Paper Citation Record · LEDGER

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space

As of 17 August 2026, this Paper Citation Record lists 40 of 40 outbound references and 0 inbound Pith citation observations for arXiv:2509.04998.

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

pith.paper-citation-record.v1
2509.04998 v1

Coverage vector

measured 40 of 40 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-05T05:45:31.196893Z

measured 40 of 40 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 0 of 0 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links

measured 0 of 1 external citation measurements

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

Source: cited_works

Reference resolution

40 of 40 outbound references displayed

verified exact2
verified fuzzy34
unresolved4
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External citation measurements

No source-named external measurement is stored.

Outbound references

Observation a7c416db-e089-4005-bd85-e9392bb35f80 · outbound

This paper cites Protein engineering: A brief overview methodologies and applications,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Protein engineering: A brief overview methodologies and applications,

Reference 1

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Observation bed58c5a-e5dd-4231-a127-b553f1d7e7da · outbound

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

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Machine-learning-guided directed evolution for protein engineering,

Reference 2

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:37.441264Z

Source-reported events for the cited work

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Observation 4c6b0b77-6dda-469e-8d97-746dacc163bf · outbound

This paper cites Directed evolution: methodologies and applications,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Directed evolution: methodologies and applications,

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:37.288184Z

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Observation 4140f955-5fdf-4b03-8159-c8d280c1daf3 · outbound

This paper cites Taking the human out of the loop: A review of bayesian optimization,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Taking the human out of the loop: A review of bayesian optimization,

Reference 4

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Source-reported events for the cited work

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Observation 5caf284f-a54c-4636-983c-d05e1c684dd5 · outbound

This paper cites Machine learning-assisted directed protein evolution with combinatorial libraries,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Machine learning-assisted directed protein evolution with combinatorial libraries,

Reference 5

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:37.172215Z

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Observation e480b04f-e6ec-4015-9fe5-e775a595822a · outbound

This paper cites Informed training set design enables efficient machine learning-assisted directed protein evolution,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Informed training set design enables efficient machine learning-assisted directed protein evolution,

Reference 6

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:37.013603Z

Source-reported events for the cited work

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Observation 77be2a33-a0a1-495f-8056-32ebf8c0fc73 · outbound

This paper cites Cluster learning-assisted directed evolution,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Cluster learning-assisted directed evolution,

Reference 7

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:36.825844Z

Source-reported events for the cited work

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Observation aa55eaa4-f8fb-492f-844b-df856cac96cb · outbound

This paper cites Clade 2.0: evolution-driven cluster learning- assisted directed evolution,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Clade 2.0: evolution-driven cluster learning- assisted directed evolution,

Reference 8

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:36.644968Z

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Observation c3892d6a-0fcc-40af-a869-8ec2465985eb · outbound

This paper cites Active finetuning protein language model: A budget-friendly method for directed evolution,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Active finetuning protein language model: A budget-friendly method for directed evolution,

Reference 9

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:36.471146Z

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Observation 897b42f2-0598-4f80-ad90-dd311d674798 · outbound

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

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Adaptation in protein fitness landscapes is facilitated by indirect paths,

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:36.303425Z

Source-reported events for the cited work

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Observation c746513d-a623-4043-adba-12a3c5c92810 · outbound

This paper cites Fitness landscape analysis around the optimum in computational protein design,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Fitness landscape analysis around the optimum in computational protein design,

Reference 11

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:36.111494Z

Source-reported events for the cited work

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Observation d39f5c07-2417-44b0-a12e-2efa53d1454b · outbound

This paper cites Navigating the protein fitness landscape with gaussian processes,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Navigating the protein fitness landscape with gaussian processes,

Reference 12

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:35.950888Z

Source-reported events for the cited work

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Observation e1b3d10e-a503-4b74-9e83-6a12288a23ba · outbound

This paper cites Leveraging uncertainty in machine learning accelerates biological discovery and design,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Leveraging uncertainty in machine learning accelerates biological discovery and design,

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:35.816318Z

Source-reported events for the cited work

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Observation c7adc4bc-0f57-4f45-b9c7-0a375f2f40dd · outbound

This paper cites Gaussian Process Optimization in the Bandit Setting: No Regret and Experimental Design.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Gaussian Process Optimization in the Bandit Setting: No Regret and Experimental Design

Reference 14

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Source-reported events for the cited work

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Observation b55c209b-2c01-41ae-a3c2-bdaca44da701 · outbound

This paper cites Convergence rates of efficient global optimization algo- rithms.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Convergence rates of efficient global optimization algo- rithms

Reference 15

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:35.659674Z

Source-reported events for the cited work

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Observation 4762bb50-1137-4ae0-bf88-f3870f506b33 · outbound

This paper cites Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization,

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:35.477651Z

Source-reported events for the cited work

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Observation 4baeaebd-a94d-40fa-824d-30a327338803 · outbound

This paper cites The form and function of channel- rhodopsin,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space The form and function of channel- rhodopsin,

Reference 17

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:35.288736Z

Source-reported events for the cited work

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Observation 9ea1190c-e38a-4d57-b820-5ca8f4be102d · outbound

This paper cites Machine learning-guided acyl-acp reductase engineering for improved in vivo fatty alcohol production,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Machine learning-guided acyl-acp reductase engineering for improved in vivo fatty alcohol production,

Reference 18

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:35.153672Z

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Observation aa68aa27-c955-488c-9341-3db220e44874 · outbound

This paper cites Fold family-regularized bayesian optimization for directed protein evolution,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Fold family-regularized bayesian optimization for directed protein evolution,

