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Paper Citation Record · LEDGER

Improving Protein Sequence Design through Designability Preference Optimization

As of 8 August 2026, this Paper Citation Record lists 47 of 47 outbound references and 1 inbound Pith citation observation for arXiv:2506.00297.

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

pith.paper-citation-record.v1
2506.00297 v1

Coverage vector

measured 47 of 47 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-07T12:12:14.333339Z

measured 48 of 48 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-08T06:32:00.761636+00:00

measured 1 of 1 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-02T09:46:04.299810Z

measured 0 of 1 external citation measurements

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

Source: cited_works

Reference resolution

47 of 47 outbound references displayed

  • verified exact0
  • verified fuzzy37
  • unresolved10
  • parse uncertain0
  • malformed identifier0
  • metadata mismatch0

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 2af98852-9dd0-4ac9-9c28-b4a53e00b860 · outbound

This paper cites Boyken, and David Baker.

Improving Protein Sequence Design through Designability Preference Optimization Boyken, and David Baker

Reference 1

Resolution
verified fuzzy
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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

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Observation 8d904d26-b77f-4c10-aa52-ceab52555064 · outbound

This paper cites Watson, David Juergens, Nathaniel R.

Improving Protein Sequence Design through Designability Preference Optimization Watson, David Juergens, Nathaniel R

Reference 2

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:22.314937Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:07.553580Z digest=sha256:211221ea3d27f6933f08f93b7f33b928f695b9ada26df36d6ab51474a26366ac

Observation a9a4082f-7a6b-4c37-a596-e9f50e19118f · outbound

This paper cites Mackessy, Stefanie K.

Improving Protein Sequence Design through Designability Preference Optimization Mackessy, Stefanie K

Reference 3

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:22.132229Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:07.781176Z digest=sha256:48b356b647860d33694d3bed19a947a6f54f24e1ca49fc5b685264daa1384d4a

Observation 0d6e696c-87ab-429b-b79a-805adb881a63 · outbound

This paper cites Woodbury, Woody Ahern, Indrek Kalvet, Nikita Hanikel, Saman Salike, Samuel J.

Improving Protein Sequence Design through Designability Preference Optimization Woodbury, Woody Ahern, Indrek Kalvet, Nikita Hanikel, Saman Salike, Samuel J

Reference 4

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:21.979880Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:07.931756Z digest=sha256:74dc65b8dc94e4d0f7897fbbf31aa4bf22eac313a59e403548d7ca9792f48cdb

Observation f8ef5b18-ce88-4eae-8f0b-046824bf33ec · outbound

This paper cites Dauparas, I.

Improving Protein Sequence Design through Designability Preference Optimization Dauparas, I

Reference 5

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:21.829624Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:08.037654Z digest=sha256:6f8ce8718d1b93d572ac02ff071256405847de7d8bac2e4ba2362be1d0535c55

Observation b278819a-fceb-4727-81ee-212a26949612 · outbound

This paper cites Generative Models for Graph-Based Protein Design.

Improving Protein Sequence Design through Designability Preference Optimization Generative Models for Graph-Based Protein Design

Reference 6

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:21.616535Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:08.175173Z digest=sha256:7f46c3ab7529df8c085e0659b2ffde708471da0b1285b37d21b1eaa2fab1bb81

Observation a51273d9-e6a7-4ac0-98a3-58d26e415223 · outbound

This paper cites Learning from Protein Structure with Geometric Vector Perceptrons.

Improving Protein Sequence Design through Designability Preference Optimization Learning from Protein Structure with Geometric Vector Perceptrons

Reference 7

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:21.445057Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:08.282188Z digest=sha256:dc412635d516ed104ed12257517ee4d76dce6932d52bfd48bac86d5f79048ffc

Observation 2d6a61ec-fc6b-4da4-a248-d8b91dc018ae · outbound

This paper cites Rotamer-free protein sequence design based on deep learning and self-consistency.Nature Computational Science, 2(7):451–462, July 2022.

