Paper Citation Record · LEDGER

Diffusion Sequence Models for Enhanced Protein Representation and Generation

As of 8 August 2026, this Paper Citation Record lists 76 of 76 outbound references and 2 inbound Pith citation observations for arXiv:2506.08293.

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

pith.paper-citation-record.v1
2506.08293 v1

Coverage vector

measured 76 of 76 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-08-07T05:22:25.325006Z

measured 78 of 78 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 2 of 2 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links, observed 2026-08-05T20:15:24.647617Z

measured 1 of 1 external citation measurements

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

Source: arxiv_reference, observed 2026-08-05T02:28:24.338817Z

Reference resolution

76 of 76 outbound references displayed

verified exact32
verified fuzzy5
unresolved36
parse uncertain0
malformed identifier1
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External citation measurements

1
arxiv_reference, observed 2026-08-05T02:28:24.338817Z

Outbound references

Observation ce7de5cd-ea4f-4fad-8894-7f388d1d212b · outbound

This paper cites Synonymous mutations in representative yeast genes are mostly strongly non-neutral.Nature, 606(7915): 725–731, June 2022.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Synonymous mutations in representative yeast genes are mostly strongly non-neutral.Nature, 606(7915): 725–731, June 2022

Reference 1

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.746747Z

Source-reported events for the cited work

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Observation d4f8e3d5-de63-47ed-923e-58714b4cff33 · outbound

This paper cites an unresolved cited work.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Unresolved cited work

Reference 2

Resolution: verified exact; raw_fallback, observed 2026-08-07T05:22:28.138967Z

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.

Observation 752d26bb-d509-425e-88ce-f862b940817b · outbound

This paper cites Gleghorn.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Gleghorn

Reference 3

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T05:22:28.213373Z

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.

Observation 69abfa95-ae04-463d-a497-f151392fcaf8 · outbound

This paper cites Uniprot: the universal protein knowledgebase in 2023.Nucleic Acids Research, 51(D1):D523–D531, January 2023.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Uniprot: the universal protein knowledgebase in 2023.Nucleic Acids Research, 51(D1):D523–D531, January 2023

Reference 4

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:19.569760Z

Source-reported events for the cited work

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Observation cc0cf82a-064e-4be6-92fb-969e49adcb76 · outbound

This paper cites Estimating the annotation error rate of curated GO database sequence annotations.BMC Bioinformatics, 8:170, 2007.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Estimating the annotation error rate of curated GO database sequence annotations.BMC Bioinformatics, 8:170, 2007

Reference 5

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.729918Z

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.

Observation 75525131-f062-43dc-b630-15649b6ea164 · outbound

This paper cites Enzymap: Exploiting protein annotation for modeling and predicting ec number changes in uniprot/swiss-prot.PLOS ONE, 9(2):e89162, February 2014.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Enzymap: Exploiting protein annotation for modeling and predicting ec number changes in uniprot/swiss-prot.PLOS ONE, 9(2):e89162, February 2014

Reference 6

Resolution: malformed identifier; no resolver link, observed 2026-08-07T05:22:19.720094Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 0aa1dad0-2812-4e0c-9d84-fdd86f6a6942 · outbound

This paper cites Accelerating biocatalysis discovery with machine learning: A paradigm shift in enzyme engineering, discovery, and design.ACS Catalysis, 13(21):14454–14469, November 2023.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Accelerating biocatalysis discovery with machine learning: A paradigm shift in enzyme engineering, discovery, and design.ACS Catalysis, 13(21):14454–14469, November 2023

Reference 7

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.719568Z

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.

Observation baeac285-bf1e-48ad-89b5-f97f789d2f10 · outbound

This paper cites Millar-Haskell, Allyson M.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Millar-Haskell, Allyson M

Reference 8

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.713026Z

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.

Observation 6c505807-2d81-485c-bba4-1874f106a822 · outbound

This paper cites Edwards, Elias McComb, Jason P.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Edwards, Elias McComb, Jason P

Reference 9

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.707069Z

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.

Observation 76cadf5f-6b56-4199-9c84-cc7167aee6eb · outbound

This paper cites DeLong, Maitham A.

Diffusion Sequence Models for Enhanced Protein Representation and Generation DeLong, Maitham A

Reference 10

Resolution: verified exact; doi, observed 2026-08-07T05:22:28.207215Z

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.

