24 accepted papers
Multi-objective molecular optimization is a fundamental yet inherently challenging task in drug discovery, as it requires simultaneously optimizing multiple, often conflicting, molecular properties. Although recent deep learning methods have shown promise, they often lack objective-specific special
Current chemical large language models (LLMs) predominantly rely on explicit Chain-of-Thought (CoT) to solve complex reasoning problems. However, forcing nonverbal tacit chemical logic into discrete natural language imposes a fundamental ``modality mismatch,'' creating an artificial bottleneck for r…
Precise property prediction of organic materials is pivotal for next-generation electronic and energy devices. In density functional theory (DFT), the electron density (ED) serves as the fundamental determinant of material properties. Yet, establishing it as an input modality for material property p…
Large language models (LLMs) are widely applied in various natural language processing tasks such as question answering and machine translation. However, due to the lack of labeled data and the difficulty of manual annotation for biochemical properties, the performance for molecule generation tasks
Recent genomic foundation models largely adopt large language model architectures that treat DNA as a one-dimensional token sequence. However, exhaustive sequential reading is structurally misaligned with sparse and discontinuous genomic semantics, leading to wasted computation on low-information ba…
Whole-Slide Images (WSIs) are widely used for estimating the prognosis of cancer patients. Current studies generally follow a cancer-specific learning paradigm. However, the available training samples for one cancer type are usually scarce in pathology. Consequently, the model often struggles to lea
Identifying suitable reaction conditions is critical for chemical synthesis, as they directly affect yield, selectivity, and transformation feasibility. While recent methods have shown promising results, most approaches either encode reactants and products independently or rely on rule-based reactio
Multi-step retrosynthetic planning aims to decompose target molecules into available starting materials by iteratively invoking single-step prediction models within a search algorithm. The success of retrosynthetic planning depends on the joint guidance of single-step reasoning and global search acr
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in models like the series of ESM and AlphaFold2. Despite these…
Existing molecular machine learning force fields (MLFFs) generally focus on the learning of atoms, molecules, and simple quantum chemical properties (such as energy and force), but ignore the importance of electron density (ED) $\rho(r)$ in accurately understanding molecular force fields (MFFs). ED…
Electron density (ED), which describes the probability distribution of electrons in space, is crucial for accurately understanding the energy and force distribution in molecular force fields (MFF). Existing machine learning force fields (MLFF) focus on mining appropriate physical quantities from the
Chemical reaction and retrosynthesis prediction are fundamental tasks in drug discovery. Recently, large language models (LLMs) have shown potential in many domains. However, directly applying LLMs to these tasks faces two major challenges: (i) lacking a large-scale chemical synthesis-related instru
Drug repurposing plays a critical role in accelerating treatment discovery, especially for complex and rare diseases. Biomedical knowledge graphs (KGs), which encode rich clinical associations, have been widely adopted to support this task. However, existing methods largely overlook common-sense bio
Predicting the types and affinities of protein-protein interactions (PPIs) is crucial for understanding biological processes and developing novel therapeutic approaches. While encoding proteins themselves is essential, PPI networks can also provide rich prior knowledge for these predictive tasks. Ho…
Molecular design inherently involves the optimization of multiple conflicting objectives, such as enhancing bio-activity and ensuring synthesizability. Evaluating these objectives often requires resource-intensive computations or physical experiments. Current molecular design methodologies typically…
Identifying drug-drug interactions (DDIs) is critical for ensuring drug safety and advancing drug development, a topic that has garnered significant research interest. While existing methods have made considerable progress, approaches relying solely on known DDIs face a key challenge when applied to…
Inductive Knowledge Graph Completion (KGC) aims to infer missing facts between newly emerged entities within knowledge graphs (KGs), posing a significant challenge. While recent studies have shown promising results in inferring such entities through knowledge subgraph reasoning, they suffer from (i)…
Knowledge graph completion (KGC) aims to alleviate the inherent incompleteness of knowledge graphs (KGs), a crucial task for numerous applications such as recommendation systems and drug repurposing. The success of knowledge graph embedding (KGE) models provokes the question about the explainability…
Extracting rich molecular representation is a crucial prerequisite for accurate drug discovery. Recent molecular representation learning methods achieve impressive progress, but the paradigm of learning from a single modality gradually encounters the bottleneck of limited representation capabilities…
This paper focuses on continual meta-learning, where few-shot tasks are heterogeneous and sequentially available. Recent works use a mixture model for meta-knowledge to deal with the heterogeneity. However, these methods suffer from parameter inefficiency caused by two reasons: (1) the underlying as…
Optimizing molecules with desired properties is a crucial step in de novo drug design. While translation-based methods have achieved initial success, they continue to face the challenge of the “exposure bias” problem. The challenge of preventing the “exposure bias” problem of molecule optimization…
Molecular representation learning is a fundamental problem in the field of drug discovery and molecular science. Whereas incorporating molecular 3D information in the representations of molecule seems beneficial, which is related to computational chemistry with the basic task of predicting stable 3D…
Recent dynamic hypergraph neural networks (DHGNNs) are designed to adaptively optimize the hypergraph structure to avoid the dependence on the initial hypergraph structure, thus capturing more hidden information for representation learning. However, most existing DHGNNs cannot adjust the hyperedge n…
Drug-drug interaction (DDI) prediction is a challenging problem in pharmacology and clinical application, and effectively identifying potential DDIs during clinical trials is critical for patients and society. Most of existing computational models with AI techniques often concentrate on integrating…