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Paper Citation Record · LEDGER

Transformers in Protein: A Survey

As of 10 August 2026, this Paper Citation Record lists 100 of 107 outbound references and 0 inbound Pith citation observations for arXiv:2505.20098.

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

pith.paper-citation-record.v1
2505.20098 v2

Coverage vector

measured 100 of 107 reference resolution

Typed states for the displayed outbound observations.

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measured 100 of 100 standing notices

One-hop event checks from named stored sources.

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measured 0 of 0 inbound itemization

Pith citing papers itemized under the disclosed page cap.

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measured 0 of 1 external citation measurements

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Source: cited_works

Reference resolution

100 of 107 outbound references displayed

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External citation measurements

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Outbound references

Observation 11f9741d-2bb3-468a-9498-7e053a227839 · outbound

This paper cites Attention is all you need,.

Transformers in Protein: A Survey Attention is all you need,

Reference 1

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Observation 153e6353-24bb-4412-8fd0-96baf27807a9 · outbound

This paper cites Bert: Pretraining of deep bidirectional transformers for language understanding,.

Transformers in Protein: A Survey Bert: Pretraining of deep bidirectional transformers for language understanding,

Reference 2

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Observation 2f5b2514-e1b9-42fa-abdc-085d177a2c42 · outbound

This paper cites Language Models are Few-Shot Learners.

Transformers in Protein: A Survey Language Models are Few-Shot Learners

Reference 3

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Observation a9a09f96-0851-4169-88b5-434d62c160d6 · outbound

This paper cites Pmanet: Malicious url detection via post-trained language model guided multi-level feature attention network,.

Transformers in Protein: A Survey Pmanet: Malicious url detection via post-trained language model guided multi-level feature attention network,

Reference 4

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Observation 3d4d026b-2edb-4b24-b5b5-94803bff3829 · outbound

This paper cites Vul- lmgnns: Fusing language models and online-distilled graph neural networks for code vulnerability detection,.

Transformers in Protein: A Survey Vul- lmgnns: Fusing language models and online-distilled graph neural networks for code vulnerability detection,

Reference 5

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Observation 090e8977-48b0-4283-bb5f-3aa03b0c2eac · outbound

This paper cites Ethereum fraud detection via joint transaction language model and graph representation learning,.

Transformers in Protein: A Survey Ethereum fraud detection via joint transaction language model and graph representation learning,

Reference 6

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Observation cbc9fc81-2788-449c-9928-8de7f178a3bc · outbound

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

Transformers in Protein: A Survey Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences,

Reference 7

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Observation ec6c8986-89f2-46a0-9ea0-38ffaca4f5ae · outbound

This paper cites Highly accurate protein structure prediction with alphafold,.

Transformers in Protein: A Survey Highly accurate protein structure prediction with alphafold,

Reference 8

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Observation 1f10aad7-8ae2-4257-b491-645d10d96d31 · outbound

This paper cites Evaluating protein transfer learning with tape,.

Transformers in Protein: A Survey Evaluating protein transfer learning with tape,

Reference 9

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Observation 67c759d0-de49-469b-9b02-38d3efa00956 · outbound

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

Transformers in Protein: A Survey Evolutionary velocity with protein language models predicts evolutionary dynamics of diverse proteins,

Reference 10

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Observation 541af0e6-d586-43b3-b98f-ad7e4843aedc · outbound

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

Transformers in Protein: A Survey Language models of protein sequences at the scale of evolution enable accurate structure prediction,

Reference 11

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Observation bd9d9d93-3e98-4a94-9062-b22a947bb7dc · outbound

This paper cites Deep learning in bioinformatics,.

Transformers in Protein: A Survey Deep learning in bioinformatics,

Reference 12

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Observation cb1a694b-c43c-4ac8-888a-2191a3a807af · outbound

This paper cites Machine learning solutions for predicting protein–protein interactions,.

Transformers in Protein: A Survey Machine learning solutions for predicting protein–protein interactions,

Reference 13

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Observation a63d47f9-65a1-47a2-9bd5-5557f04428d6 · outbound

This paper cites Unified rational protein engineering with sequence-based deep representation learning,.

Transformers in Protein: A Survey Unified rational protein engineering with sequence-based deep representation learning,

Reference 14

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Observation fadd9d83-7fd7-4c6c-957b-24875e26299e · outbound

This paper cites Protein- bert: a universal deep-learning model of protein sequence and function,.

Transformers in Protein: A Survey Protein- bert: a universal deep-learning model of protein sequence and function,

Reference 15

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Observation 5b67f996-2976-4c25-ace5-fe44a74258ff · outbound

This paper cites Deep learning in proteomics,.

