Paper Citation Record · LEDGER

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation

As of 16 August 2026, this Paper Citation Record lists 49 of 49 outbound references and 1 inbound Pith citation observation for arXiv:2412.18827.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2412.18827 v1

Coverage vector

measured 49 of 49 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-11T04:30:15.138767Z

measured 50 of 50 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-16T06:30:59.297886+00:00

measured 1 of 1 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-05-22T03:04:41.050362Z

measured 0 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: arxiv_reference, observed 2026-05-22T03:05:58.028647Z

Reference resolution

49 of 49 outbound references displayed

verified exact1
verified fuzzy20
unresolved28
parse uncertain0
malformed identifier0
metadata mismatch0

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 81255992-9646-47d3-8a3e-cefa51e3eb53 · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 1

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.965689Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation a591fcf8-b257-48cd-a65c-0804134872d0 · outbound

This paper cites Diaconis.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Diaconis

Reference 2

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.949086Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 233179e8-d91b-4394-a136-dcb0456d9feb · outbound

This paper cites Franceschi, M.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Franceschi, M

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.935722Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 16e98331-b248-4b14-bcab-a7d4154fcde0 · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 4

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.921471Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation dc94478a-4590-4bdd-a9d0-11c1afcaa59b · outbound

This paper cites He and X.-S.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation He and X.-S

Reference 5

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.907206Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation d88a65ac-f961-4f3b-a201-e6867bd3a46d · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 6

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.892167Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation dbd728a4-7ba1-4f15-b435-c97357a1f842 · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 7

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.873907Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 1a561afa-0512-4ed6-935c-3289c1a1642d · outbound

This paper cites Höhna and A.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Höhna and A

Reference 8

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.849493Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 637b5946-1b20-4f24-8467-44d55f09104f · outbound

This paper cites Höhna, M.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Höhna, M

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.834625Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation e8f45bb3-3b27-4445-b3cd-2f68d7d778dc · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 10

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.819796Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 30047e50-5f22-4f1b-a5e2-8377da9dc705 · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 11

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.803661Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation c6044562-6eef-4c59-9fc4-b2e498ffd10b · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 12

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.784400Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 788195e4-711a-4c6e-9331-9c3b6b476571 · outbound

This paper cites Kapli, Z.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Kapli, Z

Reference 13

Resolution: unresolved; no resolver link, observed 2026-08-11T04:30:14.939396Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 64057528-7914-4180-8a2b-f377fcc8dbb4 · outbound

This paper cites Adam: A Method for Stochastic Optimization.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Adam: A Method for Stochastic Optimization

Reference 14

Resolution: unresolved; no resolver link, observed 2026-08-11T04:30:14.946618Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 7a8d6239-884f-4c58-b95b-e0d27957d22e · outbound

This paper cites Auto-Encoding Variational Bayes.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Auto-Encoding Variational Bayes

Reference 15

Resolution: unresolved; no resolver link, observed 2026-08-11T04:30:14.953682Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation da8b6f8c-852a-4d15-b75e-a764770970c6 · outbound

This paper cites Koptagel, O.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Koptagel, O

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.757527Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 5fced048-7cae-4fbb-adf6-72a9fc290c06 · outbound

This paper cites Lakner, P.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Lakner, P

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.743523Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation d1d74dcd-40e2-4168-8426-cac227c7e815 · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 18

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.727976Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 2e31c2fb-9841-48e1-902b-80644194de05 · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 19

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.706781Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 15b936f9-9e38-4927-a651-739382238e58 · outbound

This paper cites Malkin, M.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Malkin, M

Reference 20

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.690456Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation f8989a43-e9e0-494b-993f-8c0291629678 · outbound

This paper cites GFlowNets and variational inference.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation GFlowNets and variational inference

Reference 21

Resolution: unresolved; no resolver link, observed 2026-08-11T04:30:14.989325Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 56688c2d-a856-45ef-9053-10979600723d · outbound

This paper cites Mimori and M.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Mimori and M

Reference 22

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.673421Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation a841b970-12a4-4d7b-b02c-ae8ee033b98b · outbound

This paper cites Mnih and D.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Mnih and D

Reference 23

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.657199Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation ce0d4426-864e-4dea-9914-89a7813a1a4e · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 24

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.643886Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 08e415e2-e06f-4682-8daa-2cefa8d897d9 · outbound

