14 accepted papers
Retrosynthesis prediction is a cornerstone of drug discovery, enabling the synthesis of novel therapeutic candidates. However, current deep learning models falter when navigating the unexplored chemical space essential for innovation. In these realistic scenarios, models face a challenging mixed out
Molecular interactions are a common phenomenon in physical chemistry field, which could produce unexpected biochemical properties harmful to humans, such as drug-drug interactions. Machine learning has the potential to deliver rapid and accurate predictions. However, the complexity of molecular stru…
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…
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…
Accurate protein identification from mass spectrometry (MS) data is fundamental to unraveling the complex roles of proteins in biological systems, with peptide sequencing being a pivotal step in this process. The two main paradigms for peptide sequencing are database search, which matches experiment…
Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. Recently, Large Language Models (LLMs), with their extensive knowledge bases and advanced reasoning capabilities, have emerged as powerful tools for
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
Molecular relational learning (MRL) seeks to understand the interaction behaviors between molecules, a pivotal task in domains such as drug discovery and materials science. Recently, extracting core substructures and modeling their interactions have emerged as mainstream approaches within machine le…
Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. With the recent development of large language models (LLMs), a growing number of studies have explored the integration of MRL with LLMs and achieved…
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…
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…
Molecular relational learning (MRL) is crucial for understanding the interaction behaviors between molecular pairs, a critical aspect of drug discovery and development. However, the large feasible model space of MRL poses significant challenges to benchmarking, and existing MRL frameworks face limit…