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The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…

Graph Self-Supervised Learning (GSSL) offers a powerful paradigm for learning graph representations without labeled data. However, existing work assumes clean, manually curated graphs. Recent advances in NLP enable the large-scale automatic…

Recent years have witnessed the rapid development of concept map generation techniques due to their advantages in providing well-structured summarization of knowledge from free texts. Traditional unsupervised methods do not generate…

Predicting molecular properties with data-driven methods has drawn much attention in recent years. Particularly, Graph Neural Networks (GNNs) have demonstrated remarkable success in various molecular generation and prediction tasks. In…

Synthesis planning is the process of recursively decomposing target molecules into available precursors. Computer-aided retrosynthesis can potentially assist chemists in designing synthetic routes, but at present it is cumbersome and…

In structure-based drug design, accurately estimating the binding affinity between a candidate ligand and its protein receptor is a central challenge. Recent advances in artificial intelligence, particularly deep learning, have demonstrated…

Molecular graph representation learning is widely used in chemical and biomedical research. While pre-trained 2D graph encoders have demonstrated strong performance, they overlook the rich molecular domain knowledge associated with…

Retrosynthesis is a procedure where a target molecule is transformed into potential reactants and thus the synthesis routes can be identified. Recently, computational approaches have been developed to accelerate the design of synthesis…

Flow-guided Localization (FGL) enables the identification of spatial regions within the human body that contain an event of diagnostic interest. FGL does that by leveraging the passive movement of energy-constrained nanodevices circulating…

De novo molecular generation from tandem mass spectra is a challenging inverse problem whose core difficulty lies in the circular dependency between atom-level and bond-level reasoning: determining a bond's type requires knowing its…

The emergence of deep learning (DL) has provided great opportunities for the high-throughput analysis of atomic-resolution micrographs. However, the DL models trained by image patches in fixed size generally lack efficiency and flexibility…

Predicting the ground-state 3D molecular conformations from 2D molecular graphs is critical in computational chemistry due to its profound impact on molecular properties. Deep learning (DL) approaches have recently emerged as promising…

We present an extension of our Molecular Transformer architecture combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention. The single-step retrosynthetic model sets a new state…

Graph Transformers have recently attracted attention for molecular property prediction by combining the inductive biases of graph neural networks (GNNs) with the global receptive field of Transformers. However, many existing hybrid…

Node classification on static graphs has achieved significant success, but achieving accurate node classification on dynamic graphs where node topology, attributes, and labels change over time has not been well addressed. Existing methods…

The computational prediction of atomistic structure is a long-standing problem in physics, chemistry, materials, and biology. Within conventional force-field or {\em ab initio} calculations, structure is determined through energy…

Dynamic graphs (DGs), which capture time-evolving relationships between graph entities, have widespread real-world applications. To efficiently encode DGs for downstream tasks, most dynamic graph neural networks follow the traditional…

Graph neural networks frequently encounter significant performance degradation when confronted with structural noise or non-homophilous topologies. To address these systemic vulnerabilities, we present AdvSynGNN, a comprehensive…

The understanding of inorganic reactions, especially those far from the equilibrium state, is relatively limited due to their inherent complexity. Poor understandings on the underlying synthetic chemistry have constrained the design of…

Molecular dynamics is a powerful simulation tool to explore material properties. Most of the realistic material systems are too large to be simulated with first-principles molecular dynamics. Classical molecular dynamics has lower…