Observation 9f786aa8-0a34-474c-beb6-fe6fc9a59cd2 · outbound

This paper cites Nelson, N’Dea Irvin-Choy, Matthew K.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Nelson, N’Dea Irvin-Choy, Matthew K

Reference 11

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.700411Z

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.

Observation 9aa08611-f599-426e-b269-7f4fe7edcc3f · outbound

This paper cites Gilbert and Jason P.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Gilbert and Jason P

Reference 12

Resolution: verified exact; raw_fallback, observed 2026-08-07T05:22:28.084955Z

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.

Observation 93abe646-f52e-462c-ba06-482f0b7bf7a6 · outbound

This paper cites Gleghorn.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Gleghorn

Reference 13

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.693858Z

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.

Observation 2702cd44-e972-4f13-827e-d63972d6f23e · outbound

This paper cites Roberts, Logan Hallee, and Chi Keung Lam.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Roberts, Logan Hallee, and Chi Keung Lam

Reference 14

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.687043Z

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.

Observation 950b4829-a576-4c1a-9c2a-effff7326b60 · outbound

This paper cites The potential of gamma secretase as a therapeutic target for cardiac diseases.J Pers Med, 11(12):1294, 2021.

Diffusion Sequence Models for Enhanced Protein Representation and Generation The potential of gamma secretase as a therapeutic target for cardiac diseases.J Pers Med, 11(12):1294, 2021

Reference 15

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.680734Z

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.

Observation 860fee61-9ba8-4317-b6ea-c17a30cd56f0 · outbound

This paper cites an unresolved cited work.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Unresolved cited work

Reference 16

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.674236Z

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.

Observation 36c68896-d1f3-4e83-8f82-5f1227100d4c · outbound

This paper cites The catalytic role of rubisco for in situ co2 recycling in escherichia coli.Frontiers in Bioengineering and Biotechnology, 8, November 2020.

Diffusion Sequence Models for Enhanced Protein Representation and Generation The catalytic role of rubisco for in situ co2 recycling in escherichia coli.Frontiers in Bioengineering and Biotechnology, 8, November 2020

Reference 17

Resolution: metadata mismatch; raw_fallback, observed 2026-08-07T05:22:28.014081Z

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.

Observation 530beadb-9368-44f6-b831-76f2f57ca7a3 · outbound

This paper cites Protein-based biological materials: Molecular design and artificial production.Chemical Reviews, 123(5):2049–2111, March 2023.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Protein-based biological materials: Molecular design and artificial production.Chemical Reviews, 123(5):2049–2111, March 2023

Reference 18

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.667243Z

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.

Observation a0666225-f5c0-4694-83cb-e2b5016a5c4e · outbound

This paper cites ProtTrans: Toward understanding the language of life through self-supervised learning.IEEE Trans Pattern Anal Mach Intell, 44 (10):7112–7127, 2022.

Diffusion Sequence Models for Enhanced Protein Representation and Generation ProtTrans: Toward understanding the language of life through self-supervised learning.IEEE Trans Pattern Anal Mach Intell, 44 (10):7112–7127, 2022

Reference 19

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:20.963990Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation cc74f997-ab5c-4540-9368-d8241ce7a82e · outbound

This paper cites Gleghorn.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Gleghorn

Reference 20

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.660139Z

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.

Observation 0155d60d-984c-4740-9220-e45cd556f667 · outbound

This paper cites CodonBERT: Large language models for mRNA design and optimization.bioRxiv, 2023.

Diffusion Sequence Models for Enhanced Protein Representation and Generation CodonBERT: Large language models for mRNA design and optimization.bioRxiv, 2023

Reference 21

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:21.153782Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 86b28f52-19bd-4596-af40-551b108e0e90 · outbound

This paper cites CodonBERT: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism.Bioinformatics, page btae330, 2024.

Diffusion Sequence Models for Enhanced Protein Representation and Generation CodonBERT: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism.Bioinformatics, page btae330, 2024

Reference 22

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:21.233317Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 84d11b7c-4d1c-4df8-a407-602eaec69655 · outbound

This paper cites Durrant, Armin W.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Durrant, Armin W

Reference 23

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.643763Z

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.

