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Paper Citation Record · LEDGER

Transformers in Protein: A Survey

As of 15 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

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measured 0 of 0 inbound itemization

Pith citing papers itemized under the disclosed page cap.

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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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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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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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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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This paper cites Deformable convolutional networks,.

Transformers in Protein: A Survey Deformable convolutional networks,

Reference 25

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

Reference 28

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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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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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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

Resolution
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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:07.038041Z digest=sha256:3c5801c2ee553e7a95d8226970b16e05e2919375acb638db2012f59e6627ef98

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:07.151872Z digest=sha256:539f475f1f51b10388c6d274209d80a16f3a8f71f8fdd403533621bdd9fa2084

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:07.218288Z digest=sha256:4104d16a7ba617cbd3fc6b961a8b48b82539178fd14bec79afb8cd55c96ec93a

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:07.302444Z digest=sha256:ebda60945e603804d8044e664377ca007adb87c7eba627934c83d4370c4ba38d

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:07.485993Z digest=sha256:61ab4472228421c7cfde8b52a927cfcd43bc8f0650903deb8f28d91f545d665c

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:07.781130Z digest=sha256:09c66803b02923241678279649c17d1d4db648f17a5f6d3488f4b17e955a6f2b

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:07.848752Z digest=sha256:f475c5b67d5d5cc8791ed53a5a9ade22bba579c52a90d0505d7ec81dd02f0634

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:07.962479Z digest=sha256:c6614031cdcae57da21dbe0f3eb6c537dd164aa174f8ad0c4476b4c9d9aba279

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.015387Z digest=sha256:5d848afc15e2b0ea0ba2b69ef50109420fc958a900e5fdf29d129969d303e799

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.060222Z digest=sha256:1649d8b3ed6938be25e99746cc20a17f07218e0b7521cd9e7af07ce8e7d51c3a

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.132680Z digest=sha256:0727539fb37590f4a22851a86c6117af7c80ffdbe11fa437a7a2c85463cfde70

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.181838Z digest=sha256:48a36334ff3f1cd3c8597058d5ac55e3a90a454118c91d388ba9a111f0f5428d

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=sha256:889e0250cf34e7c54e1dabbf6ba2d3c93583fc7a45a5f6ad56d822061e972129

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.331914Z digest=sha256:59702630ab0765b1ed8e1349ce4fd2442f0f1c1b1c00b5a9a6a50e59bf852447

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.388821Z digest=sha256:a4ad44ecb6b024f22daa69392edaf103a87fda842dfec176a6a10ed533663577

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.460803Z digest=sha256:d1a1eabeb284712da45bf1cb0d85cbdbf78cd20066d22de7187121488d6bf996

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.538032Z digest=sha256:1337760bab61c4d22d551936ce2dfb6dbb5c1ccd1e2c4a859c1846316213512f

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=sha256:63fbb6ec48fa0e52d5a452cd0bfbb29f1818bc45778b650fa61a0c931eb87a7d

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.712012Z digest=sha256:1915375da863446ec6c70ce1d5512e8f9d0e5b2ab75de027d343758838ee860b

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.781480Z digest=sha256:1add4c5357492a84ac67133ec1d81f86f79cab5e298a5c5b98d741f358c3e9b6

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.846323Z digest=sha256:d619a1c37fb1547a7d9d1159152dfd32af9441714186f4c9999508016ecdfdea

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.910694Z digest=sha256:8c167fdbc33fb394dfeeb18940047f9f7e768fee30fa009c612747f320cda6f3

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:08.980470Z digest=sha256:3eeee877265a1f213b13a8d604e0650ae718a4cd833d4e77fd81b3d21b2c7e80

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:09.153144Z digest=sha256:b1ad216bc441733024fbf9f0b6e424e73709a984d6422c89ad769746e9beddb5

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:09.208982Z digest=sha256:a396ddd1a526d352a2206535537c0e675cb2cc7fc5090bd2d6633474832dad94

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:09.283462Z digest=sha256:eeb8bbbdb269fbd2b3821e007e46af73378d75ef6d604b1cc7bf6cad12829e97

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:09.359999Z digest=sha256:860e6e418afdd90847d7d2263e2f2e2606b989c814397f5e1017d98b97f4e3f7

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:09.440718Z digest=sha256:ab3955516b4256bf154104f0a5fdee733b47dad60ba4eeca467c19474c8a0008

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:09.509224Z digest=sha256:7fb3412c2a908c13c07e48bd096848f8ca54a74d8343a9d6c727cae706e92cb8

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:09.604746Z digest=sha256:401bb37271b545f67f000ae5128a54362add5a98fb64f0c23875ef868302ba0f

