Paper Citation Record · LEDGER

Towards A Generative Protein Evolution Machine with DPLM-Evo

As of 5 August 2026, this Paper Citation Record lists 61 of 61 outbound references and 1 inbound Pith citation observation for arXiv:2605.00182.

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pith.paper-citation-record.v1
2605.00182 v3

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Reference resolution

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Outbound references

Observation 2c9f8769-3867-4208-9e7d-5f6319a47fb7 · outbound

This paper cites Protein generation with evolutionary diffusion: sequence is all you need.bioRxiv, pages 2023–09.

Towards A Generative Protein Evolution Machine with DPLM-Evo Protein generation with evolutionary diffusion: sequence is all you need.bioRxiv, pages 2023–09

Reference 1

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Observation 0a2b7f48-c9f7-469e-b582-17d05f947b56 · outbound

This paper cites Structured denoising diffusion models in discrete state-spaces.

Towards A Generative Protein Evolution Machine with DPLM-Evo Structured denoising diffusion models in discrete state-spaces

Reference 2

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Observation 63b71cc1-ee9a-4366-b543-3fe4d9c8fe9e · outbound

This paper cites A diffusion model to shrink proteins while maintaining their function.

Towards A Generative Protein Evolution Machine with DPLM-Evo A diffusion model to shrink proteins while maintaining their function

Reference 3

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Observation a1941042-ca7d-4259-80fb-f77e3c621b9f · outbound

This paper cites Protein sequence profile prediction using protalbert transformer.Computational Biology and Chemistry, 99:107717.

Towards A Generative Protein Evolution Machine with DPLM-Evo Protein sequence profile prediction using protalbert transformer.Computational Biology and Chemistry, 99:107717

Reference 4

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Observation 90618837-703d-45da-b1fe-f5a9318b686a · outbound

This paper cites Proteinbert: a universal deep- learning model of protein sequence and function.Bioinformatics, 38(8):2102–2110.

Towards A Generative Protein Evolution Machine with DPLM-Evo Proteinbert: a universal deep- learning model of protein sequence and function.Bioinformatics, 38(8):2102–2110

Reference 5

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Observation 1b887bdf-77f2-4b26-83c7-94bf60042a1f · outbound

This paper cites Famsa: Fast and accurate multiple se- quence alignment of huge protein families.Scientific reports, 6(1):33964.

Towards A Generative Protein Evolution Machine with DPLM-Evo Famsa: Fast and accurate multiple se- quence alignment of huge protein families.Scientific reports, 6(1):33964

Reference 6

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Observation a24f8a2a-0e7e-4e92-a52e-9542ba1d026d · outbound

This paper cites Prottrans: Toward understanding the language of life through self-supervised learning.

Towards A Generative Protein Evolution Machine with DPLM-Evo Prottrans: Toward understanding the language of life through self-supervised learning

Reference 7

Resolution: verified fuzzy; raw_fallback, observed 2026-07-06T13:42:37.524808Z

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This paper cites Esm cambrian: Revealing the mysteries of proteins with unsupervised learning.

Towards A Generative Protein Evolution Machine with DPLM-Evo Esm cambrian: Revealing the mysteries of proteins with unsupervised learning

Reference 8

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Observation 481fc757-18a5-4e8c-9615-760540fe6fc4 · outbound

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

Towards A Generative Protein Evolution Machine with DPLM-Evo Disease variant prediction with deep generative models of evolutionary data.Nature, 599(7883):91–95

Reference 9

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Observation 2ebcecf7-7b15-4d35-881a-96dde1d02908 · outbound

This paper cites Scaling diffusion language models via adaptation from autoregressive models.

Towards A Generative Protein Evolution Machine with DPLM-Evo Scaling diffusion language models via adaptation from autoregressive models

Reference 10

Resolution: verified fuzzy; raw_fallback, observed 2026-07-06T13:42:37.493611Z

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This paper cites Connectionist temporal clas- sification: labelling unsegmented sequence data with recurrent neural networks.

