The adoption of machine learning (ML) and deep learning methods has revolutionized molecular medicine by driving breakthroughs in genomics, transcriptomics, drug discovery, and biological systems modeling. The increasing quantity, multimodality, and heterogeneity of biological datasets demand automated methods that can produce generalizable predictive models. Recent developments in large language model-based agents have shown promise for automating end-to-end ML experimentation on structured benchmarks. However, when applied to heterogeneous computational biology datasets, these methods struggle with generalization and success rates. Here, we introduce Agentomics-ML, a fully autonomous agent-based system designed to produce a classification model and the necessary files for reproducible training and inference. Our method follows predefined steps of an ML experimentation process, repeatedly interacting with the file system through Bash to complete individual steps. Once an ML model is produced, training and validation metrics provide scalar feedback to a reflection step to identify issues such as overfitting. This step then creates verbal feedback for future iterations, suggesting adjustments to steps such as data representation, model architecture, and hyperparameter choices. We have evaluated Agentomics-ML on several established genomic and transcriptomic benchmark datasets and show that it outperforms existing state-of-the-art agent-based methods in both generalization and success rates. While state-of-the-art models built by domain experts still lead in absolute performance on the majority of the computational biology datasets used in this work, Agentomics-ML narrows the gap for fully autonomous systems and achieves state-of-the-art performance on one of the used benchmark datasets. The code is available at https://github.com/BioGeMT/Agentomics-ML.

Cloud native deployment with Kubernetes orchestration has enabled the "Write Once, Deploy Anywhere" paradigm for applications. This application development and deployment model enables scale and agility in today's hybrid and multi-cloud environments. Applications or services packaged as containers can be deployed and managed with the same Kubernetes based eco-system tools in the public cloud, on premise or Edge locations. Microsoft Azure Arc-Enabled Kubernetes (Reference 1) could be viewed as one such ecosystem tool the enables central management of Kubernetes clusters deployed on premises locations or across different public clouds. Kubernetes based offerings from different vendors are supported and they need not be based on Azure Kubernetes Service (AKS) (Reference 2).

Data scientists often train their models locally and look for a proper hosting service to deploy their models. Unfortunately, there's no one set mechanism or guide to deploying pre-trained models to the cloud. In this post, we look at deploying trained models to Amazon SageMaker hosting to reduce your deployment time. SageMaker is a fully managed machine learning (ML) service. With SageMaker, you can quickly build and train ML models and directly deploy them into a production-ready hosted environment.