Related papers: Automating Exploratory Proteomics Research via Lan…

This paper introduces PROTEUS, a fully automated system that produces data-driven hypotheses from raw data files. We apply PROTEUS to clinical proteogenomics, a field where effective downstream data analysis and hypothesis proposal is…

Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or…

Hypothesis generation is a fundamental step in scientific discovery, yet it is increasingly challenged by information overload and disciplinary fragmentation. Recent advances in Large Language Models (LLMs) have sparked growing interest in…

Significant scientific discoveries have driven the progress of human civilisation. The explosion of scientific literature and data has created information barriers across disciplines that have slowed the pace of scientific discovery. Large…

With recent Nobel Prizes recognising AI contributions to science, Large Language Models (LLMs) are transforming scientific research by enhancing productivity and reshaping the scientific method. LLMs are now involved in experimental design,…

Large language models can extract local causal claims from text, but those claims become more useful when organized as persistent, navigable world models rather than as flat summaries. We introduce PROMETHEUS, a framework that turns…

Large Language Models (LLMs) are catalyzing a paradigm shift in scientific discovery, evolving from task-specific automation tools into increasingly autonomous agents and fundamentally redefining research processes and human-AI…

Can we leverage LLMs to model the process of discovering novel language model (LM) architectures? Inspired by real research, we propose a multi-agent LLM approach that simulates the conventional stages of research, from ideation and…

Designing de novo proteins beyond those found in nature holds significant promise for advancements in both scientific and engineering applications. Current methodologies for protein design often rely on AI-based models, such as surrogate…

Numerous algorithms have been proposed for detecting anomalies (outliers, novelties) in an unsupervised manner. Unfortunately, it is not trivial, in general, to understand why a given sample (record) is labelled as an anomaly and thus…

Large Language Models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent…

Large Language Models (LLMs) are transforming scientific hypothesis generation and validation by enabling information synthesis, latent relationship discovery, and reasoning augmentation. This survey provides a structured overview of…

Given the remarkable performance of Large Language Models (LLMs), an important question arises: Can LLMs conduct human-like scientific research and discover new knowledge, and act as an AI scientist? Scientific discovery is an iterative…

The rapid growth of biomedical knowledge has outpaced our ability to efficiently extract insights and generate novel hypotheses. Large language models (LLMs) have emerged as a promising tool to revolutionize knowledge interaction and…

Emerging topics in biomedical research are continuously expanding, providing a wealth of information about genes and their function. This rapid proliferation of knowledge presents unprecedented opportunities for scientific discovery and…

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new…

Deep learning is an advanced technology that relies on large-scale data and complex models for feature extraction and pattern recognition. It has been widely applied across various fields, including computer vision, natural language…

Large language models (LLMs) and vision-language models (VLMs) have the potential to transform biological research by enabling autonomous experimentation. Yet, their application remains constrained by rigid protocol design, limited…

Large Language Models (LLMs) perform best with well-crafted prompts, yet prompt engineering remains manual, inconsistent, and inaccessible to non-experts. We introduce Promptomatix, an automatic prompt optimization framework that transforms…

Large Language Models (LLMs) are revolutionizing bioinformatics, enabling advanced analysis of DNA, RNA, proteins, and single-cell data. This survey provides a systematic review of recent advancements, focusing on genomic sequence modeling,…