Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs | Paper Citation Record

Observation a49ee2b1-4337-437e-9da8-f8c32b1ab933 · outbound

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

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Accurate structure prediction of biomolecular interactions with alphafold 3.Nature, 630(8016):493–500, 2024

Reference 1

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Observation 674cfacc-d7d7-42f6-b692-8f62b7a935e1 · outbound

This paper cites OpenProteinSet: Training data for structural biology at scale.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs OpenProteinSet: Training data for structural biology at scale

Reference 2

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Observation 69b182e8-fd20-4ca6-a44b-056be9dccc30 · outbound

This paper cites Principles that govern the folding of protein chains.Science, 181(4096): 223–230, 1973.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Principles that govern the folding of protein chains.Science, 181(4096): 223–230, 1973

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Observation 7ae8bfbf-4a3d-4219-b79e-281b86e7e226 · outbound

This paper cites Accurate prediction of protein structures and interactions using a three-track neural network.Science, 373(6557):871–876, 2021.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Accurate prediction of protein structures and interactions using a three-track neural network.Science, 373(6557):871–876, 2021

Reference 4

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Unresolved cited work

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Observation 32e9ba2b-c7db-406b-a743-5ddd7e72237d · outbound

This paper cites Sampling alternative conformational states of transporters and receptors with alphafold2.elife, 11:e75751, 2022.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Sampling alternative conformational states of transporters and receptors with alphafold2.elife, 11:e75751, 2022

Reference 6

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Observation 1b2f8a15-8584-48f2-8eaf-41ca7f70216d · outbound

This paper cites BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding

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Observation a726a7ea-09ab-4ebb-8e15-0ae78e0532ca · outbound

This paper cites The protein-folding problem, 50 years on.science, 338 (6110):1042–1046, 2012.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs The protein-folding problem, 50 years on.science, 338 (6110):1042–1046, 2012

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Observation 69768981-84de-46ad-944c-31b3cb4ba276 · outbound

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

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Prottrans: toward understanding the language of life through self-supervised learning.IEEE transactions on pattern analysis and machine intelligence, 44(10):7112–7127, 2021

Reference 9

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Observation dd4193e6-6210-4c6f-a8fe-c9bf61132817 · outbound

This paper cites Protein complex prediction with alphafold-multimer.biorxiv, pages 2021–10, 2021.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Protein complex prediction with alphafold-multimer.biorxiv, pages 2021–10, 2021

Reference 10

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Observation 1fe8e66d-95bd-4116-ba16-dbea3012de6d · outbound

This paper cites Disease variant prediction with deep generative models of evolutionary data.Nature, 599(7883):91–95, 2021.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Disease variant prediction with deep generative models of evolutionary data.Nature, 599(7883):91–95, 2021

Reference 11

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Observation fab5fd39-e3f6-4d88-bbd3-438d9a3a0d57 · outbound

This paper cites Mixture modeling by affinity propagation.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Mixture modeling by affinity propagation

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Observation 6e7df2b7-e447-4eb5-8ef2-dbd9602e47a2 · outbound

This paper cites Frey and Delbert Dueck.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Frey and Delbert Dueck

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Observation f0409904-f310-48aa-af92-a6b1bb2431b5 · outbound

This paper cites Modeling aspects of the language of life through transfer-learning protein sequences.BMC bioinformatics, 20(1):723, 2019.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Modeling aspects of the language of life through transfer-learning protein sequences.BMC bioinformatics, 20(1):723, 2019

Reference 14

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Observation b5260e0e-8a94-4baf-8b75-67e67ac184b3 · outbound

This paper cites Hofmann and A.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Hofmann and A

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Observation 34845c5f-e986-478f-a434-64c88ebbb488 · outbound

This paper cites A-prot: protein structure modeling using msa trans- former.BMC bioinformatics, 23(1):93, 2022.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs A-prot: protein structure modeling using msa trans- former.BMC bioinformatics, 23(1):93, 2022

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Observation f46270bf-b3de-48fe-aab5-d8bdf7d46a66 · outbound

This paper cites Mutation effects predicted from sequence co-variation.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Mutation effects predicted from sequence co-variation

Reference 17

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Observation 3021d039-770c-4498-9170-1124965fe662 · outbound

This paper cites Bidirectional LSTM-CRF Models for Sequence Tagging.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Bidirectional LSTM-CRF Models for Sequence Tagging

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Observation c27a97fc-65f3-4630-856a-c5a99a61ad61 · outbound

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Unresolved cited work

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Observation 06458d3e-499d-4fa0-b1af-c72612279b84 · outbound

This paper cites Efficient inference in fully connected crfs with gaussian edge potentials.Advances in neural information processing systems, 24, 2011.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Efficient inference in fully connected crfs with gaussian edge potentials.Advances in neural information processing systems, 24, 2011

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Observation 20a6c54a-e323-404e-9929-0f7e4cbfd307 · outbound

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Unresolved cited work

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Resolution: verified exact; doi, observed 2026-08-01T05:13:20.970815Z

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Observation b69502ed-dbbc-452e-8934-b0c7923f2a89 · outbound

This paper cites Factor graphs and the sum-product algorithm.IEEE Transactions on information theory, 47(2):498–519, 2001.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Factor graphs and the sum-product algorithm.IEEE Transactions on information theory, 47(2):498–519, 2001

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Observation 4d5079ad-3e6b-4984-9929-65536ddb223c · outbound

This paper cites Conditional random fields: Probabilistic models for segmenting and labeling sequence data.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Conditional random fields: Probabilistic models for segmenting and labeling sequence data