This paper cites Nei and S.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Nei and S

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.628523Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 53684bda-bd39-44c4-a0b2-2e23c156c0a3 · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 26

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.613758Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 098a0bcb-0be9-43c6-8100-d4ebdf0bde6e · outbound

This paper cites Paszke, S.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Paszke, S

Reference 27

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.599423Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 9abdfde0-dea8-488d-a7c2-22bfb95a217f · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 28

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.582722Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 6c46ffee-89d1-4b33-8f18-3002f5c1b8ff · outbound

This paper cites Ronquist, M.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Ronquist, M

Reference 29

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.561140Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation cc674aa9-93a9-4b6a-a1d1-d6d7cefffca1 · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 30

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.545185Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 028b3ae0-c954-4a8d-9dda-33bdd7ad5448 · outbound

This paper cites Saitou and M.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Saitou and M

Reference 31

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.531798Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 012d86cc-8359-4ffd-86cb-74d4dfc556da · outbound

This paper cites Shendure, S.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Shendure, S

Reference 32

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.519167Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 2e53ff85-ed84-4d94-a223-2f7ee1d0b939 · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 33

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.505195Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 979c14d3-07c3-4171-9442-91acc5045c9d · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 34

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.487919Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation ad75d159-4598-4437-a7f9-d2b27598850b · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 35

Resolution: unresolved; no resolver link, observed 2026-08-11T04:30:15.055141Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 76c44193-2999-42ec-b7da-4524453539af · outbound

This paper cites Xie and C.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Xie and C

Reference 36

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.455208Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 2a2f3f93-c59d-4c85-a0ba-2df39c563529 · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 37

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.436307Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation f0553d60-89e4-46ba-a097-42f72680a11e · outbound

This paper cites Yang and A.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Yang and A

Reference 38

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.419968Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation f3dc2852-141e-46fa-b153-5460fb04a9ec · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 39

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.405739Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation a94eb0a1-ddf2-4582-9396-d7ea80eb495a · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 40

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.392106Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 417bd816-5c5a-42fe-862c-31e1cecfbafa · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 41

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.371784Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation cdaf95cd-557a-4173-a851-264f2de495dd · outbound

This paper cites A Review of BioTree Construction in the Context of Information Fusion: Priors, Methods, Applications and Trends.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation A Review of BioTree Construction in the Context of Information Fusion: Priors, Methods, Applications and Trends

Reference 42

Resolution: verified exact; local_arxiv, observed 2026-08-11T04:30:15.228180Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 88aad942-9313-4e1b-9fba-78543f51dea3 · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 43

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.355899Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 15b9304a-611c-484f-8e66-31a217c1f80c · outbound

This paper cites an unresolved cited work.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Unresolved cited work

Reference 44

Resolution: unresolved; raw_fallback, observed 2026-08-11T04:30:15.341142Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 85fdd222-5dd3-4a8e-b62d-32e35eaa82be · outbound

This paper cites Zhang and F.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Zhang and F

Reference 45

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.326427Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation 858cf30d-978e-429a-aae5-91f1355679a0 · outbound

This paper cites Zhang and F.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Zhang and F

Reference 46

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.311085Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation ceab218c-bdee-48e7-8bbe-100da90c0f7a · outbound

This paper cites Zhang and M.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation Zhang and M

Reference 47

Resolution: verified fuzzy; raw_fallback, observed 2026-08-11T04:30:15.295716Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

Observation cabc2bd4-60b9-458e-a024-a10226ff34ae · outbound

This paper cites PhyloGFN: Phylogenetic inference with generative flow networks.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation PhyloGFN: Phylogenetic inference with generative flow networks

Reference 48

Resolution: unresolved; no resolver link, observed 2026-08-11T04:30:15.132335Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 3934f65c-3186-4ce1-a459-9daab215778a · outbound

This paper cites DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome.

PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome

Reference 49

Resolution: unresolved; no resolver link, observed 2026-08-11T04:30:15.138767Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Pith citing papers

Observation 664c6ab3-ee87-48de-b115-7aa8536f9dce · inbound

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

PhylaFlow: Hybrid Flow Matching in Billera-Holmes-Vogtmann Tree Space for Phylogenetic Inference PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation

Reference 5

Resolution: verified exact; arxiv_id, observed 2026-05-22T03:05:58.031587Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.