Observation b0c5b22e-bc4f-4f38-913a-03ddf9de9c9d · outbound

This paper cites ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling.

Diffusion Sequence Models for Enhanced Protein Representation and Generation ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling

Reference 24

Resolution: verified exact; local_arxiv, observed 2026-08-07T05:22:27.450271Z

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.

Observation 34a51f2e-acb4-4977-aac0-a53b4b6085a6 · outbound

This paper cites Durrant, Jerome Ku, Michael Poli, Greg Brockman, Daniel Chang, Gabriel A.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Durrant, Jerome Ku, Michael Poli, Greg Brockman, Daniel Chang, Gabriel A

Reference 25

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:21.477735Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation a5782868-1dca-46be-a7fd-7420fcc07ae6 · outbound

This paper cites Lawrence Zitnick, Jerry Ma, and Rob Fergus.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Lawrence Zitnick, Jerry Ma, and Rob Fergus

Reference 26

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:21.557776Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation d21e3fed-4aa5-4496-b2ac-06900a018aae · outbound

This paper cites Amini, Yisong Yue, Kevin K.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Amini, Yisong Yue, Kevin K

Reference 27

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.298605Z

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.

Observation 0df3b15d-cca8-4dda-90f9-6a26e8a861e7 · outbound

This paper cites Ankh: Optimized Protein Language Model Unlocks General-Purpose Modelling.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Ankh: Optimized Protein Language Model Unlocks General-Purpose Modelling

Reference 28

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:21.725863Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation b01295a1-381a-4fa0-a8da-ea1bde9c43e7 · outbound

This paper cites Vernon, Almer van der Sloot, Benjamin Schulz, Sarath Chandar, and Christopher James Langmead.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Vernon, Almer van der Sloot, Benjamin Schulz, Sarath Chandar, and Christopher James Langmead

Reference 30

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:21.873643Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 27186080-1df4-4ed6-8a53-c25bb934ce8d · outbound

This paper cites Siddiqui, Albert Gu, Michael D.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Siddiqui, Albert Gu, Michael D

Reference 31

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.158459Z

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.

Observation fcd429d2-ca06-4e9d-a8ca-c9b41a67c20a · outbound

This paper cites Large Language Diffusion Models.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Large Language Diffusion Models

Reference 32

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:22.008195Z

Source-reported events for the cited work

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Observation be989c85-2eac-49a0-ab7f-c13a4728f99d · outbound

This paper cites Evolutionary-scale prediction of atomic-level protein structure with a language model.Science, 379 (6637):1123–1130, March 2023.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Evolutionary-scale prediction of atomic-level protein structure with a language model.Science, 379 (6637):1123–1130, March 2023

Reference 33

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:22.056572Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation bb9fb219-f21d-462a-95fc-a3f238600805 · outbound

This paper cites Calia, Chance A.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Calia, Chance A

Reference 34

Resolution: verified exact; doi, observed 2026-08-07T05:22:28.196768Z

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.

Observation 911a2b0d-a033-4548-8362-a7b2b9eceaeb · outbound

This paper cites an unresolved cited work.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Unresolved cited work

Reference 35

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:22.224688Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation dc9dad0f-9b85-46bc-9039-30462a9db17f · outbound

This paper cites The omg dataset: An open metagenomic corpus for mixed-modality genomic language modeling.bioRxiv, August 2024.

Diffusion Sequence Models for Enhanced Protein Representation and Generation The omg dataset: An open metagenomic corpus for mixed-modality genomic language modeling.bioRxiv, August 2024

Reference 36

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:22.289104Z

Source-reported events for the cited work

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Observation 2c3b6cd6-bdf0-472f-8a3a-2a8a017d313a · outbound

This paper cites Gemma 2: Improving Open Language Models at a Practical Size.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Gemma 2: Improving Open Language Models at a Practical Size

Reference 37

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:22.382751Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 366b682f-b0ed-4f64-a99d-6307c4554dad · outbound

This paper cites Neural Combinatorial Optimization with Reinforcement Learning.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Neural Combinatorial Optimization with Reinforcement Learning

Reference 38

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:22.471203Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 85110463-ea5a-4f13-b6d1-d89dd81ce1f3 · outbound

This paper cites DeBERTaV3: Improving DeBERTa using ELECTRA-Style Pre-Training with Gradient-Disentangled Embedding Sharing.

