Task- and dataset-specific information in protein language models | Paper Citation Record

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Reference 1

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This paper cites Comparative assessment of protein large language models for enzyme commission number prediction.BMC bioinfor- matics, 26(1):68, 2025.

Task- and dataset-specific information in protein language models Comparative assessment of protein large language models for enzyme commission number prediction.BMC bioinfor- matics, 26(1):68, 2025

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This paper cites Language mod- els can identify enzymatic binding sites in pro- tein sequences.Computational and structural biotechnology journal, 23:1929–1937, 2024.

Task- and dataset-specific information in protein language models Language mod- els can identify enzymatic binding sites in pro- tein sequences.Computational and structural biotechnology journal, 23:1929–1937, 2024

Reference 3

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This paper cites Iglm: Infilling language model- ing for antibody sequence design.Cell systems, 14(11):979–989, 2023.

Task- and dataset-specific information in protein language models Iglm: Infilling language model- ing for antibody sequence design.Cell systems, 14(11):979–989, 2023

Reference 4

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This paper cites Protein language models: Applications and perspectives.

Task- and dataset-specific information in protein language models Protein language models: Applications and perspectives

Reference 5

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This paper cites Understanding intermediate layers using linear classifier probes.

Task- and dataset-specific information in protein language models Understanding intermediate layers using linear classifier probes

Reference 6

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This paper cites Deep residual learning for image recognition.

Task- and dataset-specific information in protein language models Deep residual learning for image recognition

Reference 7

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This paper cites Imagenet: A large-scale hierarchical image database.

Task- and dataset-specific information in protein language models Imagenet: A large-scale hierarchical image database

Reference 8

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This paper cites Bert: Pre-training of deep bidirectional transformers for language un- derstanding.

Task- and dataset-specific information in protein language models Bert: Pre-training of deep bidirectional transformers for language un- derstanding

Reference 9

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This paper cites The geometry of hidden representations of large transformer models.Ad- vances in Neural Information Processing Sys- tems, 36:51234–51252, 2023.

Task- and dataset-specific information in protein language models The geometry of hidden representations of large transformer models.Ad- vances in Neural Information Processing Sys- tems, 36:51234–51252, 2023

Reference 10

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Observation 5d0dcaff-3911-463d-9c45-99b05533631d · outbound

This paper cites BERTology Meets Biology: Interpreting Attention in Protein Language Models.

Task- and dataset-specific information in protein language models BERTology Meets Biology: Interpreting Attention in Protein Language Models

Reference 11

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Observation 62f72406-c10e-48c5-811f-6bbf8a4b46d6 · outbound

This paper cites Layer by Layer: Uncovering Hidden Representations in Language Models.

Task- and dataset-specific information in protein language models Layer by Layer: Uncovering Hidden Representations in Language Models

Reference 12

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This paper cites The underlying structures of self-attention: symmetry, directionality, and emergent dynamics in Transformer training.

Task- and dataset-specific information in protein language models The underlying structures of self-attention: symmetry, directionality, and emergent dynamics in Transformer training

Reference 13

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This paper cites Generative pretraining from pixels.

Task- and dataset-specific information in protein language models Generative pretraining from pixels

Reference 14

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

Task- and dataset-specific information in protein language models Evolutionary-scale prediction of atomic-level protein structure with a language model.Sci- ence, 379(6637):1123–1130, 2023

Reference 15

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Observation 9a6fbca4-6151-4207-a1c1-f91619c249eb · outbound

This paper cites Layer probing improves kinase functional prediction with protein language models.arXiv preprint arXiv:2512.00376, 2025.

Task- and dataset-specific information in protein language models Layer probing improves kinase functional prediction with protein language models.arXiv preprint arXiv:2512.00376, 2025

Reference 16

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This paper cites Visualizing and understanding convolutional networks.

Task- and dataset-specific information in protein language models Visualizing and understanding convolutional networks

Reference 17

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Observation 787edd45-84a6-490c-93e8-b5a8cf46d50b · outbound

This paper cites Quantify- ing uncertainty in protein representations across models and tasks.Nature Methods, pages 1–9, 2026.

Task- and dataset-specific information in protein language models Quantify- ing uncertainty in protein representations across models and tasks.Nature Methods, pages 1–9, 2026

Reference 18

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This paper cites Local fitness land- scape of the green fluorescent protein.Nature, 533(7603):397–401, 2016.

Task- and dataset-specific information in protein language models Local fitness land- scape of the green fluorescent protein.Nature, 533(7603):397–401, 2016

Reference 19

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This paper cites A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain.Current biology, 24(22):2643–2651, 2014.