Towards A Generative Protein Evolution Machine with DPLM-Evo Connectionist temporal clas- sification: labelling unsegmented sequence data with recurrent neural networks

Reference 11

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Observation e876c95e-748f-4124-9ca7-2176ca203750 · outbound

This paper cites Protein design with guided discrete diffusion.

Towards A Generative Protein Evolution Machine with DPLM-Evo Protein design with guided discrete diffusion

Reference 12

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Observation 11c85d11-b102-47be-8f35-82c7e728cae8 · outbound

This paper cites Fully non-autoregressive neural machine translation: Tricks of the trade.

Towards A Generative Protein Evolution Machine with DPLM-Evo Fully non-autoregressive neural machine translation: Tricks of the trade

Reference 13

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Observation 3f6e1e8a-c030-4dfd-a3e3-91838e377985 · outbound

This paper cites Levenshtein transformer.

Towards A Generative Protein Evolution Machine with DPLM-Evo Levenshtein transformer

Reference 14

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This paper cites Nat: Neural architecture transformer for accurate and compact architectures.Advances in Neural Information Processing Systems, 32.

Towards A Generative Protein Evolution Machine with DPLM-Evo Nat: Neural architecture transformer for accurate and compact architectures.Advances in Neural Information Processing Systems, 32

Reference 15

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Observation c7898c00-3bdb-4285-b71f-61a6e28872b1 · outbound

This paper cites Edit flows: Flow matching with edit operations.arXiv preprint arXiv:2506.09018.

Towards A Generative Protein Evolution Machine with DPLM-Evo Edit flows: Flow matching with edit operations.arXiv preprint arXiv:2506.09018

Reference 16

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Observation c4cae6a3-b3b8-4a91-b7b2-d3d9cbcda3cd · outbound

This paper cites Simulating 500 million years of evolution with a language model.

Towards A Generative Protein Evolution Machine with DPLM-Evo Simulating 500 million years of evolution with a language model

Reference 17

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This paper cites Diffusionbert: Improving gen- erative masked language models with diffusion models.

Towards A Generative Protein Evolution Machine with DPLM-Evo Diffusionbert: Improving gen- erative masked language models with diffusion models

Reference 18

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Observation bcdd867e-2da9-49cd-9e40-c0f9ea6d99a7 · outbound

This paper cites Denoising diffusion probabilistic models.

Towards A Generative Protein Evolution Machine with DPLM-Evo Denoising diffusion probabilistic models

Reference 19

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Observation e4bc9871-2074-4400-913e-bfad792d3d48 · outbound

This paper cites Argmax flows and multinomial diffusion: Learning categorical distributions.

Towards A Generative Protein Evolution Machine with DPLM-Evo Argmax flows and multinomial diffusion: Learning categorical distributions

Reference 20

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Observation 8c1c896a-0ee0-4401-9c78-b74dbfb4288b · outbound

This paper cites Elucidatingthedesignspaceofmultimodalproteinlanguagemodels.

Towards A Generative Protein Evolution Machine with DPLM-Evo Elucidatingthedesignspaceofmultimodalproteinlanguagemodels

Reference 21

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Observation 0e69cfe6-7ac7-4850-a5ba-adc57a436982 · outbound

This paper cites Learning inverse folding from millions of predicted structures.

Towards A Generative Protein Evolution Machine with DPLM-Evo Learning inverse folding from millions of predicted structures

Reference 22

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This paper cites Gemme: a simple and fast global epistatic model predicting mutational effects.Molecular biology and evolution, 36(11):2604–2619.

Towards A Generative Protein Evolution Machine with DPLM-Evo Gemme: a simple and fast global epistatic model predicting mutational effects.Molecular biology and evolution, 36(11):2604–2619

Reference 23

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Observation 740a0637-06a7-4e9c-893b-1b14410a6342 · outbound

This paper cites Language models of protein sequences at the scale of evolution enable accurate structure prediction.BioRxiv.

