Related papers: 3D Interaction Geometric Pre-training for Molecula…

Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top…

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…

Molecular representation pretraining is critical in various applications for drug and material discovery due to the limited number of labeled molecules, and most existing work focuses on pretraining on 2D molecular graphs. However, the…

Graph based molecular representation learning is essential for accurately predicting molecular properties in drug discovery and materials science; however, it faces significant challenges due to the intricate relationships among molecules…

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…

Machine learning has the potential to automate molecular design and drastically accelerate the discovery of new functional compounds. Towards this goal, generative models and reinforcement learning (RL) using string and graph…

In the real world, a molecule is a 3D geometric structure. Compared to 1D SMILES sequences and 2D molecular graphs, 3D molecules represent the most informative molecular modality. Despite the rapid progress of autoregressive-based language…

Effective molecular representation learning is of great importance to facilitate molecular property prediction, which is a fundamental task for the drug and material industry. Recent advances in graph neural networks (GNNs) have shown great…

Molecular representation learning has attracted much attention recently. A molecule can be viewed as a 2D graph with nodes/atoms connected by edges/bonds, and can also be represented by a 3D conformation with 3-dimensional coordinates of…

Rapid advancements in machine learning (ML) are transforming materials science by significantly speeding up material property calculations. However, the proliferation of ML approaches has made it challenging for scientists to keep up with…

Molecular property prediction is an important problem in drug discovery and materials science. As geometric structures have been demonstrated necessary for molecular property prediction, 3D information has been combined with various graph…

In recent years, molecular graph representation learning (GRL) has drawn much more attention in molecular property prediction (MPP) problems. The existing graph methods have demonstrated that 3D geometric information is significant for…

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…

Molecule representation learning (MRL) methods aim to embed molecules into a real vector space. However, existing SMILES-based (Simplified Molecular-Input Line-Entry System) or GNN-based (Graph Neural Networks) MRL methods either take…

Accurate molecular property predictions require 3D geometries, which are typically obtained using expensive methods such as density functional theory (DFT). Here, we attempt to obtain molecular geometries by relying solely on machine…

Molecular property prediction is one of the fastest-growing applications of deep learning with critical real-world impacts. Including 3D molecular structure as input to learned models improves their performance for many molecular tasks.…

Deep Metric Learning (DML), a widely-used technique, involves learning a distance metric between pairs of samples. DML uses deep neural architectures to learn semantic embeddings of the input, where the distance between similar examples is…

Recent advances in molecular representation integrates molecular topological and visual modalities, opening new avenues for precise Molecular Relational Learning (MRL). Existing MRL methods focus on intra-domain modeling, and their inherent…

Ground-state 3D geometries of molecules are essential for many molecular analysis tasks. Modern quantum mechanical methods can compute accurate 3D geometries but are computationally prohibitive. Currently, an efficient alternative to…

Molecular property prediction constitutes a cornerstone of drug discovery and materials science, necessitating models capable of disentangling complex structure-property relationships across diverse molecular modalities. Existing approaches…