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Observation b697ed62-a959-4d93-918b-456801a493ef · outbound

This paper cites Schafer, Jeshuwin Prabakaran, Devlina Chakravarty, Madeleine F.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Schafer, Jeshuwin Prabakaran, Devlina Chakravarty, Madeleine F

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Observation 77dd7a3d-90cb-4b83-ba45-464458077e85 · outbound

This paper cites Clustering by soft-constraint affinity propaga- tion: applications to gene-expression data.Bioinformatics, 23(20):2708–2715, 2007.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Clustering by soft-constraint affinity propaga- tion: applications to gene-expression data.Bioinformatics, 23(20):2708–2715, 2007

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Resolution: verified exact; doi, observed 2026-08-01T05:13:20.842545Z

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Observation a6d67c9e-1586-44b5-832e-f7d3c43bd1e0 · outbound

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

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Evolutionary-scale prediction of atomic-level protein structure with a language model.Science, 379(6637):1123–1130, 2023

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Observation 1f67af7e-f148-403f-a07e-ba1013d0d98b · outbound

This paper cites Large language models generate functional protein sequences across diverse families.Nature biotechnology, 41 (8):1099–1106, 2023.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Large language models generate functional protein sequences across diverse families.Nature biotechnology, 41 (8):1099–1106, 2023

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Observation c385733e-25bd-46ac-a9e5-2bb29d913cec · outbound

This paper cites Protein 3d structure computed from evolutionary sequence variation.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Protein 3d structure computed from evolutionary sequence variation

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Observation 0c30c93d-bdd1-4998-80f8-d200f763c037 · outbound

This paper cites Colabfold: making protein folding accessible to all.Nature methods, 19(6): 679–682, 2022.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Colabfold: making protein folding accessible to all.Nature methods, 19(6): 679–682, 2022

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Observation dd259027-70b7-4736-8d73-3eb4c9937b15 · outbound

This paper cites Cui, David C.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Cui, David C

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correction dated 2024-04-10. Source: crossref record 10.1038/s41467-024-47504-0->10.1038/s41467-024-46715-9:correction, observed 2026-07-11T03:04:19.271678+00:00. This notice travels one citation hop only.

Observation a98c429b-d445-4c44-a836-0e9525e147ff · outbound

This paper cites Direct-coupling analysis of residue coevolution captures native contacts across many protein families.Proceedings of the National Academy of Sciences, 108(49):E1293–E1301, 2011.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Direct-coupling analysis of residue coevolution captures native contacts across many protein families.Proceedings of the National Academy of Sciences, 108(49):E1293–E1301, 2011

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Observation 8411ff79-a9b5-4f52-bd23-7270fb5d3a89 · outbound

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval

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Observation 9f4d6f0e-5a7c-448a-8d58-df009e31163c · outbound

This paper cites Elsevier, 2014.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Elsevier, 2014

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Observation 5e11a770-f394-4df2-8df8-ef46f07f8266 · outbound

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Scikit- learn: Machine learning in python.the Journal of machine Learning research, 12:2825–2830, 2011

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Observation ef5e654d-1286-4fc6-869e-7389e23800e6 · outbound

This paper cites End-to-end learning of multiple sequence alignments with differentiable smith–waterman.Bioinformatics, 39(1):btac724, 2023.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs End-to-end learning of multiple sequence alignments with differentiable smith–waterman.Bioinformatics, 39(1):btac724, 2023

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This paper cites Collaborative summarization: When collaborative filtering meets document summarization.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Collaborative summarization: When collaborative filtering meets document summarization

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Evaluating Protein Transfer Learning with TAPE

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

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Transformer protein language models are unsupervised structure learners

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Observation 6e72cbe2-db2c-487e-81d9-b1be5b2b41b7 · outbound

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Msa transformer

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Unresolved cited work

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Observation 34c13b54-f7f9-4aec-b50b-f1e11e5dc558 · outbound

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Improved protein structure prediction using potentials from deep learning.Nature, 577(7792):706–710, 2020

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This paper cites Stein and Hassane S.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Stein and Hassane S

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Observation eab2edd5-313e-48dd-b6ae-585afe224ee7 · outbound

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Speach_af: Sampling protein ensembles and conformational heterogeneity with alphafold2.PLoS computational biology, 18(8):e1010483, 2022

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.Nature Biotechnology, 35(11):1026–1028, 2017

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Observation f8cf44d6-82a3-47df-afac-ee6d42df52c9 · outbound

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Hh-suite3 for fast remote homology detection and deep protein annotation

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Observation 8ba3225c-1616-4875-baf9-0b3dfa1209cb · outbound

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs BERTology Meets Biology: Interpreting Attention in Protein Language Models

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Observation d489ac5f-2751-466e-bc94-3696dd831a27 · outbound

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Graphical models, exponential families, and variational inference.Foundations and Trends® in Machine Learning, 1(1-2):1–305, 2008

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This paper cites Accurate de novo prediction of protein contact map by ultra-deep learning model.PLoS computational biology, 13(1): e1005324, 2017.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Accurate de novo prediction of protein contact map by ultra-deep learning model.PLoS computational biology, 13(1): e1005324, 2017

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This paper cites Predicting multiple conformations via sequence clustering and alphafold2.Nature, 625(7996):832–839, 2024.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Predicting multiple conformations via sequence clustering and alphafold2.Nature, 625(7996):832–839, 2024

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This paper cites Improved protein structure prediction using predicted interresidue orientations.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Improved protein structure prediction using predicted interresidue orientations

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Unresolved cited work

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Unresolved cited work

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This paper cites orphan folds.

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs orphan folds

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Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs Unresolved cited work

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