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Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network
v1v2v3 (latest)

Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network

13 September 2017
Wengong Jin
Connor W. Coley
Regina Barzilay
Tommi Jaakkola
ArXiv (abs)PDFHTML

Papers citing "Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network"

50 / 122 papers shown
Teaching Language Models Mechanistic Explainability Through MechSMILES
Teaching Language Models Mechanistic Explainability Through MechSMILES
Theo A Neukomm
Zlatko Joncev
Philippe Schwaller
LRM
149
0
0
05 Dec 2025
SynthStrategy: Extracting and Formalizing Latent Strategic Insights from LLMs in Organic Chemistry
SynthStrategy: Extracting and Formalizing Latent Strategic Insights from LLMs in Organic Chemistry
Daniel Armstrong
Zlatko Joncev
Andres M Bran
Philippe Schwaller
132
0
0
01 Dec 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
105
0
0
21 Nov 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
129
2
0
16 Oct 2025
Prime Implicant Explanations for Reaction Feasibility Prediction
Prime Implicant Explanations for Reaction Feasibility Prediction
Klaus Weinbauer
Tieu-Long Phan
Peter F. Stadler
Thomas Gärtner
Sagar Malhotra
FAttLRM
239
0
0
10 Oct 2025
oMeBench: Towards Robust Benchmarking of LLMs in Organic Mechanism Elucidation and Reasoning
oMeBench: Towards Robust Benchmarking of LLMs in Organic Mechanism Elucidation and Reasoning
R. Xu
Y. Zhang
Qingyun Wang
Carl Edwards
Heng Ji
LRM
161
2
0
09 Oct 2025
Round-trip Reinforcement Learning: Self-Consistent Training for Better Chemical LLMs
Round-trip Reinforcement Learning: Self-Consistent Training for Better Chemical LLMs
Lecheng Kong
Xiyuan Wang
Yixin Chen
Muhan Zhang
AI4CELRM
142
1
0
01 Oct 2025
FragmentRetro: A Quadratic Retrosynthetic Method Based on Fragmentation Algorithms
FragmentRetro: A Quadratic Retrosynthetic Method Based on Fragmentation Algorithms
Yu Shee
Anthony M. Smaldone
Anton Morgunov
Gregory W. Kyro
Victor S. Batista
190
0
0
18 Sep 2025
Uni-Mol3: A Multi-Molecular Foundation Model for Advancing Organic Reaction Modeling
Uni-Mol3: A Multi-Molecular Foundation Model for Advancing Organic Reaction Modeling
Lirong Wu
Junjie Wang
Zhifeng Gao
Xiaohong Ji
Rong Zhu
X. Li
Linfeng Zhang
Guolin Ke
Weinan E
AI4CE
234
1
0
30 Jul 2025
ChemDFM-R: A Chemical Reasoning LLM Enhanced with Atomized Chemical Knowledge
ChemDFM-R: A Chemical Reasoning LLM Enhanced with Atomized Chemical Knowledge
Zihan Zhao
B. Chen
Ziping Wan
Lu Chen
Xuanze Lin
...
Huayang Wang
Zhongyang Dai
Liyang Wen
Xin Chen
Kai Yu
AI4CELRM
310
4
0
29 Jul 2025
Domain Specific Benchmarks for Evaluating Multimodal Large Language Models
Domain Specific Benchmarks for Evaluating Multimodal Large Language Models
Khizar Anjuma
Muhammad Arbab Arshad
Kadhim Hayawi
Efstathios Polyzos
A. Tariq
...
