Paper Citation Record · LEDGER

Large Language Model is Secretly a Protein Sequence Optimizer

As of 20 August 2026, this Paper Citation Record lists 27 of 27 outbound references and 3 inbound Pith citation observations for arXiv:2501.09274.

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

pith.paper-citation-record.v1
2501.09274 v2

Coverage vector

measured 27 of 27 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-10T20:10:52.893429Z

measured 30 of 30 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-20T06:33:59.587034+00:00

measured 3 of 3 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-04T20:55:41.916450Z

measured 0 of 1 external citation measurements

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

Source: arxiv_reference, observed 2026-07-03T04:07:36.964600Z

Reference resolution

27 of 27 outbound references displayed

verified exact1
verified fuzzy14
unresolved12
parse uncertain0
malformed identifier0
metadata mismatch0

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation b4cb0224-a333-4f9c-b4e9-fb17880c889d · outbound

This paper cites Design by directed evolution.

Large Language Model is Secretly a Protein Sequence Optimizer Design by directed evolution

Reference 1

Resolution: unresolved; no resolver link, observed 2026-08-10T20:10:52.799942Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 11f9d901-d3f7-4c61-a4f9-bac6fd0be97e · outbound

This paper cites Conditioning by adaptive sampling for robust design.

Large Language Model is Secretly a Protein Sequence Optimizer Conditioning by adaptive sampling for robust design

Reference 2

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.258807Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation e0016b4e-82e3-40bd-bf3c-f7dabb0cbd71 · outbound

This paper cites Deep diversification of an aav capsid protein by machine learning.

Large Language Model is Secretly a Protein Sequence Optimizer Deep diversification of an aav capsid protein by machine learning

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.247851Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation bfcec33e-e2d4-4177-b44e-ca4ba28466f4 · outbound

This paper cites Generalists vs. Specialists: Evaluating LLMs on Highly-Constrained Biophysical Sequence Optimization Tasks.

Large Language Model is Secretly a Protein Sequence Optimizer Generalists vs. Specialists: Evaluating LLMs on Highly-Constrained Biophysical Sequence Optimization Tasks

Reference 4

Resolution: unresolved; no resolver link, observed 2026-08-10T20:10:52.809550Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation bfce81a8-eb0f-48ac-b90b-6f9583c4c82c · outbound

This paper cites Flip: Benchmark tasks in fitness landscape inference for proteins.

Large Language Model is Secretly a Protein Sequence Optimizer Flip: Benchmark tasks in fitness landscape inference for proteins

Reference 5

Resolution: unresolved; no resolver link, observed 2026-08-10T20:10:52.813340Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation da4c3c52-0da3-4c2f-b777-c74dba3c24cf · outbound

This paper cites Deep mutational scanning: a new style of protein science.

Large Language Model is Secretly a Protein Sequence Optimizer Deep mutational scanning: a new style of protein science

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.230322Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation f3a784c4-729c-48af-adc8-51bab59e9985 · outbound

This paper cites Mutation effects predicted from sequence co-variation.

Large Language Model is Secretly a Protein Sequence Optimizer Mutation effects predicted from sequence co-variation

Reference 7

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.218767Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation 03d5914f-99ce-4572-a099-c7dd7aa51904 · outbound

This paper cites Biological sequence design with gflownets.

Large Language Model is Secretly a Protein Sequence Optimizer Biological sequence design with gflownets

Reference 8

Resolution: unresolved; no resolver link, observed 2026-08-10T20:10:52.823344Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e71a733a-283c-4c1c-9a10-2e5cd0f163a1 · outbound

This paper cites A combinatorially complete epistatic fitness landscape in an enzyme active site.

Large Language Model is Secretly a Protein Sequence Optimizer A combinatorially complete epistatic fitness landscape in an enzyme active site

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.199633Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation 5e575411-3870-4459-ab6c-6c62e05e3555 · outbound

This paper cites Highly accurate protein structure prediction with alphafold.

Large Language Model is Secretly a Protein Sequence Optimizer Highly accurate protein structure prediction with alphafold

Reference 10

Resolution: unresolved; no resolver link, observed 2026-08-10T20:10:52.831447Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation bebdca3e-7445-4ade-9fc0-2c230a62830e · outbound

This paper cites Improving protein optimization with smoothed fitness landscapes.

Large Language Model is Secretly a Protein Sequence Optimizer Improving protein optimization with smoothed fitness landscapes

Reference 11

Resolution: unresolved; no resolver link, observed 2026-08-10T20:10:52.835278Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 2f33d543-121c-458c-a8ec-5b6f2f588d8e · outbound

This paper cites Evolutionary-scale prediction of atomic-level protein structure with a language model.

Large Language Model is Secretly a Protein Sequence Optimizer Evolutionary-scale prediction of atomic-level protein structure with a language model

Reference 12

Resolution: unresolved; no resolver link, observed 2026-08-10T20:10:52.839155Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation d7f02d13-fbda-4b6b-9e51-345bfc29aea7 · outbound

This paper cites Generative Design of Functional Metal Complexes Utilizing the Internal Knowledge of Large Language Models.

Large Language Model is Secretly a Protein Sequence Optimizer Generative Design of Functional Metal Complexes Utilizing the Internal Knowledge of Large Language Models

Reference 13

Resolution: verified exact; local_arxiv, observed 2026-08-10T20:10:53.040056Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation 2f3782b1-65ac-4a13-b571-bc327ead024a · outbound

This paper cites Proximal exploration for model-guided protein sequence design.

