C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation | Paper Citation Record

Observation 125538cd-db8d-43a1-a3bb-774b61335a64 · outbound

This paper cites Joint-Embedding vs Reconstruction: Provable Benefits of Latent Space Prediction for Self-Supervised Learning.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Joint-Embedding vs Reconstruction: Provable Benefits of Latent Space Prediction for Self-Supervised Learning

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This paper cites Ledsam, Agnieszka Grabska- Barwinska, Kyle R.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Ledsam, Agnieszka Grabska- Barwinska, Kyle R

Reference 2

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Unresolved cited work

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This paper cites Baumgart, Ji Eun Lee, Asaf Salamov, David J.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Baumgart, Ji Eun Lee, Asaf Salamov, David J

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This paper cites Durrant, Jerome Ku, Mohsen Naghipourfar, Michael Poli, Gwang- gyu Sun, Greg Brockman, Daniel Chang, Alison Fanton, Gabriel A.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Durrant, Jerome Ku, Mohsen Naghipourfar, Michael Poli, Gwang- gyu Sun, Greg Brockman, Daniel Chang, Alison Fanton, Gabriel A

Reference 5

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Observation f8fcab5d-d5b1-4534-a672-cf30c49e0352 · outbound

This paper cites Exploring Simple Siamese Representation Learning, November.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Exploring Simple Siamese Representation Learning, November

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This paper cites Exploring Simple Siamese Representation Learning.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Exploring Simple Siamese Representation Learning

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This paper cites Consens, Cameron Dufault, Michael Wainberg, Duncan Forster, Mehran Karimzadeh, Hani Goodarzi, Fabian J.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Consens, Cameron Dufault, Michael Wainberg, Duncan Forster, Mehran Karimzadeh, Hani Goodarzi, Fabian J

Reference 8

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This paper cites The OMG dataset: An open metagenomic corpus for mixed-modality genomic language modeling.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation The OMG dataset: An open metagenomic corpus for mixed-modality genomic language modeling

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Observation 9915b7b9-f9c7-4fc6-b773-199a9ee00c76 · outbound

This paper cites Eisen, Paul T.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Eisen, Paul T

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Observation ba30f21e-c534-439a-9b48-44ed57b763db · outbound

This paper cites Learning Visual Representations via Language-Guided Sampling.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Learning Visual Representations via Language-Guided Sampling

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Observation 73e39f7d-bed0-472c-aeb9-443957f1a8b6 · outbound

This paper cites Frey, Leo J.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Frey, Leo J

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Observation c5cd39d4-8ffe-4a47-93c0-e66cb84ad085 · outbound

This paper cites NCBI RefSeq: reference sequence standards through 25 years of curation and annotation.Nucleic Acids Research, 53(D1):D243–D257, January 2025.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation NCBI RefSeq: reference sequence standards through 25 years of curation and annotation.Nucleic Acids Research, 53(D1):D243–D257, January 2025

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Observation 7efd8edb-cebd-4310-95e0-e1bc2b98768f · outbound

This paper cites Halper, Daniel P.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Halper, Daniel P

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This paper cites Scaling up visual and vision-language representation learning with noisy text supervision.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Scaling up visual and vision-language representation learning with noisy text supervision

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Unresolved cited work

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This paper cites Scaling Laws for Neural Language Models.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Scaling Laws for Neural Language Models

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Observation 80a9ad3c-076a-4688-b2b3-3b14567ffc51 · outbound

This paper cites Flexible comparative genomics of prokaryotic transcriptional regulatory networks.BMC Genomics, 21(5):466, December 2020.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Flexible comparative genomics of prokaryotic transcriptional regulatory networks.BMC Genomics, 21(5):466, December 2020

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Observation a858646d-c015-4dd3-a61a-112e555d627e · outbound

This paper cites LaFleur, Ayaan Hossain, and Howard M.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation LaFleur, Ayaan Hossain, and Howard M

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This paper cites Harnessing a unified multi-modal sequence modeling to unveil protein-dna interdependency.bioRxiv, pages 2025–02, 2025.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Harnessing a unified multi-modal sequence modeling to unveil protein-dna interdependency.bioRxiv, pages 2025–02, 2025