Improving Protein Sequence Design through Designability Preference Optimization Rotamer-free protein sequence design based on deep learning and self-consistency.Nature Computational Science, 2(7):451–462, July 2022

Reference 8

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:21.217687Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:08.362935Z digest=sha256:c756d55ebd9cec522ba72dcac2623faa9f3da2eb619b4c1c4a0066c225250be5

Observation e2e86d6c-32ee-4184-b709-ee4ba3b1ada8 · outbound

This paper cites Protein sequence design by deep learning.Nature Computational Science, 2(7):416– 417, July 2022.

Improving Protein Sequence Design through Designability Preference Optimization Protein sequence design by deep learning.Nature Computational Science, 2(7):416– 417, July 2022

Reference 9

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:21.070739Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:08.463298Z digest=sha256:d28993125557c728452031823b2d7a4bb8979932f12f328ad3a338a9e96c702d

Observation 64aa0f28-23b3-4699-9f13-2140b9e63aaf · outbound

This paper cites an unresolved cited work.

Improving Protein Sequence Design through Designability Preference Optimization Unresolved cited work

Reference 10

Resolution
unresolved
raw_fallback, observed 2026-08-07T12:12:20.971485Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:08.574989Z digest=sha256:b7f184eb4e21f6c1ea2a3a28ddc0b47819a86dd87a0b5175d32b285bfdc3a4e3

Observation df37c098-33e2-4787-ad4b-7eb202472eae · outbound

This paper cites Mathews, Carla P.

Improving Protein Sequence Design through Designability Preference Optimization Mathews, Carla P

Reference 11

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:20.784350Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:08.687842Z digest=sha256:0676002970dba7814a018ba190059b227d9cf1413afb9abdc98168ceae4081f4

Observation 7794d9b9-9b41-4d28-bb48-9dcec654c7a2 · outbound

This paper cites an unresolved cited work.

Improving Protein Sequence Design through Designability Preference Optimization Unresolved cited work

Reference 12

Resolution
unresolved
raw_fallback, observed 2026-08-07T12:12:20.604167Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:08.785633Z digest=sha256:0aef32c1cc27d7bf64386337cbeb014d427e0734b42e56270ed313a1b635be6f

Observation d796f56d-8a1c-47d8-a240-ff942a4c2489 · outbound

This paper cites ProRefiner: An entropy-based refining strategy for inverse protein folding with global graph attention.Nature Communications, 14(1):7434, November 2023.

Improving Protein Sequence Design through Designability Preference Optimization ProRefiner: An entropy-based refining strategy for inverse protein folding with global graph attention.Nature Communications, 14(1):7434, November 2023

Reference 13

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:20.411220Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:08.981341Z digest=sha256:c5f01d10b305e84c1edb861cb7222073825cd0abf6ca711f368a7d692757f8b5

Observation d2b07b4d-ee82-4e02-a169-71601157e8b7 · outbound

This paper cites Structure- informed Language Models Are Protein Designers.

Improving Protein Sequence Design through Designability Preference Optimization Structure- informed Language Models Are Protein Designers

Reference 14

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:20.194159Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:09.166436Z digest=sha256:5ec52e252dd9ce17af655c56116bd7929242ccb25d99ba5db87032ccad24a65e

Observation f540e3be-e341-42f6-af36-1577547af512 · outbound

This paper cites an unresolved cited work.

Improving Protein Sequence Design through Designability Preference Optimization Unresolved cited work

Reference 15

Resolution
unresolved
raw_fallback, observed 2026-08-07T12:12:20.029022Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:09.313410Z digest=sha256:6ea8bbd13b3a1f0791c5e359bab516023c780eec2f8469230a33a6c8ff41a6c7

Observation b61ce0f0-3e92-42be-9acd-8ec51a33f714 · outbound

This paper cites an unresolved cited work.