Nishith Reddy Mannuru
Ravi Varma Kumar Bevara
Taslim Mahbub
Muhammad Zeeshan Akram
Sakib Shahriar
ELMLRM
483
8
0
15 Jun 2025
Training a Scientific Reasoning Model for Chemistry
Training a Scientific Reasoning Model for Chemistry
Siddharth Narayanan
James D. Braza
Ryan-Rhys Griffiths
Albert Bou
Geemi P Wellawatte
Mayk Caldas Ramos
Ludovico Mitchener
Samuel G. Rodriques
A. White
LRM
294
31
0
04 Jun 2025
ChemHGNN: A Hierarchical Hypergraph Neural Network for Reaction Virtual Screening and Discovery
ChemHGNN: A Hierarchical Hypergraph Neural Network for Reaction Virtual Screening and Discovery
Xiaobao Huang
Yihong Ma
Anjali Gurajapu
Jules Schleinitz
Zhichun Guo
Sarah E. Reisman
Nitesh Chawla
171
0
0
21 May 2025
Chem42: a Family of chemical Language Models for Target-aware Ligand Generation
Chem42: a Family of chemical Language Models for Target-aware Ligand Generation
A. Singh
Engin Tekin
Maryam Nadeem
Nancy A. ElNaker
Mohammad Amaan Sayeed
Natalia Vassilieva
Boulbaba Ben Amor
457
1
0
20 Mar 2025
Predicting Chemical Reaction Outcomes Based on Electron Movements Using Machine Learning
Predicting Chemical Reaction Outcomes Based on Electron Movements Using Machine Learning
Shuan Chen
Kye Sung Park
Taewan Kim
Sunkyu Han
Yousung Jung
407
1
0
13 Mar 2025
Performance Heterogeneity in Graph Neural Networks: Lessons for Architecture Design and Preprocessing
Performance Heterogeneity in Graph Neural Networks: Lessons for Architecture Design and Preprocessing
Lukas Fesser
Melanie Weber
274
1
0
01 Mar 2025
Chemical knowledge-informed framework for privacy-aware retrosynthesis learning
Chemical knowledge-informed framework for privacy-aware retrosynthesis learningNature Communications (Nat Commun), 2025
Guikun Chen
Xu Zhang
Yue Yang
Yong Liu
Yi Yang
Wenguan Wang
352
0
0
26 Feb 2025
Challenging reaction prediction models to generalize to novel chemistry
Challenging reaction prediction models to generalize to novel chemistryACS Central Science (ACS Cent. Sci.), 2025
John Bradshaw
Anji Zhang
Babak Mahjour
David E. Graff
Marwin H. S. Segler
Connor W. Coley
236
10
0
11 Jan 2025
Question Rephrasing for Quantifying Uncertainty in Large Language
  Models: Applications in Molecular Chemistry Tasks
Question Rephrasing for Quantifying Uncertainty in Large Language Models: Applications in Molecular Chemistry Tasks
Zizhang Chen
Pengyu Hong
Sandeep Madireddy
281
3
0
07 Aug 2024
ReactAIvate: A Deep Learning Approach to Predicting Reaction Mechanisms
  and Unmasking Reactivity Hotspots
ReactAIvate: A Deep Learning Approach to Predicting Reaction Mechanisms and Unmasking Reactivity Hotspots
Ajnabiul Hoque
Manajit Das
Mayank Baranwal
R. B. Sunoj
171
1
0
14 Jul 2024
RetroGFN: Diverse and Feasible Retrosynthesis using GFlowNets
RetroGFN: Diverse and Feasible Retrosynthesis using GFlowNets
Piotr Gaiñski
Michał Koziarski
Krzysztof Maziarz
Marwin H. S. Segler
Jacek Tabor
Marek Śmieja
434
11
0
26 Jun 2024
A Comprehensive Survey of Scientific Large Language Models and Their
  Applications in Scientific Discovery
A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery
Yu Zhang
Xiusi Chen
Sara Szymkuć
Sheng Wang
Shuiwang Ji
Wei Wang
Jiawei Han
489
106
0
16 Jun 2024
SciKnowEval: Evaluating Multi-level Scientific Knowledge of Large Language Models
SciKnowEval: Evaluating Multi-level Scientific Knowledge of Large Language Models
Kehua Feng
Keyan Ding
Weijie Wang
Xiang Zhuang
Yuqi Tang
Ming Qin
Yu Zhao
ELM
422
12
0
13 Jun 2024
Probabilistic Graph Rewiring via Virtual Nodes
Probabilistic Graph Rewiring via Virtual Nodes
Chendi Qian
Andrei Manolache
Christopher Morris
Mathias Niepert
AI4CE
428
14
0
27 May 2024
