Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders

23 March 2022

Samuel Stanton

Wesley J. Maddox

Nate Gruver

Phillip M. Maffettone

Papers citing "Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders"

50 / 63 papers shown

Title
Latent Bayesian Optimization via Autoregressive Normalizing Flows Seunghun Lee Jinyoung Park Jaewon Chu Minseo Yoon H. Kim BDL 19 1 0 21 Apr 2025
GOLLuM: Gaussian Process Optimized LLMs -- Reframing LLM Finetuning through Bayesian Optimization Bojana Ranković P. Schwaller BDL 65 0 0 08 Apr 2025
Global-Order GFlowNets Lluís Pastor-Pérez Javier Alonso García Lukas Mauch 24 0 0 03 Apr 2025
Preference-Guided Diffusion for Multi-Objective Offline Optimization Yashas Annadani Syrine Belakaria Stefano Ermon Stefan Bauer Barbara Engelhardt 37 0 0 21 Mar 2025
Offline Model-Based Optimization: Comprehensive Review Minsu Kim Jiayao Gu Ye Yuan Taeyoung Yun Z. Liu Yoshua Bengio Can Chen OffRL 53 2 0 21 Mar 2025
Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization N. Maus Kyurae Kim Yimeng Zeng Haydn Jones Fangping Wan Marcelo Der Torossian Torres Cesar de la Fuente-Nunez J. Gardner 75 0 0 31 Jan 2025
Bayesian Optimization with Preference Exploration by Monotonic Neural Network Ensemble Hanyang Wang Juergen Branke Matthias Poloczek 97 0 0 30 Jan 2025
Indirect Query Bayesian Optimization with Integrated Feedback Mengyan Zhang S. Bouabid Cheng Soon Ong Seth Flaxman Dino Sejdinovic 65 0 0 18 Dec 2024
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 20 4 0 09 Nov 2024
Respecting the limit:Bayesian optimization with a bound on the optimal value Hanyang Wang Juergen Branke Matthias Poloczek 26 0 0 07 Nov 2024
MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering Yizhen Luo Zikun Nie Massimo Hong Suyuan Zhao Hao Zhou Zaiqing Nie 26 0 0 30 Oct 2024
Offline Model-Based Optimization by Learning to Rank Rong-Xi Tan Ke Xue Shen-Huan Lyu Haopu Shang Yao Wang Yaoyuan Wang Sheng Fu Chao Qian OffRL 78 2 0 15 Oct 2024
Batched Energy-Entropy acquisition for Bayesian Optimization Felix Teufel Carsten Stahlhut J. Ferkinghoff-Borg 16 0 0 11 Oct 2024
Optimistic Games for Combinatorial Bayesian Optimization with Application to Protein Design Melis Ilayda Bal Pier Giuseppe Sessa Mojmír Mutný Andreas Krause 20 0 0 27 Sep 2024
Recent advances in interpretable machine learning using structure-based protein representations L. Vecchietti Minji Lee Begench Hangeldiyev Hyunkyu Jung Hahnbeom Park Tae-Kyun Kim Meeyoung Cha Ho Min Kim AI4CE 13 1 0 26 Sep 2024
Variational Search Distributions Daniel M. Steinberg Rafael Oliveira Cheng Soon Ong Edwin V. Bonilla 27 0 0 10 Sep 2024
PROUD: PaRetO-gUided Diffusion Model for Multi-objective Generation Yinghua Yao Yuangang Pan Jing Li Ivor Tsang Xin Yao 44 6 0 05 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 30 0 0 03 Jul 2024
Diffusion-BBO: Diffusion-Based Inverse Modeling for Online Black-Box Optimization D. Wu Nikki Lijing Kuang Ruijia Niu Yi-An Ma Rose Yu 22 0 0 30 Jun 2024
Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms Samuel Stanton R. Alberstein Nathan C. Frey Andrew Watkins Kyunghyun Cho 20 4 0 28 Jun 2024
CATBench: A Compiler Autotuning Benchmarking Suite for Black-box Optimization Jacob O. Tørring Carl Hvarfner Luigi Nardi Magnus Sjalander 39 0 0 24 Jun 2024
Training Greedy Policy for Proposal Batch Selection in Expensive Multi-Objective Combinatorial Optimization Deokjae Lee Hyun Oh Song Kyunghyun Cho OffRL 34 0 0 21 Jun 2024
Active learning for affinity prediction of antibodies Alexandra Gessner Sebastian W. Ober Owen Vickery Dino Oglic Talip Uçar AI4CE 19 4 0 11 Jun 2024
A survey and benchmark of high-dimensional Bayesian optimization of discrete sequences Miguel González Duque Richard Michael Simon Bartels Yevgen Zainchkovskyy Søren Hauberg Wouter Boomsma 19 4 0 07 Jun 2024
Approximation-Aware Bayesian Optimization N. Maus Kyurae Kim Geoff Pleiss David Eriksson John P. Cunningham Jacob R. Gardner 21 1 0 06 Jun 2024
