Related papers: SELFIES and the future of molecular string represe…

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…

String-based molecular representations play a crucial role in cheminformatics applications, and with the growing success of deep learning in chemistry, have been readily adopted into machine learning pipelines. However, traditional…

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…

Automated computational analysis of the vast chemical space is critical for numerous fields of research such as drug discovery and material science. Representation learning techniques have recently been employed with the primary objective…

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…

Chemical representation learning has gained increasing interest due to the limited availability of supervised data in fields such as drug and materials design. This interest particularly extends to chemical language representation learning,…

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…

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…

The simplified molecular-input line-entry system (SMILES) is the most popular representation of chemical compounds. Therefore, many SMILES-based molecular property prediction models have been developed. In particular, transformer-based…

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…

Deep learning, a subfield of machine learning, has gained importance in various application areas in recent years. Its growing popularity has led it to enter the natural sciences as well. This has created the need for molecular…

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 recent years, artificial intelligence has played an important role on accelerating the whole process of drug discovery. Various of molecular representation schemes of different modals (e.g. textual sequence or graph) are developed. By…

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance,…

Effective representation of molecules is a crucial factor affecting the performance of artificial intelligence models. This study introduces a flexible, fragment-based, multiscale molecular representation framework called t-SMILES…

Molecule generation is key to drug discovery and materials science, enabling the design of novel compounds with specific properties. Large language models (LLMs) can learn to perform a wide range of tasks from just a few examples. However,…

This study introduces a novel approach, combining substruct counting, $k$-mers, and Daylight-like fingerprints, to expand the representation of chemical structures in SMILES strings. The integrated method generates comprehensive molecular…

Purpose: Large Language Models (LLMs) like GPT (Generative Pre-trained Transformer) from OpenAI and LLaMA (Large Language Model Meta AI) from Meta AI are increasingly recognized for their potential in the field of cheminformatics,…

In the field of chemical structure recognition, the task of converting molecular images into machine-readable data formats such as SMILES string stands as a significant challenge, primarily due to the varied drawing styles and conventions…