Related papers: t-SMILES: A Scalable Fragment-based Molecular Repr…

Language models demonstrate fundamental abilities in syntax, semantics, and reasoning, though their performance often depends significantly on the inputs they process. This study introduces TSIS (Simplified TSID) and its variants:TSISD…

Traditional molecular string representations, such as SMILES, often pose challenges for AI-driven molecular design due to their non-sequential depiction of molecular substructures. To address this issue, we introduce Sequential…

Retrosynthesis prediction is fundamental to drug discovery and chemical synthesis, requiring the identification of reactants that can produce a target molecule. Current template-free methods struggle to capture the structural invariance…

In the intersection of molecular science and deep learning, tasks like virtual screening have driven the need for a high-throughput molecular representation generator on large chemical databases. However, as SMILES strings are the most…

Recent advancements in computational chemistry have leveraged the power of trans-former-based language models, such as MoLFormer, pre-trained using a vast amount of simplified molecular-input line-entry system (SMILES) sequences, to…

In this work, we propose a simple transformer-based baseline for multimodal molecular representation learning, integrating three distinct modalities: SMILES strings, 2D graph representations, and 3D conformers of molecules. A key aspect of…

Representing molecular structures effectively in chemistry remains a challenging task. Language models and graph-based models are extensively utilized within this domain, consistently achieving state-of-the-art results across an array of…

In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated…

SMILES is a linear representation of chemical structures which encodes the connection table, and the stereochemistry of a molecule as a line of text with a grammar structure denoting atoms, bonds, rings and chains, and this information can…

We introduce Group SELFIES, a molecular string representation that leverages group tokens to represent functional groups or entire substructures while maintaining chemical robustness guarantees. Molecular string representations, such as…

Molecular property prediction aims to learn representations that map chemical structures to functional properties. While multimodal learning has emerged as a powerful paradigm to learn molecular representations, prior works have largely…

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…

Chemical reaction prediction, involving forward synthesis and retrosynthesis prediction, is a fundamental problem in organic synthesis. A popular computational paradigm formulates synthesis prediction as a sequence-to-sequence translation…

Deep generative models have recently been applied to molecule design. If the molecules are encoded in linear SMILES strings, modeling becomes convenient. However, models relying on string representations tend to generate invalid samples and…

Artificial intelligence (AI) and machine learning (ML) are expanding in popularity for broad applications to challenging tasks in chemistry and materials science. Examples include the prediction of properties, the discovery of new reaction…

Simplified Molecular Input Line Entry System (SMILES) is a single line text representation of a unique molecule. One molecule can however have multiple SMILES strings, which is a reason that canonical SMILES have been defined, which ensures…

The discovery of novel materials and functional molecules can help to solve some of society's most urgent challenges, ranging from efficient energy harvesting and storage to uncovering novel pharmaceutical drug candidates. Traditionally…

Variational autoencoders (VAEs) defined over SMILES string and graph-based representations of molecules promise to improve the optimization of molecular properties, thereby revolutionizing the pharmaceuticals and materials industries.…

Molecules are commonly represented as SMILES strings, which can be readily converted to fixed-size molecular fingerprints. These fingerprints serve as feature vectors to train ML/DL models for molecular property prediction tasks in the…

SMILES-based molecular generative models have been pivotal in drug design but face challenges in fragment-constrained tasks. To address this, the Sequential Attachment-based Fragment Embedding (SAFE) representation was recently introduced…