Diffusion Sequence Models for Enhanced Protein Representation and Generation DeBERTaV3: Improving DeBERTa using ELECTRA-Style Pre-Training with Gradient-Disentangled Embedding Sharing

Reference 39

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:22.545068Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation b9890295-a074-412c-87b7-c2ccd7febe86 · outbound

This paper cites Smarter, Better, Faster, Longer: A Modern Bidirectional Encoder for Fast, Memory Efficient, and Long Context Finetuning and Inference.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Smarter, Better, Faster, Longer: A Modern Bidirectional Encoder for Fast, Memory Efficient, and Long Context Finetuning and Inference

Reference 40

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:22.615602Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 9fd75fce-0950-4296-9741-9fb2a207e872 · outbound

This paper cites SGDR: Stochastic Gradient Descent with Warm Restarts.

Diffusion Sequence Models for Enhanced Protein Representation and Generation SGDR: Stochastic Gradient Descent with Warm Restarts

Reference 41

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:22.726343Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 6f117678-bc04-4f27-9316-adb6fafc1e4d · outbound

This paper cites Decoupled Weight Decay Regularization.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Decoupled Weight Decay Regularization

Reference 42

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:22.854151Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation b3d444a0-99e2-433e-979a-70a802b18759 · outbound

This paper cites Algorithmic Capabilities of Random Transformers.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Algorithmic Capabilities of Random Transformers

Reference 43

Resolution: verified exact; local_arxiv, observed 2026-08-07T05:22:26.948583Z

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.

Observation aa91c55a-fbc3-4c9d-810e-3416a6c1d325 · outbound

This paper cites Training compute-optimal protein language models.bioRxiv, 2024.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Training compute-optimal protein language models.bioRxiv, 2024

Reference 44

Resolution: verified exact; doi, observed 2026-08-07T05:22:26.793088Z

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.

Observation f8ca1fd5-505d-4290-ae14-6fb205bef5c7 · outbound

This paper cites Esm cambrian: Revealing the mysteries of proteins with unsupervised learning.Evolutionary Scale Blog, December 2024.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Esm cambrian: Revealing the mysteries of proteins with unsupervised learning.Evolutionary Scale Blog, December 2024

Reference 45

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T05:22:28.190309Z

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.

Observation 9130ed50-b98a-4808-912f-29b30a407126 · outbound

This paper cites Gleghorn.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Gleghorn

Reference 46

Resolution: verified exact; doi, observed 2026-08-07T05:22:26.681384Z

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.

Observation 24c65ec4-fce3-41d8-b671-d4e740704824 · outbound

This paper cites Diffusion Language Models Are Versatile Protein Learners.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Diffusion Language Models Are Versatile Protein Learners

Reference 47

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:23.278913Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 47a84989-8769-4b40-ba81-1c3728280cb5 · outbound

This paper cites Attention Is All You Need.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Attention Is All You Need

Reference 48

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:23.341052Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 24944dc4-1c63-4b9d-b315-fc3757f9e6cf · outbound

This paper cites RoFormer: Enhanced Transformer with Rotary Position Embedding.

Diffusion Sequence Models for Enhanced Protein Representation and Generation RoFormer: Enhanced Transformer with Rotary Position Embedding

Reference 49

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:23.431986Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation e814403e-4d89-4d09-87a5-d883dd427b23 · outbound

This paper cites LoRA: Low-Rank Adaptation of Large Language Models.

Diffusion Sequence Models for Enhanced Protein Representation and Generation LoRA: Low-Rank Adaptation of Large Language Models

Reference 50

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:23.549959Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

Observation 3ef324b7-b32b-4f4c-8d5b-f100a75cbe7b · outbound

This paper cites an unresolved cited work.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Unresolved cited work

Reference 51

Resolution: unresolved; raw_fallback, observed 2026-08-07T05:22:28.182100Z

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.

Observation 571335e8-639c-4900-86d6-60be97540723 · outbound

This paper cites Divergence measures based on the shannon entropy.IEEE Transactions on Information Theory, 37(1):145–151, January 1991.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Divergence measures based on the shannon entropy.IEEE Transactions on Information Theory, 37(1):145–151, January 1991

Reference 52

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T05:22:28.175594Z

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.

