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Protein Design with Guided Discrete Diffusion

Protein Design with Guided Discrete Diffusion

31 May 2023
Nate Gruver
Samuel Stanton
Nathan C. Frey
Tim G. J. Rudner
I. Hotzel
J. Lafrance-Vanasse
A. Rajpal
Kyunghyun Cho
A. Wilson
    DiffM
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Papers citing "Protein Design with Guided Discrete Diffusion"

27 / 27 papers shown
Title
Multi-Step Consistency Models: Fast Generation with Theoretical Guarantees
Multi-Step Consistency Models: Fast Generation with Theoretical Guarantees
Nishant Jain
Xunpeng Huang
Yian Ma
Tong Zhang
46
0
0
02 May 2025
Latent Bayesian Optimization via Autoregressive Normalizing Flows
Latent Bayesian Optimization via Autoregressive Normalizing Flows
Seunghun Lee
Jinyoung Park
Jaewon Chu
Minseo Yoon
H. Kim
BDL
30
1
0
21 Apr 2025
Fine-Tuning Discrete Diffusion Models with Policy Gradient Methods
Fine-Tuning Discrete Diffusion Models with Policy Gradient Methods
Oussama Zekri
Nicolas Boullé
DiffM
62
3
0
03 Feb 2025
Simplified and Generalized Masked Diffusion for Discrete Data
Simplified and Generalized Masked Diffusion for Discrete Data
Jiaxin Shi
Kehang Han
Z. Wang
Arnaud Doucet
Michalis K. Titsias
DiffM
79
62
0
17 Jan 2025
Bayesian Flow Is All You Need to Sample Out-of-Distribution Chemical Spaces
Bayesian Flow Is All You Need to Sample Out-of-Distribution Chemical Spaces
Nianze Tao
OOD
OODD
BDL
97
0
0
16 Dec 2024
DiffGAD: A Diffusion-based Unsupervised Graph Anomaly Detector
DiffGAD: A Diffusion-based Unsupervised Graph Anomaly Detector
Jinghan Li
Yuan Gao
Jinda Lu
Junfeng Fang
Congcong Wen
Hui Lin
Xiang Wang
50
1
0
09 Oct 2024
Chemistry-Inspired Diffusion with Non-Differentiable Guidance
Chemistry-Inspired Diffusion with Non-Differentiable Guidance
Yuchen Shen
Chenhao Zhang
Sijie Fu
Chenghui Zhou
Newell Washburn
Barnabás Póczos
50
0
0
09 Oct 2024
How Discrete and Continuous Diffusion Meet: Comprehensive Analysis of Discrete Diffusion Models via a Stochastic Integral Framework
How Discrete and Continuous Diffusion Meet: Comprehensive Analysis of Discrete Diffusion Models via a Stochastic Integral Framework
Yinuo Ren
Haoxuan Chen
Grant M. Rotskoff
Lexing Ying
47
3
0
04 Oct 2024
Convergence of Score-Based Discrete Diffusion Models: A Discrete-Time Analysis
Convergence of Score-Based Discrete Diffusion Models: A Discrete-Time Analysis
Zikun Zhang
Zixiang Chen
Quanquan Gu
DiffM
58
3
0
03 Oct 2024
Discrete Copula Diffusion
Discrete Copula Diffusion
Anji Liu
Oliver Broadrick
Mathias Niepert
Guy Van den Broeck
DiffM
59
4
0
02 Oct 2024
Variational Search Distributions
Variational Search Distributions
Daniel M. Steinberg
Rafael Oliveira
Cheng Soon Ong
Edwin V. Bonilla
33
0
0
10 Sep 2024
Molecular Diffusion Models with Virtual Receptors
Molecular Diffusion Models with Virtual Receptors
Matan Halfon
Eyal Rozenberg
Ehud Rivlin
Daniel Freedman
50
0
0
26 Jun 2024
Training Greedy Policy for Proposal Batch Selection in Expensive
  Multi-Objective Combinatorial Optimization
Training Greedy Policy for Proposal Batch Selection in Expensive Multi-Objective Combinatorial Optimization
Deokjae Lee
Hyun Oh Song
Kyunghyun Cho
OffRL
38
0
0
21 Jun 2024
Unlocking Guidance for Discrete State-Space Diffusion and Flow Models
Unlocking Guidance for Discrete State-Space Diffusion and Flow Models
