Title
ProSpero: Active Learning for Robust Protein Design Beyond Wild-Type Neighborhoods Michal Kmicikiewicz Vincent Fortuin Ewa Szczurek OnRL 62 0 0 28 May 2025
DDPS: Discrete Diffusion Posterior Sampling for Paths in Layered Graphs Hao Luan See-Kiong Ng Chun Kai Ling 103 1 0 29 Apr 2025
ProtFlow: Fast Protein Sequence Design via Flow Matching on Compressed Protein Language Model Embeddings Zitai Kong Yiheng Zhu Yinlong Xu Hanjing Zhou Mingzhe Yin Jialu Wu Hongxia Xu Chang-Yu Hsieh Tingjun Hou Jian Wu 53 0 0 15 Apr 2025
$α$ -Flow: A Unified Framework for Continuous-State Discrete Flow Matching Models Chaoran Cheng Jiahan Li Jiajun Fan Ge Liu 57 0 0 14 Apr 2025
Offline Model-Based Optimization: Comprehensive Review Minsu Kim Jiayao Gu Ye Yuan Taeyoung Yun Ziqiang Liu Yoshua Bengio Can Chen OffRL 123 4 0 21 Mar 2025
Overconfident Oracles: Limitations of In Silico Sequence Design Benchmarking Shikha Surana Nathan Grinsztajn Timothy Atkinson Paul Duckworth Thomas D. Barrett 126 4 0 24 Feb 2025
Decoupled Sequence and Structure Generation for Realistic Antibody Design Nayoung Kim Minsu Kim SungSoo Ahn Jinkyoo Park 114 0 0 20 Jan 2025
Score-based 3D molecule generation with neural fields Matthieu Kirchmeyer Pedro H. O. Pinheiro Saeed Saremi DiffM 155 2 0 15 Jan 2025
Concept Bottleneck Language Models For protein design Aya Abdelsalam Ismail Tuomas Oikarinen Amy Wang Julius Adebayo Samuel Stanton ... J. Kleinhenz Allen Goodman H. C. Bravo Kyunghyun Cho Nathan C. Frey 124 6 0 09 Nov 2024
Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization Zichen Wang Yaokun Ji Jianing Tian Shuangjia Zheng DiffM 126 3 0 19 Oct 2024
JAMUN: Transferable Molecular Conformational Ensemble Generation with Walk-Jump Sampling Ameya Daigavane Bodhi P. Vani Saeed Saremi J. Kleinhenz Joshua Rackers 75 1 0 18 Oct 2024
A noise-corrected Langevin algorithm and sampling by half-denoising Aapo Hyvärinen DiffM 107 1 0 08 Oct 2024
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 115 9 0 04 Oct 2024
Understanding Reinforcement Learning-Based Fine-Tuning of Diffusion Models: A Tutorial and Review Masatoshi Uehara Yulai Zhao Tommaso Biancalani Sergey Levine 149 32 0 18 Jul 2024
Antibody DomainBed: Out-of-Distribution Generalization in Therapeutic Protein Design Natavsa Tagasovska Ji Won Park Matthieu Kirchmeyer Nathan C. Frey Andrew Watkins ... Arian R. Jamasb Edith Lee Tyler Bryson Stephen Ra Kyunghyun Cho OOD 137 6 0 15 Jul 2024
Reinforcement Learning for Sequence Design Leveraging Protein Language Models Jithendaraa Subramanian Shivakanth Sujit Niloy Irtisam Umong Sain Derek Nowrouzezahrai Samira Ebrahimi Kahou Riashat Islam 71 0 0 03 Jul 2024
Unlocking Guidance for Discrete State-Space Diffusion and Flow Models Hunter Nisonoff Junhao Xiong Stephan Allenspach Jennifer Listgarten 165 44 0 03 Jun 2024
Full-Atom Peptide Design based on Multi-modal Flow Matching Jiahan Li Chaoran Cheng Zuofan Wu Ruihan Guo Shitong Luo Zhizhou Ren Jian-wei Peng Jianzhu Ma 115 18 0 02 Jun 2024
Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Backbone Generation Guillaume Huguet James Vuckovic Kilian Fatras Eric Thibodeau-Laufer Pablo Lemos ... Jarrid Rector-Brooks Tara Akhound-Sadegh Michael M. Bronstein Alexander Tong A. Bose 108 32 0 30 May 2024
Robust Optimization in Protein Fitness Landscapes Using Reinforcement Learning in Latent Space Minji Lee L. Vecchietti Hyunkyu Jung Hyun Joo Ro Meeyoung Cha Ho Min Kim 104 9 0 29 May 2024
Implicitly Guided Design with PropEn: Match your Data to Follow the Gradient Natavsa Tagasovska Vladimir Gligorijević Kyunghyun Cho Andreas Loukas DiffM 96 5 0 28 May 2024
Structure-based drug design by denoising voxel grids Pedro H. O. Pinheiro Arian R. Jamasb Omar Mahmood Vishnu Sresht Saeed Saremi DiffM 65 9 0 07 May 2024
Dirichlet Flow Matching with Applications to DNA Sequence Design Hannes Stärk Bowen Jing Chenyu Wang Gabriele Corso Bonnie Berger Regina Barzilay Tommi Jaakkola BDL 123 58 0 08 Feb 2024
Evolution Guided Generative Flow Networks Zarif Ikram Ling Pan Dianbo Liu 160 1 0 03 Feb 2024
Improving Protein Optimization with Smoothed Fitness Landscapes Andrew Kirjner Jason Yim Raman Samusevich Shahar Bracha Tommi Jaakkola Regina Barzilay Ila Fiete 113 17 0 02 Jul 2023
Generative Antibody Design for Complementary Chain Pairing Sequences through Encoder-Decoder Language Model S. K. Chu K. Wei AI4CE 58 7 0 06 Jan 2023