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

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

7 October 2016
Rafael Gómez-Bombarelli
Jennifer N. Wei
D. Duvenaud
José Miguel Hernández-Lobato
Benjamín Sánchez-Lengeling
Dennis Sheberla
J. Aguilera-Iparraguirre
Timothy D. Hirzel
Ryan P. Adams
Alán Aspuru-Guzik
    3DV
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Papers citing "Automatic chemical design using a data-driven continuous representation of molecules"

50 / 832 papers shown
Title
Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks
Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks
Xinyu Wang
Jinbo Bi
Minghu Song
CLL
62
0
0
01 May 2025
JTreeformer: Graph-Transformer via Latent-Diffusion Model for Molecular Generation
JTreeformer: Graph-Transformer via Latent-Diffusion Model for Molecular Generation
J. Q. Shi
Chengxun Xie
Zhonghao Li
Xinming Zhang
Miao Zhang
MedIm
28
0
0
29 Apr 2025
Heterophily-informed Message Passing
Heterophily-informed Message Passing
Haishan Wang
Arno Solin
Vikas K. Garg
27
0
0
28 Apr 2025
Improved Molecular Generation through Attribute-Driven Integrative Embeddings and GAN Selectivity
Improved Molecular Generation through Attribute-Driven Integrative Embeddings and GAN Selectivity
Nandan Joshi
Erhan Guven
33
0
0
26 Apr 2025
Unified Molecule Generation and Property Prediction
Unified Molecule Generation and Property Prediction
Adam Izdebski
Jan Olszewski
Pankhil Gawade
Krzysztof Koras
Serra Korkmaz
Valentin Rauscher
Jakub M. Tomczak
E. Szczurek
31
0
0
23 Apr 2025
Latent Bayesian Optimization via Autoregressive Normalizing Flows
Latent Bayesian Optimization via Autoregressive Normalizing Flows
Seunghun Lee
Jinyoung Park
Jaewon Chu
Minseo Yoon
H. Kim
BDL
30
1
0
21 Apr 2025
Generating new coordination compounds via multireference simulations, genetic algorithms and machine learning: the case of Co(II) molecular magnets
Generating new coordination compounds via multireference simulations, genetic algorithms and machine learning: the case of Co(II) molecular magnets
Lion Frangoulis
Zahra Khatibi
Lorenzo A. Mariano
Alessandro Lunghi
15
0
0
18 Apr 2025
Data Fusion of Deep Learned Molecular Embeddings for Property Prediction
Data Fusion of Deep Learned Molecular Embeddings for Property Prediction
Robert Appleton
Brian C Barnes
Alejandro Strachan
FedML
AI4CE
34
0
0
09 Apr 2025
DMol: A Schedule-Driven Diffusion Model for Highly Efficient and Versatile Molecule Generation
DMol: A Schedule-Driven Diffusion Model for Highly Efficient and Versatile Molecule Generation
Peizhi Niu
Yu-Hsiang Wang
Vishal Rana
Chetan Rupakheti
Abhishek Pandey
O. Milenkovic
30
0
0
08 Apr 2025
Critical Iterative Denoising: A Discrete Generative Model Applied to Graphs
Critical Iterative Denoising: A Discrete Generative Model Applied to Graphs
Yoann Boget
Alexandros Kalousis
DiffM
58
0
0
27 Mar 2025
Offline Model-Based Optimization: Comprehensive Review
Offline Model-Based Optimization: Comprehensive Review
Minsu Kim
Jiayao Gu
Ye Yuan
Taeyoung Yun
Z. Liu
Yoshua Bengio
Can Chen
OffRL
67
2
0
21 Mar 2025
InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization
Yifan Niu
Ziqi Gao
Tingyang Xu
Yang Liu
Yatao Bian
Yu Rong
Junzhou Huang
Jia Li
68
0
0
03 Mar 2025
Molecule Generation for Target Protein Binding with Hierarchical Consistency Diffusion Model
G. Li
Chenran Jiang
Ziqi Gao
Yu Liu
Chenyang Liu
Jiean Chen
Yong Huang
Jia Li
46
0
0
02 Mar 2025
LLM-Fusion: A Novel Multimodal Fusion Model for Accelerated Material Discovery
Onur Boyar
Indra Priyadarsini
Seiji Takeda
Lisa Hamada
42
0
0
02 Mar 2025
Virtual Nodes Can Help: Tackling Distribution Shifts in Federated Graph Learning
Virtual Nodes Can Help: Tackling Distribution Shifts in Federated Graph Learning
Xingbo Fu
Zihan Chen
Yinhan He
Song Wang
Binchi Zhang
Chen Chen
Jundong Li
OOD
FedML
61
1
0
24 Feb 2025
Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks
Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks
Maya Bechler-Speicher
Ben Finkelshtein
Fabrizio Frasca
Luis Muller
Jan Tonshoff
...
