Related papers: MolGA: Molecular Graph Adaptation with Pre-trained…

Domain adaptation (DA) tries to tackle the scenarios when the test data does not fully follow the same distribution of the training data, and multi-source domain adaptation (MSDA) is very attractive for real world applications. By learning…

Geometric deep learning (GDL) has demonstrated huge power and enormous potential in molecular data analysis. However, a great challenge still remains for highly efficient molecular representations. Currently, covalent-bond-based molecular…

Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to…

Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve drug discovery processes. Automatic predictors of side-effects generally are not able to process the…

Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…

Chart-to-code generation is a critical task in automated data visualization, translating complex chart structures into executable programs. While recent Multi-modal Large Language Models (MLLMs) improve chart representation, existing…

Existing domain adaptation methods tend to treat every domain equally and align them all perfectly. Such uniform alignment ignores topological structures among different domains; therefore it may be beneficial for nearby domains, but not…

Molecular property prediction is one of the fastest-growing applications of deep learning with critical real-world impacts. Including 3D molecular structure as input to learned models improves their performance for many molecular tasks.…

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize…

Recently, transformers have shown promising performance in learning graph representations. However, there are still some challenges when applying transformers to real-world scenarios due to the fact that deep transformers are hard to train…

Molecule and text representation learning has gained increasing interest due to its potential for enhancing the understanding of chemical information. However, existing models often struggle to capture subtle differences between molecules…

Our work introduces an innovative approach to graph learning by leveraging Hyperdimensional Computing. Graphs serve as a widely embraced method for conveying information, and their utilization in learning has gained significant attention.…

Accurate prediction of molecular properties is essential in drug discovery and related fields. However, existing graph neural networks (GNNs) often struggle to simultaneously capture both local and global molecular structures. In this work,…

Molecular understanding is central to advancing areas such as scientific discovery, yet Large Language Models (LLMs) struggle to understand molecular graphs effectively. Existing graph-LLM bridges often adapt the Q-Former-style connector…

Benefiting from the powerful expressive capability of graphs, graph-based approaches have been popularly applied to handle multi-modal medical data and achieved impressive performance in various biomedical applications. For disease…

Unlike vision and language data which usually has a unique format, molecules can naturally be characterized using different chemical formulations. One can view a molecule as a 2D graph or define it as a collection of atoms located in a 3D…

Self-supervised learning has recently gained growing interest in molecular modeling for scientific tasks such as AI-assisted drug discovery. Current studies consider leveraging both 2D and 3D molecular structures for representation…

The enhanced representational power and broad applicability of deep learning models have attracted significant interest from the research community in recent years. However, these models often struggle to perform effectively under domain…

Recent advancements in computational chemistry have leveraged the power of trans-former-based language models, such as MoLFormer, pre-trained using a vast amount of simplified molecular-input line-entry system (SMILES) sequences, to…

Learning on molecule graphs has become an increasingly important topic in AI for science, which takes full advantage of AI to facilitate scientific discovery. Existing solutions on modeling molecules utilize Graph Neural Networks (GNNs) to…