Observation 04e1af43-9b24-49f3-a350-4a18a2163edc · outbound

This paper cites Introduction to information retrieval.Cambridge UP, 2009.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Introduction to information retrieval.Cambridge UP, 2009

Reference 53

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T05:22:28.169008Z

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Observation d9052c7a-97b7-4c5c-b0c5-22ebb3665d4d · outbound

This paper cites Gable, Tao Fang, Nadezhda T.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Gable, Tao Fang, Nadezhda T

Reference 54

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:23.775297Z

Source-reported events for the cited work

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Observation a570a944-c943-4955-80e1-881f802a7cd1 · outbound

This paper cites Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.Bioinformatics (Oxford, England), 22 (13):1658–1659, July 2006.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.Bioinformatics (Oxford, England), 22 (13):1658–1659, July 2006

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Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:23.847654Z

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Observation e144e8de-e650-47cd-8df0-f15f2a1cf613 · outbound

This paper cites Gleghorn.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Gleghorn

Reference 56

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:23.918419Z

Source-reported events for the cited work

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Observation 6c2521d7-97ec-48a1-8043-311b3be0df50 · outbound

This paper cites Ballard, Joshua Bambrick, Sebastian W.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Ballard, Joshua Bambrick, Sebastian W

Reference 57

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:23.988269Z

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Observation 4434fce3-38ce-4e31-9dc7-7dc702997c32 · outbound

This paper cites SaProt: Protein language modeling with structure-aware vocabulary.bioRxiv, 2023.

Diffusion Sequence Models for Enhanced Protein Representation and Generation SaProt: Protein language modeling with structure-aware vocabulary.bioRxiv, 2023

Reference 58

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:24.039163Z

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Observation 947a2718-41f3-4c94-b282-3c5e2d7611e5 · outbound

This paper cites Protokens: Probabilistic vocabulary for compact and informative encodings of all-atom protein structures.bioRxiv, page 2023.11.27.568722, July 2024.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Protokens: Probabilistic vocabulary for compact and informative encodings of all-atom protein structures.bioRxiv, page 2023.11.27.568722, July 2024

Reference 59

Resolution: verified exact; doi, observed 2026-08-07T05:22:26.529197Z

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Observation ba388abb-537f-445e-8927-b939ae8e5785 · outbound

This paper cites Khomtchouk.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Khomtchouk

Reference 60

Resolution: verified exact; doi, observed 2026-08-07T05:22:26.392312Z

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Observation d09a8043-c27a-4b87-9a80-753bfebddca6 · outbound

This paper cites Gleghorn, and Bohdan B.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Gleghorn, and Bohdan B

Reference 61

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:24.254681Z

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Observation d66fe8c3-aa6a-4fa6-98fd-792774f34779 · outbound

This paper cites Carter, Samuel Curtis, Claudia Emerson, Jeffrey Gray, Ian C.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Carter, Samuel Curtis, Claudia Emerson, Jeffrey Gray, Ian C

Reference 62

Resolution: verified fuzzy; raw_fallback, observed 2026-08-07T05:22:28.158525Z

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Observation a6b2d5e5-3c30-4046-bd8e-e6232bea109e · outbound

This paper cites an unresolved cited work.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Unresolved cited work

Reference 63

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:24.362032Z

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Observation 118c6da4-95e7-4a3c-bc83-74ac2e6ed991 · outbound

This paper cites Deep Learning using Rectified Linear Units (ReLU).

Diffusion Sequence Models for Enhanced Protein Representation and Generation Deep Learning using Rectified Linear Units (ReLU)

Reference 64

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:24.416161Z

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Observation 5bb7c414-346d-4fec-b8c8-725a1c83179b · outbound

This paper cites Improving neural networks by preventing co-adaptation of feature detectors.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Improving neural networks by preventing co-adaptation of feature detectors

Reference 65

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:24.490092Z

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Observation f3ee38f8-8bce-455c-8c8e-ed1496dbc5cc · outbound

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Diffusion Sequence Models for Enhanced Protein Representation and Generation Unresolved cited work

Reference 66

Resolution: verified exact; doi, observed 2026-08-07T05:22:26.251311Z

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Observation fae71bfb-1a9b-47f8-ad9e-ea375d89ba32 · outbound

This paper cites Sixty-five years of the long march in protein secondary structure prediction: the final stretch?Briefings in Bioinformatics, 19(3):482–494, May 2018.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Sixty-five years of the long march in protein secondary structure prediction: the final stretch?Briefings in Bioinformatics, 19(3):482–494, May 2018

Reference 67

Resolution: verified exact; doi, observed 2026-08-07T05:22:26.068403Z

Source-reported events for the cited work

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Observation 118ca2aa-88aa-43d5-b6e0-24fb714d61cc · outbound

This paper cites Ghamary, Laura Vinué, Brahm J.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Ghamary, Laura Vinué, Brahm J

Reference 68

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:24.667539Z

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Unavailable: canonical work link unavailable.

