Other Cell Lines

Other cell lines (H1 / HepG2 / HUVEC / NHEK) — RNA only

No CAGE labels exist for these four cells, so expression is RNA-only. Their enhancer encoders train on pre-built activity CSVs, and the gene HDF5 is built from precomputed ABC links (scripts/build_gene_h5_for_cell.py — no raw BAMs needed; contact = ABC average Hi-C).

Per cell (e.g. HepG2):

# 1) encoder
CELL=HepG2 sbatch slurm/train_seqencoder_12fold.slurm
#    -> results/seqencoder/HepG2/checkpoints

# 2) gene HDF5 from precomputed ABC links
CELL=HepG2 sbatch slurm/build_gene_h5.slurm
#    -> batch_output/HepG2/encoding/HepG2_samples.h5

# 3) expression (f3, RNA)
CELL=HepG2 EXPR_TYPE=RNA USE_PRM_SIGNAL=1 \
  PRETRAINED_DIR=results/seqencoder/HepG2/checkpoints \
  OUTPUT_DIR=EPInformer_models/HepG2_RNA sbatch slurm/train_epinformer_12fold.slurm

# 4) evaluate
python evaluate.py expression --pred_dir EPInformer_models/HepG2_RNA

Expected RNA (pooled out-of-fold Pearson R): H1 0.781 · HepG2 0.845 · HUVEC 0.839 · NHEK 0.828.

These four cells' expression numbers are new — upstream EPInformer reports expression for K562/GM12878 only.