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Paper Citation Record · LEDGER

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction

As of 17 August 2026, this Paper Citation Record lists 40 of 40 outbound references and 0 inbound Pith citation observations for arXiv:2505.20036.

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

pith.paper-citation-record.v1
2505.20036 v1

Coverage vector

measured 40 of 40 reference resolution

Typed states for the displayed outbound observations.

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measured 40 of 40 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.

Source: paper_references, paper_reference_links

measured 0 of 1 external citation measurements

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

Source: cited_works

Reference resolution

40 of 40 outbound references displayed

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External citation measurements

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Outbound references

Observation 6c99f1a4-4f96-45e0-a519-2ae2cc16936c · outbound

This paper cites History of protein–protein interactions: From egg- white to complex networks.Proteomics, 12(10):1478–1498, 2012.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction History of protein–protein interactions: From egg- white to complex networks.Proteomics, 12(10):1478–1498, 2012

Reference 1

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Observation 54fba32a-49cb-4730-a82c-70e0bbd8f7a4 · outbound

This paper cites Recent advances in the development of protein–protein interactions modulators: mechanisms and clinical trials.Signal transduction and targeted therapy, 5(1):213, 2020.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Recent advances in the development of protein–protein interactions modulators: mechanisms and clinical trials.Signal transduction and targeted therapy, 5(1):213, 2020

Reference 2

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Observation cf8e6e20-4a42-433c-a33d-403e7ecb03a2 · outbound

This paper cites A novel method for protein-ligand binding affinity prediction and the related descriptors exploration.Journal of computational chemistry, 30(6):900–909, 2009.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction A novel method for protein-ligand binding affinity prediction and the related descriptors exploration.Journal of computational chemistry, 30(6):900–909, 2009

Reference 3

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Observation 35cbf112-ba71-4aa2-9917-eb63c43dd95c · outbound

This paper cites Ensembling methods for protein-ligand binding affinity prediction.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Ensembling methods for protein-ligand binding affinity prediction

Reference 4

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Source-reported events for the cited work

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Observation 03d228a8-939d-4278-a627-d94a6553fdfa · outbound

This paper cites Exploring the computational methods for protein- ligand binding site prediction.Computational and structural biotechnology journal, 18:417–426, 2020.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Exploring the computational methods for protein- ligand binding site prediction.Computational and structural biotechnology journal, 18:417–426, 2020

Reference 5

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Source-reported events for the cited work

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Observation 35c37617-1fc2-4c7b-88f7-ce7263913fae · outbound

This paper cites Binding affinity prediction for protein–ligand complex using deep attention mechanism based on intermolecular interactions.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Binding affinity prediction for protein–ligand complex using deep attention mechanism based on intermolecular interactions

Reference 6

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

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Observation 8319a97b-3175-4465-adb5-43238858ac5b · outbound

This paper cites Uniref clusters: a comprehensive and scalable alternative for improving sequence similarity searches.Bioinformatics, 31(6):926–932, 2015.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Uniref clusters: a comprehensive and scalable alternative for improving sequence similarity searches.Bioinformatics, 31(6):926–932, 2015

Reference 7

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Observation dc5e8668-fa35-4e41-86d0-5d2857008978 · outbound

This paper cites Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold.Nature methods, 16(7):603–606, 2019.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold.Nature methods, 16(7):603–606, 2019

Reference 8

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Observation 1d6c816e-ddbc-45ba-bac8-b12b9effc773 · outbound

This paper cites an unresolved cited work.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Unresolved cited work

Reference 9

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Observation 046315f6-3306-400c-817d-d44d5a48c158 · outbound

This paper cites Prottrans: Towards cracking the language of life’s code through 500 self-supervised deep learning and high performance computing [j].

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Prottrans: Towards cracking the language of life’s code through 500 self-supervised deep learning and high performance computing [j]

Reference 10

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Observation 7a196524-b7d5-4509-9e3f-e456bd65916a · outbound

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

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Evolutionary-scale prediction of atomic-level protein structure with a language model.Science, 379(6637):1123–1130, 2023

Reference 11

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Observation bc68fa91-3975-4693-943b-101514512a0d · outbound

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

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Ankh: Optimized Protein Language Model Unlocks General-Purpose Modelling

Reference 12

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Observation 3ae4d8a5-5b9a-42bb-95f4-e5c2fe023a0b · outbound

This paper cites ankh2-ext1 (revision 286cb6e), 2025.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction ankh2-ext1 (revision 286cb6e), 2025

Reference 13

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Observation 59b32593-7fcd-4003-80db-7389d59a7116 · outbound

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Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction ankh2-ext2 (revision 4c155ee), 2025