Task- and dataset-specific information in protein language models A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain.Current biology, 24(22):2643–2651, 2014

Reference 20

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This paper cites Global analysis of protein folding using mas- sively parallel design, synthesis, and testing.Sci- ence, 357(6347):168–175, 2017.

Task- and dataset-specific information in protein language models Global analysis of protein folding using mas- sively parallel design, synthesis, and testing.Sci- ence, 357(6347):168–175, 2017

Reference 21

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This paper cites Mega-scale experimental analysis of protein folding stability in biology and design.Nature, 620(7973):434–444, 2023.

Task- and dataset-specific information in protein language models Mega-scale experimental analysis of protein folding stability in biology and design.Nature, 620(7973):434–444, 2023

Reference 22

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This paper cites Large language models generate functional protein se- quences across diverse families.Nature biotech- nology, 41(8):1099–1106, 2023.

Task- and dataset-specific information in protein language models Large language models generate functional protein se- quences across diverse families.Nature biotech- nology, 41(8):1099–1106, 2023

Reference 23

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This paper cites Meltome atlas—thermal proteome stability across the tree of life.Nature methods, 17(5):495–503, 2020.

Task- and dataset-specific information in protein language models Meltome atlas—thermal proteome stability across the tree of life.Nature methods, 17(5):495–503, 2020

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This paper cites Deepsol: a deep learning framework for sequence-based protein solubility prediction.Bioinformatics, 34(15):2605–2613, 2018.

Task- and dataset-specific information in protein language models Deepsol: a deep learning framework for sequence-based protein solubility prediction.Bioinformatics, 34(15):2605–2613, 2018

Reference 25

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This paper cites Deeploc 2.0: multi-label subcellular localization prediction using protein language models.Nucleic acids research, 50(W1):W228–W234, 2022.

Task- and dataset-specific information in protein language models Deeploc 2.0: multi-label subcellular localization prediction using protein language models.Nucleic acids research, 50(W1):W228–W234, 2022

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Task- and dataset-specific information in protein language models Unresolved cited work

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This paper cites Protein embeddings and deep learning pre- dict binding residues for various ligand classes.

Task- and dataset-specific information in protein language models Protein embeddings and deep learning pre- dict binding residues for various ligand classes

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Task- and dataset-specific information in protein language models Unresolved cited work

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This paper cites ESM Cambrian: Revealing the mysteries of proteins with unsupervised learn- ing.EvolutionaryScale Website, 12 2024.

Task- and dataset-specific information in protein language models ESM Cambrian: Revealing the mysteries of proteins with unsupervised learn- ing.EvolutionaryScale Website, 12 2024

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This paper cites Prottrans: to- ward understanding the language of life through self-supervised learning.IEEE transactions on pattern analysis and machine intelligence, 44(10):7112–7127, 2021.

Task- and dataset-specific information in protein language models Prottrans: to- ward understanding the language of life through self-supervised learning.IEEE transactions on pattern analysis and machine intelligence, 44(10):7112–7127, 2021

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This paper cites Bilingual language model for protein sequence and structure.NAR Genomics and Bioinformat- ics, 6(4):lqae150, 2024.

Task- and dataset-specific information in protein language models Bilingual language model for protein sequence and structure.NAR Genomics and Bioinformat- ics, 6(4):lqae150, 2024

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This paper cites Progen2: exploring the boundaries of protein language models.Cell systems, 14(11):968–978, 2023.

Task- and dataset-specific information in protein language models Progen2: exploring the boundaries of protein language models.Cell systems, 14(11):968–978, 2023

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This paper cites Protgpt2 is a deep unsupervised lan- guage model for protein design.Nature commu- nications, 13(1):4348, 2022.

Task- and dataset-specific information in protein language models Protgpt2 is a deep unsupervised lan- guage model for protein design.Nature commu- nications, 13(1):4348, 2022

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This paper cites A new algorithm for data com- pression.The C Users Journal, 12(2):23–38, 1994.

Task- and dataset-specific information in protein language models A new algorithm for data com- pression.The C Users Journal, 12(2):23–38, 1994

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This paper cites Attention is all you need.Advances in neural information processing systems, 30, 2017.

Task- and dataset-specific information in protein language models Attention is all you need.Advances in neural information processing systems, 30, 2017

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This paper cites Exploring the limits of transfer learning with a unified text- to-text transformer.Journal of machine learning research, 21(140):1–67, 2020.

