Related papers: NovoMolGen: Rethinking Molecular Language Model Pr…

Most current molecular language models transfer the masked language model or image-text generation model from natural language processing to molecular field. However, molecules are not solely characterized by atom/bond symbols; they…

We explore optimally training protein language models, an area of significant interest in biological research where guidance on best practices is limited. Most models are trained with extensive compute resources until performance gains…

"How to evaluate the de novo designs proposed by a generative model?" Despite the transformative potential of generative deep learning in drug discovery, this seemingly simple question has no clear answer. The absence of standardized…

While large language models have facilitated breakthroughs in many applications of artificial intelligence, their inherent largeness makes them computationally expensive and challenging to deploy in resource-constrained settings. In this…

Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered…

Modelica is a widely adopted language for simulating complex physical systems, yet effective model creation and optimization require substantial domain expertise. Although large language models (LLMs) have demonstrated promising…

Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the…

Large language models (LLMs) demonstrate remarkable ability to comprehend, reason, and generate following nature language instructions. However, the development of LLMs has been primarily focused on high-resource languages, such as English,…

Drug discovery can be viewed as a combinatorial search over an immense chemical space, motivating the development of deep generative models for de novo molecular design. Among these, GPT-based molecular language models (MLM) have shown…

The modeling of bio-molecular system across molecular scales remains a central challenge in scientific research. Large language models (LLMs) are increasingly applied to bio-molecular discovery, yet systematic evaluation across multi-scale…

Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields. However, their proficiency within specialized domains such as…

Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of Natural Language Processing is to understand sequences of words, a major…

Large Language Models (LLMs) and Vision Language Models (VLMs) have recently shown promising capabilities in various scientific domain. In particular, these advances have opened new opportunities in drug discovery, where the ability to…

Large Language Models (LLMs) and pre-trained Language Models (LMs) have achieved impressive success on many software engineering tasks (e.g., code completion and code generation). By leveraging huge existing code corpora (e.g., GitHub),…

Precise recognition, editing, and generation of molecules are essential prerequisites for both chemists and AI systems tackling various chemical tasks. We present MolLangBench, a comprehensive benchmark designed to evaluate fundamental…

The rapid advancement of large language models (LLMs) has led to significant improvements in natural language processing but also poses challenges due to their high computational and energy demands. This paper introduces a series of…

General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and performance required for drug discovery tasks. Simply increasing model size or introducing reasoning…

The development of large language models and multi-modal models has enabled the appealing idea of generating novel molecules from text descriptions. Generative modeling would shift the paradigm from relying on large-scale chemical screening…

In the space of only a few years, deep generative modeling has revolutionized how we think of artificial creativity, yielding autonomous systems which produce original images, music, and text. Inspired by these successes, researchers are…

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…