Observation a2131314-7c4e-4355-9bd2-e631507e9ace · outbound

This paper cites De novo design of high-affinity protein binders with AlphaProteo.

Diffusion Sequence Models for Enhanced Protein Representation and Generation De novo design of high-affinity protein binders with AlphaProteo

Reference 69

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:24.747354Z

Source-reported events for the cited work

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Observation 99d85c52-ebec-4b84-9dcf-965262de6feb · outbound

This paper cites Hutter, Fabian M.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Hutter, Fabian M

Reference 70

Resolution: verified exact; doi, observed 2026-08-07T05:22:25.885430Z

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Observation b05906c6-1c4c-403b-8818-bc3196190103 · outbound

This paper cites an unresolved cited work.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Unresolved cited work

Reference 71

Resolution: verified exact; doi, observed 2026-08-07T05:22:25.726649Z

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Observation 32545265-3de6-4b8e-aae2-19ed050f1b31 · outbound

This paper cites Desbien, John W.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Desbien, John W

Reference 72

Resolution: verified exact; doi, observed 2026-08-07T05:22:25.492649Z

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

Observation 5a60698b-692b-4f71-8693-155f0b824190 · outbound

This paper cites De novo design protein binders for mbp and gst tags.Biochemical and Biophysical Research Communications, 748:151322, February 2025.

Diffusion Sequence Models for Enhanced Protein Representation and Generation De novo design protein binders for mbp and gst tags.Biochemical and Biophysical Research Communications, 748:151322, February 2025

Reference 73

Resolution: metadata mismatch; raw_fallback, observed 2026-08-07T05:22:27.849857Z

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

Observation e2487525-3bdd-42f0-86ed-bd3d5406bf65 · outbound

This paper cites Hicks, Agnidipta Ghosh, Tristin A.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Hicks, Agnidipta Ghosh, Tristin A

Reference 74

Resolution: verified exact; doi, observed 2026-08-07T05:22:28.151857Z

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.

Observation cf75b812-87f2-4fc1-b1d2-17ac2c76190a · outbound

This paper cites an unresolved cited work.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Unresolved cited work

Reference 75

Resolution: unresolved; raw_fallback, observed 2026-08-07T05:22:28.145372Z

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Observation 0de04804-d7a5-4f3a-9628-e28a17ca44bc · outbound

This paper cites an unresolved cited work.

Diffusion Sequence Models for Enhanced Protein Representation and Generation Unresolved cited work

Reference 76

Resolution: unresolved; no resolver link, observed 2026-08-07T05:22:25.325006Z

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Observation 488b6a06-5c79-4b53-a894-86fafc67c79a · outbound

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Diffusion Sequence Models for Enhanced Protein Representation and Generation Unresolved cited work

Reference 2024

Resolution: verified exact; doi, observed 2026-08-07T05:22:27.740117Z

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Pith citing papers

Observation 7dfcc7df-7c19-44a3-90de-185395c623d9 · inbound

A Survey on Diffusion Language Models cites this paper.

A Survey on Diffusion Language Models Diffusion Sequence Models for Enhanced Protein Representation and Generation

Reference 127

Resolution: unresolved; no resolver link, observed 2026-08-05T20:15:24.647617Z

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Observation 09b943d3-37bc-45d3-b493-3b5910f21a8c · inbound

Dual Triangle Attention: Effective Bidirectional Attention Without Positional Embeddings cites this paper.

Dual Triangle Attention: Effective Bidirectional Attention Without Positional Embeddings Diffusion Sequence Models for Enhanced Protein Representation and Generation

Reference 8

Resolution: verified exact; arxiv_id, observed 2026-05-10T21:20:51.587555Z

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.