Automatic chemical design using a data-driven continuous representation of molecules

7 October 2016

Rafael Gómez-Bombarelli

Jennifer N. Wei

David Duvenaud

José Miguel Hernández-Lobato

Benjamín Sánchez-Lengeling

Dennis Sheberla

J. Aguilera-Iparraguirre

Papers citing "Automatic chemical design using a data-driven continuous representation of molecules"

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Title
Unlocking Guidance for Discrete State-Space Diffusion and Flow Models Hunter Nisonoff Junhao Xiong Stephan Allenspach Jennifer Listgarten 63 31 0 03 Jun 2024
Enhancing Generative Molecular Design via Uncertainty-guided Fine-tuning of Variational Autoencoders Naﬁz Abeer Sanket R. Jantre Nathan M. Urban Byung-Jun Yoon 45 0 0 31 May 2024
Ensemble Model With Bert,Roberta and Xlnet For Molecular property prediction Junling Hu 44 1 0 30 May 2024
Bridging Model-Based Optimization and Generative Modeling via Conservative Fine-Tuning of Diffusion Models Masatoshi Uehara Yulai Zhao Ehsan Hajiramezanali Gabriele Scalia Gökçen Eraslan Avantika Lal Sergey Levine Tommaso Biancalani 53 13 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 40 5 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 52 4 0 28 May 2024
Crystal-LSBO: Automated Design of De Novo Crystals with Latent Space Bayesian Optimization O. Boyar Yanheng Gu Yuji Tanaka Shunsuke Tonogai Tomoya Itakura Ichiro Takeuchi 47 2 0 28 May 2024
Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation Jeff Guo Philippe Schwaller Mamba 56 7 0 27 May 2024
Latent Energy-Based Odyssey: Black-Box Optimization via Expanded Exploration in the Energy-Based Latent Space Peiyu Yu Dinghuai Zhang Hengzhi He Xiaojian Ma Ruiyao Miao ... Deqian Kong Ruiqi Gao Jianwen Xie Guang Cheng Ying Nian Wu 48 5 0 27 May 2024
Embedding-Aligned Language Models Guy Tennenholtz Yinlam Chow Chih-Wei Hsu Lior Shani Ethan Liang Craig Boutilier AIFin 37 1 0 24 May 2024
PILOT: Equivariant diffusion for pocket conditioned de novo ligand generation with multi-objective guidance via importance sampling Julian Cremer Tuan Le Frank Noé Djork-Arné Clevert Kristof T. Schütt DiffM 35 8 0 23 May 2024
Regressor-free Molecule Generation to Support Drug Response Prediction Kun Li Xiuwen Gong Shirui Pan Jia Wu Bo Du Wenbin Hu 44 1 0 23 May 2024
Aligning Transformers with Continuous Feedback via Energy Rank Alignment Shriram Chennakesavalu Frank Hu Sebastian Ibarraran Grant M. Rotskoff 41 3 0 21 May 2024
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design Amit Kadan Kevin Ryczko Erika Lloyd A. Roitberg Takeshi Yamazaki 93 1 0 20 May 2024
Discrete-state Continuous-time Diffusion for Graph Generation Zhe Xu Ruizhong Qiu Yuzhong Chen Huiyuan Chen Xiran Fan Menghai Pan Zhichen Zeng Mahashweta Das Hanghang Tong 46 10 0 19 May 2024
Response Matching for generating materials and molecules Bingqing Cheng DiffM 37 1 0 15 May 2024
A Review on Fragment-based De Novo 2D Molecule Generation Sergei Voloboev VLM 31 1 0 08 May 2024
ACEGEN: Reinforcement learning of generative chemical agents for drug discovery Albert Bou Morgan Thomas Sebastian Dittert Carles Navarro Ramírez Maciej Majewski ... Mazen Ahmad Vincent Moens Woody Sherman Simone Sciabola Gianni De Fabritiis 50 6 0 07 May 2024
Synthetic Data from Diffusion Models Improve Drug Discovery Prediction Bing Hu Ashish Saragadam Anita Layton Helen Chen DiffM 39 1 0 06 May 2024
Graph as Point Set Xiyuan Wang Pan Li Muhan Zhang GNN 3DPC PINN 44 4 0 05 May 2024
Quality-Weighted Vendi Scores And Their Application To Diverse Experimental Design Quan Nguyen Adji Bousso Dieng 43 7 0 03 May 2024
SynFlowNet: Design of Diverse and Novel Molecules with Synthesis Constraints M. Cretu Charles Harris Julien Roy Emmanuel Bengio Pietro Lió Bruno Correia Julien Roy Emmanuel Bengio Pietro Liò 37 2 0 02 May 2024
Leveraging Active Subspaces to Capture Epistemic Model Uncertainty in Deep Generative Models for Molecular Design A. N. M. N. Abeer Sanket R. Jantre Nathan M. Urban Byung-Jun Yoon 52 1 0 30 Apr 2024
Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation Ian Dunn D. Koes BDL DiffM 46 11 0 30 Apr 2024
