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Understanding how molecular alterations propagate across biological systems to drive disease remains a central challenge. Although high-throughput profiling enables comprehensive characterization of tumor states, most models neglect…

The idea of using fragment embedding to circumvent the high computational scaling of accurate electronic structure methods while retaining high accuracy has been a long-standing goal for quantum chemists. Traditional fragment embedding…

This work introduces a number of algebraic topology approaches, such as multicomponent persistent homology, multi-level persistent homology and electrostatic persistence for the representation, characterization, and description of small…

Molecular representation learning, a cornerstone for downstream tasks like molecular captioning and molecular property prediction, heavily relies on Graph Neural Networks (GNN). However, GNN suffers from the over-smoothing problem, where…

Representing molecular structures effectively in chemistry remains a challenging task. Language models and graph-based models are extensively utilized within this domain, consistently achieving state-of-the-art results across an array of…

Positron emission tomography (PET) combined with computed tomography (CT) imaging is routinely used in cancer diagnosis and prognosis by providing complementary information. Automatically segmenting tumors in PET/CT images can significantly…

Text-rich heterogeneous information networks (text-rich HINs) are ubiquitous in real-world applications. Hypernymy, also known as is-a relation or subclass-of relation, lays in the core of many knowledge graphs and benefits many downstream…

Drug combinations offer therapeutic benefits but also carry the risk of adverse drug-drug interactions (DDIs), especially under complex molecular structures. Accurate DDI event prediction requires capturing fine-grained inter-drug…

Machine learning models have found numerous successful applications in computational drug discovery. A large body of these models represents molecules as sequences since molecular sequences are easily available, simple, and informative. The…

Predicting user influence in social networks is a critical problem, and hypergraphs, as a prevalent higher-order modeling approach, provide new perspectives for this task. However, the absence of explicit cascade or infection probability…

Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields. However, most approaches employ a…

Capsule networks are designed to present the objects by a set of parts and their relationships, which provide an insight into the procedure of visual perception. Although recent works have shown the success of capsule networks on simple…

Multi-modal recommendation has gained traction as items possess rich attributes like text and images. Semantic ID-based approaches effectively discretize this information into compact tokens. However, two challenges persist: (1) Suboptimal…

Molecular interactions have widely been modelled as networks. The local wiring patterns around molecules in molecular networks are linked with their biological functions. However, networks model only pairwise interactions between molecules…

Deep learning methods have achieved impressive performance for multi-class medical image segmentation. However, they are limited in their ability to encode topological interactions among different classes (e.g., containment and exclusion).…

Background: Virtual Screening (VS) has become an essential tool in drug discovery, enabling the rapid and cost-effective identification of potential bioactive molecules. Among recent advancements, Graph Neural Networks (GNNs) have gained…

Characterizing materials with electron micrographs is a crucial task in fields such as semiconductors and quantum materials. The complex hierarchical structure of micrographs often poses challenges for traditional classification methods. In…

In the field of pharmacokinetics and pharmacodynamics (PKPD) modeling, which plays a pivotal role in the drug development process, traditional models frequently encounter difficulties in fully encapsulating the complexities of drug…

Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range…

The affinity and specificity of protein-molecule binding directly impact functional outcomes, uncovering the mechanisms underlying biological regulation and signal transduction. Most deep-learning-based prediction approaches focus on…