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GuacaMol: Benchmarking Models for De Novo Molecular Design
v1v2 (latest)

GuacaMol: Benchmarking Models for De Novo Molecular Design

Journal of Chemical Information and Modeling (JCIM), 2018
22 November 2018
Nathan Brown
Marco Fiscato
Marwin H. S. Segler
Alain C. Vaucher
    ELM
ArXiv (abs)PDFHTML

Papers citing "GuacaMol: Benchmarking Models for De Novo Molecular Design"

50 / 253 papers shown
We Still Don't Understand High-Dimensional Bayesian Optimization
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Colin Doumont
Donney Fan
Natalie Maus
Jacob R. Gardner
Henry B. Moss
Geoff Pleiss
AI4CE
116
2
0
10 Apr 2026
Efficient and Programmable Exploration of Synthesizable Chemical Space
Efficient and Programmable Exploration of Synthesizable Chemical Space
Shitong Luo
Connor W. Coley
98
1
0
29 Nov 2025
FRAGMENTA: End-to-end Fragmentation-based Generative Model with Agentic Tuning for Drug Lead Optimization
FRAGMENTA: End-to-end Fragmentation-based Generative Model with Agentic Tuning for Drug Lead Optimization
Yuto Suzuki
Paul Awolade
Daniel V. LaBarbera
Farnoush Banaei-Kashani
MedImVLM
406
1
0
25 Nov 2025
Artificial Intelligence Driven Workflow for Accelerating Design of Novel Photosensitizers
Artificial Intelligence Driven Workflow for Accelerating Design of Novel Photosensitizers
Hongyi Wang
Xiuli Zheng
Weimin Liu
Zitian Tang
Sheng Gong
93
1
0
24 Nov 2025
Chatbots to strengthen democracy: An interdisciplinary seminar to train identifying argumentation techniques of science denial
Chatbots to strengthen democracy: An interdisciplinary seminar to train identifying argumentation techniques of science denial
Ingo Siegert
Jan Nehring
Aranxa Márquez Ampudia
Matthias Busch
Stefan Hillmann
100
0
0
21 Nov 2025
Pharmacophore-based design by learning on voxel grids
Pharmacophore-based design by learning on voxel grids
Omar Mahmood
Pedro H. O. Pinheiro
Richard Bonneau
Saeed Saremi
Vishnu Sresht
89
0
0
19 Nov 2025
Chain-of-Generation: Progressive Latent Diffusion for Text-Guided Molecular Design
Chain-of-Generation: Progressive Latent Diffusion for Text-Guided Molecular Design
Lingxiao Li
Haobo Zhang
Bin Chen
Jiayu Zhou
DiffMAI4CE
192
0
0
14 Nov 2025
Feedback Descent: Open-Ended Text Optimization via Pairwise Comparison
Feedback Descent: Open-Ended Text Optimization via Pairwise Comparison
Yoonho Lee
Joseph Boen
Chelsea Finn
255
16
0
11 Nov 2025
Discrete Bayesian Sample Inference for Graph Generation
Discrete Bayesian Sample Inference for Graph Generation
Ole Petersen
Marcel Kollovieh
Marten Lienen
Stephan Günnemann
DiffM
328
1
0
04 Nov 2025
STAR-VAE: Latent Variable Transformers for Scalable and Controllable Molecular Generation
STAR-VAE: Latent Variable Transformers for Scalable and Controllable Molecular Generation
Bum Chul Kwon
Ben Shapira
Moshiko Raboh
Shreyans Sethi
Shruti Murarka
Joseph A. Morrone
Jianying Hu
Parthasarathy Suryanarayanan
BDL
231
0
0
04 Nov 2025
Diffusion Models at the Drug Discovery Frontier: A Review on Generating Small Molecules versus Therapeutic Peptides
Diffusion Models at the Drug Discovery Frontier: A Review on Generating Small Molecules versus Therapeutic Peptides
Yiquan Wang
Yahui Ma
Yuhan Chang
Jiayao Yan
Jialin Zhang
Minnuo Cai
Kai Wei
MedIm
490
2
0
31 Oct 2025
Distributional Multi-objective Black-box Optimization for Diffusion-model Inference-time Multi-Target Generation
Distributional Multi-objective Black-box Optimization for Diffusion-model Inference-time Multi-Target Generation
Kim yong Tan
Yueming Lyu
Ivor W. Tsang
Yew-Soon Ong
103
0
0
30 Oct 2025
Evaluating Medical LLMs by Levels of Autonomy: A Survey Moving from Benchmarks to Applications
Evaluating Medical LLMs by Levels of Autonomy: A Survey Moving from Benchmarks to Applications
Xiao Ye
Jacob Dineen
Zhaonan Li
Zhikun Xu
Weiyu Chen
...