Reference 14

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Observation 0ce834c9-3865-4e23-8ed3-c9753a38b1b0 · outbound

This paper cites Sofroniew, Deniz Oktay, Zeming Lin, Robert Verkuil, Vincent Q.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Sofroniew, Deniz Oktay, Zeming Lin, Robert Verkuil, Vincent Q

Reference 15

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Observation 2d66bb25-543c-4e94-ae1d-d9998695bf8b · outbound

This paper cites Peer: a comprehensive and multi-task benchmark for protein sequence understanding.Advances in Neural Information Processing Systems, 35:35156–35173, 2022.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Peer: a comprehensive and multi-task benchmark for protein sequence understanding.Advances in Neural Information Processing Systems, 35:35156–35173, 2022

Reference 16

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Observation aaa02c3b-c96d-4904-9e09-cd3dea683729 · outbound

This paper cites D-script translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions.Cell Systems, 12(10):969–982, 2021.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction D-script translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions.Cell Systems, 12(10):969–982, 2021

Reference 17

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Observation 07f4ed01-0fda-43ad-b5ef-419565e2159e · outbound

This paper cites Topsy- turvy: integrating a global view into sequence-based ppi prediction.Bioinformatics, 38 (Supplement_1):i264–i272, 2022.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Topsy- turvy: integrating a global view into sequence-based ppi prediction.Bioinformatics, 38 (Supplement_1):i264–i272, 2022

Reference 18

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Observation eabbc64b-cf0c-47b6-a6e8-7217735105f1 · outbound

This paper cites Saprot: Protein language modeling with structure-aware vocabulary.bioRxiv, pages 2023–10, 2023.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Saprot: Protein language modeling with structure-aware vocabulary.bioRxiv, pages 2023–10, 2023

Reference 19

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Observation 751f973b-1c5e-4032-ab91-44166b08a455 · outbound

This paper cites Multifaceted protein–protein interaction prediction based on siamese residual rcnn.Bioinformatics, 35(14):i305–i314, 2019.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Multifaceted protein–protein interaction prediction based on siamese residual rcnn.Bioinformatics, 35(14):i305–i314, 2019

Reference 20

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Observation cb2c1cfa-ab1d-4c1d-8c57-bf9750ef46fe · outbound

This paper cites Mu- tation effect estimation on protein–protein interactions using deep contextualized representation learning.NAR genomics and bioinformatics, 2(2):lqaa015, 2020.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Mu- tation effect estimation on protein–protein interactions using deep contextualized representation learning.NAR genomics and bioinformatics, 2(2):lqaa015, 2020

Reference 21

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Observation f12e7de8-760a-4dfa-aba8-302a8b4b42f1 · outbound

This paper cites Ddmut-ppi: predicting effects of mutations on protein–protein interactions using graph-based deep learning.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Ddmut-ppi: predicting effects of mutations on protein–protein interactions using graph-based deep learning

Reference 22

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Observation b38f9df0-c5da-48fd-8e1f-9807adf81de7 · outbound

This paper cites Ppb-affinity: Protein-protein binding affinity dataset for ai-based protein drug discovery.Scientific Data, 11(1):1–11, 2024.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Ppb-affinity: Protein-protein binding affinity dataset for ai-based protein drug discovery.Scientific Data, 11(1):1–11, 2024

Reference 23

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Observation c870f26a-3973-4ed8-b586-29029ab0b941 · outbound

This paper cites Datasets: A Community Library for Natural Language Processing.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Datasets: A Community Library for Natural Language Processing

Reference 24

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Observation 93432789-213f-40e3-8c00-535b5959f681 · outbound

This paper cites Skempi 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation.Bioinformatics, 35(3):462–469, 2019.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Skempi 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation.Bioinformatics, 35(3):462–469, 2019

Reference 25

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Observation d4f5649f-1435-4732-a0cd-45e6b3fcf200 · outbound

This paper cites Proteinflow: a python library to pre-process protein structure data for deep learning applications.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Proteinflow: a python library to pre-process protein structure data for deep learning applications

Reference 26

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Source-reported events for the cited work

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Observation e8938a73-b40c-4fc3-9bc3-c256a7feafeb · outbound

This paper cites Deeploc: prediction of protein subcellular localization using deep learning.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Deeploc: prediction of protein subcellular localization using deep learning

Reference 27

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Observation 57880f12-7f9c-4927-8a64-dfa7fd8ed292 · outbound

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

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Deeploc 2.0: multi-label subcellular localization prediction using protein language models.Nucleic acids research, 50(W1):W228–W234, 2022

Reference 28

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Observation 0f4f7754-5c0c-4731-9cf5-6310a615fd0e · outbound