Transformers in Protein: A Survey Deep learning in proteomics,

Reference 16

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Observation 03432406-c26b-4d04-94ed-8ec244a6fc0f · outbound

This paper cites Transformer- based deep learning for predicting protein properties in the life sci- ences,.

Transformers in Protein: A Survey Transformer- based deep learning for predicting protein properties in the life sci- ences,

Reference 17

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Observation 726c8010-dff6-4829-bad3-529769afefb9 · outbound

This paper cites Machine learning: its challenges and opportunities in plant system biology,.

Transformers in Protein: A Survey Machine learning: its challenges and opportunities in plant system biology,

Reference 18

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Observation 67a5439a-fc11-471a-9aa3-2fe1e8e56d82 · outbound

This paper cites Artificial intelligence in the prediction of protein–ligand interactions: recent advances and future directions,.

Transformers in Protein: A Survey Artificial intelligence in the prediction of protein–ligand interactions: recent advances and future directions,

Reference 19

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Observation abc0a439-80a7-4c82-856e-1dfffd390980 · outbound

This paper cites Roberta: A robustly optimized bert pretraining approach,.

Transformers in Protein: A Survey Roberta: A robustly optimized bert pretraining approach,

Reference 20

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Observation 66a8fca6-a8c8-4f2b-96db-8122db9aa916 · outbound

This paper cites Linformer: Self- attention with linear complexity,.

Transformers in Protein: A Survey Linformer: Self- attention with linear complexity,

Reference 21

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Observation b9d15f7a-2b29-4276-a802-79e344bfc57d · outbound

This paper cites An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale.

Transformers in Protein: A Survey An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale

Reference 22

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Observation d1a97527-1b71-4e8d-853a-965c416ec943 · outbound

This paper cites On the turing completeness of modern neural network architectures,.

Transformers in Protein: A Survey On the turing completeness of modern neural network architectures,

Reference 23

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Observation edaa7f6f-29ef-46d4-8212-50afbc622043 · outbound

This paper cites On the relationship between self-attention and convolutional layers,.

Transformers in Protein: A Survey On the relationship between self-attention and convolutional layers,

Reference 24

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Observation 149f5466-658c-4ea0-93ff-ac0c19101a84 · outbound

This paper cites Deformable convolutional networks,.

Transformers in Protein: A Survey Deformable convolutional networks,

Reference 25

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Observation d9416745-fb67-4044-b307-5a2050200300 · outbound

This paper cites Prottrans: Towards cracking the language of life’s code through self-supervised deep learning and high performance computing,.

Transformers in Protein: A Survey Prottrans: Towards cracking the language of life’s code through self-supervised deep learning and high performance computing,

Reference 26

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Observation ecb48275-bb3d-4bad-8174-e91806388abc · outbound

This paper cites PeptideBERT: A Language Model based on Transformers for Peptide Property Prediction.

Transformers in Protein: A Survey PeptideBERT: A Language Model based on Transformers for Peptide Property Prediction

Reference 28

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Observation 8aacccda-8aca-4e94-8b81-f5c2e0c22272 · outbound

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

Transformers in Protein: A Survey Language models of protein sequences at the scale of evolution enable accurate structure prediction,

Reference 29

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Transformers in Protein: A Survey Msa transformer,

Reference 30

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Transformers in Protein: A Survey Endowing Protein Language Models with Structural Knowledge

Reference 31

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Transformers in Protein: A Survey Alberts, D

Reference 32

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Transformers in Protein: A Survey Prediction of protein conformation,

Reference 33

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This paper cites Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins,.

Transformers in Protein: A Survey Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins,

Reference 35

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Transformers in Protein: A Survey Modeling aspects of the language of life through transfer-learning protein sequences,

Reference 36

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Transformers in Protein: A Survey Tm-align: a protein structure alignment algorithm based on the tm-score,

Reference 39

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This paper cites Prottrans: towards cracking the language of life’s code through self-supervised learning,.

Transformers in Protein: A Survey Prottrans: towards cracking the language of life’s code through self-supervised learning,

Reference 40

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Transformers in Protein: A Survey The protein-folding problem, 50 years on,

Reference 41

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This paper cites Protein folding and misfolding,.

Transformers in Protein: A Survey Protein folding and misfolding,

Reference 42

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Transformers in Protein: A Survey Goap: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction,

Reference 48

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verified fuzzy
raw_fallback, observed 2026-08-07T14:03:25.018365Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:07.038041Z digest=sha256:b0bbe473ef9338849dfa38d7073379156d78f86b568dddee1e998ef23315de67

Observation d4d6aa8c-7305-4efb-9537-7e651be703f5 · outbound

This paper cites Protein secondary structure prediction based on position- specific scoring matrices,.

