Cover Image

Explaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective for Molecular Property Prediction

Fuente: arXiv

Saved in:

Bibliographic Details
Main Authors:	He, Yinhan, Zheng, Zaiyi, Soga, Patrick, Zhu, Yaozhen, Dong, yushun, Li, Jundong
Format:	Preprint
Published:	2024
Subjects:	Machine Learning Computation and Language Biomolecules
Online Access:	Acceder al recurso
Tags:	Add Tag No Tags, Be the first to tag this record!

Similar Items

GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text
by: Liu, Pengfei, et al.
Published: (2023)

TwinBooster: Synergising Large Language Models with Barlow Twins and Gradient Boosting for Enhanced Molecular Property Prediction
by: Schuh, Maximilian G., et al.
Published: (2024)

MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction
by: Edwards, Carl, et al.
Published: (2024)

A Large-Scale Dataset for Molecular Structure-Language Description via a Rule-Regularized Method
by: Cai, Feiyang, et al.
Published: (2026)

MoleculeQA: A Dataset to Evaluate Factual Accuracy in Molecular Comprehension
by: Lu, Xingyu, et al.
Published: (2024)

Investigating Graph Neural Networks and Classical Feature-Extraction Techniques in Activity-Cliff and Molecular Property Prediction
by: Dablander, Markus
Published: (2024)

Ligandformer: A Graph Neural Network for Predicting Compound Property with Robust Interpretation
by: Guo, Jinjiang, et al.
Published: (2022)

IDP-Bert: Predicting Properties of Intrinsically Disordered Proteins (IDP) Using Large Language Models
by: Mollaei, Parisa, et al.
Published: (2024)

MD-LLM-1: A Large Language Model for Molecular Dynamics
by: Murtada, Mhd Hussein, et al.
Published: (2025)

Uncertainty Quantification for Molecular Property Predictions with Graph Neural Architecture Search
by: Jiang, Shengli, et al.
Published: (2023)

3M-Diffusion: Latent Multi-Modal Diffusion for Language-Guided Molecular Structure Generation
by: Zhu, Huaisheng, et al.
Published: (2024)

Global Human-guided Counterfactual Explanations for Molecular Properties via Reinforcement Learning
by: Wang, Danqing, et al.
Published: (2024)

How Creative Are Large Language Models in Generating Molecules?
by: Tao, Wen, et al.
Published: (2026)

The Role of Model Architecture and Scale in Predicting Molecular Properties: Insights from Fine-Tuning RoBERTa, BART, and LLaMA
by: Youngmin, Lee, et al.
Published: (2024)

Graph Neural Networks Are More Than Filters: Revisiting and Benchmarking from A Spectral Perspective
by: Dong, Yushun, et al.
Published: (2024)

Large Language Model Agent for Modular Task Execution in Drug Discovery
by: Ock, Janghoon, et al.
Published: (2025)

DrugLLM: Open Large Language Model for Few-shot Molecule Generation
by: Liu, Xianggen, et al.
Published: (2024)

Structure-Enhanced Protein Instruction Tuning: Towards General-Purpose Protein Understanding with LLMs
by: Wu, Wei, et al.
Published: (2024)

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

K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction
by: Abdullahi, Tassallah, et al.
Published: (2025)

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

MolLangBench: A Comprehensive Benchmark for Language-Prompted Molecular Structure Recognition, Editing, and Generation
by: Cai, Feiyang, et al.
Published: (2025)

Integrating Chemical Language and Molecular Graph in Multimodal Fused Deep Learning for Drug Property Prediction
by: Lu, Xiaohua, et al.
Published: (2023)

DrugImproverGPT: A Large Language Model for Drug Optimization with Fine-Tuning via Structured Policy Optimization
by: Liu, Xuefeng, et al.
Published: (2025)

BadGraph: A Backdoor Attack Against Latent Diffusion Model for Text-Guided Graph Generation
by: Ye, Liang, et al.
Published: (2025)

Language Interaction Network for Clinical Trial Approval Estimation
by: Gao, Chufan, et al.
Published: (2024)

Simple, Efficient and Scalable Structure-aware Adapter Boosts Protein Language Models
by: Tan, Yang, et al.
Published: (2024)

GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking
by: Yuan, Yiliang, et al.
Published: (2024)

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

Learning Hierarchical Interaction for Accurate Molecular Property Prediction
by: Hong, Huiyang, et al.
Published: (2025)

Can Large Language Models Understand Molecules?
by: Sadeghi, Shaghayegh, et al.
Published: (2024)

Predicting ATP binding sites in protein sequences using Deep Learning and Natural Language Processing
by: V, Shreyas, et al.
Published: (2024)

Multi-Modal Representation Learning for Molecular Property Prediction: Sequence, Graph, Geometry
by: Wang, Zeyu, et al.
Published: (2024)

Computational Protein Science in the Era of Large Language Models (LLMs)
by: Fan, Wenqi, et al.
Published: (2025)

Specialising and Analysing Instruction-Tuned and Byte-Level Language Models for Organic Reaction Prediction
by: Pang, Jiayun, et al.
Published: (2024)

Benchmarking Large Language Models for Molecule Prediction Tasks
by: Zhong, Zhiqiang, et al.
Published: (2024)

Large Language Models for Controllable Multi-property Multi-objective Molecule Optimization
by: Dey, Vishal, et al.
Published: (2025)

MolTailor: Tailoring Chemical Molecular Representation to Specific Tasks via Text Prompts
by: Guo, Haoqiang, et al.
Published: (2024)

Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey
by: Pei, Qizhi, et al.
Published: (2024)

MultiModal-Learning for Predicting Molecular Properties: A Framework Based on Image and Graph Structures
by: Wang, Zhuoyuan, et al.
Published: (2023)