Towards A Generative Protein Evolution Machine with DPLM-Evo Language models of protein sequences at the scale of evolution enable accurate structure prediction.BioRxiv

Reference 24

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Observation 75dee439-8fd0-45ad-a64b-364a02aaed75 · outbound

This paper cites Evolutionary-scale prediction of atomic-level protein structure with a language model.

Towards A Generative Protein Evolution Machine with DPLM-Evo Evolutionary-scale prediction of atomic-level protein structure with a language model

Reference 25

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This paper cites Sequential diffusion language models.

Towards A Generative Protein Evolution Machine with DPLM-Evo Sequential diffusion language models

Reference 26

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This paper cites Expert-guided pro- tein language models enable accurate and blazingly fast fitness prediction.Bioinformatics, 40(11):btae621, 11.

Towards A Generative Protein Evolution Machine with DPLM-Evo Expert-guided pro- tein language models enable accurate and blazingly fast fitness prediction.Bioinformatics, 40(11):btae621, 11

Reference 27

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This paper cites doi: 10.1093/bioinformatics/btae621.

Towards A Generative Protein Evolution Machine with DPLM-Evo doi: 10.1093/bioinformatics/btae621

Reference 28

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This paper cites Language models enable zero-shot prediction of the effects of mutations on protein function.

Towards A Generative Protein Evolution Machine with DPLM-Evo Language models enable zero-shot prediction of the effects of mutations on protein function

Reference 29

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Observation 09b03239-3521-4816-b8cc-2a9dbff7f7e1 · outbound

This paper cites Dima: Diffusion mamba – a diffusion model with state space backbone for protein design.

Towards A Generative Protein Evolution Machine with DPLM-Evo Dima: Diffusion mamba – a diffusion model with state space backbone for protein design

Reference 30

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This paper cites Transforming the language of life: transformer neural networks for protein prediction tasks.

Towards A Generative Protein Evolution Machine with DPLM-Evo Transforming the language of life: transformer neural networks for protein prediction tasks

Reference 31

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Observation 24f6fa4d-f022-46db-8e97-b0a6c27cd1a8 · outbound

This paper cites Scaling up masked diffusion models on text.

Towards A Generative Protein Evolution Machine with DPLM-Evo Scaling up masked diffusion models on text

Reference 32

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Observation 1ceb3d46-9ba3-48a3-a09a-fe5eecf211a5 · outbound

This paper cites Large Language Diffusion Models.

Towards A Generative Protein Evolution Machine with DPLM-Evo Large Language Diffusion Models

Reference 33

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This paper cites ProGen2: Exploring the Boundaries of Protein Language Models.

Towards A Generative Protein Evolution Machine with DPLM-Evo ProGen2: Exploring the Boundaries of Protein Language Models

Reference 34

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Observation e003b8f4-0f93-4afc-bfc3-da57c961eb2e · outbound

This paper cites Proteingym: Large-scale benchmarks for protein fitness prediction and design.

Towards A Generative Protein Evolution Machine with DPLM-Evo Proteingym: Large-scale benchmarks for protein fitness prediction and design

Reference 35

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This paper cites Your absorbing discrete diffusion secretly models the conditional distributions of clean data.

Towards A Generative Protein Evolution Machine with DPLM-Evo Your absorbing discrete diffusion secretly models the conditional distributions of clean data

Reference 36

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Observation e0198d34-a454-4f42-a3fd-a9e99ef6163f · outbound

This paper cites Evaluating protein transfer learning with tape.

Towards A Generative Protein Evolution Machine with DPLM-Evo Evaluating protein transfer learning with tape

Reference 37

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This paper cites Diffuser: Diffusion via edit-based reconstruction.

Towards A Generative Protein Evolution Machine with DPLM-Evo Diffuser: Diffusion via edit-based reconstruction

Reference 38

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

Towards A Generative Protein Evolution Machine with DPLM-Evo Lawrence Zitnick, Jerry Ma, and Rob Fergus

Reference 39

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This paper cites Simpleandeffectivemaskeddiffusionlanguagemodels.

Towards A Generative Protein Evolution Machine with DPLM-Evo Simpleandeffectivemaskeddiffusionlanguagemodels

Reference 40

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This paper cites The diffusion duality.