Reference 19

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Observation c93d1a2b-5a14-42db-bd45-53f80bc6e764 · outbound

This paper cites ODBO: Bayesian Optimization with Search Space Prescreening for Directed Protein Evolution.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space ODBO: Bayesian Optimization with Search Space Prescreening for Directed Protein Evolution

Reference 20

Resolution: verified exact; local_arxiv, observed 2026-08-05T05:45:31.545918Z

Source-reported events for the cited work

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Observation 40ab7207-afae-4229-9880-95e4f5749642 · outbound

This paper cites Xgbod: improving supervised outlier detection with unsupervised representation learning,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Xgbod: improving supervised outlier detection with unsupervised representation learning,

Reference 21

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:34.784064Z

Source-reported events for the cited work

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Observation fb76dbf3-5309-46d0-b0d5-9be422b959c6 · outbound

This paper cites Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences,

Reference 22

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:34.592826Z

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Observation 40f59fe9-8ee2-4b18-a167-c6a166372103 · outbound

This paper cites BERTology Meets Biology: Interpreting Attention in Protein Language Models.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space BERTology Meets Biology: Interpreting Attention in Protein Language Models

Reference 23

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Source-reported events for the cited work

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Observation f91e9e58-e9f8-4a34-9bd7-8c9a980808f4 · outbound

This paper cites Transformer protein language models are unsupervised structure learners,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Transformer protein language models are unsupervised structure learners,

Reference 24

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:34.323436Z

Source-reported events for the cited work

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Observation cb8fac2e-d774-4398-81a7-ed2cd41eadf0 · outbound

This paper cites Prottrans: Toward understanding the language of life through self- supervised learning,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Prottrans: Toward understanding the language of life through self- supervised learning,

Reference 25

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:34.084632Z

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 7192fda2-4613-4240-b048-3417f56cbfa7 · outbound

This paper cites Active learning-assisted directed evolution,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Active learning-assisted directed evolution,

Reference 26

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Observation ad6650d5-b662-481e-a4ac-48b0375adaae · outbound

This paper cites Biochemistry, essential amino acids,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Biochemistry, essential amino acids,

Reference 27

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Source-reported events for the cited work

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Observation 0f492dfd-7e97-4d65-adff-1bfcdbcad264 · outbound

This paper cites Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins,

Reference 28

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:33.427583Z

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Observation abd3c291-7d4e-4142-a6e0-c98e8a60c30a · outbound

This paper cites Language models of protein sequences at the scale of evolution enable accurate structure prediction,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Language models of protein sequences at the scale of evolution enable accurate structure prediction,

Reference 29

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Observation d19832c5-5590-4bb8-bdde-e17b655d7791 · outbound

This paper cites RITA: a Study on Scaling Up Generative Protein Sequence Models.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space RITA: a Study on Scaling Up Generative Protein Sequence Models

Reference 30

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Observation 7e00e57a-fda3-4c40-9be3-493524206dd6 · outbound

This paper cites Protgpt2 is a deep unsupervised language model for protein design,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Protgpt2 is a deep unsupervised language model for protein design,

Reference 31

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Observation f7b4d142-78b6-43e3-b217-815a69899054 · outbound

This paper cites BOSS.jl (Bayesian Optimization with Semiparametric Surrogate).

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space BOSS.jl (Bayesian Optimization with Semiparametric Surrogate)

Reference 32

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:32.804010Z

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

Observation 081d51eb-5760-42ff-93c0-72c68888dfbc · outbound

This paper cites The newuoa software for unconstrained optimization without derivatives,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space The newuoa software for unconstrained optimization without derivatives,

Reference 33

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:32.619100Z

Source-reported events for the cited work

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Observation cd68e343-59b6-43c6-9c49-da0b5f5c6b71 · outbound

This paper cites DESilico.jl (Directed Evolution in Silico).

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space DESilico.jl (Directed Evolution in Silico)

Reference 34

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:32.432961Z

Source-reported events for the cited work

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Observation 6d5dda02-c44e-4e97-b151-ed4d320f4aa7 · outbound

This paper cites Pervasive degeneracy and epistasis in a protein-protein interface,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Pervasive degeneracy and epistasis in a protein-protein interface,

Reference 35

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:32.270843Z

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Observation 5dca8913-a77a-4db1-ba22-95e0e4559870 · outbound

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

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Mutation effects predicted from sequence co-variation,

Reference 36

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:32.042186Z

Source-reported events for the cited work

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Observation 457fb911-eae9-425c-bb4d-e655f8f140db · outbound

This paper cites Msa transformer,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Msa transformer,

Reference 37

Resolution: verified exact; doi, observed 2026-08-05T05:45:31.361156Z

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Observation a90d07d0-bb2e-4429-a0c7-44437891f8eb · outbound

This paper cites Protein engineering with large language models,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Protein engineering with large language models,

Reference 38

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:31.941760Z

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 52bd6eed-13f7-41fe-82dd-20aaba7165c1 · outbound

This paper cites Scalable global optimization via local bayesian optimization,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Scalable global optimization via local bayesian optimization,

Reference 39

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:31.816889Z

Source-reported events for the cited work

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Observation 6d8e32c1-29a6-4bfd-90c9-988942c610e5 · outbound

This paper cites Practical bayesian optimization in the presence of outliers,.

Directed Evolution of Proteins via Bayesian Optimization in Embedding Space Practical bayesian optimization in the presence of outliers,

Reference 40

Resolution: verified fuzzy; raw_fallback, observed 2026-08-05T05:45:31.680047Z

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.

Pith citing papers

No inbound Pith citation observations are available.