Ji-Eun Irene Yum
Muhammad Ali Khan
Muhammad Umar Afzal
Irbaz B. Riaz
Ben Zhou
LM&MAELM
257
1
0
20 Oct 2025
Controllable Graph Generation with Diffusion Models via Inference-Time Tree Search Guidance
Controllable Graph Generation with Diffusion Models via Inference-Time Tree Search Guidance
Jiachi Zhao
Zehong Wang
Yamei Liao
Chuxu Zhang
Yanfang Ye
AI4CE
189
3
0
12 Oct 2025
Graph Diffusion Transformers are In-Context Molecular Designers
Graph Diffusion Transformers are In-Context Molecular Designers
Gang Liu
Jie Chen
Yihan Zhu
Michael Sun
Tengfei Luo
Nitesh Chawla
Meng Jiang
DiffMAI4CE
140
2
0
09 Oct 2025
PolyGraph Discrepancy: a classifier-based metric for graph generation
PolyGraph Discrepancy: a classifier-based metric for graph generation
Markus Krimmel
Philip Hartout
Karsten Borgwardt
Dexiong Chen
216
2
0
07 Oct 2025
A Genetic Algorithm for Navigating Synthesizable Molecular Spaces
A Genetic Algorithm for Navigating Synthesizable Molecular Spaces
Alston Lo
Connor W. Coley
Wojciech Matusik
189
3
0
25 Sep 2025
ExMolRL: Phenotype-Target Joint Generation of De Novo Molecules via Multi-Objective Reinforcement Learning
ExMolRL: Phenotype-Target Joint Generation of De Novo Molecules via Multi-Objective Reinforcement Learning
Haotian Guo
Hui Liu
97
0
0
25 Sep 2025
NMR-Solver: Automated Structure Elucidation via Large-Scale Spectral Matching and Physics-Guided Fragment Optimization
NMR-Solver: Automated Structure Elucidation via Large-Scale Spectral Matching and Physics-Guided Fragment Optimization
Yongqi Jin
Jun-Jie Wang
Fanjie Xu
Xiaohong Ji
Zhifeng Gao
Linfeng Zhang
Guolin Ke
Rong Zhu
Weinan E
80
7
0
30 Aug 2025
A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Design
A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Design
Haydn Thomas Jones
Natalie Maus
Josh Magnus Ludan
Maggie Ziyu Huan
Jiaming Liang
...
Z. Ives
Yoseph Barash
Cesar de la Fuente-Nunez
Jacob R. Gardner
Mark Yatskar
220
2
0
14 Aug 2025
Sparse Probabilistic Graph Circuits
Sparse Probabilistic Graph Circuits
Martin Rektoris
Milan Papez
Václav Smídl
Tomás Pevný
TPM
342
0
0
11 Aug 2025
MolSnap: Snap-Fast Molecular Generation with Latent Variational Mean Flow
MolSnap: Snap-Fast Molecular Generation with Latent Variational Mean Flow
Md Atik Ahamed
Qiang Ye
Q. Cheng
BDL
188
3
0
07 Aug 2025
Look the Other Way: Designing 'Positive' Molecules with Negative Data via Task Arithmetic
Look the Other Way: Designing 'Positive' Molecules with Negative Data via Task Arithmetic
Rıza Özçelik
Sarah de Ruiter
F. Grisoni
259
0
0
23 Jul 2025
A study of EHVI vs fixed scalarization for molecule design
A study of EHVI vs fixed scalarization for molecule design
Anabel Yong
Austin Tripp
Layla Hosseini-Gerami
Brooks Paige
276
2
0
18 Jul 2025
Bures-Wasserstein Flow Matching for Graph Generation
Bures-Wasserstein Flow Matching for Graph Generation
Keyue Jiang
Jiahao Cui
Xiaowen Dong
Laura Toni
376
2
0
16 Jun 2025
Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?
Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?
Fei Lin
Ziyang Gong
Cong Wang
Yonglin Tian
Tengchao Zhang
...