Equivariant Denoisers Cannot Copy Graphs: Align Your Graph Diffusion Models
Equivariant Denoisers Cannot Copy Graphs: Align Your Graph Diffusion Models
Najwa Laabid
Severi Rissanen
Markus Heinonen
Arno Solin
Vikas Garg
DiffM
426
1
0
27 May 2024
Gradient Propagation in Retrosynthetic Space: An Efficient Framework for Synthesis Plan Generation
Gradient Propagation in Retrosynthetic Space: An Efficient Framework for Synthesis Plan Generation
Chengyang Tian
Yuhang Chang
Yangpeng Zhang
Yang Liu
214
0
0
25 May 2024
UAlign: Pushing the Limit of Template-free Retrosynthesis Prediction
  with Unsupervised SMILES Alignment
UAlign: Pushing the Limit of Template-free Retrosynthesis Prediction with Unsupervised SMILES Alignment
Kaipeng Zeng
Bo Yang
Xin Zhao
Yu Zhang
Fan Nie
Yunbo Wang
Yaohui Jin
Yanyan Xu
324
21
0
25 Mar 2024
Assessing the Extrapolation Capability of Template-Free Retrosynthesis
  Models
Assessing the Extrapolation Capability of Template-Free Retrosynthesis Models
Shuan Chen
Yousung Jung
ELM
183
3
0
29 Feb 2024
Contextual Molecule Representation Learning from Chemical Reaction
  Knowledge
Contextual Molecule Representation Learning from Chemical Reaction Knowledge
Han Tang
Shikun Feng
Bicheng Lin
Yuyan Ni
Jingjing Liu
Wei-Ying Ma
Yanyan Lan
300
3
0
21 Feb 2024
Retrosynthesis prediction enhanced by in-silico reaction data
  augmentation
Retrosynthesis prediction enhanced by in-silico reaction data augmentation
Xu Zhang
Yiming Mo
Wenguan Wang
Yi Yang
303
4
0
31 Jan 2024
ChemDFM: Dialogue Foundation Model for Chemistry
ChemDFM: Dialogue Foundation Model for ChemistryCell Reports Physical Science (Cell Rep Phys Sci), 2024
Zihan Zhao
Da Ma
Lu Chen
Liangtai Sun
Zihao Li
...
Su Zhu
Shuai Fan
Guodong Shen
Xin Chen
Kai Yu
AI4CE
166
13
0
26 Jan 2024
T-Rex: Text-assisted Retrosynthesis Prediction
T-Rex: Text-assisted Retrosynthesis Prediction
Yifeng Liu
Hanwen Xu
Tangqi Fang
Haocheng Xi
Zixuan Liu
Sheng Zhang
Hoifung Poon
Sheng Wang
246
1
0
26 Jan 2024
RetroOOD: Understanding Out-of-Distribution Generalization in
  Retrosynthesis Prediction
RetroOOD: Understanding Out-of-Distribution Generalization in Retrosynthesis Prediction
Yemin Yu
Luotian Yuan
Ying Wei
Hanyu Gao
Xinhai Ye
Zhihua Wang
Leilei Gan
OOD
308
5
0
18 Dec 2023
Holistic chemical evaluation reveals pitfalls in reaction prediction
  models
Holistic chemical evaluation reveals pitfalls in reaction prediction models
Victor Sabanza Gil
Andres M Bran
Malte Franke
Remi Schlama
J. Luterbacher
Philippe Schwaller
ELM
309
1
0
14 Dec 2023
Efficient interpolation of molecular properties across chemical compound
  space with low-dimensional descriptors
Efficient interpolation of molecular properties across chemical compound space with low-dimensional descriptors
Yun-Wen Mao
R. Krems
106
4
0
26 Nov 2023
ReactionT5: a large-scale pre-trained model towards application of
  limited reaction data
ReactionT5: a large-scale pre-trained model towards application of limited reaction data
Tatsuya Sagawa
Ryosuke Kojima
AI4CE
247
13
0
12 Nov 2023
AI for Interpretable Chemistry: Predicting Radical Mechanistic Pathways
  via Contrastive Learning
AI for Interpretable Chemistry: Predicting Radical Mechanistic Pathways via Contrastive LearningNeural Information Processing Systems (NeurIPS), 2023
Mohammadamin Tavakoli
Y. T. T. Chiu
Alexander Shmakov
Ann Marie Carlton
David Van Vranken
Pierre Baldi
274
5
0
02 Nov 2023
De-novo Chemical Reaction Generation by Means of Temporal Convolutional
  Neural Networks
De-novo Chemical Reaction Generation by Means of Temporal Convolutional Neural Networks
A. Buin
Hung Yi Chiang
S. A. Gadsden
Faraz A. Alderson
208
0
0
