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Multi-Objective De Novo Drug Design with Conditional Graph Generative
  Model
v1v2v3 (latest)

Multi-Objective De Novo Drug Design with Conditional Graph Generative Model

18 January 2018
Yibo Li
L. Zhang
Zhenming Liu
ArXiv (abs)PDFHTML

Papers citing "Multi-Objective De Novo Drug Design with Conditional Graph Generative Model"

50 / 128 papers shown
Graph VQ-Transformer (GVT): Fast and Accurate Molecular Generation via High-Fidelity Discrete Latents
Graph VQ-Transformer (GVT): Fast and Accurate Molecular Generation via High-Fidelity Discrete Latents
Haozhuo Zheng
Cheng Wang
Yang Liu
89
0
0
02 Dec 2025
Scaffold-Aware Generative Augmentation and Reranking for Enhanced Virtual Screening
Scaffold-Aware Generative Augmentation and Reranking for Enhanced Virtual Screening
Xin Eric Wang
Y. Wang
Yunchao Liu
J. Meiler
Tyler Derr
196
1
0
18 Oct 2025
Coder as Editor: Code-driven Interpretable Molecular Optimization
Coder as Editor: Code-driven Interpretable Molecular Optimization
Wenyu Zhu
Chengzhu Li
Xiaohe Tian
Yifan Wang
Yinjun Jia
Jianhui Wang
Bowen Gao
Ya Zhang
Wei-Ying Ma
Yanyan Lan
122
2
0
16 Oct 2025
Graph Generation with Spectral Geodesic Flow Matching
Graph Generation with Spectral Geodesic Flow Matching
Xikun Huang
Tianyu Ruan
Chihao Zhang
Shihua Zhang
243
1
0
02 Oct 2025
AReUReDi: Annealed Rectified Updates for Refining Discrete Flows with Multi-Objective Guidance
AReUReDi: Annealed Rectified Updates for Refining Discrete Flows with Multi-Objective Guidance
Tong Chen
Yinuo Zhang
Pranam Chatterjee
226
4
0
30 Sep 2025
A Genetic Algorithm for Navigating Synthesizable Molecular Spaces
A Genetic Algorithm for Navigating Synthesizable Molecular Spaces
Alston Lo
Connor W. Coley
Wojciech Matusik
190
3
0
25 Sep 2025
SBGD: Improving Graph Diffusion Generative Model via Stochastic Block Diffusion
SBGD: Improving Graph Diffusion Generative Model via Stochastic Block Diffusion
Junwei Su
Shan Wu
DiffM
251
0
0
20 Aug 2025
Diverse Mini-Batch Selection in Reinforcement Learning for Efficient Chemical Exploration in de novo Drug Design
Diverse Mini-Batch Selection in Reinforcement Learning for Efficient Chemical Exploration in de novo Drug Design
Hampus Gummesson Svensson
Ola Engkvist
J. Janet
C. Tyrchan
M. Chehreghani
OffRL
391
1
0
26 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
252
5
0
10 Jun 2025
Multi-Objective-Guided Discrete Flow Matching for Controllable Biological Sequence Design
Multi-Objective-Guided Discrete Flow Matching for Controllable Biological Sequence Design
Tong Chen
Yinuo Zhang
Sophia Tang
Pranam Chatterjee
519
17
0
11 May 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
Yang Liu
Yatao Bian
Yu Rong
Junzhou Huang
Jia Li
327
2
0
03 Mar 2025
Auto-encoding Molecules: Graph-Matching Capabilities Matter
Auto-encoding Molecules: Graph-Matching Capabilities Matter
Magnus Cunow
Gerrit Großmann
GNN
239
0
0
01 Mar 2025
Genetic-guided GFlowNets for Sample Efficient Molecular Optimization
Genetic-guided GFlowNets for Sample Efficient Molecular OptimizationNeural Information Processing Systems (NeurIPS), 2024
Hyeon-Seob Kim
Minsu Kim
Sanghyeok Choi
Jinkyoo Park
439
24
0
31 Dec 2024
GraphXForm: Graph transformer for computer-aided molecular design
GraphXForm: Graph transformer for computer-aided molecular designDigital Discovery (DD), 2024
Jonathan Pirnay
Jan G. Rittig
Alexander B. Wolf
Martin Grohe
Jakob Burger
Alexander Mitsos
D. G. Grimm
AI4CE
528
7
0
03 Nov 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 TabletabilityNeural Information Processing Systems (NeurIPS), 2024
Nina Gubina
Andrei Dmitrenko
Gleb Solovev
Lyubov Yamshchikova
Oleg Petrov
Ivan Lebedev
N. Serov
Grigorii Kirgizov
Nikolay Nikitin
Vladimir Vinogradov
259