Improving Protein Sequence Design through Designability Preference Optimization Unresolved cited work

Reference 16

Resolution
unresolved
raw_fallback, observed 2026-08-07T12:12:19.835745Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:09.463803Z digest=sha256:e1dc02a73d832629ab5bd5f9cffe24b964eca10c83de34c2982f6ba909e9196e

Observation 845a05a9-76e5-4317-a454-6b3e8d5b1be5 · outbound

This paper cites PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes.Journal of Chemical Information and Modeling, 60(10):4894–4903, October 2020.

Improving Protein Sequence Design through Designability Preference Optimization PRosettaC: Rosetta Based Modeling of PROTAC Mediated Ternary Complexes.Journal of Chemical Information and Modeling, 60(10):4894–4903, October 2020

Reference 17

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:19.647308Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

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Observation 3f2cfc53-ba5f-4c6a-b2b1-30bc0c36ea6c · outbound

This paper cites an unresolved cited work.

Improving Protein Sequence Design through Designability Preference Optimization Unresolved cited work

Reference 18

Resolution
unresolved
raw_fallback, observed 2026-08-07T12:12:19.471632Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:09.820582Z digest=sha256:51c527926784e6c57eb284b0094300469decfc1042c618d44ce4d43e1b7d99c1

Observation 34c1f102-df3a-4f80-9188-fabbd9e0c52d · outbound

This paper cites ProteinBench: A Holistic Evaluation of Protein Foundation Models.

Improving Protein Sequence Design through Designability Preference Optimization ProteinBench: A Holistic Evaluation of Protein Foundation Models

Reference 19

Resolution
unresolved
no resolver link, observed 2026-08-07T12:12:09.974745Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-07T12:12:09.974745Z digest=sha256:345c179312b5f5ae86e5b78425e80b99c69aa2bdc375516b6e9e50f1d920c1d2

Observation c1448df6-5d28-4510-ba04-9c9259ac8b6b · outbound

This paper cites Christiano, Jan Leike, Tom B.

Improving Protein Sequence Design through Designability Preference Optimization Christiano, Jan Leike, Tom B

Reference 20

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:19.265635Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:10.130405Z digest=sha256:44ba6d77381b3d2a3dc58f3335100eb1fd594f2b1cf70afbae34dbb865d2f270

Observation 3d566225-5afd-4df3-8d11-c6b25a5e4479 · outbound

This paper cites https://ai.meta.com/blog/llama-3-2-connect-2024-vision-edge-mobile-devices/.

Improving Protein Sequence Design through Designability Preference Optimization https://ai.meta.com/blog/llama-3-2-connect-2024-vision-edge-mobile-devices/

Reference 21

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:19.083292Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:10.298914Z digest=sha256:1319fae8b092aea0304b060e1da51d7f8f7905e0cb9a50e0f2ba7bb2ec07ff77

Observation b3d94b92-dc9c-46ad-b59d-55f741806825 · outbound

This paper cites DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning, January 2025.

Improving Protein Sequence Design through Designability Preference Optimization DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning, January 2025

Reference 22

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:18.920335Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:10.461367Z digest=sha256:f8befd4383cab94bfd7adafae7e25c2f6365b4adb5eab55122f28ee188c00459

Observation f83dcc5d-4f4e-47b3-9b44-ab2db36b73d0 · outbound

This paper cites Ab initio characterization of protein molecular dynamics with AI2BMD.

Improving Protein Sequence Design through Designability Preference Optimization Ab initio characterization of protein molecular dynamics with AI2BMD

Reference 23

Resolution
verified fuzzy
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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:10.647012Z digest=sha256:ff4c1d803443b4d615836cc02ba0a38d6f16a2c8a34c362afcc306fc543ffaa4

Observation 74e9f29f-9f9f-45f9-aa4a-7379c92b715c · outbound

This paper cites Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander W.

