Agentic AI

Introduction: Beyond the Chatbot When you ask ChatGPT a question, it answers. When you ask an agentic AI system a question, it acts. This distinction — between passive assistance and autonomous execution — marks one of the most significant shifts in artificial intelligence since the transformer architecture itself. Agentic AI systems are not merely more sophisticated chatbots. They are autonomous entities capable of perception, reasoning, planning, tool use, action, and memory. They can independently execute multi-step workflows, make decisions when faced with uncertainty, and adapt their approach based on feedback from the environment. In scientific contexts, this means agents that can read literature, formulate hypotheses, design experiments, execute computational analyses, interpret results, and iterate — all with varying degrees of human oversight. ...

Introduction: The Cellular Resolution Frontier Biology has always been a story of scale. For decades, we studied organisms, then tissues, then cell populations — averaging signals across thousands or millions of cells. But tissues are not homogeneous. A tumor contains cancer cells, immune cells, fibroblasts, and endothelial cells, each with distinct molecular profiles. The brain contains hundreds of neuronal subtypes, each with unique functions. Even “identical” cells in culture exhibit stochastic variation in gene expression that can determine cell fate. ...

AI for Metagenomics: Decoding the Microbiome The human microbiome is often referred to as our “second genome.” Comprising trillions of microorganisms—bacteria, archaea, fungi, and viruses—these hidden ecosystems outnumber human cells and contain vastly more genetic diversity than our own DNA. But where human genomics deals with a single species and a relatively static genome, metagenomics is the study of a dynamic, highly complex, and constantly shifting multi-species community. Decoding the microbiome is arguably one of the most data-rich and complex challenges in modern biology. Traditional bioinformatics tools, while foundational, have struggled with the compositionality, sparsity, and high dimensionality of metagenomic data. ...

Protein artificial intelligence is, without question, the most mature and publicly celebrated discipline within the “omics” family. When we discuss AI in biology, the conversation inevitably drifts toward the 2024 Nobel Prize in Chemistry—awarded jointly to David Baker for computational protein design, and to Demis Hassabis and John Jumper for protein structure prediction via AlphaFold. However, structure prediction was merely the opening act. Today, the frontier has rapidly shifted from static structure prediction to protein design (creating entirely new proteins), function prediction, and complex interaction modeling. In this seventh installment of the Agentic Omics series, we will dissect the current state of AI in proteomics, evaluate the monumental shifts from AlphaFold 2 to AlphaFold 3 and ESM-3, explore generative models like ProGen and RFdiffusion, and critically assess their real-world clinical impact in drug discovery. ...

When a new foundation model in computational biology is released, the accompanying paper inevitably features tables of bolded numbers demonstrating state-of-the-art performance. Whether it is predicting protein structures or annotating single-cell data, the claims are often spectacular. But how do we truly know if these AI systems work in ways that matter to biology, rather than just optimizing arbitrary computational metrics? For the vision of Agentic Omics to become reality—where autonomous agents orchestrate models like AlphaFold and DNABERT-2 to drive drug discovery—we need a rigorous understanding of when these models succeed, when they hallucinate, and when their benchmarks deceive us. Claims of AI breakthroughs are only as strong as their evaluation methodologies. ...

The bottleneck for AI in computational biology is rarely a shortage of sophisticated models; it is the sheer difficulty of making biological data AI-ready. The “Agentic Omics” vision—where autonomous AI agents orchestrate domain-specific models to accelerate drug discovery—fundamentally rests on the assumption that these agents have access to standardized, clean, and computable data. In this post, we explore the unglamorous but critical foundation of omics AI: the data infrastructure. We trace the journey from raw sequencing reads to the structured tensor formats required by modern foundation models, exploring the evolving standards, the scale of the challenge, and how cloud infrastructure is adapting. ...