3
0
22 Oct 2024
Heterogeneous Graph Generation: A Hierarchical Approach using Node
  Feature Pooling
Heterogeneous Graph Generation: A Hierarchical Approach using Node Feature Pooling
Hritaban Ghosh
Chen Changyu
Arunesh Sinha
Shamik Sural
197
0
0
15 Oct 2024
Chemistry-Inspired Diffusion with Non-Differentiable Guidance
Chemistry-Inspired Diffusion with Non-Differentiable GuidanceInternational Conference on Learning Representations (ICLR), 2024
Yuchen Shen
Chenhao Zhang
Sijie Fu
Chenghui Zhou
Newell Washburn
Barnabás Póczos
398
5
0
09 Oct 2024
Generative Artificial Intelligence for Navigating Synthesizable Chemical
  Space
Generative Artificial Intelligence for Navigating Synthesizable Chemical Space
Wenhao Gao
Shitong Luo
Connor W. Coley
297
20
0
04 Oct 2024
Quantum-inspired Reinforcement Learning for Synthesizable Drug Design
Quantum-inspired Reinforcement Learning for Synthesizable Drug Design
Dannong Wang
Jintai Chen
Zhiding Liang
Tianfan Fu
Xiao-Yang Liu
265
6
0
13 Sep 2024
Instruction-Based Molecular Graph Generation with Unified Text-Graph Diffusion Model
Instruction-Based Molecular Graph Generation with Unified Text-Graph Diffusion Model
Yuran Xiang
Haiteng Zhao
Chang Ma
Zhi-Hong Deng
325
3
0
19 Aug 2024
A Bayesian Flow Network Framework for Chemistry Tasks
A Bayesian Flow Network Framework for Chemistry TasksJournal of Chemical Information and Modeling (JCIM), 2024
Nianze Tao
Minori Abe
BDL
379
10
0
28 Jul 2024
LICO: Large Language Models for In-Context Molecular Optimization
LICO: Large Language Models for In-Context Molecular OptimizationInternational Conference on Learning Representations (ICLR), 2024
Tung Nguyen
Aditya Grover
371
27
0
27 Jun 2024
Diffusion Models in $\textit{De Novo}$ Drug Design
Diffusion Models in De Novo\textit{De Novo}De Novo Drug DesignJournal of Chemical Information and Modeling (JCIM), 2024
Amira Alakhdar
Barnabas Poczos
Newell Washburn
MedIm
250
68
0
07 Jun 2024
Enhancing Generative Molecular Design via Uncertainty-guided Fine-tuning
  of Variational Autoencoders
Enhancing Generative Molecular Design via Uncertainty-guided Fine-tuning of Variational Autoencoders
Nafiz Abeer
Sanket Jantre
Nathan M. Urban
Byung-Jun Yoon
331
2
0
31 May 2024
DrugLLM: Open Large Language Model for Few-shot Molecule Generation
DrugLLM: Open Large Language Model for Few-shot Molecule Generation
Xianggen Liu
Yan Guo
Haoran Li
Jin Liu
Shudong Huang
Bowen Ke
Jiancheng Lv
181
20
0
07 May 2024
Leveraging Active Subspaces to Capture Epistemic Model Uncertainty in
  Deep Generative Models for Molecular Design
Leveraging Active Subspaces to Capture Epistemic Model Uncertainty in Deep Generative Models for Molecular Design
A. N. M. N. Abeer
Sanket Jantre
Nathan M. Urban
Byung-Jun Yoon
271
2
0
30 Apr 2024
Optimizing OOD Detection in Molecular Graphs: A Novel Approach with
  Diffusion Models
Optimizing OOD Detection in Molecular Graphs: A Novel Approach with Diffusion Models
Xu Shen
Yili Wang
Kaixiong Zhou
Shirui Pan
Xin Wang
356
27
0
24 Apr 2024
Mol-AIR: Molecular Reinforcement Learning with Adaptive Intrinsic
  Rewards for Goal-directed Molecular Generation
Mol-AIR: Molecular Reinforcement Learning with Adaptive Intrinsic Rewards for Goal-directed Molecular Generation
Jinyeong Park
Jaegyoon Ahn
Jonghwan Choi
Jibum Kim
263
13
0
29 Mar 2024
GLAD: Improving Latent Graph Generative Modeling with Simple
  Quantization
GLAD: Improving Latent Graph Generative Modeling with Simple Quantization
Van Khoa Nguyen
Yoann Boget
Frantzeska Lavda
Alexandros Kalousis
459
6
0
25 Mar 2024
Instruction Multi-Constraint Molecular Generation Using a
  Teacher-Student Large Language Model
Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model
Peng Zhou
Jianmin Wang
Chunyan Li
Zixu Wang
Yiping Liu
...
