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Generative modeling of discrete data underlies important applications spanning text-based agents like ChatGPT to the design of the very building blocks of life in protein sequences.
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Tm-align: a protein structure alignment algorithm based on the tm-score
Y. Zhang and J. Skolnick · 2005
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Deep reinforcement learning from human preferences
P. F. Christiano, J. Leike, T. Brown, M. Martic, S. Legg, and D. Amodei · 2017
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T. Salimans, A. Karpathy, X. Chen, and D. P. Kingma · 2017
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Mmseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
M. Steinegger and J. Söding · 2017
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Bert: Pre-training of deep bidirectional transformers for language understanding
J. Devlin · 2018
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Large-scale celebfaces attributes (celeba) dataset
Z. Liu, P. Luo, X. Wang, and X. Tang · 2018
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Roberta: A robustly optimized bert pretraining approach
Y. Liu · 2019
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Language models are unsupervised multitask learners
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Bayesflow: Learning complex stochastic models with invertible neural networks
S. T. Radev, U. K. Mertens, A. Voss, L. Ardizzone, and U. Köthe · 2020
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Learning to summarize with human feedback
N. Stiennon, L. Ouyang, J. Wu, D. Ziegler, R. Lowe, C. Voss, A. Radford, D. Amodei, and P. F. Christiano · 2020
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Structured denoising diffusion models in discrete state-spaces
J. Austin, D. D. Johnson, J. Ho, D. Tarlow, and R. Van Den Berg · 2021
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Flow network based generative models for non-iterative diverse candidate generation
E. Bengio, M. Jain, M. Korablyov, D. Precup, and Y. Bengio · 2021
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Diffusion models beat gans on image synthesis
P. Dhariwal and A. Nichol · 2021
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Webgpt: Browser-assisted question-answering with human feedback
R. Nakano, J. Hilton, S. Balaji, J. Wu, L. Ouyang, C. Kim, C. Hesse, S. Jain, V. Kosaraju, W. Saunders, et al · 2021
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A continuous time framework for discrete denoising models
A. Campbell, J. Benton, V. De Bortoli, T. Rainforth, G. Deligiannidis, and A. Doucet · 2022
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Analog bits: Generating discrete data using diffusion models with self-conditioning
T. Chen, R. Zhang, and G. Hinton · 2022
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Robust deep learning–based protein sequence design using proteinmpnn
J. Dauparas, I. Anishchenko, N. Bennett, H. Bai, R. J. Ragotte, L. F. Milles, B. I. Wicky, A. Courbet, R. J. de Haas, N. Bethel, et al · 2022
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A high-level programming language for generative protein design
B. Hie, S. Candido, Z. Lin, O. Kabeli, R. Rao, N. Smetanin, T. Sercu, and A. Rives · 2022
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Classifier-free diffusion guidance
J. Ho and T. Salimans · 2022
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Diffusion-lm improves controllable text generation
X. Li, J. Thickstun, I. Gulrajani, P. S. Liang, and T. B. Hashimoto · 2022
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Language models of protein sequences at the scale of evolution enable accurate structure prediction
Z. Lin, H. Akin, R. Rao, B. Hie, Z. Zhu, W. Lu, N. Smetanin, A. dos Santos Costa, M. Fazel-Zarandi, T. Sercu, S. Candido, et al · 2022
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Learning gflownets from partial episodes for improved convergence and stability. iclr’2023
K. Madan, J. Rector-Brooks, M. Korablyov, E. Bengio, M. Jain, A. Nica, T. Bosc, Y. Bengio, and N. Malkin · 2022
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Trajectory balance: Improved credit assignment in gflownets
N. Malkin, M. Jain, E. Bengio, C. Sun, and Y. Bengio · 2022
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Concrete score matching: Generalized score matching for discrete data
C. Meng, K. Choi, J. Song, and S. Ermon · 2022
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Training language models to follow instructions with human feedback
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Red teaming language models with language models
E. Perez, S. Huang, F. Song, T. Cai, R. Ring, J. Aslanides, A. Glaese, N. McAleese, and G. Irving · 2022
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Foldseek: fast and accurate protein structure search
M. van Kempen, S. S. Kim, C. Tumescheit, M. Mirdita, C. L. Gilchrist, J. Söding, and M. Steinegger · 2022
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Language models generalize beyond natural proteins
R. Verkuil, O. Kabeli, Y. Du, B. I. Wicky, L. F. Milles, J. Dauparas, D. Baker, S. Ovchinnikov, T. Sercu, and A. Rives · 2022
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Digress: Discrete denoising diffusion for graph generation
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A. Campbell, J. Yim, R. Barzilay, T. Rainforth, and T. Jaakkola · 2024
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Categorical flow matching on statistical manifolds
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Fisher flow matching for generative modeling over discrete data
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V. De Bortoli, M. Hutchinson, P. Wirnsberger, and A. Doucet · 2024
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Miniaturizing, modifying, and augmenting nature’s proteins with raygun
K. Devkota, D. Shonai, J. Mao, S. H. Soderling, and R. Singh · 2024
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Gflownet foundations
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Simple and effective masked diffusion language models
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