Task- and dataset-specific information in protein language models Exploring the limits of transfer learning with a unified text- to-text transformer.Journal of machine learning research, 21(140):1–67, 2020

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Task- and dataset-specific information in protein language models Improving language understanding by generative pre-training, 2018

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Observation 505a94e6-87b6-4391-b8c7-4cdf28040293 · outbound

This paper cites Estimating the intrinsic dimension of datasets by a minimal neighbor- hood information.Scientific reports, 7(1):12140, 2017.

Task- and dataset-specific information in protein language models Estimating the intrinsic dimension of datasets by a minimal neighbor- hood information.Scientific reports, 7(1):12140, 2017

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Observation c7e8de6a-1124-4b18-bdbb-ee0359f5db26 · outbound

This paper cites Hierarchical nucleation in deep neural networks.Advances in Neural Information Processing Systems, 33:7526–7536, 2020.

Task- and dataset-specific information in protein language models Hierarchical nucleation in deep neural networks.Advances in Neural Information Processing Systems, 33:7526–7536, 2020

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Task- and dataset-specific information in protein language models Unresolved cited work

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Task- and dataset-specific information in protein language models Supervised learning of protein melting temperature: Cross-species vs

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This paper cites Data splitting to avoid information leakage with datasail.Nature Communications, 16(1):3337, 2025.

Task- and dataset-specific information in protein language models Data splitting to avoid information leakage with datasail.Nature Communications, 16(1):3337, 2025

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This paper cites Bert rediscovers the classical nlp pipeline.

Task- and dataset-specific information in protein language models Bert rediscovers the classical nlp pipeline

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This paper cites Uniprot: the universal protein knowledgebase in 2025.Nucleic acids research, 52(D 1):D609– D617, 2024.

Task- and dataset-specific information in protein language models Uniprot: the universal protein knowledgebase in 2025.Nucleic acids research, 52(D 1):D609– D617, 2024

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This paper cites Mgnify: the microbiome sequence data analy- sis resource in 2023.Nucleic acids research, 51(D1):D753–D759, 2023.

Task- and dataset-specific information in protein language models Mgnify: the microbiome sequence data analy- sis resource in 2023.Nucleic acids research, 51(D1):D753–D759, 2023

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This paper cites The genome portal of the de- partment of energy joint genome institute: 2014 updates.Nucleic acids research, 42(D1):D26– D31, 2014.

Task- and dataset-specific information in protein language models The genome portal of the de- partment of energy joint genome institute: 2014 updates.Nucleic acids research, 42(D1):D26– D31, 2014

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Observation c4204ce7-ed48-4e50-aa84-2c4e76e6257b · outbound

This paper cites Protein-level assembly increases pro- tein sequence recovery from metagenomic sam- 17 ples manyfold.Nature methods, 16(7):603–606, 2019.

Task- and dataset-specific information in protein language models Protein-level assembly increases pro- tein sequence recovery from metagenomic sam- 17 ples manyfold.Nature methods, 16(7):603–606, 2019

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Observation d753ca65-2053-4d42-afab-7dde942d2669 · outbound

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

Task- and dataset-specific information in protein language models Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.Bioinformat- ics, 22(13):1658–1659, 2006

Reference 49

Resolution: verified fuzzy; raw_fallback, observed 2026-08-16T00:21:22.861405Z

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Observation c4231b2b-06df-411c-bea7-74a50a8568ae · outbound

This paper cites Evaluating protein transfer learning with tape.Advances in neural information processing systems, 32, 2019.

Task- and dataset-specific information in protein language models Evaluating protein transfer learning with tape.Advances in neural information processing systems, 32, 2019

Reference 50

Resolution: unresolved; no resolver link, observed 2026-08-16T00:21:22.653467Z

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Observation e8f0e8f7-6f26-4c0e-92fb-f1baf6f94c3c · outbound

This paper cites Proteingym: Large- scale benchmarks for protein fitness prediction and design.Advances in neural information processing systems, 36:64331–64379, 2023.

Task- and dataset-specific information in protein language models Proteingym: Large- scale benchmarks for protein fitness prediction and design.Advances in neural information processing systems, 36:64331–64379, 2023

Reference 51

Resolution: verified fuzzy; raw_fallback, observed 2026-08-16T00:21:22.839603Z

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Observation 6a449864-71e8-4a6e-aabb-9a2d6ab84b6b · outbound

This paper cites Kalinina.

Task- and dataset-specific information in protein language models Kalinina

Reference 52

Resolution: malformed identifier; raw_fallback, observed 2026-08-16T00:21:22.826276Z

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