Related papers: MolGA: Molecular Graph Adaptation with Pre-trained…

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…

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular…

Molecular representation learning methods typically tokenize molecules as individual atoms or use rigid, rule-based fragment decompositions, limiting their ability to capture meaningful chemical substructure context. We introduce…

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D…

Recent years have seen a rapid growth of utilizing graph neural networks (GNNs) in the biomedical domain for tackling drug-related problems. However, like any other deep architectures, GNNs are data hungry. While requiring labels in real…

Molecular representation learning is pivotal in predicting molecular properties and advancing drug design. Traditional methodologies, which predominantly rely on homogeneous graph encoding, are limited by their inability to integrate…

Molecular property prediction, crucial for early drug candidate screening and optimization, has seen advancements with deep learning-based methods. While deep learning-based methods have advanced considerably, they often fall short in fully…

Artificial Intelligence predicts drug properties by encoding drug molecules, aiding in the rapid screening of candidates. Different molecular representations, such as SMILES and molecule graphs, contain complementary information for…

Graph embedding aims to transfer a graph into vectors to facilitate subsequent graph analytics tasks like link prediction and graph clustering. Most approaches on graph embedding focus on preserving the graph structure or minimizing the…

Molecular graph representation learning is a fundamental problem in modern drug and material discovery. Molecular graphs are typically modeled by their 2D topological structures, but it has been recently discovered that 3D geometric…

We propose a combination of a variational autoencoder and a transformer based model which fully utilises graph convolutional and graph pooling layers to operate directly on graphs. The transformer model implements a novel node encoding…

The latest biological findings observe that the traditional motionless 'lock-and-key' theory is not generally applicable because the receptor and ligand are constantly moving. Nonetheless, remarkable changes in associated atomic sites and…

Graph transformers typically lack third-order interactions, limiting their geometric understanding which is crucial for tasks like molecular geometry prediction. We propose the Triplet Graph Transformer (TGT) that enables direct…

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.…

As graph representation learning often suffers from label scarcity problems in real-world applications, researchers have proposed graph domain adaptation (GDA) as an effective knowledge-transfer paradigm across graphs. In particular, to…

Tackling molecular optimization problems using conventional computational methods is challenging, because the determination of the optimized configuration is known to be an NP-hard problem. Recently, there has been increasing interest in…

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…

Scaling deep learning models has been at the heart of recent revolutions in language modelling and image generation. Practitioners have observed a strong relationship between model size, dataset size, and performance. However,…

We propose Adjustable Molecular Representation (AdaMR), a new large-scale uniform pre-training strategy for small-molecule drugs, as a novel unified pre-training strategy. AdaMR utilizes a granularity-adjustable molecular encoding strategy,…

Accurately predicting drug-target binding affinity (DTA) in silico is a key task in drug discovery. Most of the conventional DTA prediction methods are simulation-based, which rely heavily on domain knowledge or the assumption of having the…