Researchers improve tree model recovery from noisy data.
problem Learning tree structured models from corrupted data.
method Linear latent tree models and continuous corruption model.
result Chow-Liu algorithm consistently learns tree from noisy data.
Paper proposes learnable topological features for efficient phylogenetic inference.
problem Finding appropriate topological structures for phylogenetic inference tasks requires significant design effort and domain expertise.
method Combines raw node features with graph neural networks to automatically adapt to different tasks.
result Demonstrates effectiveness and efficiency on simulated and real data phylogenetic inference tasks.
Develops a new method to recover large latent tree models efficiently.
problem Inference of large latent tree structures from terminal node observations.
method Spectral Top-Down Recovery (STDR) using Fiedler vector partitioning.
result Proves statistical consistency and sample complexity for accurate tree recovery.
Improved phylogenetic inference with normalizing flows.
problem Limitations of current diagonal Lognormal branch length approximation in VBPI.
method Proposes VBPI-NF using normalizing flows to handle non-Euclidean branch length space.
result Significantly improves phylogenetic posterior estimation on real data.
New method embeds phylogenetic trees for clustering, recovering evolutionary relationships.
problem Lack of a meaningful way to embed phylogenetic trees into a vector space.
method Split-weight embedding to fit clustering algorithms to phylogenetic trees.
result Split-weight embedding recovers meaningful evolutionary relationships in simulated and real data.
PhyloGFN uses GFlowNets to infer phylogenetic trees from sequence data.
problem Challenging phylogenetic tree inference from sequence data due to high complexity.
method Adopting GFlowNets for parsimony-based and Bayesian phylogenetic inference.
result PhyloGFN produces diverse and high-quality evolutionary hypotheses.
PhyloVAE learns tree topologies without supervision.
problem Learning accurate tree representations from evolutionary data.
method Unsupervised learning via variational autoencoders with efficient tree generation.
result PhyloVAE generates high-resolution tree topologies efficiently.
GeoPhy uses geometric gradients to efficiently infer phylogenetic trees from molecular data.
problem Challenges in accurately inferring species relationships from molecular data due to combinatorially vast tree topologies.
method Introduces a novel, fully differentiable formulation of phylogenetic inference using geometric spaces and variational Bayesian methods.
result Significantly outperforms other approximate Bayesian methods in inferring phylogenetic trees.
A new variational method speeds up Bayesian phylogenetic inference.
problem Slow and inefficient MCMC methods in Bayesian phylogenetic inference.
method Combining subsplit Bayesian networks with variational inference for efficient tree topology and branch length estimation.
result Variational approach provides competitive performance with significantly fewer iterations.
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.
problem Multimodality of tree-topology posterior distributions in phylogenetic inference.
method VBPI-Mixtures algorithm that uses mixture learning within the BBVI framework.
result VBPI-Mixtures captures tree-topology distributions better than VBPI.
New model addresses instability in hierarchical clustering of social networks.
problem Instability in existing hierarchical clustering algorithms for social networks.
method Introduce T-Stochastic Graphs, a probabilistic model that relaxes ultrametric assumptions. result Prove spectral approach combining Neighbor-Joining is statistically consistent.
Develops a variational method for ultrametric phylogenetic trees.
problem Accurate and efficient approximation of posterior distributions over trees in Bayesian phylogenetics.
method Variational Bayesian approach based on coalescent times of a single-linkage clustering.
result Achieves competitive accuracy with significantly fewer gradient evaluations.
Paper improves tree probability estimation using stochastic optimization and variance reduction.
problem Improving tree probability estimation in phylogenetic inference.
method Introduces computationally efficient methods for training SBNs and variance reduction for optimization.
result Methods outperform previous baseline methods in tree topology probability estimation and Bayesian phylogenetic inference.
ARTree uses deep learning to infer tree topologies efficiently.
problem Efficient phylogenetic inference from tree topologies.
method Deep autoregressive model based on graph neural networks (GNNs).
result ARTree provides a flexible family of distributions over tree topologies.
Improved phylogenetic tree reconstruction using flexible branch length distributions.
problem Inefficient Markov chain Monte Carlo methods for large sequence datasets.
method Variational Bayesian phylogenetic inference with semi-implicit branch length distributions.
result Proposed method improves marginal likelihood estimation and branch length posterior approximation.
New method uses hyperbolic space for faster phylogenetic tree inference.
problem Inefficient Euclidean-based phylogenetic inference in high dimensions.
method Developed novel hyperbolic extensions of sequential search algorithms and variational inference methods.
result Improved speed, scalability and performance in phylogenetic inference.
