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A Refined Generalization Analysis for Extreme Multi-class Supervised Contrastive Representation Learning Ensemble Distributionally Robust Bayesian Optimisation The Proxy Presumption: From Semantic Embeddings to Valid Social Measures Modulated learning for private and distributed regression with just a single sample per client device Query-efficient model evaluation using cached responses Functional-prior-based approaches to Bayesian PDE-constrained inversion using physics-informed neural networks Optimal Experiments for Partial Causal Effect Identification Order-Agnostic Autoregressive Modelling with Missing Data Grokking or Glitching? How Low-Precision Drives Slingshot Loss Spikes Tuning Derivatives for Causal Fairness in Machine Learning Spherical Flows for Sampling Categorical Data Bayesian Rain Field Reconstruction using Commercial Microwave Links and Diffusion Model Priors GRALIS: A Unified Canonical Framework for Linear Attribution Methods via Riesz Representation Sharp Capacity Thresholds in Linear Associative Memory: From Winner-Take-All to Listwise Retrieval Unified Framework of Distributional Regret in Multi-Armed Bandits and Reinforcement Learning Jacobian-Velocity Bounds for Deployment Risk Under Covariate Drift Self-Attention as Transport: Limits of Symmetric Spectral Diagnostics Perturbation is All You Need for Extrapolating Language Models Adapt or Forget: Provable Tradeoffs Between Adam and SGD in Nonstationary Optimization Realizable Bayes-Consistency for General Metric Losses Graph Convolutional Support Vector Regression for Robust Spatiotemporal Forecasting of Urban Air Pollution Segmenting Human-LLM Co-authored Text via Change Point Detection Stochastic Schrödinger Diffusion Models for Pure-State Ensemble Generation Understanding Self-Supervised Learning via Latent Distribution Matching The Geometric Mechanics of Contrastive Representation Learning: Alignment Potentials, Entropic Dispersion, and Cross-modal Divergence Imbalanced Classification under Capacity Constraints On the Spectral Structure and Objective Equivalence of Orthogonal Multilabel Fisher Discriminants Partially Observed Structural Causal Models First-Order Efficiency for Probabilistic Value Estimation via A Statistical Viewpoint Robust and Fast Training via Per-Sample Clipping
PhyloGFN: Phylogenetic inference with generative flow net...
Mingyang Zhou, Zichao Yan, Elliot Layne, Nikolay Malkin, Dinghua · 2023-10-13 · via stat updates on arXiv.org

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.