Transformers in Protein: A Survey Protein secondary structure prediction based on position- specific scoring matrices,

Reference 49

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:24.826837Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:07.151872Z digest=sha256:049dd917aa982f8c407fa06bbf20740a6618880e56f06eaed93334b20432f44e

Observation a66d5f8e-cea0-4994-9b36-7efaa7e99d9e · outbound

This paper cites Prediction of protein secondary structure at better than 70% accuracy,.

Transformers in Protein: A Survey Prediction of protein secondary structure at better than 70% accuracy,

Reference 50

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:27.120378Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:07.218288Z digest=sha256:4afa96bef7ecb4835ba53fb817b2ca3ccf7289a99ec0aa9c3bae2aa3f87d9a90

Observation 20f0a81d-c60e-4240-b9ba-b695ab249108 · outbound

This paper cites Protein-folding dynamics: overview of molecular simulation techniques,.

Transformers in Protein: A Survey Protein-folding dynamics: overview of molecular simulation techniques,

Reference 51

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:24.672367Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:07.302444Z digest=sha256:6ad22b10b3add89b339a7f9e8013cd922ba0e219706c1caa5ec33d41850abba1

Observation 7dbea9a1-6407-467e-aaad-16c7c698ba78 · outbound

This paper cites Protein modeling by e-mail,.

Transformers in Protein: A Survey Protein modeling by e-mail,

Reference 53

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:24.316687Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:07.485993Z digest=sha256:5e117c07133c3bc3c7b72c96d043a49a2972172663dbe219063a0c5266d01a56

Observation 39513a6c-cb9e-4960-af97-9422230166ae · outbound

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

Transformers in Protein: A Survey Language models of protein sequences at the scale of evolution enable accurate structure prediction,

Reference 57

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:23.935691Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:07.781130Z digest=sha256:a4be052f7c12c43987f7e9396ea42ae40e11b46076a05221236fca656d4a5df5

Observation 3b472261-bf11-4e39-a63d-78e394de49bb · outbound

This paper cites Suppression of alpha-band power underlies exogenous attention to emotional distractors,.

Transformers in Protein: A Survey Suppression of alpha-band power underlies exogenous attention to emotional distractors,

Reference 58

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:23.706325Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:07.848752Z digest=sha256:ff91db59e9e005df1a2f4723f8d5bda86ceabd10384350b15746cc93ece79c29

Observation 566780d4-7a88-4014-a5a4-4f14e81b5dde · outbound

This paper cites Improved protein structure prediction using potentials from deep learning,.

Transformers in Protein: A Survey Improved protein structure prediction using potentials from deep learning,

Reference 60

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:23.543272Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:07.962479Z digest=sha256:6c39e597ccc88fd2214c4813b14d9409bb4d13a34b213da637a059aa60df10a6

Observation b669394d-c0e7-4567-bc20-2234f7734254 · outbound

This paper cites Evaluating protein transfer learning with tape,.

Transformers in Protein: A Survey Evaluating protein transfer learning with tape,

Reference 61

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:23.314244Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.015387Z digest=sha256:a124e87c6c7eff02aa51ec9849a24ba3756920f867aed05aec0cdd560324274f

Observation a19f3cdb-fcbf-445e-8a85-76fef5604b8a · outbound

This paper cites A Protein Structure Prediction Approach Leveraging Transformer and CNN Integration.

Transformers in Protein: A Survey A Protein Structure Prediction Approach Leveraging Transformer and CNN Integration

Reference 62

Resolution
verified exact
local_arxiv, observed 2026-08-07T14:03:16.412661Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.060222Z digest=sha256:d98c79ba4b1303ed90dc3b372d0aa2b88b38d9fc57a6ecb7a448487f0f1e4102

Observation 6b6543db-9c39-4ebd-8861-29c1526b9d74 · outbound

This paper cites Protein- bert: a universal deep-learning model of protein sequence and function,.

Transformers in Protein: A Survey Protein- bert: a universal deep-learning model of protein sequence and function,

Reference 63

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:23.026562Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.132680Z digest=sha256:af42d1de4a47da6aeb397c997194f968551b020a923561e6c80489ffc90055c3

Observation e5b59e50-b941-4f07-b0b6-f86f3de997fd · outbound

This paper cites Trans-morfs: A disordered protein predictor based on the transformer architecture,.