Michael M. Bronstein
Mathias Niepert
Bryan Perozzi
Mikhail Galkin
Christopher Morris
OOD
97
2
0
21 Feb 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation
Zhiyuan Liu
Yanchen Luo
Han Huang
Enzhi Zhang
Sihang Li
Junfeng Fang
Yaorui Shi
X. Wang
Kenji Kawaguchi
Tat-Seng Chua
100
3
0
18 Feb 2025
MOLLM: Multi-Objective Large Language Model for Molecular Design -- Optimizing with Experts
MOLLM: Multi-Objective Large Language Model for Molecular Design -- Optimizing with Experts
Nian Ran
Yue Wang
Richard Allmendinger
75
0
0
18 Feb 2025
Survey on Recent Progress of AI for Chemistry: Methods, Applications, and Opportunities
Survey on Recent Progress of AI for Chemistry: Methods, Applications, and Opportunities
Ding Hu
Pengxiang Hua
Zhen Huang
88
0
0
09 Feb 2025
Generating 3D Binding Molecules Using Shape-Conditioned Diffusion Models with Guidance
Ziqi Chen
B. Peng
Tianhua Zhai
Daniel Adu-Ampratwum
Xia Ning
63
1
0
09 Feb 2025
Using Random Noise Equivariantly to Boost Graph Neural Networks Universally
Using Random Noise Equivariantly to Boost Graph Neural Networks Universally
X. Wang
Muhan Zhang
107
0
0
04 Feb 2025
A Metric for the Balance of Information in Graph Learning
A Metric for the Balance of Information in Graph Learning
Alex O. Davies
Nirav Ajmeri
Telmo de Menezes e Silva Filho
46
0
0
31 Jan 2025
Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization
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
80
0
0
31 Jan 2025
FIT-GNN: Faster Inference Time for GNNs Using Coarsening
FIT-GNN: Faster Inference Time for GNNs Using Coarsening
Shubhajit Roy
Hrriday Ruparel
Kishan Ved
Anirban Dasgupta
GNN
AI4CE
65
0
0
28 Jan 2025
KAA: Kolmogorov-Arnold Attention for Enhancing Attentive Graph Neural Networks
KAA: Kolmogorov-Arnold Attention for Enhancing Attentive Graph Neural Networks
Taoran Fang
Tianhong Gao
Chunping Wang
Yihao Shang
Wei Chow
Lei Chen
Yang Yang
46
1
0
23 Jan 2025
Balancing Efficiency and Expressiveness: Subgraph GNNs with Walk-Based Centrality
Joshua Southern
Yam Eitan
Guy Bar-Shalom
Michael M. Bronstein
Haggai Maron
Fabrizio Frasca
33
1
0
06 Jan 2025
Genetic-guided GFlowNets for Sample Efficient Molecular Optimization
Genetic-guided GFlowNets for Sample Efficient Molecular Optimization
Hyeon-Seob Kim
Minsu Kim
Sanghyeok Choi
Jinkyoo Park
51
3
0
31 Dec 2024
Scalable Bayesian Optimization via Focalized Sparse Gaussian Processes
Scalable Bayesian Optimization via Focalized Sparse Gaussian Processes
Yunyue Wei
Vincent Zhuang
Saraswati Soedarmadji
Yanan Sui
126
0
0
31 Dec 2024
Safe Bayesian Optimization for the Control of High-Dimensional Embodied Systems
Safe Bayesian Optimization for the Control of High-Dimensional Embodied Systems
Yunyue Wei
Zeji Yi
Hongda Li
Saraswati Soedarmadji
Yanan Sui
28
0
0
31 Dec 2024
The Jungle of Generative Drug Discovery: Traps, Treasures, and Ways Out
Rıza Özçelik
F. Grisoni
46
0
0
24 Dec 2024
High-Dimensional Bayesian Optimization via Random Projection of Manifold
  Subspaces
High-Dimensional Bayesian Optimization via Random Projection of Manifold Subspaces
Quoc-Anh Hoang Nguyen
The Hung Tran
75
1
0
21 Dec 2024
Future Research Avenues for Artificial Intelligence in Digital Gaming:
  An Exploratory Report
Future Research Avenues for Artificial Intelligence in Digital Gaming: An Exploratory Report
Markus Dablander
75
0
0
18 Dec 2024
Bayesian Flow Is All You Need to Sample Out-of-Distribution Chemical Spaces
Bayesian Flow Is All You Need to Sample Out-of-Distribution Chemical Spaces
Nianze Tao
OOD
OODD
BDL
103
0
0
16 Dec 2024
DeepNose: An Equivariant Convolutional Neural Network Predictive Of
  Human Olfactory Percepts
DeepNose: An Equivariant Convolutional Neural Network Predictive Of Human Olfactory Percepts
Sergey A. Shuvaev
Khue Tran
Khristina Samoilova
Cyrille Mascart
A. Koulakov
72
0
0
11 Dec 2024
Towards Graph Foundation Models: A Study on the Generalization of Positional and Structural Encodings