Improving Protein Sequence Design through Designability Preference Optimization Senior, Richard Evans, John Jumper, James Kirkpatrick, Laurent Sifre, Tim Green, Chongli Qin, Augustin Žídek, Alexander W

Reference 24

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:18.659693Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:10.762169Z digest=sha256:1c9f381456250f4a76b72cd22abc59318f52f1e893074d016a001bf9f44b6341

Observation ce64660c-dca7-4d12-be18-4484e1311fe3 · outbound

This paper cites Kinch, R.

Improving Protein Sequence Design through Designability Preference Optimization Kinch, R

Reference 25

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:18.468321Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:10.868750Z digest=sha256:23335cc84bb92927302411f096f32bfeb3bcf703cf40f0237c6be4bd2865e970

Observation 46b073f5-423c-47af-92a6-0e51afd605ff · outbound

This paper cites an unresolved cited work.

Improving Protein Sequence Design through Designability Preference Optimization Unresolved cited work

Reference 26

Resolution
unresolved
no resolver link, observed 2026-08-07T12:12:11.014273Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-07T12:12:11.014273Z digest=sha256:7afc2b7c28354c7fc2946dbbc04387faccb861106dae0b50a07ee481559cf545

Observation b2e9fe4e-baa3-4dd8-bb59-4e9abbbc1400 · outbound

This paper cites Manning, Stefano Ermon, and Chelsea Finn.

Improving Protein Sequence Design through Designability Preference Optimization Manning, Stefano Ermon, and Chelsea Finn

Reference 27

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:18.306389Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:11.165970Z digest=sha256:92331c709447bae57146983959acab966e10305737e274ef139e2c8d5658cd8e

Observation 804b6a88-0724-43f8-8d1f-4ab45718be33 · outbound

This paper cites Gomez, Łukasz Kaiser, and Illia Polosukhin.

Improving Protein Sequence Design through Designability Preference Optimization Gomez, Łukasz Kaiser, and Illia Polosukhin

Reference 28

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:18.136501Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:11.356050Z digest=sha256:d3d331dc0f5221fba54e4788db5992dc06e0070a318379b1ffd81949930d8a75

Observation f99cec6a-3cb1-44be-a9ae-2be9275f2f4e · outbound

This paper cites Learning inverse folding from millions of predicted structures.

Improving Protein Sequence Design through Designability Preference Optimization Learning inverse folding from millions of predicted structures

Reference 29

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:17.943807Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:11.539350Z digest=sha256:5043f13da7567cd6d517cc706967fbcee47b1ee7562c3eebf6f1e2889c5838dc

Observation eee1b8b8-fbe8-47de-b6d5-68cb12069f3d · outbound

This paper cites an unresolved cited work.

Improving Protein Sequence Design through Designability Preference Optimization Unresolved cited work

Reference 30

Resolution
unresolved
raw_fallback, observed 2026-08-07T12:12:17.718407Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:11.692726Z digest=sha256:5de3203fc754d68bda932e77ccf8233772ff6da66400ade22bec0e7b6302f1e4

Observation b2918872-e99b-4c77-8689-59d44db28ae1 · outbound

This paper cites Nakou, Sebastian Lindner, Gavin Ayres, Lesley S.

Improving Protein Sequence Design through Designability Preference Optimization Nakou, Sebastian Lindner, Gavin Ayres, Lesley S

Reference 31

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:17.545074Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:11.888140Z digest=sha256:6b462640797f6f5fc7a5af6798f2f9053a3a30154df87e56040eae08b9e5c39e

Observation c0a7b5da-b725-4842-b101-12f5e12fb116 · outbound

This paper cites Accurate and robust protein sequence design with CarbonDesign.Nature Machine Intelligence, 6(5):536–547, May 2024.

Improving Protein Sequence Design through Designability Preference Optimization Accurate and robust protein sequence design with CarbonDesign.Nature Machine Intelligence, 6(5):536–547, May 2024

Reference 32

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:17.321653Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:12.064793Z digest=sha256:3be2a113143ae8f575d3c70ab0929ed405dfd8f4b98ad3fd2679e6bfd097eae8

Observation 05b9a618-875e-4fc0-96c7-b19cd467ef0b · outbound

This paper cites Atomic context-conditioned protein sequence design using LigandMPNN.Nature Methods, 22(4):717–723, April 2025.