26 Oct 2023
Molecule-Edit Templates for Efficient and Accurate Retrosynthesis
  Prediction
Molecule-Edit Templates for Efficient and Accurate Retrosynthesis Prediction
Mikolaj Sacha
Michal Sadowski
Piotr Kozakowski
Ruard van Workum
Stanislaw Jastrzebski
271
2
0
11 Oct 2023
Probabilistically Rewired Message-Passing Neural Networks
Probabilistically Rewired Message-Passing Neural NetworksInternational Conference on Learning Representations (ICLR), 2023
Chendi Qian
Andrei Manolache
Kareem Ahmed
Zhe Zeng
Karen Ullrich
Mathias Niepert
Christopher Morris
533
26
0
03 Oct 2023
Conformal Autoregressive Generation: Beam Search with Coverage
  Guarantees
Conformal Autoregressive Generation: Beam Search with Coverage GuaranteesAAAI Conference on Artificial Intelligence (AAAI), 2023
Nicolas Deutschmann
Marvin Alberts
María Rodríguez Martínez
UQLM
291
21
0
07 Sep 2023
A Unified View of Deep Learning for Reaction and Retrosynthesis
  Prediction: Current Status and Future Challenges
A Unified View of Deep Learning for Reaction and Retrosynthesis Prediction: Current Status and Future ChallengesInternational Joint Conference on Artificial Intelligence (IJCAI), 2023
Ziqiao Meng
Peilin Zhao
Yang Yu
Irwin King
306
10
0
28 Jun 2023
Retrosynthesis Prediction with Local Template Retrieval
Retrosynthesis Prediction with Local Template RetrievalAAAI Conference on Artificial Intelligence (AAAI), 2023
Shufang Xie
Rui Yan
Junliang Guo
Ziheng Lu
Lijun Wu
Tao Qin
274
20
0
07 Jun 2023
Doubly Stochastic Graph-based Non-autoregressive Reaction Prediction
Doubly Stochastic Graph-based Non-autoregressive Reaction PredictionInternational Joint Conference on Artificial Intelligence (IJCAI), 2023
Ziqiao Meng
Peilin Zhao
Yang Yu
Irwin King
191
9
0
05 Jun 2023
Bi-level Contrastive Learning for Knowledge-Enhanced Molecule
  Representations
Bi-level Contrastive Learning for Knowledge-Enhanced Molecule RepresentationsAAAI Conference on Artificial Intelligence (AAAI), 2023
Pengcheng Jiang
Cao Xiao
Tianfan Fu
Jimeng Sun
483
7
0
02 Jun 2023
What can Large Language Models do in chemistry? A comprehensive
  benchmark on eight tasks
What can Large Language Models do in chemistry? A comprehensive benchmark on eight tasksNeural Information Processing Systems (NeurIPS), 2023
Taicheng Guo
Kehan Guo
B. Nan
Zhengwen Liang
Zhichun Guo
Nitesh Chawla
Olaf Wiest
Xiangliang Zhang
ELM
643
242
0
27 May 2023
G-MATT: Single-step Retrosynthesis Prediction using Molecular Grammar
  Tree Transformer
G-MATT: Single-step Retrosynthesis Prediction using Molecular Grammar Tree TransformerAIChE Journal (AIChE J.), 2023
K. Zhang
Vipul Mann
V. Venkatasubramanian
380
8
0
04 May 2023
GraphGANFed: A Federated Generative Framework for Graph-Structured
  Molecules Towards Efficient Drug Discovery
GraphGANFed: A Federated Generative Framework for Graph-Structured Molecules Towards Efficient Drug DiscoveryIEEE/ACM Transactions on Computational Biology & Bioinformatics (TCBB), 2023
Daniel Manu
Jingjing Yao
Wuji Liu
Xiang Sun
FedML
288
21
0
11 Apr 2023
SELFormer: Molecular Representation Learning via SELFIES Language Models
SELFormer: Molecular Representation Learning via SELFIES Language Models
Atakan Yüksel
Erva Ulusoy
Atabey Ünlü
Tunca Dogan
343
103
0
10 Apr 2023
Bridging the Gap between Chemical Reaction Pretraining and Conditional
  Molecule Generation with a Unified Model
Bridging the Gap between Chemical Reaction Pretraining and Conditional Molecule Generation with a Unified Model
Yiran Zhou
Liangren Zhang
Yuheng Ding
Ningfeng Liu
Song Song
L. Zhang
Bowei Huang
Zhenming Liu
AI4CE
519
21
0
13 Mar 2023
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