Xibao Cai
Houtim Lai
Wei Liu
Longyue Wang
Xiangxiang Zeng
330
8
0
20 Mar 2024
Neural Graph Generator: Feature-Conditioned Graph Generation using
  Latent Diffusion Models
Neural Graph Generator: Feature-Conditioned Graph Generation using Latent Diffusion Models
Iakovos Evdaimon
Giannis Nikolentzos
Michail Chatzianastasis
Hadi Abdine
Michalis Vazirgiannis
DiffM
336
8
0
03 Mar 2024
Retrosynthesis Prediction via Search in (Hyper) Graph
Retrosynthesis Prediction via Search in (Hyper) GraphIEEE Transactions on Automation Science and Engineering (T-ASE), 2024
Zixun Lan
Binjie Hong
Jiajun Zhu
Zuo Zeng
Zhenfu Liu
Limin Yu
Fei Ma
237
1
0
09 Feb 2024
Pard: Permutation-Invariant Autoregressive Diffusion for Graph
  Generation
Pard: Permutation-Invariant Autoregressive Diffusion for Graph GenerationNeural Information Processing Systems (NeurIPS), 2024
Lingxiao Zhao
Xueying Ding
Leman Akoglu
DiffM
311
21
0
06 Feb 2024
De novo Drug Design using Reinforcement Learning with Multiple GPT
  Agents
De novo Drug Design using Reinforcement Learning with Multiple GPT Agents
Xiuyuan Hu
Guoqing Liu
Yang Zhao
Hao Zhang
330
33
0
21 Dec 2023
Gotta be SAFE: A New Framework for Molecular Design
Gotta be SAFE: A New Framework for Molecular DesignDigital Discovery (DD), 2023
Emmanuel Noutahi
Cristian Gabellini
Michael Craig
Jonathan S.C Lim
Prudencio Tossou
387
44
0
16 Oct 2023
Node-Aligned Graph-to-Graph (NAG2G): Elevating Template-Free Deep
  Learning Approaches in Single-Step Retrosynthesis
Node-Aligned Graph-to-Graph (NAG2G): Elevating Template-Free Deep Learning Approaches in Single-Step RetrosynthesisJACS Au (JACS Au), 2023
Lin Yao
Wentao Guo
Zhen Wang
Shang Xiang
Wentan Liu
Guolin Ke
337
28
0
27 Sep 2023
ChemSpaceAL: An Efficient Active Learning Methodology Applied to
  Protein-Specific Molecular Generation
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular GenerationJournal of Chemical Information and Modeling (JCIM), 2023
Gregory W. Kyro
Anton Morgunov
Rafael I. Brent
Victor S. Batista
301
19
0
11 Sep 2023
GSHOT: Few-shot Generative Modeling of Labeled Graphs
GSHOT: Few-shot Generative Modeling of Labeled GraphsLOG IN (LOG IN), 2023
S. Manchanda
Shubham Gupta
Jignesh M. Patel
Srikanta J. Bedathur
VLM
258
0
0
06 Jun 2023
Balancing Exploration and Exploitation: Disentangled $β$-CVAE in De
  Novo Drug Design
Balancing Exploration and Exploitation: Disentangled βββ-CVAE in De Novo Drug Design
Guang Jun Nicholas Ang
Deanne Chin
Bingquan Shen
236
0
0
02 Jun 2023
Symmetric Replay Training: Enhancing Sample Efficiency in Deep
  Reinforcement Learning for Combinatorial Optimization
Symmetric Replay Training: Enhancing Sample Efficiency in Deep Reinforcement Learning for Combinatorial OptimizationInternational Conference on Machine Learning (ICML), 2023
Hyeon-Seob Kim
Minsu Kim
SungSoo Ahn
