Experiments

In this folder, we collect experimental runs of models included in genomic_benchmarks.models module for benchmark datasets. Current SOTA is HyenaDNA, descriped into details at https://github.com/HazyResearch/hyena-dna.

Each run is recorded as a notebook. Currently, TensorFlow experiments are run with papermill, PyTorch experiments are run manually.

See the accuracy and F1 score on test sets in the table below.

How to add an experiment

PyTorch

To run one experiment:

papermill utils/torch_cnn_classifier.ipynb torch_cnn_experiments/[DATASET NAME].ipynb -p DATASET [DATASET NAME]

To run all experiments:

bash utils/run_all_torch_experiments.sh

TensorFlow

To run one experiment:

papermill utils/tf_cnn_classifier.ipynb tf_cnn_experiments/[DATASET NAME].ipynb -p DATASET [DATASET NAME]

To run all experiments:

bash utils/run_all_tf_experiments.sh

How to add another papermill script:

• create a notebook in utils folder following the naming convention there
• all parameters should be specified in one cell in the beginning of the notebook, tag it parameters as described here
• run experiments using papermill for all benchmark datasets

Results

HyenaDNA

Dataset	Accuracy
demo_coding_vs_intergenomic_seqs	91.3
demo_human_or_worm	96.6
drosophila_enhancers_stark	58.6
dummy_mouse_enhancers_ensembl	85.1
human_enhancers_cohn	74.2
human_enhancers_ensembl	89.2
human_ensembl_regulatory	93.8
human_nontata_promoters	96.6
human_ocr_ensembl	80.9

PyTorch CNN

Dataset	Accuracy	F1 score
demo_coding_vs_intergenomic_seqs	87.6	86.8
demo_human_or_worm	93	92.8
drosophila_enhancers_stark	58.6	44.5
dummy_mouse_enhancers_ensembl	69	70.4
human_enhancers_cohn	69.5	67.1
human_enhancers_ensembl	68.9	56.5
human_ensembl_regulatory	93.3	93.3
human_nontata_promoters	84.6	83.7
human_ocr_ensembl	68	66.1

TensorFlow CNN

Dataset	Loss	Accuracy	F1
demo_coding_vs_intergenomic_seqs	0.258	89.6	89.4
demo_human_or_worm	0.148	94.2	93.2
drosophila_enhancers_stark	0.959	52.4	69.1
dummy_mouse_enhancers_ensembl	0.919	50	66.9
human_enhancers_cohn	0.589	68.9	71.3
human_enhancers_ensembl	0.421	81.1	74.6
human_ensembl_regulatory	0.505	79.3	79.3
human_nontata_promoters	0.319	86.5	84.4
human_ocr_ensembl	0.585	68.8	72