Hunter Nisonoff
Junhao Xiong
Stephan Allenspach
Jennifer Listgarten
55
31
0
03 Jun 2024
Implicitly Guided Design with PropEn: Match your Data to Follow the
  Gradient
Implicitly Guided Design with PropEn: Match your Data to Follow the Gradient
Natavsa Tagasovska
Vladimir Gligorijević
Kyunghyun Cho
Andreas Loukas
DiffM
52
4
0
28 May 2024
Preference optimization of protein language models as a multi-objective
  binder design paradigm
Preference optimization of protein language models as a multi-objective binder design paradigm
Pouria A. Mistani
Venkatesh Mysore
32
6
0
07 Mar 2024
Fine-Tuned Language Models Generate Stable Inorganic Materials as Text
Fine-Tuned Language Models Generate Stable Inorganic Materials as Text
Nate Gruver
Anuroop Sriram
Andrea Madotto
A. Wilson
C. L. Zitnick
Zachary W. Ulissi
27
55
0
06 Feb 2024
Resurrecting Recurrent Neural Networks for Long Sequences
Resurrecting Recurrent Neural Networks for Long Sequences
Antonio Orvieto
Samuel L. Smith
Albert Gu
Anushan Fernando
Çağlar Gülçehre
Razvan Pascanu
Soham De
88
265
0
11 Mar 2023
Muse: Text-To-Image Generation via Masked Generative Transformers
Muse: Text-To-Image Generation via Masked Generative Transformers
Huiwen Chang
Han Zhang
Jarred Barber
AJ Maschinot
José Lezama
...
Kevin Patrick Murphy
William T. Freeman
Michael Rubinstein
Yuanzhen Li
Dilip Krishnan
DiffM
197
519
0
02 Jan 2023
DiffusER: Discrete Diffusion via Edit-based Reconstruction
DiffusER: Discrete Diffusion via Edit-based Reconstruction
Machel Reid
Vincent J. Hellendoorn
Graham Neubig
DiffM
45
39
0
30 Oct 2022
Diffusion-LM Improves Controllable Text Generation
Diffusion-LM Improves Controllable Text Generation
Xiang Lisa Li
John Thickstun
Ishaan Gulrajani
Percy Liang
Tatsunori B. Hashimoto
AI4CE
173
773
0
27 May 2022
Protein Structure and Sequence Generation with Equivariant Denoising
  Diffusion Probabilistic Models
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models
N. Anand
Tudor Achim
DiffM
187
173
0
26 May 2022
RePaint: Inpainting using Denoising Diffusion Probabilistic Models
RePaint: Inpainting using Denoising Diffusion Probabilistic Models
Andreas Lugmayr
Martin Danelljan
Andrés Romero
F. I. F. Richard Yu
Radu Timofte
Luc Van Gool
DiffM
213
1,354
0
24 Jan 2022
"Will You Find These Shortcuts?" A Protocol for Evaluating the
  Faithfulness of Input Salience Methods for Text Classification
"Will You Find These Shortcuts?" A Protocol for Evaluating the Faithfulness of Input Salience Methods for Text Classification
Jasmijn Bastings
Sebastian Ebert
Polina Zablotskaia
Anders Sandholm
Katja Filippova
115
75
0
14 Nov 2021
Benchmarking deep generative models for diverse antibody sequence design
Benchmarking deep generative models for diverse antibody sequence design
Igor Melnyk
Payel Das
Vijil Chenthamarakshan
A. Lozano
DiffM
40
17
0
12 Nov 2021
Generalization in NLI: Ways (Not) To Go Beyond Simple Heuristics
Generalization in NLI: Ways (Not) To Go Beyond Simple Heuristics
Prajjwal Bhargava
Aleksandr Drozd
Anna Rogers
95
101
0
04 Oct 2021
Argmax Flows and Multinomial Diffusion: Learning Categorical
  Distributions
Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions
Emiel Hoogeboom
Didrik Nielsen
P. Jaini
Patrick Forré
Max Welling
DiffM
207
394
0
10 Feb 2021
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