Scientific large language models: A survey on biological & chemical domains

Q Zhang, K Ding, T Lv, X Wang, Q Yin, Y Zhang… - ACM Computing …, 2025 - dl.acm.org
Large Language Models (LLMs) have emerged as a transformative power in enhancing
natural language comprehension, representing a significant stride toward artificial general …

Invariant graph learning meets information bottleneck for out-of-distribution generalization

W Mao, J Wu, H Liu, Y Sui, X Wang - arxiv preprint arxiv:2408.01697, 2024 - arxiv.org
Graph out-of-distribution (OOD) generalization remains a major challenge in graph learning
since graph neural networks (GNNs) often suffer from severe performance degradation …

Unimot: Unified molecule-text language model with discrete token representation

J Zhang, Y Bian, Y Chen, Q Yao - arxiv preprint arxiv:2408.00863, 2024 - arxiv.org
The remarkable success of Large Language Models (LLMs) across diverse tasks has driven
the research community to extend their capabilities to molecular applications. However …

Discrete Dictionary-based Decomposition Layer for Structured Representation Learning

T Park, HC Kim, M Lee - Advances in Neural Information …, 2025 - proceedings.neurips.cc
Neuro-symbolic neural networks have been extensively studied to integrate symbolic
operations with neural networks, thereby improving systematic generalization. Specifically …

Unraveling and Mitigating Endogenous Task-oriented Spurious Correlations in Ego-graphs via Automated Counterfactual Contrastive Learning

T Lin, Y Kang, Z Jiang, K Song, K Kuang, C Sun… - Expert Systems with …, 2025 - Elsevier
Abstract Graph Neural Networks (GNNs) have been proven to easily overfit spurious
subgraphs in the available data, which reduces their trustworthiness in high-stakes real …

A survey of out‐of‐distribution generalization for graph machine learning from a causal view

J Ma - AI Magazine, 2024 - Wiley Online Library
Graph machine learning (GML) has been successfully applied across a wide range of tasks.
Nonetheless, GML faces significant challenges in generalizing over out‐of‐distribution …

Advancing Molecule Invariant Representation via Privileged Substructure Identification

R Wang, H Dai, C Yang, L Song, C Shi - Proceedings of the 30th ACM …, 2024 - dl.acm.org
Graph neural networks (GNNs) have revolutionized molecule representation learning by
modeling molecules as graphs, with atoms represented as nodes and chemical bonds as …

When graph neural network meets causality: Opportunities, methodologies and an outlook

W Jiang, H Liu, H **ong - arxiv preprint arxiv:2312.12477, 2023 - arxiv.org
Graph Neural Networks (GNNs) have emerged as powerful representation learning tools for
capturing complex dependencies within diverse graph-structured data. Despite their …

A Survey of Quantized Graph Representation Learning: Connecting Graph Structures with Large Language Models

Q Lin, Z Peng, K Shi, K He, Y Xu, E Cambria… - arxiv preprint arxiv …, 2025 - arxiv.org
Recent years have witnessed rapid advances in graph representation learning, with the
continuous embedding approach emerging as the dominant paradigm. However, such …

Raising the Bar in Graph OOD Generalization: Invariant Learning Beyond Explicit Environment Modeling

X Shen, Y Liu, Y Wang, R Miao, Y Dai, S Pan… - arxiv preprint arxiv …, 2025 - arxiv.org
Out-of-distribution (OOD) generalization has emerged as a critical challenge in graph
learning, as real-world graph data often exhibit diverse and shifting environments that …