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:09.720351Z digest=sha256:a0f6a05bee67752c85ac5f38b064577c5f31f6c67e7e0b9bc752e9f3fc3b2db6

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:09.816536Z digest=sha256:1a4f6107b585cc427c42954e09132e901c65a848c919d029f6da99453f9d9b95

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:09.887645Z digest=sha256:66bf25c1f9cffa4a774123b67005be4ab89de8394f4608a7d5bf5495f770cc12

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=sha256:9b168f44403838e717ea0ba7b155a4a682459aec1062ea0aedbaa700e8eec345

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:10.089363Z digest=sha256:722d4e09c090e9cfe647d343014104eaabc08cd820e84b237a2a32d94e411193

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:10.169600Z digest=sha256:99e0c4d1956bfb518d20f69e9ffa1977c019f883df78d7238cb223529d268317

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:10.324134Z digest=sha256:0c0d26eb7833d1cc8336632e247578c6e62049e35cf6e9666d9f721659ca6616

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
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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:10.419312Z digest=sha256:627a1ab1cc649e54e58a9cc5d472774a09756ca3fb915e2984637d0843074ae1

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:10.709283Z digest=sha256:4eabaf4970575b3307eb325dde161c32e2fc0a5a9e4a9663dc4e6e7e92a40c75

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:10.801603Z digest=sha256:eccb6109b7d0c431ee687c317a8c37dd93a8d2b1cdb5bedff21a31f0db510596

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
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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:10.894662Z digest=sha256:827366582d9d0d75125bb696bac3215860883e3817be76117674aca38c18a680

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
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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:10.966982Z digest=sha256:b8e4e0cf51bfcbfbaeb039b4c20d78e55d9cb57acf4f1322f60ce3e23ca8ac31

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
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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:11.097147Z digest=sha256:9f8cd6fca068430deb0166d4da3df9383a57b325acb6f1f94af7f3bb564c2940

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 2026-08-15T06:32:42.880941+00:00.

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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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:11.256767Z digest=sha256:6e9b3ec7742d2055a55a6ff12584c9f4c1f5eb48411673aa8b3732e97d486c3c

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:11.461782Z digest=sha256:af79b6cecae927a74723382005cb45b8408f416766bde4fb7bbce8824edb2ff4

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:cddf309ddfa6301f134001ef3c5200352bcefa40a7965eca78c3405950faeffd

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:11.604904Z digest=sha256:0ca485c0e118c2a3d8ec19d53ab96033d8b05c9ecbbb271d930610198297413d

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:11.750672Z digest=sha256:a353cf361b50352d683c0d00344f5d7d1020df70f57ced8b8d79ef6eeec05f43

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=sha256:2eb1905676b0d73558602778a8881a24110a5471d76872fb2cffbad1db779582

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=sha256:99770a178e1bf28de90de2f4adaf3b6e1b92e99919e0bb2eabab3c13c6ab8899

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:12.303384Z digest=sha256:a41b2980e5c0168706b11181b12b76cac3555fe1086c42da24547b4cbe74d7fc

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:12.420865Z digest=sha256:f6a342e1e89559b100781b2c8b48d68c81873d483b458248a7cccc8216ca685b

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:12.509487Z digest=sha256:c5bb39b0227698158ecdc9d6ea1066c23a560070c62d0d08fd2e05b62eb51b4d

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:12.664339Z digest=sha256:393a9ef2d8d9d772f57e08ebecafb4a0abd22c4292e40f7be53b455a515a119f

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:12.838435Z digest=sha256:a288f8e104633d77283dbda5e0d6baff8065fa640e09e275b23f411709e6580a

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:13.113047Z digest=sha256:03f2847b17f36038af09c6a02c839af8612844421a6db1e5bf84311448dfbda8

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.

source=pdf_text observed=2026-08-07T14:03:13.225771Z digest=sha256:17707dbc9d86674e925307a7896ad7d461766b06f932f951e887a744046da244

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=sha256:31359832aec03b3f6e1c411fc5ce218aaa2a1c36c62e13f65c56a335c62004b7

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:13.462283Z digest=sha256:301bcb831e5d0dcf61749147fca26a68e4c071f204e6ac297e0f3f33b3385033

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 2026-08-15T06:32:42.880941+00:00.

source=pdf_text observed=2026-08-07T14:03:13.623313Z digest=sha256:174ff87aa99a76562c7295930b6e9769ac847e0c136e545ffbacdcea27ed5096

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=sha256:914031ba7d0b84132fa5f37a3982ec262729c4a77758b176c58f167a36ccc768

Pith citing papers

No inbound Pith citation observations are available.