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We investigate the possibility of learning the representations of cosmological multifield dataset from the CAMELS project. We train a very deep variational encoder on images which comprise three channels, namely gas density (Mgas), neutral…

Molecular representation learning plays an essential role in cheminformatics. Recently, language model-based approaches have gained popularity as an alternative to traditional expert-designed features to encode molecules. However, these…

Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design…

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…

Recent advances in generative models have made exploring design spaces easier for de novo molecule generation. However, popular generative models like GANs and normalizing flows face challenges such as training instabilities due to…

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…

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…

Machine learning approaches have become popular for molecular modeling tasks, including molecular force fields and properties prediction. Traditional supervised learning methods suffer from scarcity of labeled data for particular tasks,…

Molecular property prediction is essential in chemistry, especially for drug discovery applications. However, available molecular property data is often limited, encouraging the transfer of information from related data. Transfer learning…

We propose a latent space energy-based prior model for text generation and classification. The model stands on a generator network that generates the text sequence based on a continuous latent vector. The energy term of the prior model…

Generative models have demonstrated substantial promise in Natural Language Processing (NLP) and have found application in designing molecules, as seen in General Pretrained Transformer (GPT) models. In our efforts to develop such a tool…

Template-free SMILES-to-SMILES translation models for reaction prediction and single-step retrosynthesis are of interest for industrial applications in computer-aided synthesis planning systems due to their state-of-the-art accuracy.…

Deep generative models have emerged as an exciting avenue for inverse molecular design, with progress coming from the interplay between training algorithms and molecular representations. One of the key challenges in their applicability to…

Generating peptides with desired properties is crucial for drug discovery and biotechnology. Traditional sequence-based and structure-based methods often require extensive datasets, which limits their effectiveness. In this study, we…

Recent years have seen rapid development of descriptor generation based on representation learning of extremely diverse molecules, especially those that apply natural language processing (NLP) models to SMILES, a literal representation of…

Deep generative models have been wildly successful at learning coherent latent representations for continuous data such as video and audio. However, generative modeling of discrete data such as arithmetic expressions and molecular…

We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of…

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%…

Training generative models that capture rich semantics of the data and interpreting the latent representations encoded by such models are very important problems in un-/self-supervised learning. In this work, we provide a simple algorithm…

Deep learning models for anticipating the products of organic reactions have found many use cases, including validating retrosynthetic pathways and constraining synthesis-based molecular design tools. Despite compelling performance on…