Improving Protein Sequence Design through Designability Preference Optimization Atomic context-conditioned protein sequence design using LigandMPNN.Nature Methods, 22(4):717–723, April 2025

Reference 33

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:17.151456Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:12.217191Z digest=sha256:4a02b33f69b9fca354d123da3797754f366032cfb989ebceca0b4c2c4b0a6fa4

Observation 3d1291ec-e201-4752-8828-e1f79dc13430 · outbound

This paper cites A General Theoretical Paradigm to Understand Learning from Human Preferences.

Improving Protein Sequence Design through Designability Preference Optimization A General Theoretical Paradigm to Understand Learning from Human Preferences

Reference 34

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:16.963653Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:12.373676Z digest=sha256:45a398e812cdfed19686eac0eb61740260cf32d26582f6a11cf523fa9fe3930f

Observation da771f2d-8b0a-4ba6-a67a-3e474c2d0448 · outbound

This paper cites Liu, and Xuanhui Wang.

Improving Protein Sequence Design through Designability Preference Optimization Liu, and Xuanhui Wang

Reference 35

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:16.746479Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:12.524103Z digest=sha256:11cbebbdd41e6c4c1a14c2bf81ebbb503d4b7d717eada2de8006ed24c872d5ae

Observation 000427cf-eae3-4b98-a095-893f0e343dbe · outbound

This paper cites SimPO: Simple Preference Optimization with a Reference-Free Reward.

Improving Protein Sequence Design through Designability Preference Optimization SimPO: Simple Preference Optimization with a Reference-Free Reward

Reference 36

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:16.609037Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:12.690730Z digest=sha256:2767b94943e9fff354c14d33f32ff00d7ad00dd096ebafce4fda1d95c1039460

Observation bb228053-06d5-4e03-81ad-8d498a325946 · outbound

This paper cites an unresolved cited work.

Improving Protein Sequence Design through Designability Preference Optimization Unresolved cited work

Reference 37

Resolution
unresolved
raw_fallback, observed 2026-08-07T12:12:16.378423Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:12.824852Z digest=sha256:bac8826e24535bd9421825bebe5ba2eb1d386085042794843d61eb77f902c38c

Observation b92069dd-0cb0-4314-bbe1-8e5100a3bf59 · outbound

This paper cites The Llama 3 Herd of Models, November 2024.

Improving Protein Sequence Design through Designability Preference Optimization The Llama 3 Herd of Models, November 2024

Reference 38

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:16.198763Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:12.971901Z digest=sha256:23a1b433049aa0b40564066dedd7c6b958ea3aa09415d612fa3efaed7eea9d45

Observation 50185078-b27c-4bc9-9743-3e1b3e693585 · outbound

This paper cites Berman, John Westbrook, Zukang Feng, Gary Gilliland, T.

Improving Protein Sequence Design through Designability Preference Optimization Berman, John Westbrook, Zukang Feng, Gary Gilliland, T

Reference 39

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:16.036068Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:13.139713Z digest=sha256:878563805fc3a52025908afe19bfc6b6a79b2b677af2291b935772bfea121e15

Observation d5d5940f-8e84-4629-aaf0-f8ea471e7464 · outbound

This paper cites Ballard, Joshua Bambrick, Sebastian W.

Improving Protein Sequence Design through Designability Preference Optimization Ballard, Joshua Bambrick, Sebastian W

Reference 40

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:15.808729Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:13.301543Z digest=sha256:1519816b0a905a8c4b811c71b2c08b326247111f1f080cd3f3b532bd711726a1

Observation 2b3dd517-8cfe-422b-90cc-320a0eff7f60 · outbound

This paper cites an unresolved cited work.