Generative AI for Visualization: State of the Art and Future Directions Yilin Ye Jianing Hao Yihan Hou Zhan Wang Shishi Xiao Yuyu Luo Wei Zeng 42 39 0 28 Apr 2024
GRANOLA: Adaptive Normalization for Graph Neural Networks Moshe Eliasof Beatrice Bevilacqua Carola-Bibiane Schönlieb Haggai Maron 33 5 0 20 Apr 2024
A Quadrature Approach for General-Purpose Batch Bayesian Optimization via Probabilistic Lifting Masaki Adachi Satoshi Hayakawa Martin Jørgensen Saad Hamid Harald Oberhauser Michael A. Osborne GP 32 3 0 18 Apr 2024
MolCRAFT: Structure-Based Drug Design in Continuous Parameter Space Yanru Qu Keyue Qiu Yuxuan Song Jingjing Gong Jiawei Han Mingyue Zheng Hao Zhou Wei-Ying Ma 35 18 0 18 Apr 2024
GP-MoLFormer: A Foundation Model For Molecular Generation Jerret Ross Brian M. Belgodere Samuel C. Hoffman Vijil Chenthamarakshan Youssef Mroueh Payel Das Payel Das 38 5 0 04 Apr 2024
CM-TTS: Enhancing Real Time Text-to-Speech Synthesis Efficiency through Weighted Samplers and Consistency Models Xiang Li Fan Bu Ambuj Mehrish Yingting Li Jiale Han Bo Cheng Soujanya Poria DiffM 37 6 0 31 Mar 2024
Mol-AIR: Molecular Reinforcement Learning with Adaptive Intrinsic Rewards for Goal-directed Molecular Generation Jinyeong Park Jaegyoon Ahn Jonghwan Choi Jibum Kim 36 2 0 29 Mar 2024
Space Group Informed Transformer for Crystalline Materials Generation Zhendong Cao Xiaoshan Luo Jianwei Lv Lei Wang AI4CE 39 16 0 23 Mar 2024
CardioGenAI: A Machine Learning-Based Framework for Re-Engineering Drugs for Reduced hERG Liability Gregory W. Kyro Matthew T. Martin Eric D. Watt Victor S. Batista 43 2 0 12 Mar 2024
3M-Diffusion: Latent Multi-Modal Diffusion for Text-Guided Generation of Molecular Graphs Huaisheng Zhu Teng Xiao V. Honavar DiffM 40 1 0 11 Mar 2024
Materials science in the era of large language models: a perspective Ge Lei Ronan Docherty Samuel J. Cooper 45 18 0 11 Mar 2024
Improving Variational Autoencoder Estimation from Incomplete Data with Mixture Variational Families Vaidotas Šimkus Michael U. Gutmann 43 2 0 05 Mar 2024
When SMILES have Language: Drug Classification using Text Classification Methods on Drug SMILES Strings Azmine Toushik Wasi vSerbetar Karlo Raima Islam Taki Hasan Rafi Dong-Kyu Chae 25 1 0 03 Mar 2024
Reinforced In-Context Black-Box Optimization Lei Song Chenxiao Gao Ke Xue Chenyang Wu Dong Li Haifeng Zhang Zongzhang Zhang Chao Qian 35 3 0 27 Feb 2024
Material Microstructure Design Using VAE-Regression with Multimodal Prior Avadhut Sardeshmukh Sreedhar Reddy B. Gautham Pushpak Bhattacharyya 21 0 0 27 Feb 2024
TrustMol: Trustworthy Inverse Molecular Design via Alignment with Molecular Dynamics Kevin Tirta Wijaya Navid Ansari Hans-Peter Seidel Vahid Babaei 35 0 0 26 Feb 2024
Feedback Efficient Online Fine-Tuning of Diffusion Models Masatoshi Uehara Yulai Zhao Kevin Black Ehsan Hajiramezanali Gabriele Scalia N. Diamant Alex Tseng Sergey Levine Tommaso Biancalani 39 21 0 26 Feb 2024
A Statistical Analysis of Wasserstein Autoencoders for Intrinsically Low-dimensional Data Saptarshi Chakraborty Peter L. Bartlett 44 1 0 24 Feb 2024
Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling Yuwei Yang Siqi Ouyang Xueyu Hu Mingyue Zheng Hao Zhou Lei Li 45 1 0 22 Feb 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 37 6 0 16 Feb 2024
MFBind: a Multi-Fidelity Approach for Evaluating Drug Compounds in Practical Generative Modeling Peter Eckmann D. Wu G. Heinzelmann Michael K. Gilson Rose Yu AI4CE 36 4 0 16 Feb 2024
A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation Xiangru Tang Howard Dai Elizabeth Knight Fang Wu Yunyang Li Tianxiao Li Mark B. Gerstein 24 26 0 13 Feb 2024
Subgraphormer: Unifying Subgraph GNNs and Graph Transformers via Graph Products Guy Bar-Shalom Beatrice Bevilacqua Haggai Maron AI4CE 35 6 0 13 Feb 2024
Quantum Computing-Enhanced Algorithm Unveils Novel Inhibitors for KRAS Mohammad Ghazi Vakili Christoph Gorgulla AkshatKumar Nigam Dmitry Bezrukov Daniel Varoli ... Feng Ren Yudong Cao Igor Štagljar Alán Aspuru-Guzik Alex Zhavoronkov 37 6 0 13 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 32 21 0 07 Feb 2024
Sign Rank Limitations for Inner Product Graph Decoders Su Hyeong Lee Qingqi Zhang Risi Kondor 33 0 0 06 Feb 2024