Phylogenetic Inference

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Overview

Phylogenetic inference uses observed traits to estimate evolutionary trees, including their branching patterns and divergence times, helping explain how species, genes, languages, and other evolving systems are related. Classical approaches include likelihood-based and Bayesian methods, parsimony, and distance-based algorithms; species-tree methods must also account for discordance among gene histories. Newer work uses neural networks and generative models to propose trees, estimate distances, or sample posterior distributions, sometimes incorporating tree-space geometry or multimodal data. A central challenge is scaling to large datasets while retaining accurate, calibrated uncertainty under complex evolutionary processes and avoiding poor generalization beyond training data.

Latest papers

CardsList

12 papers2 papers in the last four weeks, against 1 the four weeks before. 0.0% of all new papers.

  1. Deep Generative Models for Phylogenetic Inference with Complex Evolutionary Processes

    Oct 13, 2026Ethan Baron, Alan N. Amin, Andrew Gordon WilsonPhylogenetic InferenceGenerative Modeling

    New York University

  2. Algorithmically Aligned Neural Agglomerative Tree Construction

    Oct 5, 2026Robert R Nerem, Pranav Singh, Cheyenne Ward +1ClusteringHierarchical Clustering

    University of California San Diego · University of Washington

  3. Self-Supervised Lexical Representation Learning for Fast, Large-Scale Phylogenetic Inference

    Sep 4, 2026Tim WientzekPhylogenetic InferenceSelf-Supervised Learning

  4. Approximating SPR Distance Between Phylogenetic Trees with Graph Neural Networks

    Jul 17, 2026Renata Martins Castanheira, Miguel Bugalho, Cátia VazGraph Neural NetworksPhylogenetic Inference

    ISEL – Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Portugal · ALGORITMI Research Center/CCPM, Portugal · INESC-ID Lisboa, Portugal

  5. Morphology-Aware Multimodal Representation Learning for Insect Phylogenetic Reconstruction

    Jun 20, 2026Zixuan Liu, Kaijie Yu, Chun He +5Cross-Modal AlignmentPhylogenetic Inference

    Zhejiang Key Lab of Accessible Perception and Intelligent Systems, Zhejiang University, Hangzhou 310027, China · State Key Laboratory of Rice Biology and Breeding & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China · Rural Development Academy, Zhejiang University, Hangzhou 310058, China +1

  6. MalTree: Tracing Malware Evolution from Embeddings at Scale

    Jun 4, 2026Akash Amalan, Georgios Smaragdakis, Tom J. VieringPhylogenetic InferenceMalware Analysis

    Delft University of Technology, Delft, The Netherlands.

  7. PhylaFlow: Hybrid Flow Matching in Billera-Holmes-Vogtmann Tree Space for Phylogenetic Inference

    May 21, 2026Yasha Ektefaie, Leo Cui, Shrey Jain +2Flow MatchingTree Search

    Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard · Department of Biomedical Informatics, Harvard Medical School · Centennial High School +1

  8. Phylogenetic Tree Inference with Tropical Axial Attention

    May 12, 2026Chris Teska, Kurt Pasque, Ruriko Yoshida +1Phylogenetic InferenceAttention Mechanisms

    In this work, we introduce a Tropical Axial Attention neural reasoning architecture...

  9. Tree-Conditioned Edit Flows for Ancestral Sequence Reconstruction

    May 5, 2026Emil Sharafutdinov, Ingemar AndréFlow MatchingPhylogenetic Inference

    Center for Molecular Protein Science Lund University Box 124, 221 00 Lund

  10. Phonological distances for linguistic typology and the origin of Indo-European languages

    Apr 13, 2026Marius Mavridis, Juan De Gregorio, Raul Toral +1Linguistic TypologyPhylogenetic Inference

    Institute for Cross-Disciplinary Physics and Complex Systems IFISC (UIB-CSIC), Campus Universitat de les Illes Balears, E-07122 Palma de Mallorca, Spain · Universit´e Paris-Saclay, ENS Paris-Saclay, DER de Physique, 91190, Gif-sur-Yvette, France

  11. SDSR: A Spectral Divide-and-Conquer Approach for Species Tree Reconstruction

    Mar 10, 2026Ortal Reshef, Ofer Glassman, Or Zuk +3Phylogenetic Inference

    Hebrew University of Jerusalem · Department of Statistics and Data Science, Hebrew University of Jerusalem · Weizmann Institute of Science +3

  12. PhyloGFN: Phylogenetic inference with generative flow networks

    Oct 12, 2023Mingyang Zhou, Zichao Yan, Elliot Layne +5Bayesian InferencePosterior Sampling

    McGill University · McGill University, Mila · Universit´e de Montr´eal, Mila