Improving Protein Sequence Design through Designability Preference Optimization Unresolved cited work

Reference 41

Resolution
unresolved
raw_fallback, observed 2026-08-07T12:12:15.622282Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:13.468454Z digest=sha256:6b457c9d788922ae3872c07d8564ccfa99fa71895d84108698fff7eed4d5c9d8

Observation 96f9a0fb-986b-431a-9939-963d48408a0e · outbound

This paper cites Woodbury, Donghyo Kim, Indrek Kalvet, Yakov Kipnis, Brian Coventry, Han Raut Altae-Tran, Magnus Bauer, Regina Barzilay, Tommi S.

Improving Protein Sequence Design through Designability Preference Optimization Woodbury, Donghyo Kim, Indrek Kalvet, Yakov Kipnis, Brian Coventry, Han Raut Altae-Tran, Magnus Bauer, Regina Barzilay, Tommi S

Reference 42

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:15.423051Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:13.640287Z digest=sha256:fddca5d7322ccd44eee1c6e82213a394bcdd470cf3eec575ca02631e9e2c17fb

Observation ed509beb-2032-4162-8b9b-62704cf3adc4 · outbound

This paper cites Provably Robust DPO: Aligning Language Models with Noisy Feedback.

Improving Protein Sequence Design through Designability Preference Optimization Provably Robust DPO: Aligning Language Models with Noisy Feedback

Reference 43

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:15.237489Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:13.774395Z digest=sha256:48d39e361b420169bdd431e77fb16774947df39ef92068a4cd98a28ebc52fa69

Observation c9cd7396-0fb0-4ea2-a89e-bf9a7185745f · outbound

This paper cites Liu, and Jialu Liu.

Improving Protein Sequence Design through Designability Preference Optimization Liu, and Jialu Liu

Reference 44

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:15.058823Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:13.899877Z digest=sha256:733a1f6fb9993c9ef8646580709f0f0d71d43f55349c2d8b60ce86c6d6741e37

Observation 8e71d8e0-ff20-4c12-99e2-54940b8b4b52 · outbound

This paper cites Model Alignment as Prospect Theoretic Optimization.

Improving Protein Sequence Design through Designability Preference Optimization Model Alignment as Prospect Theoretic Optimization

Reference 45

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:14.894163Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:14.065811Z digest=sha256:783b01e5666c00ebf52f3c1a94ca7047bb9d350aa8c41ec4269ebd8760117c79

Observation a3fc7719-a9fa-4705-97ce-588deb2af574 · outbound

This paper cites Noise Contrastive Alignment of Language Models with Explicit Rewards.NeurIPS, 37:117784–117812, December 2024.

Improving Protein Sequence Design through Designability Preference Optimization Noise Contrastive Alignment of Language Models with Explicit Rewards.NeurIPS, 37:117784–117812, December 2024

Reference 46

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:14.735242Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:14.225058Z digest=sha256:cde781d8c56c58ea63380c994b0d44c095a7632deec5ee38c4aa1f0568a9187f

Observation e136365a-18d0-4fa0-8fbe-d2eb9d22e159 · outbound

This paper cites designability.

Improving Protein Sequence Design through Designability Preference Optimization designability

Reference 47

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T12:12:14.539902Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-08T06:32:00.761636+00:00.

source=pdf_text observed=2026-08-07T12:12:14.333339Z digest=sha256:f9360b35ab3152c00fc3568adb6bba695240a3321e17d9380d0258f8c78af551

Pith citing papers

Observation 8f2eeb86-c8d2-4625-9aaa-101d7f166783 · inbound

Preference-based Antibody Expression Ranking: Scaling with Large-scale Weak Supervision cites this paper.

Preference-based Antibody Expression Ranking: Scaling with Large-scale Weak Supervision Improving Protein Sequence Design through Designability Preference Optimization

Reference 21

Resolution
unresolved
no resolver link, observed 2026-08-02T09:46:04.299810Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=arxiv_source observed=2026-08-02T09:46:04.299810Z digest=sha256:8dcf9171422eb94ccc372ce3a390328dc55c0caf88f82f06252536079019ffe3