider probabilistic programming for birth-death models of evolution and introduce a new widely-applicable inference method that combines an extension of the alive particle filter (APF) with automatic Rao-Blackwellization via delayed sampling. Birth-death models of evolution are an important family of phylogenetic…
Develops a new method to recover large latent tree models efficiently.
SDSR reconstructs species trees from genetic markers efficiently.
The orientable cover of the moduli space of real genus zero algebraic curves with marked points is a compact aspherical manifold tiled by associahedra, which resolves the singularities of the space of phylogenetic trees. The resolution maps planar metric trees to their underlying abstract representatives, collapsing an…
Scientific investigations that incorporate next generation sequencing involve analyses of high-dimensional data where the need to organize, collate and interpret the outcomes are pressingly important. Currently, data can be collected at the microbiome level leading to the possibility of personalized medicine whereby tr…
We present a technique for clustering categorical data by generating many dissimilarity matrices and averaging over them. We begin by demonstrating our technique on low dimensional categorical data and comparing it to several other techniques that have been proposed. Then we give conditions under which our method shoul…
A Bayesian treatment of latent directed graph structure for non-iid data is provided where each child datum is sampled with a directed conditional dependence on a single unknown parent datum. The latent graph structure is assumed to lie in the family of directed out-tree graphs which leads to efficient Bayesian inferen…
The analysis of Belief Propagation and other algorithms for the {\em reconstruction problem} plays a key role in the analysis of community detection in inference on graphs, phylogenetic reconstruction in bioinformatics, and the cavity method in statistical physics. We prove a conjecture of Evans, Kenyon, Peres, and Sch…
Traditional anatomical analyses captured only a fraction of real phenomic information. Here, we apply deep learning to quantify total phenotypic similarity across 2468 butterfly photographs, covering 38 subspecies from the polymorphic mimicry complex of and . E…
A common assumption in multiple scientific applications is that the distribution of observed data can be modeled by a latent tree graphical model. An important example is phylogenetics, where the tree models the evolutionary lineages of a set of observed organisms. Given a set of independent realizations of the random …
Hierarchical clustering is a fundamental task often used to discover meaningful structures in data, such as phylogenetic trees, taxonomies of concepts, subtypes of cancer, and cascades of particle decays in particle physics. Typically approximate algorithms are used for inference due to the combinatorial number of poss…
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons …