Fetching the paper…
Reading the bibliography…
Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences.
Plug and play language models: A simple approach to controlled text generation
Dathathri, S., A. Madotto, J. Lan, J. Hung, E. Frank, P. Molino, J. Yosinski, and R. Liu (2019) · 1912
Earlier work this paper cites.
ZINC- a free database of commercially available compounds for virtual screening
Irwin, J. J. and B. K. Shoichet (2005) · 2005
Earlier work this paper cites.
Denoising diffusion implicit models
Song, J., C. Meng, and S. Ermon (2020) · 2010
Earlier work this paper cites.
Autodock vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
Trott, O. and A. J. Olson (2010) · 2010
Earlier work this paper cites.
Score-based generative modeling through stochastic differential equations
Song, Y., J. Sohl-Dickstein, D. P. Kingma, A. Kumar, S. Ermon, and B. Poole (2020) · 2011
Earlier work this paper cites.
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets
van Westen, G. J., R. F. Swier, I. Cortes-Ciriano, J. K. Wegner, J. P. Overington, A. P. IJzerman, H. W. van Vlijmen, and A. Bender (2013) · 2013
Earlier work this paper cites.
Particle methods: An introduction with applications
Del Moral, P. and A. Doucet (2014) · 2014
Earlier work this paper cites.
Fast, accurate, and reliable molecular docking with quickvina 2
Alhossary, A., S. D. Handoko, Y. Mu, and C.-K. Kwoh (2015) · 2015
Earlier work this paper cites.
Big data of materials science: critical role of the descriptor
Ghiringhelli, L. M., J. Vybiral, S. V. Levchenko, C. Draxl, and M. Scheffler (2015) · 2015
Earlier work this paper cites.
Nested sequential monte carlo methods
Naesseth, C., F. Lindsten, and T. Schon (2015) · 2015
Earlier work this paper cites.
Towards better decoding and language model integration in sequence to sequence models
Chorowski, J. and N. Jaitly (2016) · 2016
Earlier work this paper cites.
Rdkit: Open-source cheminformatics software, 2016
Landrum, G. et al. (2016) · 2016
Earlier work this paper cites.
Google’s neural machine translation system: Bridging the gap between human and machine translation
Wu, Y., M. Schuster, Z. Chen, Q. V. Le, M. Norouzi, W. Macherey, M. Krikun, Y. Cao, Q. Gao, K. Macherey, et al. (2016) · 2016
Earlier work this paper cites.
Adding conditional control to diffusion models with reinforcement learning
Zhao, Y., M. Uehara, G. Scalia, T. Biancalani, S. Levine, and E. Hajiramezanali (2024) · 2016
Earlier work this paper cites.
The rosetta all-atom energy function for macromolecular modeling and design
Alford, R. F., A. Leaver-Fay, J. R. Jeliazkov, M. J. O’Meara, F. P. DiMaio, H. Park, M. V. Shapovalov, P. D. Renfrew, V. K. Mulligan, K. Kappel, et al. (2017) · 2017
Earlier work this paper cites.
Gate-variants of gated recurrent unit (gru) neural networks
Dey, R. and F. M. Salem (2017) · 2017
Earlier work this paper cites.
Reinforcement learning with deep energy-based policies
Haarnoja, T., H. Tang, P. Abbeel, and S. Levine (2017) · 2017
Earlier work this paper cites.
Optimization of mrna untranslated regions for improved expression of therapeutic mrna
Asrani, K. H., J. D. Farelli, M. R. Stahley, R. L. Miller, C. J. Cheng, R. R. Subramanian, and J. M. Brown (2018) · 2018
Earlier work this paper cites.
Junction tree variational autoencoder for molecular graph generation
Jin, W., R. Barzilay, and T. Jaakkola (2018) · 2018
Earlier work this paper cites.
Reinforcement learning and control as probabilistic inference: Tutorial and review
Levine, S. (2018) · 2018
Earlier work this paper cites.
How powerful are graph neural networks?
Xu, K., W. Hu, J. Leskovec, and S. Jegelka (2018) · 2018
Earlier work this paper cites.
A theory of regularized markov decision processes
Geist, M., B. Scherrer, and O. Pietquin (2019) · 2019
Earlier work this paper cites.
Identification and massively parallel characterization of regulatory elements driving neural induction
Inoue, F., A. Kreimer, T. Ashuach, N. Ahituv, and N. Yosef (2019) · 2019
Earlier work this paper cites.
Elements of sequential monte carlo
Naesseth, C. A., F. Lindsten, T. B. Schön, et al. (2019) · 2019
Earlier work this paper cites.
Pytorch: An imperative style, high-performance deep learning library
Paszke, A., S. Gross, F. Massa, A. Lerer, J. Bradbury, G. Chanan, T. Killeen, Z. Lin, N. Gimelshein, L. Antiga, et al. (2019) · 2019
Earlier work this paper cites.
Human 5’utr design and variant effect prediction from a massively parallel translation assay
Sample, P. J., B. Wang, D. W. Reid, V. Presnyak, I. J. McFadyen, D. R. Morris, and G. Seelig (2019) · 2019
Earlier work this paper cites.
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
Gainza, P., F. Sverrisson, F. Monti, E. Rodola, D. Boscaini, M. M. Bronstein, and B. E. Correia (2020) · 2020
Earlier work this paper cites.
Denoising diffusion probabilistic models
Ho, J., A. Jain, and P. Abbeel (2020) · 2020
Earlier work this paper cites.
Learning to summarize with human feedback
Stiennon, N., L. Ouyang, J. Wu, D. Ziegler, R. Lowe, C. Voss, A. Radford, D. Amodei, and P. F. Christiano (2020) · 2020
Earlier work this paper cites.
Structured denoising diffusion models in discrete state-spaces
Austin, J., D. D. Johnson, J. Ho, D. Tarlow, and R. Van Den Berg (2021) · 2021
Earlier work this paper cites.
Effective gene expression prediction from sequence by integrating long-range interactions
Avsec, Ž., V. Agarwal, D. Visentin, J. R. Ledsam, A. Grabska-Barwinska, K. R. Taylor, Y. Assael, J. Jumper, P. Kohli, and D. R. Kelley (2021) · 2021
Earlier work this paper cites.
Machine learning for designing next-generation mrna therapeutics
Castillo-Hair, S. M. and G. Seelig (2021) · 2021
Cited alongside, same era.
Diffusion models beat gans on image synthesis
Dhariwal, P. and A. Nichol (2021) · 2021
Cited alongside, same era.
Machine translation decoding beyond beam search
Leblond, R., J.-B. Alayrac, L. Sifre, M. Pislar, J.-B. Lespiau, I. Antonoglou, K. Simonyan, and O. Vinyals (2021) · 2021
Cited alongside, same era.
Webgpt: Browser-assisted question-answering with human feedback
Nakano, R., J. Hilton, S. Balaji, J. Wu, L. Ouyang, C. Kim, C. Hesse, S. Jain, V. Kosaraju, W. Saunders, et al. (2021) · 2021
Cited alongside, same era.
Fudge: Controlled text generation with future discriminators
Yang, K. and D. Klein (2021) · 2021
Cited alongside, same era.
Exploring chemical space with score-based out-of-distribution generation
Lee, S., J. Jo, and S. J. Hwang (2023) · 2023
Later among the works it cites.
Sequential monte carlo steering of large language models using probabilistic programs
Lew, A. K., T. Zhi-Xuan, G. Grand, and V. K. Mansinghka (2023) · 2023
Later among the works it cites.
Discrete diffusion language modeling by estimating the ratios of the data distribution
Lou, A., C. Meng, and S. Ermon (2023) · 2023
Later among the works it cites.
Controlled decoding from language models
Mudgal, S., J. Lee, H. Ganapathy, Y. Li, T. Wang, Y. Huang, Z. Chen, H.-T. Cheng, M. Collins, T. Strohman, et al. (2023) · 2023
Later among the works it cites.
Aligning text-to-image diffusion models with reward backpropagation
alphaXiv searches the wider corpus for related work and actual follow-ups.
alphaXiv is searching for related work…
Hit and lead discovery with explorative rl and fragment-based molecule generation
Yang, S., D. Hwang, S. Lee, S. Ryu, and S. J. Hwang (2021) · 2021
Cited alongside, same era.
A continuous time framework for discrete denoising models
Campbell, A., J. Benton, V. De Bortoli, T. Rainforth, G. Deligiannidis, and A. Doucet (2022) · 2022
Cited alongside, same era.
Diffusion posterior sampling for general noisy inverse problems
Chung, H., J. Kim, M. T. Mccann, M. L. Klasky, and J. C. Ye (2022) · 2022
Cited alongside, same era.
Classifier-free diffusion guidance
Ho, J. and T. Salimans (2022) · 2022
Cited alongside, same era.
Video diffusion models
Ho, J., T. Salimans, A. Gritsenko, W. Chan, M. Norouzi, and D. J. Fleet (2022) · 2022
Cited alongside, same era.
Score-based generative modeling of graphs via the system of stochastic differential equations
Jo, J., S. Lee, and S. J. Hwang (2022) · 2022
Cited alongside, same era.
Cold decoding: Energy-based constrained text generation with langevin dynamics
Qin, L., S. Welleck, D. Khashabi, and Y. Choi (2022) · 2022
Cited alongside, same era.
Prabhudesai, M., A. Goyal, D. Pathak, and K. Fragkiadaki (2023) · 2023
Later among the works it cites.
Llama 2: Open foundation and fine-tuned chat models
Touvron, H., L. Martin, K. Stone, P. Albert, A. Almahairi, Y. Babaei, N. Bashlykov, S. Batra, P. Bhargava, S. Bhosale, et al. (2023) · 2023
Later among the works it cites.
De novo design of protein structure and function with rfdiffusion
Watson, J. L., D. Juergens, N. R. Bennett, B. L. Trippe, J. Yim, H. E. Eisenach, W. Ahern, A. J. Borst, R. J. Ragotte, L. F. Milles, et al. (2023) · 2023
Later among the works it cites.
