Paper Citation Record · LEDGER

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design

As of 5 August 2026, this Paper Citation Record lists 16 of 16 outbound references and 1 inbound Pith citation observation for arXiv:2604.16896.

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

pith.paper-citation-record.v1
2604.16896 v1

Coverage vector

measured 16 of 16 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-05-10T07:00:46.618841Z

measured 17 of 17 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-05T06:32:48.257954+00:00

measured 1 of 1 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-05-22T01:19:00.268857Z

measured 0 of 1 external citation measurements

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

Source: pith, observed 2026-05-22T01:20:51.955094Z

Reference resolution

16 of 16 outbound references displayed

verified exact2
verified fuzzy4
unresolved4
parse uncertain0
malformed identifier1
metadata mismatch5

External citation measurements

No source-named external measurement is stored.

Outbound references

Observation 1b70cb86-5658-4677-85b0-f51c2dbad184 · outbound

This paper cites Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Alexander Pritzel, Olaf Ron- neberger, Lindsay Willmore, Andrew J.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Alexander Pritzel, Olaf Ron- neberger, Lindsay Willmore, Andrew J

Reference 1

Resolution: verified fuzzy; raw_fallback, observed 2026-05-21T14:45:14.636918Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation 8dcf03fa-aa34-4583-a592-d89a0c5a685b · outbound

This paper cites Language Models are Few-Shot Learners.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design Language Models are Few-Shot Learners

Reference 2

Resolution: metadata mismatch; arxiv_id, observed 2026-05-10T12:05:38.478916Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation ba43fd85-0df5-4c08-a6b1-51cb036325fe · outbound

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

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning

Reference 3

Resolution: metadata mismatch; local_arxiv, observed 2026-05-10T07:01:49.080389Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation 8c67d4fc-2f5a-4baf-b627-aca1edf951df · outbound

This paper cites Qwen2.5 Technical Report.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design Qwen2.5 Technical Report

Reference 4

Resolution: verified exact; local_arxiv, observed 2026-05-10T07:01:49.065260Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation c43b67da-c64a-4ff1-ab6c-104590cc7ef6 · outbound

This paper cites DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models

Reference 5

Resolution: metadata mismatch; local_arxiv, observed 2026-05-10T07:01:49.067623Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation dddcb644-2eb8-45aa-a660-ab0da4fb07df · outbound

This paper cites Finetuned Language Models Are Zero-Shot Learners.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design Finetuned Language Models Are Zero-Shot Learners

Reference 6

Resolution: metadata mismatch; arxiv_id, observed 2026-05-10T21:14:13.786069Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation 25e3e49c-c7c5-4e80-a9bb-b7981a14a940 · outbound

This paper cites Advancing Multimodal Reasoning via Reinforcement Learning with Cold Start.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design Advancing Multimodal Reasoning via Reinforcement Learning with Cold Start

Reference 7

Resolution: metadata mismatch; arxiv_id, observed 2026-05-10T07:01:49.070150Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation d6848d2a-266d-4fce-98c3-ba93397651ff · outbound

This paper cites binds Zn 2+ with a Cys 2His2 coordination motif.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design binds Zn 2+ with a Cys 2His2 coordination motif

Reference 8

Resolution: verified exact; arxiv_id, observed 2026-05-10T07:01:49.075165Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation c3e6d2fa-ab7f-402d-a5d5-40eab1091050 · outbound

This paper cites an unresolved cited work.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design Unresolved cited work

Reference 9

Resolution: unresolved; raw_fallback, observed 2026-05-21T14:45:14.644901Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation e1d444b4-8d2a-4909-9f10-7d4ee1b130d5 · outbound

This paper cites specific function in intein-mediated protein splicing, cell-cell signaling.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design specific function in intein-mediated protein splicing, cell-cell signaling

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-05-21T14:45:14.631850Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation 8ab73780-db55-4313-9f01-a568c1d3efe2 · outbound

This paper cites an unresolved cited work.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design Unresolved cited work

Reference 11

Resolution: unresolved; raw_fallback, observed 2026-05-21T14:45:14.626258Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation 357a4c3d-e040-41fe-aa04-ea6688c1322c · outbound

This paper cites no new sequences.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design no new sequences

Reference 12

Resolution: malformed identifier; arxiv_id, observed 2026-05-10T07:01:49.077757Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation d5848b17-aedd-4dc6-92f6-f7f4804f33a4 · outbound

This paper cites The case highlights two behaviors.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design The case highlights two behaviors

Reference 13

Resolution: verified fuzzy; raw_fallback, observed 2026-05-21T14:45:14.629024Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation 3d24b303-2912-40fe-9d21-efd46c0b570a · outbound

This paper cites an unresolved cited work.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design Unresolved cited work

Reference 14

Resolution: unresolved; raw_fallback, observed 2026-05-21T14:45:14.641772Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation 4ccc5e41-05f9-4f3b-924f-01c2f20b3e1d · outbound

This paper cites an unresolved cited work.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design Unresolved cited work

Reference 15

Resolution: unresolved; raw_fallback, observed 2026-05-21T14:45:14.639443Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation baa73b32-6522-4d54-812c-091e7e8b42be · outbound

This paper cites Involved in oxygen transport from the gills to the various peripheral tissues.

ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design Involved in oxygen transport from the gills to the various peripheral tissues

Reference 16

Resolution: verified fuzzy; raw_fallback, observed 2026-05-21T14:45:14.634559Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Pith citing papers

Observation 8c811739-6118-49d1-adad-19f4f0a926db · inbound

RefusalBench: Why Refusal Rate Misranks Frontier LLMs on Biological Research Prompts cites this paper.

RefusalBench: Why Refusal Rate Misranks Frontier LLMs on Biological Research Prompts ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design

Reference 7

Resolution: verified exact; local_arxiv, observed 2026-05-22T01:20:51.957519Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.