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

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Evolutionary-scale prediction of atomic- level protein structure with a language model.Science, 379(6637):1123–1130, March 2023

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Unresolved cited work

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This paper cites Decoupled weight decay regularization.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Decoupled weight decay regularization

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Observation bde52fa4-59aa-4a0f-b5b4-2fbf7727f4a1 · outbound

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation A census-based estimate of Earth’s bacterial and archaeal diversity.PLOS Biology, 17(2):e3000106, February 2019

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This paper cites Evolution Is All You Need: Phylogenetic Augmentation for Contrastive Learning.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Evolution Is All You Need: Phylogenetic Augmentation for Contrastive Learning

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Observation 8c2620c4-8ac6-4f40-94ea-287069700e3b · outbound

This paper cites Lu, Haoran Zhang, Marzyeh Ghassemi, and Alan Moses.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Lu, Haoran Zhang, Marzyeh Ghassemi, and Alan Moses

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This paper cites UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

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This paper cites Moses, Jason E.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Moses, Jason E

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This paper cites A Metric Learning Reality Check.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation A Metric Learning Reality Check

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This paper cites Durrant, Brian Kang, Dhruva Katrekar, David B.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Durrant, Brian Kang, Dhruva Katrekar, David B

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This paper cites Representation Learning with Contrastive Predictive Coding.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Representation Learning with Contrastive Predictive Coding

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This paper cites O’Leary, Eric Cox, J.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation O’Leary, Eric Cox, J

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This paper cites Pedregosa, G.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Pedregosa, G

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Stripedhyena: Moving beyond transformers with hybrid signal processing models.GitHub repository, 12, 2023

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Learning transferable visual models from natural language supervision

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Robust and Decomposable Average Precision for Image Retrieval

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This paper cites Lawrence Zitnick, Jerry Ma, and Rob Fergus.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Lawrence Zitnick, Jerry Ma, and Rob Fergus

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.Nucleic Acids Research, 49(D1):D112–D120, January 2021

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E

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This paper cites Sangster, Cameron Dufault, Haoning Qu, Denise Le, Julie D.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Sangster, Cameron Dufault, Haoning Qu, Denise Le, Julie D

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Sastry, Ye Gao, Richard Szubin, Ying Hefner, Sibei Xu, Donghyuk Kim, Kumari Sonal Choudhary, Laurence Yang, Zachary A

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation GenBank 2025 update.Nucleic Acids Research, 53(D1):D56–D61, January 2025

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.Nature Biotechnology, 35(11):1026–1028, November 2017

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation RoFormer: Enhanced Transformer with Rotary Position Embedding

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Observation fc97f99e-d03b-4c04-afdc-f23051cb78ea · outbound

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Esm cambrian: Revealing the mysteries of proteins with unsupervised learning

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Tripp, Kimberly D

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Attention is All you Need

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Tokenization to transfer: Do genomic foundation models learn good representations? InThe Fourteenth International Conference on Learning Representations, 2026

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This paper cites Weirauch and Timothy R.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Weirauch and Timothy R

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Design prokaryotic cis-regulatory elements using language model.Nucleic Acids Research, 54(4):gkag122, February 2026

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation DNASimCLR: a contrastive learning-based deep learning approach for gene sequence data classification.BMC Bioinformatics, 25(1):328, October 2024

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This paper cites Yu, Winnie L.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Yu, Winnie L

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Lit: Zero-shot transfer with locked-image text tuning

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C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation Wayment-Steele, Garyk Brixi, Haobo Wang, Dorothee Kern, and Sergey Ovchinnikov

Reference 56

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This paper cites In their evaluations the authors used the final layer embeddings of the Evo 7B model, averaged over the sequence length and having a dimensionality of 4,096.

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation In their evaluations the authors used the final layer embeddings of the Evo 7B model, averaged over the sequence length and having a dimensionality of 4,096

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This paper cites 2.4T tokens) with sequences from all domains of life (downloaded from https://huggingface.co/arcinstitute/evo2_7b, apache-2.0 license).

C3P: Contrastive promoter-protein pretraining yields representations capturing bacterial gene regulation 2.4T tokens) with sequences from all domains of life (downloaded from https://huggingface.co/arcinstitute/evo2_7b, apache-2.0 license)

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