NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation

18 February 2025

Papers citing "NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation"

50 / 82 papers shown

Title
GEOM-Drugs Revisited: Toward More Chemically Accurate Benchmarks for 3D Molecule Generation Filipp Nikitin Ian Dunn D. Koes Olexandr Isayev 339 0 0 30 Apr 2025
Text-guided Diffusion Model for 3D Molecule Generation Yanchen Luo Sihang Li Changhao Nai Zhiyuan Liu Jiancan Wu An Zhang Wenjie Du Xiang Wang 51 7 0 04 Oct 2024
An Investigation of Warning Erroneous Chat Translations in Cross-lingual Communication Yunmeng Li Jun Suzuki Makoto Morishita Kaori Abe Kentaro Inui 89 10 0 28 Aug 2024
ReactXT: Understanding Molecular "Reaction-ship" via Reaction-Contextualized Molecule-Text Pretraining Zhiyuan Liu Yaorui Shi An Zhang Changhao Nai Enzhi Zhang Xiang Wang Kenji Kawaguchi Tat-Seng Chua 59 10 0 23 May 2024
ProtT3: Protein-to-Text Generation for Text-based Protein Understanding Zhiyuan Liu An Zhang Hao Fei Enzhi Zhang Xiang Wang Kenji Kawaguchi Tat-Seng Chua 80 19 0 21 May 2024
SciAssess: Benchmarking LLM Proficiency in Scientific Literature Analysis Hengxing Cai Xiaochen Cai Junhan Chang Changhao Nai Lin Yao ... Changhong Chen Zheng Cheng Zifeng Zhao Linfeng Zhang Guolin Ke ELM 43 24 0 04 Mar 2024
MolTC: Towards Molecular Relational Modeling In Language Models Sihang Li Shuai Zhang Chang Wu Zhengyi Yang Zhiyuan Liu Changhao Nai Kun Wang Wenjie Du Xiang Wang 63 21 0 06 Feb 2024
Towards 3D Molecule-Text Interpretation in Language Models Changhao Nai Zhiyuan Liu Yancheng Luo Xiang Wang Xiangnan He Kenji Kawaguchi Tat-Seng Chua Qi Tian AI4CE 52 46 0 25 Jan 2024
TinyLlama: An Open-Source Small Language Model Peiyuan Zhang Guangtao Zeng Tianduo Wang Wei Lu ALM LRM 96 374 0 04 Jan 2024
Swallowing the Bitter Pill: Simplified Scalable Conformer Generation Yuyang Wang Ahmed A. A. Elhag Navdeep Jaitly J. Susskind Miguel Angel Bautista DiffM 52 22 0 27 Nov 2023
Rethinking Tokenizer and Decoder in Masked Graph Modeling for Molecules Zhiyuan Liu Yaorui Shi An Zhang Enzhi Zhang Kenji Kawaguchi Xiang Wang Tat-Seng Chua AI4CE 51 38 0 23 Oct 2023
ReLM: Leveraging Language Models for Enhanced Chemical Reaction Prediction Yaorui Shi An Zhang Enzhi Zhang Zhiyuan Liu Xiang Wang AI4CE 43 24 0 20 Oct 2023
Particle Guidance: non-I.I.D. Diverse Sampling with Diffusion Models Gabriele Corso Yilun Xu Valentin De Bortoli Regina Barzilay Tommi Jaakkola DiffM 34 21 0 19 Oct 2023
MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter Zhiyuan Liu Changhao Nai Yancheng Luo Hao Fei Yixin Cao Kenji Kawaguchi Xiang Wang Tat-Seng Chua 53 86 0 19 Oct 2023
Navigating the Design Space of Equivariant Diffusion-Based Generative Models for De Novo 3D Molecule Generation Tuan Le Julian Cremer Frank Noé Djork-Arné Clevert Kristof T. Schütt DiffM 45 28 0 29 Sep 2023
Redundancy-aware Transformer for Video Question Answering Yicong Li Xun Yang An Zhang Chun Feng Xiang Wang Tat-Seng Chua 38 15 0 07 Aug 2023
Discovering Spatio-Temporal Rationales for Video Question Answering Yicong Li Junbin Xiao Chun Feng Xiang Wang Tat-Seng Chua 74 13 0 22 Jul 2023
Llama 2: Open Foundation and Fine-Tuned Chat Models Hugo Touvron Louis Martin Kevin R. Stone Peter Albert Amjad Almahairi ... Sharan Narang Aurelien Rodriguez Robert Stojnic Sergey Edunov Thomas Scialom AI4MH ALM 197 11,484 0 18 Jul 2023
FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning Tri Dao LRM 60 1,221 0 17 Jul 2023
Geometric Latent Diffusion Models for 3D Molecule Generation Minkai Xu Alexander Powers R. Dror Stefano Ermon J. Leskovec DiffM AI4CE 82 142 0 02 May 2023
MUDiff: Unified Diffusion for Complete Molecule Generation Chenqing Hua Sitao Luan Minkai Xu Rex Ying Jie Fu Stefano Ermon Doina Precup DiffM 73 36 0 28 Apr 2023
PyTorch FSDP: Experiences on Scaling Fully Sharded Data Parallel Yanli Zhao Andrew Gu R. Varma Liangchen Luo Chien-chin Huang ... Bernard Nguyen Geeta Chauhan Y. Hao Ajit Mathews Shen Li FedML MoE 52 322 0 21 Apr 2023
