Related papers: Advancing Molecular Graph-Text Pre-training via Fi…

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…

Pretraining molecular representations is crucial for drug and material discovery. Recent methods focus on learning representations from geometric structures, effectively capturing 3D position information. Yet, they overlook the rich…

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…

Multimodal molecular representation learning, which jointly models molecular graphs and their textual descriptions, enhances predictive accuracy and interpretability by enabling more robust and reliable predictions of drug toxicity,…

Artificial intelligence has demonstrated immense potential in scientific research. Within molecular science, it is revolutionizing the traditional computer-aided paradigm, ushering in a new era of deep learning. With recent progress in…

Molecule property prediction has gained significant attention in recent years. The main bottleneck is the label insufficiency caused by expensive lab experiments. In order to alleviate this issue and to better leverage textual knowledge for…

Molecular property prediction is a crucial foundation for drug discovery. In recent years, pre-trained deep learning models have been widely applied to this task. Some approaches that incorporate prior biological domain knowledge into the…

The integration of deep learning, particularly AI-Generated Content, with high-quality data derived from ab initio calculations has emerged as a promising avenue for transforming the landscape of scientific research. However, the challenge…

Recent advancements in biology and chemistry have leveraged multi-modal learning, integrating molecules and their natural language descriptions to enhance drug discovery. However, current pre-training frameworks are limited to two…

Tiered graph autoencoders provide the architecture and mechanisms for learning tiered latent representations and latent spaces for molecular graphs that explicitly represent and utilize groups (e.g., functional groups). This enables the…

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating…

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

Predicting molecular properties is essential for drug discovery, and computational methods can greatly enhance this process. Molecular graphs have become a focus for representation learning, with Graph Neural Networks (GNNs) widely used.…

We consider feature representation learning problem of molecular graphs. Graph Neural Networks have been widely used in feature representation learning of molecular graphs. However, most existing methods deal with molecular graphs…

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…

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 representation is a critical element in our understanding of the physical world and the foundation for modern molecular machine learning. Previous molecular machine learning models have employed strings, fingerprints, global…

As a pioneering vision-language model, CLIP (Contrastive Language-Image Pre-training) has achieved significant success across various domains and a wide range of downstream vision-language tasks. However, the text encoders in popular CLIP…

With the advent of the era of foundation models, pre-training and fine-tuning have become common paradigms. Recently, parameter-efficient fine-tuning has garnered widespread attention due to its better balance between the number of…

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…