Related papers: Advancing biomolecular understanding and design fo…

Proteins, as essential biomolecules, play a central role in biological processes, including metabolic reactions and DNA replication. Accurate prediction of their properties and functions is crucial in biological applications. Recent…

The applications of large language models (LLMs) in various biological domains have been explored recently, but their reasoning ability in complex biological systems, such as pathways, remains underexplored, which is crucial for predicting…

Aligning molecular sequence representations (e.g., SMILES notations) with textual descriptions is critical for applications spanning drug discovery, materials design, and automated chemical literature analysis. Existing methodologies…

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance,…

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations…

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…

Molecular representations are inherently task-dependent, yet most pre-trained molecular encoders are not. Task conditioning promises representations that reorganize based on task descriptions, but existing approaches rely on expensive…

The recommendation of medication is a vital aspect of intelligent healthcare systems, as it involves prescribing the most suitable drugs based on a patient's specific health needs. Unfortunately, many sophisticated models currently in use…

Toxicity remains a leading cause of early-stage drug development failure. Despite advances in molecular design and property prediction, the task of molecular toxicity repair, generating structurally valid molecular alternatives with reduced…

Organic reaction, the foundation of modern chemical industry, is crucial for new material development and drug discovery. However, deciphering reaction mechanisms and modeling multi-molecular relationships remain formidable challenges due…

Multi-omics studies often rely on pathway enrichment to interpret heterogeneous molecular changes, but pathway enrichment (PE)-based workflows inherit structural limitations of pathway resources, including curation lag, functional…

Proteins are fundamental components of biological systems and can be represented through various modalities, including sequences, structures, and textual descriptions. Despite the advances in deep learning and scientific large language…

Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely black-box models and thus challenging to interpret, current protein LM…

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…

Protein language models (PLMs) encode rich biological information, yet their internal neuron representations are poorly understood. We introduce the first automated framework for labeling every neuron in a PLM with biologically grounded…

Human language is one of the most expressive tools for conveying intent, yet most artificial or biological systems lack mechanisms to interpret or respond meaningfully to it. Bridging this gap could enable more natural forms of control over…

The trade-off between expressiveness and interpretability remains a core challenge when building human-centric predictive models for classification and decision-making. While symbolic rules offer interpretability, they often lack…

Large language models (LLMs) have displayed an impressive ability to harness natural language to perform complex tasks. In this work, we explore whether we can leverage this learned ability to find and explain patterns in data.…

Structure determination is essential to a mechanistic understanding of diseases and the development of novel therapeutics. Machine-learning-based structure prediction methods have made significant advancements by computationally predicting…

The 21st century is presenting humankind with unprecedented environmental and medical challenges. The ability to design novel proteins tailored for specific purposes could transform our ability to respond timely to these issues. Recent…