Towards A Generative Protein Evolution Machine with DPLM-Evo The diffusion duality

Reference 41

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This paper cites Simple guidance mechanisms for discrete diffusion models.

Towards A Generative Protein Evolution Machine with DPLM-Evo Simple guidance mechanisms for discrete diffusion models

Reference 42

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This paper cites Simplified and generalized masked diffusion for discrete data.Advancesin neural information processing systems, 37:103131–103167.

Towards A Generative Protein Evolution Machine with DPLM-Evo Simplified and generalized masked diffusion for discrete data.Advancesin neural information processing systems, 37:103131–103167

Reference 43

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This paper cites Deep unsupervised learning using nonequilibrium thermodynamics.

Towards A Generative Protein Evolution Machine with DPLM-Evo Deep unsupervised learning using nonequilibrium thermodynamics

Reference 44

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This paper cites URLhttps://proceedings.mlr.press/v37/sohl-dickstein15.html.

Towards A Generative Protein Evolution Machine with DPLM-Evo URLhttps://proceedings.mlr.press/v37/sohl-dickstein15.html

Reference 45

Resolution: verified fuzzy; raw_fallback, observed 2026-07-06T13:42:37.466621Z

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This paper cites Denoising diffusion implicit models.

Towards A Generative Protein Evolution Machine with DPLM-Evo Denoising diffusion implicit models

Reference 46

Resolution: verified fuzzy; raw_fallback, observed 2026-07-06T13:42:37.469050Z

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This paper cites Score- based generative modeling through stochastic differential equations.

Towards A Generative Protein Evolution Machine with DPLM-Evo Score- based generative modeling through stochastic differential equations

Reference 47

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Observation c775ac57-9ca0-44b6-a94e-17d657b7e353 · outbound

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

Towards A Generative Protein Evolution Machine with DPLM-Evo Saprot: Protein language modeling with structure-aware vocabulary.bioRxiv, pages 2023–10

Reference 48

Resolution: verified fuzzy; raw_fallback, observed 2026-07-06T13:42:37.491406Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation d8402592-7ce7-45bf-8edb-eea239d7014c · outbound

This paper cites PoET: A generative model of protein families as sequences-of-sequences.

Towards A Generative Protein Evolution Machine with DPLM-Evo PoET: A generative model of protein families as sequences-of-sequences

Reference 49

Resolution: verified fuzzy; raw_fallback, observed 2026-07-06T13:42:37.459293Z

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Observation cfda7e34-9dd9-49f1-b785-c8913ea58c60 · outbound

This paper cites Language models generalize beyond natural proteins.bioRxiv, pages 2022–12.

Towards A Generative Protein Evolution Machine with DPLM-Evo Language models generalize beyond natural proteins.bioRxiv, pages 2022–12

Reference 50

Resolution: verified fuzzy; raw_fallback, observed 2026-07-06T13:42:37.477498Z

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Observation 45a511c8-e3ec-4911-9464-ccdb15799740 · outbound

This paper cites Gen- eralized interpolating discrete diffusion.

Towards A Generative Protein Evolution Machine with DPLM-Evo Gen- eralized interpolating discrete diffusion

Reference 51

Resolution: verified fuzzy; raw_fallback, observed 2026-07-06T13:42:37.464148Z

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Observation a4f66361-6fb8-489b-b8aa-4827172e1e17 · outbound

This paper cites DPLM-2: A Multimodal Diffusion Protein Language Model.

Towards A Generative Protein Evolution Machine with DPLM-Evo DPLM-2: A Multimodal Diffusion Protein Language Model

Reference 52

Resolution: verified exact; arxiv_id, observed 2026-07-01T08:05:30.838461Z

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Observation 2f64dcec-a684-48b6-91bc-7fdb983393be · outbound

This paper cites Diffusion Language Models Are Versatile Protein Learners.