This paper cites Mutabind2: predicting the impacts of single and multiple mutations on protein-protein interactions.Iscience, 23(3), 2020.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Mutabind2: predicting the impacts of single and multiple mutations on protein-protein interactions.Iscience, 23(3), 2020

Reference 29

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Source-reported events for the cited work

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Observation 38b63fa1-80ca-4425-8b67-7a4407c4b043 · outbound

This paper cites Saambe-3d: predicting effect of mutations on protein–protein interactions.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Saambe-3d: predicting effect of mutations on protein–protein interactions

Reference 30

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Source-reported events for the cited work

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Observation b69e8a71-6ed3-4ed6-a6c9-2ebe9c6e5a2d · outbound

This paper cites Revealing data leakage in protein interaction benchmarks.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Revealing data leakage in protein interaction benchmarks

Reference 31

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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

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Observation fe3fbb21-bcbb-49dd-8ca9-9610f90ba0dd · outbound

This paper cites Quantification of biases in predictions of protein–protein binding affinity changes upon mutations.Briefings in bioinformatics, 25(1): bbad491, 2024.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Quantification of biases in predictions of protein–protein binding affinity changes upon mutations.Briefings in bioinformatics, 25(1): bbad491, 2024

Reference 32

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verified fuzzy
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Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

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Observation 41723e62-2e4b-45dd-a65a-a2425d9f5a37 · outbound

This paper cites Mmseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.Nature biotechnology, 35(11):1026–1028, 2017.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Mmseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.Nature biotechnology, 35(11):1026–1028, 2017

Reference 33

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unresolved
no resolver link, observed 2026-08-07T14:04:45.222353Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

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Observation 124ed1fd-7dc1-4ebb-9bc1-dc21e6a23e75 · outbound

This paper cites Robust deep learning–based protein sequence design using proteinmpnn.Science, 378(6615):49–56, 2022.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Robust deep learning–based protein sequence design using proteinmpnn.Science, 378(6615):49–56, 2022

Reference 34

Resolution
unresolved
no resolver link, observed 2026-08-07T14:04:45.307846Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

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Observation 3dc52373-67e8-4d34-9c64-4f544d2cde9f · outbound

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

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Evaluating protein transfer learning with tape.Advances in neural information processing systems, 32, 2019

Reference 35

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unresolved
no resolver link, observed 2026-08-07T14:04:45.383121Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

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Observation 9540d6ef-bede-44ce-a078-3401dd7a3883 · outbound

This paper cites Deepsol: a deep learning framework for sequence-based protein solubility prediction.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Deepsol: a deep learning framework for sequence-based protein solubility prediction

Reference 36

Resolution
unresolved
no resolver link, observed 2026-08-07T14:04:45.451571Z

Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-07T14:04:45.451571Z digest=sha256:24a0d2919662ac36e2a249190f0706e32e9aff5e7e4b89b59d6d55a8ca72ede5

Observation b646c805-7ef6-490e-b377-f9cca3708d92 · outbound

This paper cites Attention is all you need.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Attention is all you need

Reference 37

Resolution
unresolved
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Source-reported events for the cited work

Unavailable: canonical work link unavailable.

source=pdf_text observed=2026-08-07T14:04:45.525142Z digest=sha256:090e13ba588d13a9c6e9c25a78b3ecf4ab75f68fe7c231e919df2dc24b1a7f98

Observation 733137e8-afab-4b87-a1f3-5c3d0fbb9f0c · outbound

This paper cites Con- vbert: Improving bert with span-based dynamic convolution.Advances in Neural Information Processing Systems, 33:12837–12848, 2020.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Con- vbert: Improving bert with span-based dynamic convolution.Advances in Neural Information Processing Systems, 33:12837–12848, 2020

Reference 38

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verified fuzzy
raw_fallback, observed 2026-08-07T14:04:46.268240Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

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Observation 3f7448f9-d861-43ac-abb7-a44bb52125e9 · outbound

This paper cites PyTorch 2: Faster Machine Learning Through Dynamic Python Bytecode Transformation and Graph Compilation.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction PyTorch 2: Faster Machine Learning Through Dynamic Python Bytecode Transformation and Graph Compilation

Reference 39

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Source-reported events for the cited work

Unavailable: canonical work link unavailable.

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Observation 31989c2d-9c9e-4769-ac6e-71e84a75238c · outbound

This paper cites Accurate structure prediction of biomolecular interactions with alphafold 3.Nature, 630(8016):493–500, 2024.

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction Accurate structure prediction of biomolecular interactions with alphafold 3.Nature, 630(8016):493–500, 2024

Reference 40

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verified fuzzy
raw_fallback, observed 2026-08-07T14:04:46.104687Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-16T06:30:59.297886+00:00.

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Pith citing papers

No inbound Pith citation observations are available.