Related papers: Chemical Language Model Linker: blending text and …

The generation of molecules with desired properties has become increasingly popular, revolutionizing the way scientists design molecular structures and providing valuable support for chemical and drug design. However, despite the potential…

Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science. A fundamental requirement for these models is the ability to accurately understand molecular structures,…

Generative machine learning models for exploring chemical space have shown immense promise, but many molecules they generate are too difficult to synthesize, making them impractical for further investigation or development. In this work, we…

This paper presents a novel training method, Conditional Masked Language Modeling (CMLM), to effectively learn sentence representations on large scale unlabeled corpora. CMLM integrates sentence representation learning into MLM training by…

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a…

The application of large language models (LLMs) to chemistry is frequently hampered by a "tokenization bottleneck", where tokenizers tuned on general-domain text tend to fragment chemical representations such as SMILES into semantically…

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…

Molecule generation requires satisfying multiple chemical and biological constraints while searching a large and structured chemical space. This makes it a non-binary problem, where effective models must identify non-obvious solutions under…

A drug molecule is a substance that changes the organism's mental or physical state. Every approved drug has an indication, which refers to the therapeutic use of that drug for treating a particular medical condition. While the Large…

Predicting chemical reactions, a fundamental challenge in chemistry, involves forecasting the resulting products from a given reaction process. Conventional techniques, notably those employing Graph Neural Networks (GNNs), are often limited…

Generative cross-modal retrieval, which treats retrieval as a generation task, has emerged as a promising direction with the rise of Multimodal Large Language Models (MLLMs). In this setting, the model responds to a text query by generating…

Retrieval-augmented Large Language Models (LLMs) offer substantial benefits in enhancing performance across knowledge-intensive scenarios. However, these methods often face challenges with complex inputs and encounter difficulties due to…

Designing de-novo molecules with desired property profiles requires efficient exploration of the vast chemical space ranging from $10^{23}$ to $10^{60}$ possible synthesizable candidates. While various deep generative models have been…

Formal languages are an integral part of modeling and simulation. They allow the distillation of knowledge into concise simulation models amenable to automatic execution, interpretation, and analysis. However, the arguably most humanly…

We present MeshLLM, a novel framework that leverages large language models (LLMs) to understand and generate text-serialized 3D meshes. Our approach addresses key limitations in existing methods, including the limited dataset scale when…

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language…

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 seek to automate the design of molecules based on specific chemical properties. Our primary contributions are a simpler method for generating SMILES strings guaranteed to be chemically valid, using a combination of a new context-free…

Large Language Models(LLMs) have revolutionized text generation and multimodal perception,but their capabilities in 3D content generation remain underexplored. Existing methods compromise by producing either low-resolution meshes or coarse…

We introduce Concept Bottleneck Protein Language Models (CB-pLM), a generative masked language model with a layer where each neuron corresponds to an interpretable concept. Our architecture offers three key benefits: i) Control: We can…