Geometric latent diffusion models for 3d molecule generation
Xu, M., A. S. Powers, R. O. Dror, S. Ermon, and J. Leskovec (2023) · 2023
Later among the works it cites.
Freedom: Training-free energy-guided conditional diffusion model
Yu, J., Y. Wang, C. Zhao, B. Ghanem, and J. Zhang (2023) · 2023
Later among the works it cites.
Theoretical guarantees on the best-of-n alignment policy
Beirami, A., A. Agarwal, J. Berant, A. D’Amour, J. Eisenstein, C. Nagpal, and A. T. Suresh (2024) · 2024
Closest in time.
Campbell, A., J. Yim, R. Barzilay, T. Rainforth, and T. Jaakkola (2024) · 2024
Closest in time.
Diffusion posterior sampling for linear inverse problem solving: A filtering perspective
Dou, Z. and Y. Song (2024) · 2024
Closest in time.
Dna-diffusion: Leveraging generative models for controlling chromatin accessibility and gene expression via synthetic regulatory elements
Ferreira DaSilva, L., S. Senan, Z. M. Patel, A. J. Reddy, S. Gabbita, Z. Nussbaum, C. M. V. Cordova, A. Wenteler, N. Weber, T. M. Tunjic, et al. (2024) · 2024
Closest in time.
Gradient guidance for diffusion models: An optimization perspective
Guo, Y., H. Yuan, Y. Yang, M. Chen, and M. Wang (2024) · 2024
Closest in time.
Value augmented sampling for language model alignment and personalization
Han, S., I. Shenfeld, A. Srivastava, Y. Kim, and P. Agrawal (2024) · 2024
Closest in time.
Simulating 500 million years of evolution with a language model
Hayes, T., R. Rao, H. Akin, N. J. Sofroniew, D. Oktay, Z. Lin, R. Verkuil, V. Q. Tran, J. Deaton, M. Wiggert, et al. (2024) · 2024
Closest in time.
reglm: Designing realistic regulatory dna with autoregressive language models
Lal, A., D. Garfield, T. Biancalani, and G. Eraslan (2024) · 2024
Closest in time.
Unlocking guidance for discrete state-space diffusion and flow models
Nisonoff, H., J. Xiong, S. Allenspach, and J. Listgarten (2024) · 2024
Closest in time.
Particle denoising diffusion sampler
Phillips, A., H.-D. Dau, M. J. Hutchinson, V. De Bortoli, G. Deligiannidis, and A. Doucet (2024) · 2024
Closest in time.
Simple and effective masked diffusion language models
Sahoo, S. S., M. Arriola, Y. Schiff, A. Gokaslan, E. Marroquin, J. T. Chiu, A. Rush, and V. Kuleshov (2024) · 2024
Closest in time.
Designing dna with tunable regulatory activity using discrete diffusion
Sarkar, A., Z. Tang, C. Zhao, and P. Koo (2024) · 2024
Closest in time.
Simplified and generalized masked diffusion for discrete data
Shi, J., K. Han, Z. Wang, A. Doucet, and M. K. Titsias (2024) · 2024
Closest in time.
Dirichlet flow matching with applications to dna sequence design
Stark, H., B. Jing, C. Wang, G. Corso, B. Berger, R. Barzilay, and T. Jaakkola (2024) · 2024
Closest in time.
Cell-type-directed design of synthetic enhancers
Taskiran, I. I., K. I. Spanier, H. Dickmänken, N. Kempynck, A. Pančíková, E. C. Ekşi, G. Hulselmans, J. N. Ismail, K. Theunis, R. Vandepoel, et al. (2024) · 2024
Closest in time.
Understanding reinforcement learning-based fine-tuning of diffusion models: A tutorial and review
Uehara, M., Y. Zhao, T. Biancalani, and S. Levine (2024) · 2024
Closest in time.
Fine-tuning of continuous-time diffusion models as entropy-regularized control
Uehara, M., Y. Zhao, K. Black, E. Hajiramezanali, G. Scalia, N. L. Diamant, A. M. Tseng, T. Biancalani, and S. Levine (2024) · 2024
Closest in time.
Uehara, M., Y. Zhao, E. Hajiramezanali, G. Scalia, G. Eraslan, A. Lal, S. Levine, and T. Biancalani (2024) · 2024
Closest in time.
Diffusion model alignment using direct preference optimization
Wallace, B., M. Dang, R. Rafailov, L. Zhou, A. Lou, S. Purushwalkam, S. Ermon, C. Xiong, S. Joty, and N. Naik (2024) · 2024
Closest in time.
Practical and asymptotically exact conditional sampling in diffusion models
Wu, L., B. Trippe, C. Naesseth, D. Blei, and J. P. Cunningham (2024) · 2024
Closest in time.
Probabilistic inference in language models via twisted sequential monte carlo
Zhao, S., R. Brekelmans, A. Makhzani, and R. Grosse (2024) · 2024
Closest in time.