Transformers in Protein: A Survey Trans-morfs: A disordered protein predictor based on the transformer architecture,

Reference 64

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:22.891967Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.181838Z digest=sha256:9acd6b7697b0e68e995ac6049a5a2ab197b3ebe5d496f273394258f6a9347cc5

Observation b7a334db-2aed-4622-89e5-e90d00cfd93a · outbound

This paper cites ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction.

Transformers in Protein: A Survey ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction

Reference 65

Resolution
unresolved
no resolver link, observed 2026-08-07T14:03:08.262064Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-07T14:03:08.262064Z digest=sha256:a9bda3d03ee2dcf78f78d5a84502e3b0632c8e39a01dc6b49ebf2dadac0f11a9

Observation 11484f55-03b6-4dab-b0be-7aa5f1194a35 · outbound

This paper cites Ramsundar, P.

Transformers in Protein: A Survey Ramsundar, P

Reference 66

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:22.723642Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.331914Z digest=sha256:0f229d94c02d3e3c5fa4ded1d3fac87f0778e8ab86f54cd800a08343dd52002f

Observation af2ce176-96ba-4f34-bbe5-850a6f28a3ae · outbound

This paper cites High-resolution de novo structure prediction from primary sequence,.

Transformers in Protein: A Survey High-resolution de novo structure prediction from primary sequence,

Reference 67

Resolution
verified exact
doi, observed 2026-08-07T14:03:15.888449Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.388821Z digest=sha256:641bcc06d140b2482c8979b03fb25f314ac03404da12d9374683857bf9c9c622

Observation 3e2a582c-01a8-4f0d-acd3-b49327338ef5 · outbound

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

Transformers in Protein: A Survey Protgpt2 is a deep unsupervised language model for protein design,

Reference 68

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:22.517669Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.460803Z digest=sha256:e6159fa278f7b97e95f34a90adf3676a87a93dbac50924355bc21b22e4f43ff6

Observation 17f62304-312b-4645-822e-c618c7c3984b · outbound

This paper cites Large language models generate functional protein sequences across diverse families,.

Transformers in Protein: A Survey Large language models generate functional protein sequences across diverse families,

Reference 69

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:22.352202Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.538032Z digest=sha256:1cc566d0e1e43553962728d85dce7341cc05a5dac62bf7eabbdf875ba2b2af7c

Observation 2b83b2bc-12d4-4801-ab1d-6ebf547bb60d · outbound

This paper cites De novo design of protein structure and function with rfdiffusion,.

Transformers in Protein: A Survey De novo design of protein structure and function with rfdiffusion,

Reference 70

Resolution
unresolved
no resolver link, observed 2026-08-07T14:03:08.593974Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-07T14:03:08.593974Z digest=sha256:8c62418e2ac59bac6fa4d1da959de0fe8802f0a88ae8c6339402ecce6046bfc7

Observation 9e84ba09-7c22-4b6d-9030-76ad1fee4f31 · outbound

This paper cites Mftrans: A multi-feature transformer network for protein secondary structure prediction,.

Transformers in Protein: A Survey Mftrans: A multi-feature transformer network for protein secondary structure prediction,

Reference 72

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:21.916212Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.712012Z digest=sha256:f9006f8b77c46a516d4588bf9d3c8a879aae64e740f8d57e899b0eec76955061

Observation 509e0b86-24b5-40ac-a3b2-af81106d7fe1 · outbound

This paper cites Transconv: Convolution-infused transformer for protein secondary structure prediction,.

Transformers in Protein: A Survey Transconv: Convolution-infused transformer for protein secondary structure prediction,

Reference 73

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:21.729242Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.781480Z digest=sha256:0ab064fb5ac734f63342547cf823dcdc1e3b7f4e93ba67ad9b4ce393e3c05717

Observation 58ebcf24-a840-4a10-9328-e230b9efd3d9 · outbound

This paper cites De novo atomic protein structure modeling for cryoem density maps using 3d transformer and hmm,.

Transformers in Protein: A Survey De novo atomic protein structure modeling for cryoem density maps using 3d transformer and hmm,

Reference 74

Resolution
verified exact
doi, observed 2026-08-07T14:03:15.651075Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.846323Z digest=sha256:705d1e80b64cb4e4d6ce03e19e8775398f07143a1bad345005f9f20d92d39162

Observation 2eb72f34-a157-481a-ab92-92356814afe9 · outbound

This paper cites A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation,.

