ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference | Paper Citation Record

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This paper cites Attwood, Sarah C.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Attwood, Sarah C

Reference 1

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Observation e2892ad8-8f49-43a5-b7ae-a0598bb8c247 · outbound

This paper cites Flow network based generative models for non-iterative diverse candidate generation.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Flow network based generative models for non-iterative diverse candidate generation

Reference 2

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This paper cites Blei, Alp Kucukelbir, and Jon D.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Blei, Alp Kucukelbir, and Jon D

Reference 3

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Observation 5012910b-c09e-4176-8bc2-f28c6a91065a · outbound

This paper cites Reweighted wake-sleep.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Reweighted wake-sleep

Reference 4

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ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Unresolved cited work

Reference 5

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Observation 39e3b7c8-7918-45f6-a193-2f0eb2c2ad4a · outbound

This paper cites Naesseth, and Itsik Pe'er.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Naesseth, and Itsik Pe'er

Reference 6

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Observation 5c483fdc-b1b4-41a4-8778-f31a22102309 · outbound

This paper cites Learning Phrase Representations using RNN Encoder-Decoder for Statistical Machine Translation.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Learning Phrase Representations using RNN Encoder-Decoder for Statistical Machine Translation

Reference 7

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This paper cites Maximum likelihood of evolutionary trees is hard.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Maximum likelihood of evolutionary trees is hard

Reference 8

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Observation cab7a274-b9a4-4617-915a-8c86ba200546 · outbound

This paper cites Fast and Accurate Deep Network Learning by Exponential Linear Units (ELUs).

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Fast and Accurate Deep Network Learning by Exponential Linear Units (ELUs)

Reference 9

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Observation c7a45c00-52b0-4844-915b-b4cd22fb6a57 · outbound

This paper cites Computational complexity of inferring phylogenies from dissimilarity matrices.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Computational complexity of inferring phylogenies from dissimilarity matrices

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:25.286574Z

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Observation 2c2dcefb-da36-423f-852a-ab23e72499e5 · outbound

This paper cites Deepseek-v2: A powerful open-source language model.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Deepseek-v2: A powerful open-source language model

Reference 11

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Observation d63a1c96-eed2-419b-8e4b-c1c1feaf5302 · outbound

This paper cites The expansion of conservation genetics.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference The expansion of conservation genetics

Reference 12

Resolution: verified exact; doi, observed 2026-08-15T18:22:24.252540Z

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Observation ad858086-44fd-4c20-8c22-f53c1d6f0267 · outbound

This paper cites Probabilistic path H amiltonian M onte C arlo.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Probabilistic path H amiltonian M onte C arlo

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:25.247850Z

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Observation 2746ec17-7105-4342-a726-b54ec55c28bb · outbound

This paper cites Beast: Bayesian evolutionary analysis by sampling trees.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Beast: Bayesian evolutionary analysis by sampling trees

Reference 14

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Observation 312cd968-ad44-4960-b680-336bbe9e6827 · outbound

This paper cites Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Reference 15

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ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Unresolved cited work

Reference 16

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Observation f39b3929-5be0-466f-85f5-2a3e341fd7f7 · outbound

This paper cites u nther, Christian T Happi, Edward C Holmes, Brima Kargbo, Sakoba Ke \.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference u nther, Christian T Happi, Edward C Holmes, Brima Kargbo, Sakoba Ke \

Reference 17

Resolution: verified exact; doi, observed 2026-08-15T18:22:25.184320Z

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Observation c0fb5838-e52a-47c3-af73-431a4f657b62 · outbound

This paper cites Felsenstein.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Felsenstein

Reference 18

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Observation 6c2e1127-56f7-49f9-b25e-9b12c77e62b5 · outbound

This paper cites Inferring Phylogenies.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Inferring Phylogenies

Reference 19

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Observation d7d6c3fe-dbdc-4660-b78e-169f46c74db8 · outbound

This paper cites Toward defining the course of evolution: minimum change for a specific tree topology.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Toward defining the course of evolution: minimum change for a specific tree topology

Reference 20

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ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Unresolved cited work

Reference 21

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Observation aa950da5-1a93-4e65-b901-f51c4de416f5 · outbound

This paper cites Neural Message Passing for Quantum Chemistry.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Neural Message Passing for Quantum Chemistry

Reference 22

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ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Unresolved cited work

Reference 23

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ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Unresolved cited work