Visual Instruction Tuning Haotian Liu Chunyuan Li Qingyang Wu Yong Jae Lee SyDa VLM MLLM 329 4,506 0 17 Apr 2023
SELFormer: Molecular Representation Learning via SELFIES Language Models Atakan Yüksel Erva Ulusoy Atabey Ünlü Tunca Dogan 52 57 0 10 Apr 2023
MiDi: Mixed Graph and 3D Denoising Diffusion for Molecule Generation Clément Vignac Nagham Osman Laura Toni P. Frossard DiffM 60 52 0 17 Feb 2023
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation Han Huang Leilei Sun Bowen Du Weifeng Lv 66 42 0 01 Jan 2023
Scalable Diffusion Models with Transformers William S. Peebles Saining Xie GNN 60 2,182 0 19 Dec 2022
Generalized Laplacian Positional Encoding for Graph Representation Learning Sohir Maskey Alipanah Parviz Maximilian Thiessen Hannes Stärk Ylli Sadikaj Haggai Maron AI4CE 65 16 0 28 Oct 2022
Equivariant Energy-Guided SDE for Inverse Molecular Design Fan Bao Min Zhao Zhongkai Hao Pei‐Yun Li Chongxuan Li Jun Zhu DiffM 211 66 0 30 Sep 2022
MDM: Molecular Diffusion Model for 3D Molecule Generation Lei Huang Hengtong Zhang Tingyang Xu Ka-Chun Wong DiffM 55 82 0 13 Sep 2022
ChemBERTa-2: Towards Chemical Foundation Models Walid Ahmad Elana Simon Seyone Chithrananda Gabriel Grand Bharath Ramsundar AI4CE 33 132 0 05 Sep 2022
Equivariant and Invariant Grounding for Video Question Answering Yicong Li Xiang Wang Junbin Xiao Tat-Seng Chua 44 25 0 26 Jul 2022
LIMO: Latent Inceptionism for Targeted Molecule Generation Peter Eckmann Kunyang Sun Bo Zhao Mudong Feng Michael K. Gilson Rose Yu BDL 58 46 0 17 Jun 2022
Let Invariant Rationale Discovery Inspire Graph Contrastive Learning Changhao Nai Xiang Wang An Zhang Y. Wu Xiangnan He Tat-Seng Chua 55 94 0 16 Jun 2022
Invariant Grounding for Video Question Answering Yicong Li Xiang Wang Junbin Xiao Wei Ji Tat-Seng Chua OOD 49 96 0 06 Jun 2022
Torsional Diffusion for Molecular Conformer Generation Bowen Jing Gabriele Corso Jeffrey Chang Regina Barzilay Tommi Jaakkola DiffM BDL 67 266 0 01 Jun 2022
GraphMAE: Self-Supervised Masked Graph Autoencoders Zhenyu Hou Xiao Liu Yukuo Cen Yuxiao Dong Hongxia Yang C. Wang Jie Tang SSL 65 559 0 22 May 2022
Equivariant Diffusion for Molecule Generation in 3D Emiel Hoogeboom Victor Garcia Satorras Clément Vignac Max Welling DiffM 68 594 0 31 Mar 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 87 89 0 28 Mar 2022
GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation Minkai Xu Lantao Yu Yang Song Chence Shi Stefano Ermon Jian Tang BDL DiffM 114 502 0 06 Mar 2022
Fine-Tuning can Distort Pretrained Features and Underperform Out-of-Distribution Ananya Kumar Aditi Raghunathan Robbie Jones Tengyu Ma Percy Liang OODD 89 655 0 21 Feb 2022
Regression Transformer: Concurrent sequence regression and generation for molecular language modeling Jannis Born Matteo Manica 27 94 0 01 Feb 2022
High-Resolution Image Synthesis with Latent Diffusion Models Robin Rombach A. Blattmann Dominik Lorenz Patrick Esser Bjorn Ommer 3DV 245 15,081 0 20 Dec 2021
Keeping it Simple: Language Models can learn Complex Molecular Distributions Daniel Flam-Shepherd Kevin Zhu A. Aspuru‐Guzik 168 144 0 06 Dec 2021
3D Infomax improves GNNs for Molecular Property Prediction Hannes Stärk Dominique Beaini Gabriele Corso Prudencio Tossou Christian Dallago Stephan Günnemann Pietro Lio AI4CE 56 205 0 08 Oct 2021
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 149 308 0 07 Oct 2021
Inverse design of 3d molecular structures with conditional generative neural networks Niklas W. A. Gebauer M. Gastegger Stefaan S. P. Hessmann Klaus-Robert Muller Kristof T. Schütt AI4CE 199 171 0 10 Sep 2021
Variational Diffusion Models Diederik P. Kingma Tim Salimans Ben Poole Jonathan Ho DiffM 132 1,089 0 01 Jul 2021
LoRA: Low-Rank Adaptation of Large Language Models J. E. Hu Yelong Shen Phillip Wallis Zeyuan Allen-Zhu Yuanzhi Li Shean Wang Lu Wang Weizhu Chen OffRL AI4TS AI4CE ALM AIMat 223 9,946 0 17 Jun 2021
GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles O. Ganea L. Pattanaik Connor W. Coley Regina Barzilay K. Jensen W. Green Tommi Jaakkola AI4CE 73 136 0 08 Jun 2021