Index

Symbols

--basedir command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] --batch-size command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] --center command line option, [1] --checkpoint-metric command line option, [1], [2], [3], [4], [5] --checkpoint-mode command line option, [1], [2], [3], [4], [5] --ckpt command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] --dropout command line option, [1], [2], [3], [4], [5] --finetune-ckpt command line option, [1], [2], [3] --flank-window command line option, [1] --genome command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] --gep-gradient-checkpoint command line option, [1] --gep-parallel-embedding command line option, [1] --gep-zero-inflation command line option, [1] --gpu command line option, [1] --grad-samples command line option, [1], [2], [3], [4], [5] --hdf5-file command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] --help command line option, [1] --hf-endpoint command line option, [1] --high-resolution command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] --ignore command line option, [1] --ignore-object command line option, [1] --kind command line option, [1], [2], [3], [4], [5] --label command line option, [1] --limit-val-batches command line option, [1], [2], [3], [4], [5] --log-every-n-steps command line option, [1], [2], [3], [4], [5] --loss command line option, [1], [2], [3], [4], [5] --lr command line option, [1], [2], [3], [4], [5] --mask command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] --max-epochs command line option, [1], [2], [3], [4], [5] --meta command line option, [1], [2], [3] --mode command line option, [1] --name command line option, [1], [2], [3], [4], [5]

--no-filter command line option, [1] --num-workers command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] --o-bw command line option, [1] --o-h5 command line option, [1] --o-table command line option, [1] --oname command line option, [1], [2], [3], [4], [5], [6], [7] --perturbation command line option, [1] --perturbation-object command line option, [1] --perturbation-value command line option, [1] --pretrain-ckpt command line option, [1], [2], [3] --pretrain-trainable command line option, [1], [2], [3], [4], [5] --prompt-celltype command line option, [1], [2], [3] --prompt-celltype-cache-file command line option, [1], [2], [3], [4], [5] --prompt-dim-external command line option, [1], [2], [3], [4], [5] --prompt-kind command line option, [1], [2], [3], [4], [5] --prompt-regulator command line option, [1], [2], [3] --prompt-regulator-cache-file command line option, [1], [2], [3], [4], [5] --prompt-regulator-cache-limit command line option, [1] --prompt-regulator-cache-pin-memory command line option, [1] --save-top-k command line option, [1], [2], [3], [4], [5] --tag command line option, [1], [2], [3], [4], [5] --test command line option, [1], [2], [3], [4], [5] --train command line option, [1], [2], [3], [4], [5] --val-check-interval command line option, [1], [2], [3], [4], [5] --valid command line option, [1], [2], [3], [4], [5] --warmup-ratio command line option, [1], [2], [3], [4], [5] -d command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] -g command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] -hr command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] -k command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] -o command line option, [1], [2], [3], [4], [5], [6], [7]

B

BED command line option, [1]

C

command line option --basedir, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19] --batch-size, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] --center, [1] --checkpoint-metric, [1], [2], [3], [4], [5] --checkpoint-mode, [1], [2], [3], [4], [5] --ckpt, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] --dropout, [1], [2], [3], [4], [5] --finetune-ckpt, [1], [2], [3] --flank-window, [1] --genome, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] --gep-gradient-checkpoint, [1] --gep-parallel-embedding, [1] --gep-zero-inflation, [1] --gpu, [1] --grad-samples, [1], [2], [3], [4], [5] --hdf5-file, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] --help, [1] --hf-endpoint, [1] --high-resolution, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] --ignore, [1] --ignore-object, [1] --kind, [1], [2], [3], [4], [5] --label, [1] --limit-val-batches, [1], [2], [3], [4], [5] --log-every-n-steps, [1], [2], [3], [4], [5] --loss, [1], [2], [3], [4], [5] --lr, [1], [2], [3], [4], [5] --mask, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] --max-epochs, [1], [2], [3], [4], [5] --meta, [1], [2], [3] --mode, [1] --name, [1], [2], [3], [4], [5] --no-filter, [1] --num-workers, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] --o-bw, [1] --o-h5, [1] --o-table, [1] --oname, [1], [2], [3], [4], [5], [6], [7] --perturbation, [1] --perturbation-object, [1] --perturbation-value, [1] --pretrain-ckpt, [1], [2], [3] --pretrain-trainable, [1], [2], [3], [4], [5] --prompt-celltype, [1], [2], [3] --prompt-celltype-cache-file, [1], [2], [3], [4], [5] --prompt-dim-external, [1], [2], [3], [4], [5] --prompt-kind, [1], [2], [3], [4], [5] --prompt-regulator, [1], [2], [3] --prompt-regulator-cache-file, [1], [2], [3], [4], [5] --prompt-regulator-cache-limit, [1] --prompt-regulator-cache-pin-memory, [1] --save-top-k, [1], [2], [3], [4], [5] --tag, [1], [2], [3], [4], [5] --test, [1], [2], [3], [4], [5] --train, [1], [2], [3], [4], [5] --val-check-interval, [1], [2], [3], [4], [5] --valid, [1], [2], [3], [4], [5] --warmup-ratio, [1], [2], [3], [4], [5] -d, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] -g, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] -hr, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17] -k, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] -o, [1], [2], [3], [4], [5], [6], [7] BED, [1] IDS, [1], [2], [3] Path, [1] Pin, [1] SUPERVISED_FILE, [1], [2], [3], [4], [5] supervised_file, [1], [2], [3] The, [1]

I

IDS command line option, [1], [2], [3]

P

Path command line option, [1]

Pin command line option, [1]

S

SUPERVISED_FILE command line option, [1], [2], [3], [4], [5]

supervised_file command line option, [1], [2], [3]

T

The command line option, [1]