Related papers: MutaPLM: Protein Language Modeling for Mutation Ex…

The conditional generation of proteins with desired functions is a key goal for generative models. Existing methods based on prompting of protein language models (PLMs) can generate proteins conditioned on a target functionality, such as a…

Protein language models (PLMs) learn probability distributions over natural protein sequences. By learning from hundreds of millions of natural protein sequences, protein understanding and design capabilities emerge. Recent works have shown…

Large Language Models excel in tasks like natural language understanding and text generation. Prompt engineering plays a critical role in leveraging LLM effectively. However, LLMs black-box nature hinders its interpretability and effective…

The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein…

Pre-trained on extensive text and image corpora, current Multi-Modal Large Language Models (MLLM) have shown strong capabilities in general visual reasoning tasks. However, their performance is still lacking in physical domains that require…

The rapid advancement of artificial intelligence, particularly with the development of Large Language Models (LLMs) built on the transformer architecture, has redefined the capabilities of natural language processing. These models now…

Designing protein mutants of both high stability and activity is a critical yet challenging task in protein engineering. Here, we introduce PRIME, a deep learning model, which can suggest protein mutants of improved stability and activity…

Large protein language models are adept at capturing the underlying evolutionary information in primary structures, offering significant practical value for protein engineering. Compared to natural language models, protein amino acid…

Optimization problems seek to find the best solution to an objective under a set of constraints, and have been widely investigated in real-world applications. Modeling and solving optimization problems in a specific domain typically require…

Large language models (LLMs) are playing an increasingly important role in science and engineering. For example, their ability to parse and understand human and computer languages makes them powerful interpreters and their use in…

Transformer-based pretrained language models (PLMs) have started a new era in modern natural language processing (NLP). These models combine the power of transformers, transfer learning, and self-supervised learning (SSL). Following the…

Despite deep learning's success in chemistry, its impact is hindered by a lack of interpretability and an inability to resolve activity cliffs, where minor structural nuances trigger drastic property shifts. Current representation learning,…

Humans possess the capability to comprehend diverse modalities and seamlessly transfer information between them. In this work, we introduce ModaVerse, a Multi-modal Large Language Model (MLLM) capable of comprehending and transforming…

The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs…

Explainability for Large Language Models (LLMs) is a critical yet challenging aspect of natural language processing. As LLMs are increasingly integral to diverse applications, their "black-box" nature sparks significant concerns regarding…

The rapid development of Large Language Models (LLMs) demonstrates remarkable multilingual capabilities in natural language processing, attracting global attention in both academia and industry. To mitigate potential discrimination and…

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…

The interaction between proteins and nucleic acids is crucial for processes that sustain cellular function, including DNA maintenance and the regulation of gene expression and translation. Amino acid mutations in protein-nucleic acid…

As developers increasingly rely on LLM-generated code summaries for documentation, testing, and review, it is important to study whether these summaries accurately reflect what the program actually does. LLMs often produce confident…

Understanding the intricate interplay among sequence, structure, and function remains a fundamental challenge in proteomics. The sequence-structure-function paradigm posits that biological roles are governed by the tertiary geometric…