Scaling Laws and Architectural Frontiers in Metagenomic Foundation Models

Foundation models for genomics have the potential to revolutionize therapeutic design, yet the optimal architectural choices for modeling the vast and diverse distribution of metagenomic data remain under-explored. In this work, we present the machine learning methodology behind EDEN, a family of metagenomic foundation models scaled up to 28 billion parameters and trained on 9.7 trillion nucleotide tokens. We provide a systematic empirical study of architectural trade-offs between autoregressive Transformers (Llama-style), State-Space Models (Mamba), and Long-convolutional architectures (Hyena) for nucleotide-level modeling. Contrary to recent trends favoring linear-time sequence models for long-range biological data, we demonstrate that the Llama architecture exhibits superior scaling efficiency and semantic retrieval capabilities as the model capacity grows. We derive a set of quality-aware scaling laws for metagenomics, showing how model performance follows predictable power-law behavior across three orders of magnitude in parameters and data. Through extensive benchmarking, spanning unsupervised zero-shot fitness prediction, semantic completion, and gene recovery, we establish a blueprint for scaling biological foundation models and provide empirical evidence demonstrating why Transformer-based architectures define the current frontier