Related papers: MolCA: Molecular Graph-Language Modeling with Cros…

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…

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus…

Molecular language modeling tasks such as molecule captioning have been recognized for their potential to further understand molecular properties that can aid drug discovery or material synthesis based on chemical reactions. Unlike the…

While Large Language Models (LLMs) have shown exceptional generalization capabilities, their ability to process graph data, such as molecular structures, remains limited. To bridge this gap, this paper proposes Graph2Token, an efficient…

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language…

We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be…

Recent advances in large language models (LLMs) have led to models that tackle diverse molecular tasks, such as chemical reaction prediction and molecular property prediction. Large-scale molecular instruction-tuning datasets have enabled…

Large Language Models (LLMs) have significantly advanced molecular discovery, but existing multimodal molecular architectures fundamentally rely on autoregressive (AR) backbones. This strict left-to-right inductive bias is sub-optimal for…

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in…

Designing molecules with desirable physiochemical properties and functionalities is a long-standing challenge in chemistry, material science, and drug discovery. Recently, machine learning-based generative models have emerged as promising…

Molecular Relational Learning (MRL), aiming to understand interactions between molecular pairs, plays a pivotal role in advancing biochemical research. Recently, the adoption of large language models (LLMs), known for their vast knowledge…

Molecular core structures and R-groups are essential concepts in drug development. Integration of these concepts with conventional graph pre-training approaches can promote deeper understanding in molecules. We propose MolPLA, a novel…

Cross-modal text-molecule retrieval model aims to learn a shared feature space of the text and molecule modalities for accurate similarity calculation, which facilitates the rapid screening of molecules with specific properties and…

Effectively integrating molecular graph structures with Large Language Models (LLMs) is a key challenge in drug discovery. Most existing multi-modal alignment methods typically process these structures by fine-tuning the LLM or adding a…

Human expertise in chemistry and biomedicine relies on contextual molecular understanding, a capability that large language models (LLMs) can extend through fine-grained alignment between molecular structures and text. Recent multimodal…

Although artificial intelligence (AI) has made significant progress in understanding molecules in a wide range of fields, existing models generally acquire the single cognitive ability from the single molecular modality. Since the hierarchy…

Large Language Models (LLMs) with their strong task-handling capabilities have shown remarkable advancements across a spectrum of fields, moving beyond natural language understanding. However, their proficiency within the chemistry domain…

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…

The remarkable success of Large Language Models (LLMs) across diverse tasks has driven the research community to extend their capabilities to molecular applications. However, most molecular LLMs employ adapter-based architectures that do…

Molecular knowledge resides within three different modalities of information sources: molecular structures, biomedical documents, and knowledge bases. Effective incorporation of molecular knowledge from these modalities holds paramount…