Related papers: SMILES Enumeration as Data Augmentation for Neural…

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…

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…

Language models for molecular design have scaled to hundreds of millions of parameters, yet how they learn chemical grammar is poorly understood. We train SMolLM, a 53K-parameter weight-shared transformer, to generate novel SMILES with 95%…

The increasing integration of large language models (LLMs) across various fields has heightened concerns about their potential to propagate dangerous information. This paper specifically explores the security vulnerabilities of LLMs within…

Chemical databases store information in text representations, and the SMILES format is a universal standard used in many cheminformatics software. Encoded in each SMILES string is structural information that can be used to predict complex…

SMILES, a crucial textual representation of molecular structures, has garnered significant attention as a foundation for pre-trained language models (LMs). However, most existing pre-trained SMILES LMs focus solely on the single-token level…

There is more and more evidence that machine learning can be successfully applied in materials science and related fields. However, datasets in these fields are often quite small ($\ll1000$ samples). It makes the most advanced machine…

Modulation-enhanced localization microscopy (MELM) has demonstrated significant improvements in both lateral and axial localization precision compared to conventional single-molecule localization microscopy (SMLM). However, lateral…

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,…

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…

Molecular property prediction is an increasingly critical task within drug discovery and development. Typically, neural networks can learn molecular properties using graph-based, language-based or feature-based methods. Recent advances in…

Molecular property prediction has attracted substantial attention recently. Accurate prediction of drug properties relies heavily on effective molecular representations. The structures of chemical compounds are commonly represented as…

The detailed analysis of molecular structures and properties holds great potential for drug development discovery through machine learning. Developing an emergent property in the model to understand molecules would broaden the horizons for…

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,…

Recurrent neural networks have been widely used to generate millions of de novo molecules in a known chemical space. These deep generative models are typically setup with LSTM or GRU units and trained with canonical SMILEs. In this study,…

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…

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…

We address the task of controlled generation of small molecules, which entails finding novel molecules with desired properties under certain constraints (e.g., similarity to a reference molecule). Here we introduce MolMIM, a probabilistic…

In molecular structure data, SMILES (Simplified Molecular Input Line Entry System) strings are used to analyze molecular structure design. Numerical feature representation of SMILES strings is a challenging task. This work proposes a…

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…