Transformers in Protein: A Survey A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation,

Reference 75

Resolution
verified exact
doi, observed 2026-08-07T14:03:15.363896Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.910694Z digest=sha256:ceab3334c3eac505d7f2d8e446bc850405a434a246a78cecad60fa10ef32c7a3

Observation 3ffbd77e-f306-48d3-9915-4ad3da1dd2f9 · outbound

This paper cites Gpcrpred: an svm-based method for prediction of families and subfamilies of g-protein coupled receptors,.

Transformers in Protein: A Survey Gpcrpred: an svm-based method for prediction of families and subfamilies of g-protein coupled receptors,

Reference 76

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:21.529936Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:08.980470Z digest=sha256:8ffcf0a4c62d03141b7721e7876053adbfe56a43e5e605b76af38131a45cb71d

Observation b01c79f0-8e6a-4b0f-9f83-8f44638e1f7c · outbound

This paper cites Multi-scale deep learning for the imbalanced multi-label protein subcellular localization prediction based on im- munohistochemistry images,.

Transformers in Protein: A Survey Multi-scale deep learning for the imbalanced multi-label protein subcellular localization prediction based on im- munohistochemistry images,

Reference 77

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:21.364194Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:09.153144Z digest=sha256:a0a9e7023cf5f7a96cd7693e45351ae410608f97d9167b6ec8bc410cfe5057d1

Observation 4c72bd69-6b51-40b4-82f0-1c107e93f1d1 · outbound

This paper cites Prog-sol: Predicting protein solubility using protein embeddings and dual-graph convolutional networks,.

Transformers in Protein: A Survey Prog-sol: Predicting protein solubility using protein embeddings and dual-graph convolutional networks,

Reference 78

Resolution
verified exact
doi, observed 2026-08-07T14:03:14.923769Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:09.208982Z digest=sha256:f9f7c12f72a60b83745440839b398ed2bbc5c46d7408cb2fc9e5d6d3643e33ab

Observation f7d1767f-cf51-49ea-84bb-7adabd13f9a3 · outbound

This paper cites Deep-probind: Bind- ing protein prediction with transformer-based deep learning model,.

Transformers in Protein: A Survey Deep-probind: Bind- ing protein prediction with transformer-based deep learning model,

Reference 79

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:21.190261Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:09.283462Z digest=sha256:6aab488748ce21577631b6e0edacc3388a58f70866cef250cd2aa3e4091416f4

Observation 58a2d6e2-2d30-4b74-a47f-f5515ea23450 · outbound

This paper cites Insights into the inner workings of transformer models for protein function prediction,.

Transformers in Protein: A Survey Insights into the inner workings of transformer models for protein function prediction,

Reference 80

Resolution
verified exact
doi, observed 2026-08-07T14:03:14.742427Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:09.359999Z digest=sha256:c0e3dcc8b4038c376fdb075a5e0bf81dfea45431f16a2523979a893fd0431b8f

Observation 05be466a-50f3-454f-9861-e34b23e4c80e · outbound

This paper cites Segt-go: a graph transformer method based on ppi serialization and explanatory artificial intelligence for protein function prediction,.

Transformers in Protein: A Survey Segt-go: a graph transformer method based on ppi serialization and explanatory artificial intelligence for protein function prediction,

Reference 81

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:20.984237Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:09.440718Z digest=sha256:8e9c5ea701e8a014c0d7d0360c4b2fafcf54c74d4327e5beac11d7ab070d39f1

Observation 35fb3eee-b421-4fd4-900e-4b4c3c7eb2fb · outbound

This paper cites Integrating transformers and automl for protein function prediction,.

Transformers in Protein: A Survey Integrating transformers and automl for protein function prediction,

Reference 82

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:20.837485Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:09.509224Z digest=sha256:21b3e0f2255a420c04b14b2cc947bfcb64def189c0ea85e9b34b22eb623726c9

Observation 36a79ae2-e10c-47b4-96a0-53e33de61c8c · outbound

This paper cites Deepppi: boosting prediction of protein–protein interactions with deep neural networks,.

Transformers in Protein: A Survey Deepppi: boosting prediction of protein–protein interactions with deep neural networks,

Reference 83

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:20.675614Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:09.604746Z digest=sha256:269ef5b79c5678fc6d515d20f221d57692d8a0003d8fe6388c33ffbd91ec5cde

Observation 5e388b23-5ee9-416a-b5a4-bf6179981660 · outbound

This paper cites Graphtrans: a software system for network conversions for simulation, structural analysis, and graph operations,.