Reference 24

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This paper cites Drummond.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Drummond

Reference 25

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Observation a6675ecb-3f34-436d-bbea-11587a5a645e · outbound

This paper cites Efficient mixture learning in black-box variational inference.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Efficient mixture learning in black-box variational inference

Reference 26

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Observation 571ced14-9722-434d-8bcb-e185c67e596f · outbound

This paper cites An introduction to variational methods for graphical models.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference An introduction to variational methods for graphical models

Reference 27

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This paper cites Evolution of protein molecules.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Evolution of protein molecules

Reference 28

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This paper cites Variational phylodynamic inference using pandemic-scale data.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Variational phylodynamic inference using pandemic-scale data

Reference 29

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ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Unresolved cited work

Reference 30

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This paper cites Kingma and Max Welling.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Kingma and Max Welling

Reference 31

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Observation c9f0e7a1-36e5-4929-9e75-f61c97939936 · outbound

This paper cites VaiPhy : a variational inference based algorithm for phylogeny.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference VaiPhy : a variational inference based algorithm for phylogeny

Reference 32

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This paper cites Lakner, P.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Lakner, P

Reference 33

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Observation 8ca3e9e8-2f3d-4a24-b2bb-fc474aa7c514 · outbound

This paper cites The estimation of tree posterior probabilities using conditional clade probability distributions.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference The estimation of tree posterior probabilities using conditional clade probability distributions

Reference 34

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This paper cites Larget and D.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Larget and D

Reference 35

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Observation 890c280c-2cf8-4254-ad8e-c8d8c3d09422 · outbound

This paper cites Trajectory balance: Improved credit assignment in GF lownets.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Trajectory balance: Improved credit assignment in GF lownets

Reference 36

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Observation 8505c93a-c83e-4dbe-9b1f-09a75e8318df · outbound

This paper cites Minimizing the average distance to a closest leaf in a phylogenetic tree.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Minimizing the average distance to a closest leaf in a phylogenetic tree

Reference 37

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ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Unresolved cited work

Reference 38

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Observation 9cf85be5-3fa0-467a-b1f5-fa8f65ae05a6 · outbound

This paper cites Geophy: Differentiable phylogenetic inference via geometric gradients of tree topologies.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Geophy: Differentiable phylogenetic inference via geometric gradients of tree topologies

Reference 39

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Observation cbdb4bfe-b39f-4663-b951-fc5196e5f29d · outbound

This paper cites Variational inference for monte carlo objectives.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Variational inference for monte carlo objectives

Reference 40

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Observation 0ebd6198-11e9-449b-aafc-fa53b71b41e4 · outbound

This paper cites Improved variational bayesian phylogenetic inference using mixtures.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Improved variational bayesian phylogenetic inference using mixtures

Reference 41

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Observation 932a54ed-ee16-46b4-87fc-22f7bf30b7a7 · outbound

This paper cites Blei, and Itsik Pe’er.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Blei, and Itsik Pe’er

Reference 42

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Observation 63a12375-4c03-4cfa-aea9-1f1b102ba3cb · outbound

This paper cites Attending to graph transformers.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Attending to graph transformers

Reference 43

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ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Unresolved cited work

Reference 44

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Observation 69a57b97-a267-4e3e-99ff-5798098b0f01 · outbound

This paper cites PyTorch : An imperative style, high-performance deep learning library.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference PyTorch : An imperative style, high-performance deep learning library

Reference 45

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.771322Z

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Observation c1b8c0d5-a113-4c00-b782-7aa070cf2551 · outbound

This paper cites Kosioreck, Tuan Anh Le, Chris J.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Kosioreck, Tuan Anh Le, Chris J

Reference 46

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.750509Z

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Observation 4549a90b-5176-43ea-a4bf-eab5876e33e8 · outbound

This paper cites MrBayes 3.2: Efficient B ayesian phylogenetic inference and model choice across a large model space.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference MrBayes 3.2: Efficient B ayesian phylogenetic inference and model choice across a large model space

Reference 47

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.732230Z

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ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Unresolved cited work

Reference 48

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Observation 9ac62806-56a3-4f5c-9509-c95ec32fc82e · outbound

This paper cites The neighbor-joining method: a new method for reconstructing phylogenetic trees.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference The neighbor-joining method: a new method for reconstructing phylogenetic trees

Reference 49

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.691944Z

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Observation 138721ae-233e-4d46-b768-65cfa631b924 · outbound