SNJ recovers latent tree models from similarity matrices.
problem Reconstructing latent tree models from observed data.
method Spectral Neighbor Joining (SNJ) method.
result SNJ is consistent and requires fewer samples for accurate tree recovery.
Bayesian supertrees method uses variational Bayes for overlapping taxon subsets.
problem Inference of phylogenetic tree topologies for overlapping taxon sets.
method Variational Bayesian approach.
result Demonstrates effectiveness of variational Bayes for Bayesian supertrees.
VCSMC improves efficiency in Bayesian phylogenetic inference.
problem Inefficient exploration of phylogenetic state space.
method Variational Combinatorial Sequential Monte Carlo (VCSMC) and nested CSMC.
result VCSMC and VNCSMC explore higher probability spaces efficiently.
Mathematical foundation for phylogenetic tree uncertainty quantification.
problem Uncertainty in evolutionary relationships between species.
method Introducing the Wald space as a subset of symmetric positive definite matrices, studying its topology and structure, and proposing a new numerical method for geodesics and curvature.
result Wald space has a topology of disjoint open cubes, is contractible, and is a Whitney stratified space of type (A).
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…
Tropical SVM tackles phylogenomics by classifying multi-locus data.
problem Classifying multi-locus data sets for phylogenetic analysis.
method Proposes tropical support vector machines (SVMs) for phylogenomics, formulated as linear programming problems.
result Developed methods for hard and soft margin tropical SVMs, proving necessary and sufficient conditions for separation.
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…
SDSR reconstructs species trees from genetic markers efficiently.
problem Challenges in reconstructing species trees from genetic data.
method Spectral divide-and-conquer approach based on graph theory.
result SDSR achieves up to 10-fold faster runtime with comparable accuracy.
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.
problem Developing a space for statistical analysis of phylogenies with biologically informed assumptions.
method Introduces wald space, a new phylogenetic tree space, and two related geometries based on Fisher information and Gaussian processes.
result Geodesics in wald space are similar to those in the Fisher information geometry, but the two geometries are distinct.
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:…
Unified framework for inference in complex nonlinear processes.
problem Challenges in inferring nonlinear continuous stochastic processes with sparse observations and complex topologies.
method Neural Backward Filtering Forward Guiding (NBFFG) framework that constructs a variational posterior using a proxy linear-Gaussian process.
result Empirical results show NBFFG outperforms baselines on synthetic benchmarks and high-dimensional phylogenetic analysis tasks.
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.
problem Challenges in applying kernel methods to matchings due to their discrete, non-Euclidean nature.
method Characterizes stationary kernels, introduces heat and Matérn kernel families, and develops a sub-exponential algorithm for efficient evaluation.
result Establishes novel negative results and identifies an open problem in transferring the framework to trees.
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 (X,d,μ1) and (X,d,μ2), we are interested in the problem of determining from finite data whether or not μ1 is μ2. 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…
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 derive an arbitrage free relationship between recovery swap rates, digital default swap spreads and conventional CDS spreads, and argue that the fair forward recovery rate used in recovery swaps must contain a convexity premium over the expected recovery value.
Method uses Seq2Seq learning to automatically generate recovery commands for ICT systems.
problem Manual decision-making for recovery commands is time-consuming and error-prone.
method Seq2Seq neural network model trained on past logs and commands.
result The model can estimate accurate recovery commands from new failures.
A new model explains U- and Swoosh-shaped stock price recovery during the COVID-19.
problem Modeling stock price recovery during the COVID-19 with V- and L-shaped recovery.
method Introducing a sentiment variable θ to quantify investor sentiment and simulate U- and Swoosh-shaped recovery. result The model explains U- and Swoosh-shaped recovery of sectoral indices with positive sentiment.
This paper improves support recovery in universal one-bit compressed sensing.
problem Support recovery in one-bit compressed sensing for sparse signals.
method Proposes approximate support recovery and superset recovery algorithms with polynomial-time complexity.
result Achieves improved support recovery with fewer measurements compared to existing methods.
This work provides a guaranteed tensor recovery method by combining low-rankness and smoothness priors.
problem Guaranteed tensor recovery with theoretical guarantees for low-rank and smoothness priors.
method Developed a new regularization term that combines low-rankness and smoothness priors, proving exact recovery guarantees.
result Rigorously proved exact recovery guarantees for tensor completion and tensor robust principal component analysis.
This paper tackles tensor recovery from noisy and multi-level quantized measurements.
problem Tensors from multi-level quantized measurements.
method Nonconvex optimization problem with alternating proximal gradient descent.
result The recovery error diminishes to zero with increasing tensor dimensions.