Large Language Model is Secretly a Protein Sequence Optimizer Proximal exploration for model-guided protein sequence design

Reference 14

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.169929Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation 2572dddf-6404-4a48-9222-841e884fb64b · outbound

This paper cites Exploring protein fitness landscapes by directed evolution.

Large Language Model is Secretly a Protein Sequence Optimizer Exploring protein fitness landscapes by directed evolution

Reference 15

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.159588Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation 979edd04-8f67-4ac1-9765-ade5f6571282 · outbound

This paper cites Local fitness landscape of the green fluorescent protein.

Large Language Model is Secretly a Protein Sequence Optimizer Local fitness landscape of the green fluorescent protein

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.150471Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation 6712293c-a35f-45d0-9090-cf622aa36151 · outbound

This paper cites Tuned fitness landscapes for benchmarking model-guided protein design.

Large Language Model is Secretly a Protein Sequence Optimizer Tuned fitness landscapes for benchmarking model-guided protein design

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.139117Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation 45d721af-c36f-4066-acb0-4c7c3459f28d · outbound

This paper cites Protein design by directed evolution guided by large language models.

Large Language Model is Secretly a Protein Sequence Optimizer Protein design by directed evolution guided by large language models

Reference 18

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.127024Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation 7de8ead5-dc67-4776-a252-91815a504cae · outbound

This paper cites Efficient Evolutionary Search Over Chemical Space with Large Language Models.

Large Language Model is Secretly a Protein Sequence Optimizer Efficient Evolutionary Search Over Chemical Space with Large Language Models

Reference 19

Resolution: unresolved; no resolver link, observed 2026-08-10T20:10:52.865174Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 82fba977-7756-461a-9432-e3bfbf72b613 · outbound

This paper cites Adaptation in protein fitness landscapes is facilitated by indirect paths.

Large Language Model is Secretly a Protein Sequence Optimizer Adaptation in protein fitness landscapes is facilitated by indirect paths

Reference 20

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.116023Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation 15c1e4a0-a150-4a78-b959-fc264ef04db8 · outbound

This paper cites Active learning-assisted directed evolution.

Large Language Model is Secretly a Protein Sequence Optimizer Active learning-assisted directed evolution

Reference 21

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.103645Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation 73277fba-128a-4273-8c10-98df0a423ddd · outbound

This paper cites Machine-learning-guided directed evolution for protein engineering.

Large Language Model is Secretly a Protein Sequence Optimizer Machine-learning-guided directed evolution for protein engineering

Reference 22

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.091723Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation 612f45ef-1736-420f-952d-b57f949b0793 · outbound

This paper cites Protein language models learn evolutionary statistics of interacting sequence motifs.

Large Language Model is Secretly a Protein Sequence Optimizer Protein language models learn evolutionary statistics of interacting sequence motifs

Reference 23

Resolution: verified fuzzy; raw_fallback, observed 2026-08-10T20:10:53.079923Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation 8266c117-45f1-4cd9-b727-1840f779eaaa · outbound

This paper cites write newline.

Large Language Model is Secretly a Protein Sequence Optimizer write newline

Reference 24

Resolution: unresolved; no resolver link, observed 2026-08-10T20:10:52.882094Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 4667a5e4-e4c8-4e74-a820-02d376f78519 · outbound

This paper cites @esa (Ref.

Large Language Model is Secretly a Protein Sequence Optimizer @esa (Ref

Reference 25

Resolution: unresolved; no resolver link, observed 2026-08-10T20:10:52.886231Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 79807b36-d894-4383-a751-c3b3ec1ce17c · outbound

This paper cites an unresolved cited work.

Large Language Model is Secretly a Protein Sequence Optimizer Unresolved cited work

Reference 26

Resolution: unresolved; no resolver link, observed 2026-08-10T20:10:52.889790Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 51dce926-717b-48f5-a6c0-2f992ca2ea2c · outbound

This paper cites an unresolved cited work.

Large Language Model is Secretly a Protein Sequence Optimizer Unresolved cited work

Reference 27

Resolution: unresolved; no resolver link, observed 2026-08-10T20:10:52.893429Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Pith citing papers

Observation 711d76bf-83f7-403e-8a8f-1bf839ec8eb9 · inbound

Towards an AI co-scientist cites this paper.

Towards an AI co-scientist Large Language Model is Secretly a Protein Sequence Optimizer

Reference 279

Resolution: verified exact; arxiv_id, observed 2026-05-11T13:02:45.541768Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.

Observation e2c469a8-6acf-486b-8f5e-d317bad7e637 · inbound

A Systematic Survey on Large Language Models for Evolutionary Optimization: From Modeling to Solving cites this paper.

A Systematic Survey on Large Language Models for Evolutionary Optimization: From Modeling to Solving Large Language Model is Secretly a Protein Sequence Optimizer

Reference 216

Resolution: unresolved; no resolver link, observed 2026-08-04T20:55:41.916450Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a062f0c5-ff33-46bf-8fcf-bfd9ee9b6403 · inbound

Towards Diverse Scientific Hypothesis Search with Large Language Models cites this paper.

Towards Diverse Scientific Hypothesis Search with Large Language Models Large Language Model is Secretly a Protein Sequence Optimizer

Reference 47

Resolution: verified exact; arxiv_id, observed 2026-07-03T04:07:36.966106Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-20T06:33:59.587034+00:00.