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Reparameterized diffusion models (RDMs) have recently matched autoregressive methods in protein generation, motivating their use for challenging tasks such as designing membrane proteins, which possess interleaved soluble and transmembrane…

Multimodal large language models (MLLMs) have made impressive progress in many applications in recent years. However, chemical MLLMs that can handle cross-modal understanding and generation remain underexplored. To fill this gap, we propose…

Generative AI presents chemists with novel ideas for drug design and facilitates the exploration of vast chemical spaces. Diffusion models (DMs), an emerging tool, have recently attracted great attention in drug R\&D. This paper…

Advances in large language models (LLMs) have recently opened new and promising avenues for small-molecule drug discovery. Yet existing LLM-based approaches for molecular generation often suffer from high rates of invalid and low-quality…

Large Language Models (LLMs) are central to the one-for-all intelligent paradigm, but they face a fundamental challenge when dealing with heterogeneous scientific data such as molecules: the inherent gap between discrete linguistic symbols…

Generating chemically valid 3D molecular conformations is critical for computational drug discovery. Classical diffusion-based models like GeoLDM perform well but require hundreds of steps, making large-scale in silico screening…

Developing an effective molecular generation framework even with a limited number of molecules is often important for its practical deployment, e.g., drug discovery, since acquiring task-related molecular data requires expensive and…

Autoregressive language models generate text one token at a time, yet natural language is inherently structured in multi-token units, including phrases, n-grams, and collocations that carry meaning jointly. This one-token bottleneck limits…

Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…

Generating molecular structures with desired properties is a critical task with broad applications in drug discovery and materials design. We propose 3M-Diffusion, a novel multi-modal molecular graph generation method, to generate diverse,…

The de novo generation of molecules with targeted properties is crucial in biology, chemistry, and drug discovery. Current generative models are limited to using single property values as conditions, struggling with complex customizations…

Molecule generation is a challenging open problem in cheminformatics. Currently, deep generative approaches addressing the challenge belong to two broad categories, differing in how molecules are represented. One approach encodes molecular…

In recent years, deep learning techniques have made significant strides in molecular generation for specific targets, driving advancements in drug discovery. However, existing molecular generation methods present significant limitations:…

We introduce G2T-LLM, a novel approach for molecule generation that uses graph-to-tree text encoding to transform graph-based molecular structures into a hierarchical text format optimized for large language models (LLMs). This encoding…

Machine learning in drug discovery has been focused on virtual screening of molecular libraries using discriminative models. Generative models are an entirely different approach that learn to represent and optimize molecules in a continuous…

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML…

This document presents some early explorations of applying Softly Masked Language Modelling (SMLM) to symbolic music generation. SMLM can be seen as a generalisation of masked language modelling (MLM), where instead of each element of the…

Molecular representation learning plays a crucial role in advancing applications such as drug discovery and material design. Existing work leverages 2D and 3D modalities of molecular information for pre-training, aiming to capture…

Bridging molecular structures and natural language is essential for controllable design. Autoregressive models struggle with long-range dependencies, while standard diffusion processes apply uniform corruption across positions, which can…

Generating molecules with desired biological activities has attracted growing attention in drug discovery. Previous molecular generation models are designed as chemocentric methods that hardly consider the drug-target interaction, limiting…