Related papers: Representation-Guided Discrete Molecular Graph Ret…

Retrosynthesis prediction is one of the fundamental challenges in organic chemistry and related fields. The goal is to find reactants molecules that can synthesize product molecules. To solve this task, we propose a new graph-to-graph…

Single-step retrosynthesis (SSR) in organic chemistry is increasingly benefiting from deep learning (DL) techniques in computer-aided synthesis design. While template-free DL models are flexible and promising for retrosynthesis prediction,…

Retrosynthesis prediction is a fundamental problem in organic synthesis, where the task is to identify precursor molecules that can be used to synthesize a target molecule. A key consideration in building neural models for this task is…

Recent advances in molecular generative models have demonstrated great promise for accelerating scientific discovery, particularly in drug design. However, these models often struggle to generate high-quality molecules, especially in…

Drug Discovery is a fundamental and ever-evolving field of research. The design of new candidate molecules requires large amounts of time and money, and computational methods are being increasingly employed to cut these costs. Machine…

Recently, generative graph models have shown promising results in learning graph representations through self-supervised methods. However, most existing generative graph representation learning (GRL) approaches rely on random masking across…

Image generation using diffusion models have demonstrated outstanding learning capabilities, effectively capturing the full distribution of the training dataset. They are known to generate wide variations in sampled images, albeit with a…

Synthesizability in generative molecular design remains a pressing challenge. Existing methods to assess synthesizability span heuristics-based methods, retrosynthesis models, and synthesizability-constrained molecular generation. The…

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…

Retrosynthesis prediction focuses on identifying reactants capable of synthesizing a target product. Typically, the retrosynthesis prediction involves two phases: Reaction Center Identification and Reactant Generation. However, we argue…

One common belief is that with complex models and pre-training on large-scale datasets, transformer-based methods for referring expression comprehension (REC) perform much better than existing graph-based methods. We observe that since most…

Retrosynthesis poses a key challenge in biopharmaceuticals, aiding chemists in finding appropriate reactant molecules for given product molecules. With reactants and products represented as 2D graphs, retrosynthesis constitutes a…

Coarse-graining (CG) of molecular simulations simplifies the particle representation by grouping selected atoms into pseudo-beads and drastically accelerates simulation. However, such CG procedure induces information losses, which makes…

The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of…

Scene Graph Generation is a critical enabler of environmental comprehension for autonomous robotic systems. Most of existing methods, however, are often thwarted by the intricate dynamics of background complexity, which limits their ability…

A fundamental problem in computational chemistry is to find a set of reactants to synthesize a target molecule, a.k.a. retrosynthesis prediction. Existing state-of-the-art methods rely on matching the target molecule with a large set of…

Geometric representation-conditioned molecule generation provides an effective paradigm that decouples molecule representation modeling from structure generation. By decoupling molecule generation into two stages-first generating a…

Graph Transformers have recently attracted attention for molecular property prediction by combining the inductive biases of graph neural networks (GNNs) with the global receptive field of Transformers. However, many existing hybrid…

De novo molecule generation often results in chemically unfeasible molecules. A natural idea to mitigate this problem is to bias the search process towards more easily synthesizable molecules using a proxy for synthetic accessibility.…

Graph generation generally aims to create new graphs that closely align with a specific graph distribution. Existing works often implicitly capture this distribution through the optimization of generators, potentially overlooking the…