Jinkyoo Park
OffRL
534
9
0
02 Jun 2023
Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation
  in 3D
Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3DInternational Conference on Machine Learning (ICML), 2023
Yiran Zhou
Yuxuan Song
Minkai Xu
Jingjing Gong
B. Gao
Hao Zhou
Weiying Ma
Yanyan Lan
DiffM
315
29
0
05 May 2023
Optimizing Drug Design by Merging Generative AI With Active Learning
  Frameworks
Optimizing Drug Design by Merging Generative AI With Active Learning Frameworks
Isaac Filella-Merce
Alexis Molina
Marek Orzechowski
Lucía Díaz
Yangnv Zhu
Julia Vilalta Mor
Laura Malo
Ajay Yekkirala
Soumya S. Ray
Víctor Guallar
AI4CE
150
9
0
04 May 2023
Towards Invertible Semantic-Preserving Embeddings of Logical Formulae
Towards Invertible Semantic-Preserving Embeddings of Logical FormulaeInternational Workshop on Neural-Symbolic Learning and Reasoning (NeSy), 2023
Gaia Saveri
Luca Bortolussi
NAI
226
3
0
03 May 2023
Modeling and design of heterogeneous hierarchical bioinspired spider web
  structures using generative deep learning and additive manufacturing
Modeling and design of heterogeneous hierarchical bioinspired spider web structures using generative deep learning and additive manufacturing
Wei Lu
Nicolas A. Lee
Markus J. Buehler
AI4CE
187
2
0
11 Apr 2023
Sample-efficient Multi-objective Molecular Optimization with GFlowNets
Sample-efficient Multi-objective Molecular Optimization with GFlowNetsNeural Information Processing Systems (NeurIPS), 2023
Yiheng Zhu
Jialun Wu
Chaowen Hu
Jiahuan Yan
Chang-Yu Hsieh
Tingjun Hou
Jian Wu
469
61
0
08 Feb 2023
De Novo Molecular Generation via Connection-aware Motif Mining
De Novo Molecular Generation via Connection-aware Motif MiningInternational Conference on Learning Representations (ICLR), 2023
Zijie Geng
Shufang Xie
Ziheng Lu
Lijun Wu
Tao Qin
Jie Wang
Yongdong Zhang
Feng Wu
Tie-Yan Liu
373
54
0
02 Feb 2023
AlignGraph: A Group of Generative Models for Graphs
AlignGraph: A Group of Generative Models for GraphsSDM (SDM), 2023
Kimia Shayestehfard
Dana Brooks
Stratis Ioannidis
222
0
0
26 Jan 2023
NVDiff: Graph Generation through the Diffusion of Node Vectors
NVDiff: Graph Generation through the Diffusion of Node Vectors
Xiaohui Chen
Yukun Li
Aonan Zhang
Liping Liu
DiffM
269
29
0
19 Nov 2022
Bidirectional Generation of Structure and Properties Through a Single
  Molecular Foundation Model
Bidirectional Generation of Structure and Properties Through a Single Molecular Foundation ModelNature Communications (Nat Commun), 2022
Jinho Chang
Jong Chul Ye
AI4CE
286
70
0
19 Nov 2022
A Transformer-based Generative Model for De Novo Molecular Design
A Transformer-based Generative Model for De Novo Molecular Design
Wenlu Wang
Ye Wang
Honggang Zhao
Simone Sciabola
148
0
0
17 Oct 2022
123
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