Transformers in Protein: A Survey Graphtrans: a software system for network conversions for simulation, structural analysis, and graph operations,

Reference 84

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:22.124288Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:09.720351Z digest=sha256:be9b5a865f8c0c0e763715da8cd822f60faaaa3237d37104b19530658749b9f1

Observation 32ed5314-19e9-40c4-8a07-c93c325096c1 · outbound

This paper cites Gact-ppis: Prediction of protein-protein interaction sites based on graph structure and transformer network,.

Transformers in Protein: A Survey Gact-ppis: Prediction of protein-protein interaction sites based on graph structure and transformer network,

Reference 85

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:20.457893Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:09.816536Z digest=sha256:80af520cbb8b0540d5b1774fc1f8451d21758b479c82de10318decca819459d8

Observation 1086db35-16c7-4d12-8e9d-7d0026f45ead · outbound

This paper cites Tranp-b-site: A transformer enhanced method for prediction of binding sites of protein-protein interactions,.

Transformers in Protein: A Survey Tranp-b-site: A transformer enhanced method for prediction of binding sites of protein-protein interactions,

Reference 86

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:20.253915Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:09.887645Z digest=sha256:c5ec96fdc00eb94bfb4ce25f1c747459f93d44ca9cbca9ee088bf69fbbc8bc3f

Observation e48d37ec-5e6f-49c8-89d8-f649a50b3ab6 · outbound

This paper cites Tuna: An uncertainty- aware transformer model for sequence-based protein–protein interaction prediction,.

Transformers in Protein: A Survey Tuna: An uncertainty- aware transformer model for sequence-based protein–protein interaction prediction,

Reference 87

Resolution
unresolved
no resolver link, observed 2026-08-07T14:03:09.972916Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-07T14:03:09.972916Z digest=sha256:831e89963421b5e7a91e6e2e65bb3f4cc8d77c9e6e5a88da9ec7f3729d3cd190

Observation 32dc7779-c7b7-4af7-b70a-e44b07e35594 · outbound

This paper cites Predicting protein-protein binding affinity with deep learning: A comparative analysis of cnn and transformer models,.

Transformers in Protein: A Survey Predicting protein-protein binding affinity with deep learning: A comparative analysis of cnn and transformer models,

Reference 88

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:20.026045Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:10.089363Z digest=sha256:e8a16154b357cd192e2ee5109f2886665f5f25ce34c95a85b93226f696a8e62f

Observation 07d8e7d2-c562-4a2b-ab64-11ef1557cf97 · outbound

This paper cites A review of transformers in drug discovery and beyond,.

Transformers in Protein: A Survey A review of transformers in drug discovery and beyond,

Reference 89

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:19.833901Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:10.169600Z digest=sha256:bbee5be4c328c81fac3f68a721851bdd170389c89fbef0dc69c58b02c85cd71b

Observation ff5502d0-a63a-4327-bea0-0be01e7a034c · outbound

This paper cites Mol-bert: An effective molecular representation with bert for molecular property prediction,.

Transformers in Protein: A Survey Mol-bert: An effective molecular representation with bert for molecular property prediction,

Reference 90

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:19.619012Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

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Observation 2baa566d-23c5-4480-be12-a6a5ce5e3f9a · outbound

This paper cites Molecular generative graph neural networks for drug discovery,.

Transformers in Protein: A Survey Molecular generative graph neural networks for drug discovery,

Reference 91

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:19.438610Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:10.419312Z digest=sha256:56ffaafcd6dafeb34bc95068ff4567fb12ce089bf8049ddf91796381de8ebf34

Observation 4489ff67-aa95-4854-887e-fa150d1feddb · outbound

This paper cites Integrating transformer-based language model for drug discovery,.

Transformers in Protein: A Survey Integrating transformer-based language model for drug discovery,

Reference 93

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:19.247088Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:10.709283Z digest=sha256:59e4ba832a561b8711e116557d943c58258f5a4e3edb3bcdd4f3686ca01676ae

Observation 1d0c8684-1a9d-414b-8c8c-0083a8808a68 · outbound

This paper cites Integrating transformers and many-objective optimization for drug design,.

Transformers in Protein: A Survey Integrating transformers and many-objective optimization for drug design,

Reference 94

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:19.064622Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:10.801603Z digest=sha256:e15956d2f3bfc5331e5016df575533247cf39efe2afa3b866169386d04d50858

Observation 81764d03-a23c-4a9c-8e3a-308eeb2466aa · outbound

This paper cites Transformers and large language models for chemistry and drug discovery,.

Transformers in Protein: A Survey Transformers and large language models for chemistry and drug discovery,

Reference 95

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:18.813725Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:10.894662Z digest=sha256:8ca589b96138d0aacf9237adf6a803e2229cc5a7e44f2874b3e3902774fce104

Observation 664b84b4-39ec-44ab-8381-4aea678813aa · outbound

This paper cites Sspro/accpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity,.