Towards Graph Foundation Models: A Study on the Generalization of Positional and Structural Encodings
Billy Joe Franks
Moshe Eliasof
Semih Cantürk
Guy Wolf
Carola-Bibiane Schönlieb
Sophie Fellenz
Marius Kloft
AI4CE
76
0
0
10 Dec 2024
LMDM:Latent Molecular Diffusion Model For 3D Molecule Generation
LMDM:Latent Molecular Diffusion Model For 3D Molecule Generation
Xiang Chen
DiffM
74
0
0
05 Dec 2024
Hierarchical VAE with a Diffusion-based VampPrior
Hierarchical VAE with a Diffusion-based VampPrior
Anna Kuzina
Jakub M. Tomczak
DiffM
TPM
BDL
87
0
0
02 Dec 2024
Generative Model for Synthesizing Ionizable Lipids: A Monte Carlo Tree
  Search Approach
Generative Model for Synthesizing Ionizable Lipids: A Monte Carlo Tree Search Approach
Jingyi Zhao
Yuxuan Ou
Austin Tripp
Morteza Rasoulianboroujeni
José Miguel Hernández-Lobato
62
0
0
01 Dec 2024
Gradient Inversion Attack on Graph Neural Networks
Gradient Inversion Attack on Graph Neural Networks
Divya Anand Sinha
Yezi Liu
Ruijie Du
Yanning Shen
FedML
66
0
0
29 Nov 2024
Multi-scale Generative Modeling for Fast Sampling
Multi-scale Generative Modeling for Fast Sampling
Xiongye Xiao
Shixuan Li
Luzhe Huang
Gengshuo Liu
Trung-Kien Nguyen
Yi Huang
Di Chang
Mykel J. Kochenderfer
Paul Bogdan
DiffM
51
1
0
14 Nov 2024
Bio-xLSTM: Generative modeling, representation and in-context learning
  of biological and chemical sequences
Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences
Niklas Schmidinger
Lisa Schneckenreiter
Philipp Seidl
Johannes Schimunek
Pieter-Jan Hoedt
Johannes Brandstetter
Andreas Mayr
Sohvi Luukkonen
Sepp Hochreiter
G. Klambauer
MedIm
61
4
0
06 Nov 2024
Pathway-Guided Optimization of Deep Generative Molecular Design Models
  for Cancer Therapy
Pathway-Guided Optimization of Deep Generative Molecular Design Models for Cancer Therapy
Alif Bin Abdul Qayyum
S. Mertins
Amanda K. Paulson
Nathan M. Urban
Byung-Jun Yoon
30
0
0
05 Nov 2024
Understanding Variational Autoencoders with Intrinsic Dimension and
  Information Imbalance
Understanding Variational Autoencoders with Intrinsic Dimension and Information Imbalance
Charles Camboulin
Diego Doimo
Aldo Glielmo
DRL
69
0
0
04 Nov 2024
Conditional Latent Space Molecular Scaffold Optimization for Accelerated
  Molecular Design
Conditional Latent Space Molecular Scaffold Optimization for Accelerated Molecular Design
O. Boyar
Hiroyuki Hanada
I. Takeuchi
BDL
40
0
0
03 Nov 2024
GraphXForm: Graph transformer for computer-aided molecular design
GraphXForm: Graph transformer for computer-aided molecular design
Jonathan Pirnay
Jan G. Rittig
Alexander B. Wolf
Martin Grohe
Jakob Burger
Alexander Mitsos
D. G. Grimm
AI4CE
51
1
0
03 Nov 2024
EARL-BO: Reinforcement Learning for Multi-Step Lookahead,
  High-Dimensional Bayesian Optimization
EARL-BO: Reinforcement Learning for Multi-Step Lookahead, High-Dimensional Bayesian Optimization
Mujin Cheon
Jay H. Lee
Dong-Yeun Koh
Calvin Tsay
28
0
0
31 Oct 2024
Diffusion Twigs with Loop Guidance for Conditional Graph Generation
Diffusion Twigs with Loop Guidance for Conditional Graph Generation
Giangiacomo Mercatali
Yogesh Verma
André Freitas
Vikas K. Garg
31
3
0
31 Oct 2024
SAFE setup for generative molecular design
SAFE setup for generative molecular design
Yassir El Mesbahi
Emmanuel Noutahi
31
0
0
26 Oct 2024
Hybrid Generative AI for De Novo Design of Co-Crystals with Enhanced
  Tabletability
Hybrid Generative AI for De Novo Design of Co-Crystals with Enhanced Tabletability
Nina Gubina
Andrei Dmitrenko
Gleb Solovev
Lyubov Yamshchikova
Oleg Petrov
Ivan Lebedev
N. Serov
Grigorii Kirgizov
Nikolay Nikitin
Vladimir Vinogradov
26
0
0
22 Oct 2024
Cliqueformer: Model-Based Optimization with Structured Transformers
Cliqueformer: Model-Based Optimization with Structured Transformers
J. Kuba
Pieter Abbeel
Sergey Levine
OffRL
AI4CE
59
2
0
17 Oct 2024
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