This paper cites Spielman.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Spielman

Reference 50

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.674743Z

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Observation c83d1087-8a9d-42d7-9654-f4cf0530631f · outbound

This paper cites PAUP* : Phylogenetic analysis using parsimony.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference PAUP* : Phylogenetic analysis using parsimony

Reference 51

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.658792Z

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Observation 75bde5b1-85d5-4dfd-8f60-43f8d76bfca2 · outbound

This paper cites Attention is all you need.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Attention is all you need

Reference 52

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ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Unresolved cited work

Reference 53

Resolution: unresolved; raw_fallback, observed 2026-08-15T18:22:24.630981Z

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This paper cites Sarma, Michael M.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Sarma, Michael M

Reference 54

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This paper cites Quantifying MCMC exploration of phylogenetic tree space.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Quantifying MCMC exploration of phylogenetic tree space

Reference 55

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This paper cites ART ree: A deep autoregressive model for phylogenetic inference.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference ART ree: A deep autoregressive model for phylogenetic inference

Reference 56

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This paper cites Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Variational Bayesian Phylogenetic Inference with Semi-implicit Branch Length Distributions

Reference 57

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This paper cites Improving tree probability estimation with stochastic optimization and variance reduction.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Improving tree probability estimation with stochastic optimization and variance reduction

Reference 58

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.576677Z

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This paper cites Phylo VAE : Unsupervised learning of phylogenetic trees via variational autoencoders.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Phylo VAE : Unsupervised learning of phylogenetic trees via variational autoencoders

Reference 59

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.558131Z

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Observation 3eb26b55-2c27-41ac-9fda-9c3e384bc83e · outbound

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ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Unresolved cited work

Reference 60

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Observation 169d44c0-d36f-46e5-a9dd-6d7eafc14516 · outbound

This paper cites On layer normalization in the transformer architecture.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference On layer normalization in the transformer architecture

Reference 61

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Observation e3db0a90-ff59-410c-9358-207fa5bca144 · outbound

This paper cites Yang and A.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Yang and A

Reference 62

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.509119Z

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This paper cites Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method

Reference 63

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.492657Z

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Observation adbc899d-ae30-4663-9c3a-15ef954fbb37 · outbound

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ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Unresolved cited work

Reference 64

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This paper cites Improved variational Bayesian phylogenetic inference with normalizing flows.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Improved variational Bayesian phylogenetic inference with normalizing flows

Reference 65

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.462000Z

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This paper cites Learnable topological features for phylogenetic inference via graph neural networks.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Learnable topological features for phylogenetic inference via graph neural networks

Reference 66

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.444562Z

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Observation 7089e9d8-7a44-4580-bed0-6d448a8ca727 · outbound

This paper cites Generalizing tree probability estimation via B ayesian networks.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Generalizing tree probability estimation via B ayesian networks

Reference 67

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.428743Z

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Observation d78ce667-26b0-4a3a-a29c-d60beaab3606 · outbound

This paper cites Variational Bayesian phylogenetic inference.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Variational Bayesian phylogenetic inference

Reference 68

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.410878Z

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Observation 9de582dc-42b4-428c-8709-704a6659e489 · outbound

This paper cites A variational approach to B ayesian phylogenetic inference.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference A variational approach to B ayesian phylogenetic inference

Reference 69

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.393549Z

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Observation e3f97487-828e-414d-8bf4-458e1b6cf07f · outbound

This paper cites Zhang and M.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Zhang and M

Reference 70

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.377743Z

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Observation aad426a0-419f-48eb-b3a1-15a3ca747f0c · outbound

This paper cites Influenza research database: An integrated bioinformatics resource for influenza virus research.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Influenza research database: An integrated bioinformatics resource for influenza virus research

Reference 71

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.361828Z

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Observation 81bc415d-c549-4a42-ba16-26b045f53cd8 · outbound

This paper cites Phylo GFN : Phylogenetic inference with generative flow networks.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference Phylo GFN : Phylogenetic inference with generative flow networks

Reference 72

Resolution: verified fuzzy; raw_fallback, observed 2026-08-15T18:22:24.345619Z

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Observation 1e31a8d6-35d6-4ee8-8720-94fc7fa9fad8 · outbound

This paper cites write newline.

ARTreeFormer: A Faster Attention-based Autoregressive Model for Phylogenetic Inference write newline

Reference 73

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