Towards A Generative Protein Evolution Machine with DPLM-Evo Diffusion Language Models Are Versatile Protein Learners

Reference 53

Resolution: verified exact; arxiv_id, observed 2026-07-01T08:05:30.820845Z

Source-reported events for the cited work

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Observation 8cf71208-9c4f-488e-a1f3-a50cdc32898f · outbound

This paper cites Dreamon: Diffusion language models for code infilling beyond fixed-size canvas.

Towards A Generative Protein Evolution Machine with DPLM-Evo Dreamon: Diffusion language models for code infilling beyond fixed-size canvas

Reference 54

Resolution: verified fuzzy; raw_fallback, observed 2026-07-06T13:42:37.482447Z

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Observation 6d1a4b5c-4ba6-4376-b501-290d3f41cd06 · outbound

This paper cites Modeling Protein Using Large-scale Pretrain Language Model.

Towards A Generative Protein Evolution Machine with DPLM-Evo Modeling Protein Using Large-scale Pretrain Language Model

Reference 55

Resolution: verified exact; arxiv_id, observed 2026-07-01T08:05:30.834844Z

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Observation 4bee2478-323c-4fcf-abf8-f9e4672436ac · outbound

This paper cites Convolutions are competitive with transformers for protein sequence pretraining.

Towards A Generative Protein Evolution Machine with DPLM-Evo Convolutions are competitive with transformers for protein sequence pretraining

Reference 56

Resolution: verified fuzzy; raw_fallback, observed 2026-07-06T13:42:37.506754Z

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Observation 7f929090-2cf1-4185-806b-0fef679a8a3f · outbound

This paper cites Dream 7B: Diffusion Large Language Models.

Towards A Generative Protein Evolution Machine with DPLM-Evo Dream 7B: Diffusion Large Language Models

Reference 57

Resolution: verified exact; local_arxiv, observed 2026-07-01T08:05:30.806849Z

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Observation 80c6884c-6355-46c5-92b7-017136da4160 · outbound

This paper cites Diffusion Language Models Can Perform Many Tasks with Scaling and Instruction-Finetuning.

Towards A Generative Protein Evolution Machine with DPLM-Evo Diffusion Language Models Can Perform Many Tasks with Scaling and Instruction-Finetuning

Reference 58

Resolution: verified exact; arxiv_id, observed 2026-07-01T08:05:30.797220Z

Source-reported events for the cited work

No event found in the named queried sources as of 2026-08-05T06:32:48.257954+00:00.

Observation 5c5e9215-b6ad-40f9-a20a-28a1af5556ca · outbound

This paper cites DINOISER: Diffused Conditional Sequence Learning by Manipulating Noises.

Towards A Generative Protein Evolution Machine with DPLM-Evo DINOISER: Diffused Conditional Sequence Learning by Manipulating Noises

Reference 59

Resolution: verified exact; arxiv_id, observed 2026-07-01T08:05:30.817387Z

Source-reported events for the cited work

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Observation 62be88ec-216a-4e6b-b625-6c7732aa79f7 · outbound

This paper cites A Reparameterized Discrete Diffusion Model for Text Generation.

Towards A Generative Protein Evolution Machine with DPLM-Evo A Reparameterized Discrete Diffusion Model for Text Generation

Reference 60

Resolution: verified exact; arxiv_id, observed 2026-07-01T08:05:30.827484Z

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Observation a36aaccd-3be1-4fd4-b5dc-260644c07a0c · outbound

This paper cites Structure-informed language models are protein designers.

Towards A Generative Protein Evolution Machine with DPLM-Evo Structure-informed language models are protein designers

Reference 61

Resolution: verified fuzzy; raw_fallback, observed 2026-07-06T13:42:37.540246Z

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Pith citing papers

Observation 0341f131-13ce-4c9a-a7d5-463f0f0c02e8 · inbound

AMix-2: Establishing Protein as a Native Modality in Large Language Models cites this paper.

AMix-2: Establishing Protein as a Native Modality in Large Language Models Towards A Generative Protein Evolution Machine with DPLM-Evo

Reference 60

Resolution: verified exact; local_arxiv, observed 2026-06-28T20:12:37.759097Z

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