Fei Wang
Xiaotong Yu
Xue Yang
Gen Luo
Fei-Yue Wang
382
3
0
12 Jun 2025
Scalable and Cost-Efficient de Novo Template-Based Molecular Generation
Scalable and Cost-Efficient de Novo Template-Based Molecular Generation
Piotr Gaiñski
Oussama Boussif
Andrei Rekesh
Dmytro Shevchuk
Ali Parviz
Mike Tyers
Robert A. Batey
Michał Koziarski
249
5
0
10 Jun 2025
A collaborative constrained graph diffusion model for the generation of realistic synthetic molecules
A collaborative constrained graph diffusion model for the generation of realistic synthetic molecules
Manuel Ruiz-Botella
Marta Sales-Pardo
Roger Guimerà
193
0
0
22 May 2025
A Survey of Large Language Models for Text-Guided Molecular Discovery: from Molecule Generation to Optimization
A Survey of Large Language Models for Text-Guided Molecular Discovery: from Molecule Generation to Optimization
Ziqing Wang
Kexin Zhang
Zihan Zhao
Yibo Wen
Abhishek Pandey
Han Liu
Kaize Ding
410
5
0
22 May 2025
Learning Flexible Forward Trajectories for Masked Molecular Diffusion
Learning Flexible Forward Trajectories for Masked Molecular Diffusion
Hyunjin Seo
Taewon Kim
Sihyun Yu
SungSoo Ahn
DiffMAI4CE
728
2
0
22 May 2025
A Comprehensive Benchmarking Platform for Deep Generative Models in Molecular Design
A Comprehensive Benchmarking Platform for Deep Generative Models in Molecular Design
Adarsh Singh
ELM
172
0
0
19 May 2025
El Agente: An Autonomous Agent for Quantum Chemistry
El Agente: An Autonomous Agent for Quantum Chemistry
Yunheng Zou
Austin H. Cheng
Abdulrahman Aldossary
Jiaru Bai
Shi Xuan Leong
...
Ilya Yakavets
Han Hao
Chris Crebolder
Varinia Bernales
Alán Aspuru-Guzik
362
1
0
05 May 2025
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
361
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01 May 2025
Latent Bayesian Optimization via Autoregressive Normalizing Flows
Latent Bayesian Optimization via Autoregressive Normalizing FlowsInternational Conference on Learning Representations (ICLR), 2025
Seunghun Lee
Jinyoung Park
Jaewon Chu
Minseo Yoon
H. Kim
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389
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DMol: A Highly Efficient and Chemical Motif-Preserving Molecule Generation Platform
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Peizhi Niu
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Vishal Rana
Chetan Rupakheti
Abhishek Pandey
O. Milenkovic
806
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Offline Model-Based Optimization: Comprehensive Review
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Minsu Kim
Jiayao Gu
Ye Yuan
Taeyoung Yun
Ziqiang Liu
Yoshua Bengio
Can Chen
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483
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Chem42: a Family of chemical Language Models for Target-aware Ligand Generation
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A. Singh
Engin Tekin
Maryam Nadeem
Nancy A. ElNaker
Mohammad Amaan Sayeed
Natalia Vassilieva
Boulbaba Ben Amor
438
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20 Mar 2025
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation
Mohit Pandey
G. Subbaraj
Artem Cherkasov
Martin Ester
Emmanuel Bengio
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619
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Backdoor Attacks on Discrete Graph Diffusion Models
Backdoor Attacks on Discrete Graph Diffusion Models
Jiawen Wang
Samin Karim
Yuan Hong
Binghui Wang
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513
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SAGE-Amine: Generative Amine Design with Multi-Property Optimization for Efficient CO2 Capture
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Hocheol Lim
Hyein Cho
Jeonghoon Kim
296
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04 Mar 2025
InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization
InversionGNN: A Dual Path Network for Multi-Property Molecular OptimizationInternational Conference on Learning Representations (ICLR), 2025
Yifan Niu
Ziqi Gao
Qifeng Bai
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Yatao Bian
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Jia Li
324
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03 Mar 2025
A Survey of Graph Transformers: Architectures, Theories and Applications
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Chaohao Yuan
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Ercan Engin Kuruoglu
Shu Wu
Qifeng Bai
Wenbing Huang
Deli Zhao
Hong Cheng
Yu Rong
542
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23 Feb 2025
Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks
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Maya Bechler-Speicher
Ben Finkelshtein
Fabrizio Frasca
Luis Muller
Jan Tönshoff
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Michael M. Bronstein
Mathias Niepert
Bryan Perozzi
Mikhail Galkin
Christopher Morris
OOD
646
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ExLLM: Experience-Enhanced LLM Optimization for Molecular Design and Beyond
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Nian Ran
Yue Wang
Xiaoyuan Zhang
Zhongzheng Li
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Richard Allmendinger
632
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HOG-Diff: Higher-Order Guided Diffusion for Graph Generation
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Tolga Birdal
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498
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Fast Graph Generation via Autoregressive Noisy Filtration Modeling
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Dexiong Chen
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Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization
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