Offline Multi-Objective Optimization Ke Xue Rong-Xi Tan Xiaobin Huang Chao Qian OffRL 33 5 0 06 Jun 2024
TAGMol: Target-Aware Gradient-guided Molecule Generation Vineeth Dorna Subhalingam D Keshav Kolluru Shreshth Tuli Mrityunjay Singh Saurabh Singal N. M. A. Krishnan Sayan Ranu 24 2 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 32 14 0 02 Jun 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 19 4 0 29 May 2024
Conformal Validity Guarantees Exist for Any Data Distribution (and How to Find Them) Drew Prinster Samuel Stanton Anqi Liu S. Saria 34 5 0 10 May 2024
Bayesian-Guided Generation of Synthetic Microbiomes with Minimized Pathogenicity N. Pillai B. Nanduri Michael J. Rothrock Zhiqian Chen Mahalingam Ramkumar MedIm 21 0 0 29 Apr 2024
Generative AI for Controllable Protein Sequence Design: A Survey Yiheng Zhu Zitai Kong Jialun Wu Weize Liu Yuqiang Han Mingze Yin Hongxia Xu Chang-Yu Hsieh Tingjun Hou AI4CE 33 6 0 16 Feb 2024
A Sober Look at LLMs for Material Discovery: Are They Actually Good for Bayesian Optimization Over Molecules? Agustinus Kristiadi Felix Strieth-Kalthoff Marta Skreta Pascal Poupart Alán Aspuru-Guzik Geoff Pleiss 15 19 0 07 Feb 2024
Fine-Tuned Language Models Generate Stable Inorganic Materials as Text Nate Gruver Anuroop Sriram Andrea Madotto A. Wilson C. L. Zitnick Zachary W. Ulissi 14 53 0 06 Feb 2024
Position: Bayesian Deep Learning is Needed in the Age of Large-Scale AI Theodore Papamarkou Maria Skoularidou Konstantina Palla Laurence Aitchison Julyan Arbel ... David Rügamer Yee Whye Teh Max Welling Andrew Gordon Wilson Ruqi Zhang UQCV BDL 32 27 0 01 Feb 2024
Bayesian Optimization through Gaussian Cox Process Models for Spatio-temporal Data Yongsheng Mei Mahdi Imani Tian-Shing Lan GP 22 5 0 25 Jan 2024
Tree Search-Based Evolutionary Bandits for Protein Sequence Optimization Jiahao Qiu Hui Yuan Jinghong Zhang Wentao Chen Huazheng Wang Mengdi Wang 11 0 0 08 Jan 2024
PG-LBO: Enhancing High-Dimensional Bayesian Optimization with Pseudo-Label and Gaussian Process Guidance Taicai Chen Yue Duan Dong Li Lei Qi Yinghuan Shi Yang Gao BDL DRL 9 5 0 28 Dec 2023
Joint Composite Latent Space Bayesian Optimization Natalie Maus Zhiyuan Jerry Lin Maximilian Balandat E. Bakshy BDL 17 2 0 03 Nov 2023
Advancing Bayesian Optimization via Learning Correlated Latent Space Seunghun Lee Jaewon Chu S. Kim Juyeon Ko Hyunwoo J. Kim BDL 25 5 0 31 Oct 2023
Order-Preserving GFlowNets Yihang Chen Lukas Mauch 20 9 0 30 Sep 2023
AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodies Karolis Martinkus J. Ludwiczak Kyunghyun Cho Weishao Lian J. Lafrance-Vanasse ... A. Rajpal Y. Wu Richard Bonneau Vladimir Gligorijević Andreas Loukas DiffM 11 36 0 28 Jul 2023
Improving Protein Optimization with Smoothed Fitness Landscapes Andrew Kirjner Jason Yim Raman Samusevich Shahar Bracha Tommi Jaakkola Regina Barzilay Ila Fiete 9 14 0 02 Jul 2023
Multi-Fidelity Active Learning with GFlowNets Alex Hernandez-Garcia Nikita Saxena Moksh Jain Cheng-Hao Liu Yoshua Bengio AI4CE 11 14 0 20 Jun 2023
Is novelty predictable? Clara Fannjiang Jennifer Listgarten AI4CE 10 14 0 01 Jun 2023
A Study of Bayesian Neural Network Surrogates for Bayesian Optimization Y. Li Tim G. J. Rudner A. Wilson BDL 11 27 0 31 May 2023
Protein Design with Guided Discrete Diffusion Nate Gruver Samuel Stanton Nathan C. Frey Tim G. J. Rudner I. Hotzel J. Lafrance-Vanasse A. Rajpal Kyunghyun Cho A. Wilson DiffM 24 100 0 31 May 2023
Inverse Protein Folding Using Deep Bayesian Optimization N. Maus Yimeng Zeng Daniel A. Anderson Phillip M. Maffettone Aaron C. Solomon Peyton Greenside Osbert Bastani Jacob R. Gardner 10 2 0 25 May 2023
The Behavior and Convergence of Local Bayesian Optimization Kaiwen Wu Kyurae Kim Roman Garnett J. Gardner 25 9 0 24 May 2023
Biological Sequence Kernels with Guaranteed Flexibility Alan N. Amin Eli N. Weinstein D. Marks 16 4 0 06 Apr 2023