Transformers in Protein: A Survey Sspro/accpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity,

Reference 96

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:24.481228Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:10.966982Z digest=sha256:483b6aa3df0265017f79563fb1d88b1cb2fc4c23286c1251bca5055ebd5351ec

Observation 19205735-2dad-4908-9e8e-cc0768992f2f · outbound

This paper cites Uniprot: the universal protein knowledgebase in 2021,.

Transformers in Protein: A Survey Uniprot: the universal protein knowledgebase in 2021,

Reference 97

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:25.320178Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:11.097147Z digest=sha256:2b05a78aa1c940f90ca169d468ce735fdf8bc4453f97640e949e7c2394c44f9a

Observation ea613f91-af85-4546-93ee-eb9491a7c1ef · outbound

This paper cites Mmseqs2 enables sensitive protein sequence searching for the analysis of massive data sets,.

Transformers in Protein: A Survey Mmseqs2 enables sensitive protein sequence searching for the analysis of massive data sets,

Reference 98

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:25.709269Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:11.162288Z digest=sha256:a85ce5ef03608e4d4dc860e168481b8a578a39fa61396881547d5dabfa170d13

Observation 7c7300b7-64d2-4927-ab96-5a4f24587eed · outbound

This paper cites Confold2: improved contact-driven ab initio protein structure modeling,.

Transformers in Protein: A Survey Confold2: improved contact-driven ab initio protein structure modeling,

Reference 99

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:25.162050Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

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Observation e74dcf80-3079-4e48-bb98-598c1a471000 · outbound

This paper cites Language models enable zero-shot prediction of the effects of mutations on protein function,.

Transformers in Protein: A Survey Language models enable zero-shot prediction of the effects of mutations on protein function,

Reference 101

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:18.416264Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

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Observation 13e188e6-4851-4a09-a590-76eeef4fd645 · outbound

This paper cites Energy and policy con- siderations for modern deep learning research,.

Transformers in Protein: A Survey Energy and policy con- siderations for modern deep learning research,

Reference 102

Resolution
unresolved
no resolver link, observed 2026-08-07T14:03:11.547056Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-07T14:03:11.547056Z digest=sha256:36c46043040c7ccb322e56fb2f09b06b15503f4f54663883a48cf682a9bba42e

Observation 3b0323c1-b835-4478-ba94-ed9fa7843598 · outbound

This paper cites Deep learning in proteomics,.

Transformers in Protein: A Survey Deep learning in proteomics,

Reference 103

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:18.240507Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:11.604904Z digest=sha256:76b89f62d9f2ad68ff1b73248b9b3e0c3cb9df37ebde7256a63a90dc68b21c27

Observation 011ba748-bb11-4b40-88f6-4c3b9c138ca6 · outbound

This paper cites Deep multi-view learning methods: A review,.

Transformers in Protein: A Survey Deep multi-view learning methods: A review,

Reference 104

Resolution
verified fuzzy
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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:11.750672Z digest=sha256:289e02e41991b91f21a39ae716689c151036cab74d337042a2d90823aa8993c5

Observation dc50b9cb-37df-44a5-950c-48b896926721 · outbound

This paper cites Towards A Rigorous Science of Interpretable Machine Learning.

Transformers in Protein: A Survey Towards A Rigorous Science of Interpretable Machine Learning

Reference 106

Resolution
unresolved
no resolver link, observed 2026-08-07T14:03:12.045481Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-07T14:03:12.045481Z digest=sha256:51b2e10fb85c41010ae6859686549de66fc4ff741af169d61b4f92f64a121686

Observation 606b836a-83dc-4743-af30-738b150c4f93 · outbound

This paper cites Explainable Artificial Intelligence: Understanding, Visualizing and Interpreting Deep Learning Models.

Transformers in Protein: A Survey Explainable Artificial Intelligence: Understanding, Visualizing and Interpreting Deep Learning Models

Reference 107

Resolution
unresolved
no resolver link, observed 2026-08-07T14:03:12.178432Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-07T14:03:12.178432Z digest=sha256:cfb198b9056f67a9d2ac09ac601c518828b5db73cc3b0c15192a3f5b7fe731e3

Observation f5e44775-b372-4eaa-9dcf-8680729f41e5 · outbound

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

Transformers in Protein: A Survey Transformer protein language models are unsupervised structure learners,

Reference 108

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:18.634300Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:12.303384Z digest=sha256:2469841bcb12d7439474913ef79e5a081b09c7f410d72b0154106a74ff9cea3b

Observation 24bfbff4-4e82-4449-a1f5-576b491f2131 · outbound

This paper cites Protein tertiary structure prediction and refinement using deep learning and rosetta in casp14,.

