Evo 2 sparse autoencoder activations for the Escherichia coli K-12 MG1655 genome

Whole-genome sparse-autoencoder activations for every base of the Escherichia coli K-12 MG1655 chromosome (RefSeq GCF_000005845.2, NC_000913.3), computed from the blocks.26 embedding of Evo 2 7B with the Goodfire BatchTopK SAE, stored as a CSR matrix of 4,641,652 rows x 32,768 features. Includes the embeddings, annotation and protein structures used by an accompanying hands-on notebook that reproduces the E. coli panels of Figure 4 of the Evo 2 paper. See README.md in the files below for the file list, the byte layout of the CSR files, and how to read one region over HTTP Range without downloading the whole 2.4 GB matrix. Version 4 rebuilds the activation matrix with the encode used by the Evo 2 notebook: relu(x W + b_enc) followed by BatchTopK over the window read. Rows hold the largest 128 activations per base, and class_sums.npz is recomputed from them.