Cover Image

PharMolixFM: All-Atom Foundation Models for Molecular Modeling and Generation

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	Luo, Yizhen, Wang, Jiashuo, Fan, Siqi, Nie, Zaiqing
Format:	Preprint
Published:	2025
Subjects:	Biomolecules Machine Learning
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

Learning Multi-view Molecular Representations with Structured and Unstructured Knowledge
by: Luo, Yizhen, et al.
Published: (2024)

MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering
by: Luo, Yizhen, et al.
Published: (2024)

ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling
by: Zheng, Kangjie, et al.
Published: (2024)

MarS-FM: Generative Modeling of Molecular Dynamics via Markov State Models
by: Kapuśniak, Kacper, et al.
Published: (2025)

Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling
by: Lu, Shuqi, et al.
Published: (2025)

Towards Faster and More Compact Foundation Models for Molecular Property Prediction
by: Ghunaim, Yasir, et al.
Published: (2025)

Generative Modeling of Molecular Dynamics Trajectories
by: Jing, Bowen, et al.
Published: (2024)

GP-MoLFormer: A Foundation Model For Molecular Generation
by: Ross, Jerret, et al.
Published: (2024)

Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings
by: Sengar, Aditya, et al.
Published: (2025)

Structure-Based Drug Design via 3D Molecular Generative Pre-training and Sampling
by: Yang, Yuwei, et al.
Published: (2024)

Multi-Objective Latent Space Optimization of Generative Molecular Design Models
by: Abeer, A N M Nafiz, et al.
Published: (2022)

Graph Diffusion Transformers for Multi-Conditional Molecular Generation
by: Liu, Gang, et al.
Published: (2024)

Beyond Atoms: Evaluating Electron Density Representation for 3D Molecular Learning
by: Suriana, Patricia, et al.
Published: (2025)

Collaborative Expert LLMs Guided Multi-Objective Molecular Optimization
by: Yu, Jiajun, et al.
Published: (2025)

An End-to-End Framework for Molecular Conformation Generation via Bilevel Programming
by: Xu, Minkai, et al.
Published: (2021)

Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling
by: Zhou, Xiangxin, et al.
Published: (2025)

Molecular Diffusion Models with Virtual Receptors
by: Halfon, Matan, et al.
Published: (2024)

Rethinking Molecular Design: Integrating Latent Variable and Auto-Regressive Models for Goal Directed Generation
by: Arthur-Loui, Heath, et al.
Published: (2024)

Tokenization for Molecular Foundation Models
by: Wadell, Alexius, et al.
Published: (2024)

AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodies
by: Martinkus, Karolis, et al.
Published: (2023)

OneProt: Towards Multi-Modal Protein Foundation Models
by: Flöge, Klemens, et al.
Published: (2024)

Guided Generation for Developable Antibodies
by: Zhao, Siqi, et al.
Published: (2025)

DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization
by: Zhou, Xiangxin, et al.
Published: (2024)

Molecular Fingerprints Are Strong Models for Peptide Function Prediction
by: Adamczyk, Jakub, et al.
Published: (2025)

Unveiling Scaling Behaviors in Molecular Language Models: Effects of Model Size, Data, and Representation
by: Xu, Dong, et al.
Published: (2026)

ModuLM: Enabling Modular and Multimodal Molecular Relational Learning with Large Language Models
by: Chen, Zhuo, et al.
Published: (2025)

MolPIF: A Parameter Interpolation Flow Model for Molecule Generation
by: Jin, Yaowei, et al.
Published: (2025)

Towards Efficient Molecular Property Optimization with Graph Energy Based Models
by: Miglior, Luca, et al.
Published: (2025)

QuickBind: A Light-Weight And Interpretable Molecular Docking Model
by: Treyde, Wojtek, et al.
Published: (2024)

Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure
by: Dunn, Ian, et al.
Published: (2023)

Unified Guidance for Geometry-Conditioned Molecular Generation
by: Ayadi, Sirine, et al.
Published: (2025)

CryoFM: A Flow-based Foundation Model for Cryo-EM Densities
by: Zhou, Yi, et al.
Published: (2024)

Generative Molecular Design with Steerable and Granular Synthesizability Control
by: Guo, Jeff, et al.
Published: (2025)

Towards More Accurate Full-Atom Antibody Co-Design
by: Wu, Jiayang, et al.
Published: (2025)

Protein Conformation Generation via Force-Guided SE(3) Diffusion Models
by: Wang, Yan, et al.
Published: (2024)

PFMBench: Protein Foundation Model Benchmark
by: Gao, Zhangyang, et al.
Published: (2025)

Calibrating Generative Models to Distributional Constraints
by: Smith, Henry D., et al.
Published: (2025)

Training-Free Guidance for Discrete Diffusion Models for Molecular Generation
by: Kerby, Thomas J., et al.
Published: (2024)

Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation
by: Guo, Jeff, et al.
Published: (2024)

Lift Your Molecules: Molecular Graph Generation in Latent Euclidean Space
by: Ketata, Mohamed Amine, et al.
Published: (2024)