Transformers in Protein: A Survey Protein tertiary structure prediction and refinement using deep learning and rosetta in casp14,

Reference 109

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:17.722242Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:12.420865Z digest=sha256:2821b0bad9cc4454d520aae61aa925becad0a7f0b7ae4bc869376f219f08fe3f

Observation 93f1b046-098d-472a-a6d8-66a12ec95006 · outbound

This paper cites Deepaffinity: interpretable deep learning of compound–protein affinity through unified recurrent and convolutional neural networks,.

Transformers in Protein: A Survey Deepaffinity: interpretable deep learning of compound–protein affinity through unified recurrent and convolutional neural networks,

Reference 110

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:17.518518Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:12.509487Z digest=sha256:4e081f9fc05bf94235081d2c195c421f644af74e9731608e948b47dc21d344e2

Observation 783a8155-2014-4996-a1b2-c039bd54024f · outbound

This paper cites Grandmaster level in starcraft ii using multi-agent reinforcement learning,.

Transformers in Protein: A Survey Grandmaster level in starcraft ii using multi-agent reinforcement learning,

Reference 111

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:17.331316Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:12.664339Z digest=sha256:42a59b03948a61c4181db7b6515fe1c59f607d7496885e7f9326235b01a6bc54

Observation 7ba9d5bb-e8b4-4b82-86bd-cc8ef6b67cd0 · outbound

This paper cites Toward a shared vision for cancer genomic data,.

Transformers in Protein: A Survey Toward a shared vision for cancer genomic data,

Reference 112

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:17.131373Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:12.838435Z digest=sha256:0d47892d15be5ca35e31d3609fb6e0eb1bc531404a1c4b1c6c1eedbc40e42e8d

Observation 203cac42-87ae-4618-98cc-09752ef89b2a · outbound

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

Transformers in Protein: A Survey Prottrans: Toward understanding the language of life through self-supervised learning,

Reference 114

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:24.151134Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

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Observation 70a97fb9-a971-476c-be20-39a89c9e819a · outbound

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

Transformers in Protein: A Survey Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences,

Reference 115

Resolution
unresolved
no resolver link, observed 2026-08-07T14:03:13.225771Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

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Observation 5b9238b1-ee7e-43b0-9a14-05faa089b9c7 · outbound

This paper cites Accurate prediction of protein structures and interactions using a three- track neural network,.

Transformers in Protein: A Survey Accurate prediction of protein structures and interactions using a three- track neural network,

Reference 116

Resolution
unresolved
no resolver link, observed 2026-08-07T14:03:13.362425Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-07T14:03:13.362425Z digest=sha256:4e15d93c3de15d3c1c2e6f79e8e975fc294db02934730da89005984fac60d4ef

Observation 321c2afe-540e-4991-a851-571bebac858d · outbound

This paper cites Molmol: a program for dis- play and analysis of macromolecular structures,.

Transformers in Protein: A Survey Molmol: a program for dis- play and analysis of macromolecular structures,

Reference 117

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:25.521265Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:13.462283Z digest=sha256:b3d72e77012d5e0ab8c130976c09db077f7c27507bf7a6ebeae0f5931621d683

Observation f81f4e42-28fc-4085-9b55-caebfb4a2618 · outbound

This paper cites Transformer architecture and attention mech- anisms in genome data analysis: a comprehensive review,.

Transformers in Protein: A Survey Transformer architecture and attention mech- anisms in genome data analysis: a comprehensive review,

Reference 118

Resolution
verified fuzzy
raw_fallback, observed 2026-08-07T14:03:16.884822Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-10T06:31:04.303077+00:00.

source=pdf_text observed=2026-08-07T14:03:13.623313Z digest=sha256:7d220ec46d06e8b13187667d85c6edcf3f9a1a930a41929c35d1c8df3d1b5fc8

Observation dd09bc71-1e03-468a-a493-56a1e19628a3 · outbound

This paper cites A Unified Approach to Interpreting Model Predictions.

Transformers in Protein: A Survey A Unified Approach to Interpreting Model Predictions

Reference 119

Resolution
unresolved
no resolver link, observed 2026-08-07T14:03:13.766676Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-07T14:03:13.766676Z digest=sha256:5b24bc3bc038936041754b182a1b782b89eeee5e5d3f99135ec7ba3629bb53ef

Pith citing papers

No inbound Pith citation observations are available.