├── .gitignore ├── LICENSE ├── README.md ├── amber ├── __init__.py ├── _deprecated │ ├── bootstrap │ │ ├── analyze.py │ │ ├── dense_skipcon_space.py │ │ ├── explore_lambda.py │ │ ├── gold_standard.py │ │ ├── grid_search.py │ │ └── simple_conv1d_space.py │ ├── convert_fasta_to_encoded_h5py.py │ ├── convert_fasta_to_h5py.py │ ├── draw_samples.py │ ├── interpret │ │ ├── __init__.py │ │ ├── heritability.py │ │ ├── interpret.py │ │ ├── scores.py │ │ └── sequenceModel.py │ ├── objective │ │ ├── __init__.py │ │ ├── generalObjFunc.py │ │ ├── generalObjMath.py │ │ ├── graph.py │ │ ├── motif.py │ │ └── motifUtils.py │ ├── plots │ │ ├── plot_all_stats.py │ │ └── plotsV1.py │ └── split_samples.py ├── architect │ ├── __init__.py │ ├── base.py │ ├── buffer.py │ ├── commonOps.py │ ├── manager.py │ ├── modelSpace.py │ ├── optim │ │ ├── __init__.py │ │ ├── controller │ │ │ ├── __init__.py │ │ │ ├── base.py │ │ │ ├── controllerTrainEnv.py │ │ │ ├── pytorch │ │ │ │ ├── __init__.py │ │ │ │ └── generalController.py │ │ │ ├── tf1 │ │ │ │ ├── __init__.py │ │ │ │ ├── generalController.py │ │ │ │ ├── multiioController.py │ │ │ │ ├── operationController.py │ │ │ │ └── zeroShotController.py │ │ │ └── tf2 │ │ │ │ ├── __init__.py │ │ │ │ └── generalController.py │ │ └── pmbga │ │ │ ├── __init__.py │ │ │ ├── bayes_prob.py │ │ │ └── genetic_algo.py │ ├── reward.py │ ├── store.py │ └── trainEnv.py ├── backend │ ├── __init__.py │ ├── amber_ops.py │ ├── backend.py │ ├── pytorch │ │ ├── __init__.py │ │ ├── cache.py │ │ ├── layer.py │ │ ├── math.py │ │ ├── model.py │ │ ├── session.py │ │ ├── tensor.py │ │ └── utils.py │ ├── set_default_backend.py │ ├── tensorflow_1 │ │ ├── __init__.py │ │ ├── _operators │ │ │ ├── __init__.py │ │ │ ├── denovo_motif_conv.py │ │ │ ├── sepfc.py │ │ │ └── topk.py │ │ ├── math.py │ │ ├── model.py │ │ ├── session.py │ │ └── tensor.py │ └── tensorflow_2 │ │ ├── __init__.py │ │ ├── _operators │ │ ├── __init__.py │ │ ├── denovo_motif_conv.py │ │ ├── sepfc.py │ │ └── topk.py │ │ ├── cache.py │ │ ├── math.py │ │ ├── model.py │ │ ├── session.py │ │ └── tensor.py ├── getter.py ├── modeler │ ├── __init__.py │ ├── _deprecated │ │ ├── child.py │ │ ├── dag.py │ │ ├── enasModeler.py │ │ └── preprocess │ │ │ ├── __init__.py │ │ │ ├── cluster.py │ │ │ └── pipeline.py │ ├── architectureDecoder.py │ ├── base.py │ ├── resnet │ │ ├── __init__.py │ │ ├── keras_resnet.py │ │ └── pytorch_resnet.py │ ├── sequential │ │ ├── __init__.py │ │ ├── keras_sequential.py │ │ └── pytorch_sequential.py │ ├── sparse_ffnn │ │ ├── __init__.py │ │ ├── keras_ffnn.py │ │ ├── pytorch_ffnn.py │ │ └── tf1_featmod_ffnn.py │ └── supernet │ │ ├── __init__.py │ │ ├── base.py │ │ ├── pytorch_supernet.py │ │ └── tf1_supernet.py ├── offline_learn │ ├── __init__.py │ └── mock_manager.py ├── plots │ ├── __init__.py │ ├── heatmap2.py │ ├── ontology.py │ ├── plotsV1.py │ └── sankey.py ├── utils │ ├── __init__.py │ ├── data_parser.py │ ├── io.py │ ├── logging.py │ ├── motif.py │ ├── saliency.py │ ├── sampler.py │ ├── sequences.py │ ├── simulator.py │ ├── tensorflowMem.py │ ├── testing_utils.py │ └── tests │ │ ├── files │ │ ├── small_genome.encoded.h5 │ │ ├── small_genome.fa │ │ ├── small_genome.fa.fai │ │ └── small_genome.h5 │ │ ├── test_encoded_genome.py │ │ ├── test_encoded_hdf5_genome.py │ │ ├── test_genome.py │ │ └── test_hdf5_genome.py └── wrapper.py ├── bin └── amber-cli ├── dev.md ├── docs ├── Makefile ├── _config.yml ├── make.bat └── source │ ├── _static │ └── img │ │ ├── amber-logo.png │ │ ├── controller.png │ │ └── package_layout.png │ ├── amber-cli.rst │ ├── amber.architect.rst │ ├── amber.bootstrap.rst │ ├── amber.interpret.rst │ ├── amber.modeler.rst │ ├── amber.objective.rst │ ├── amber.plots.rst │ ├── amber.resources.rst │ ├── amber.utils.rst │ ├── conf.py │ ├── index.rst │ ├── modules.rst │ ├── overview │ ├── faq.rst │ ├── installation.rst │ ├── overview.rst │ └── reference.rst │ ├── resource │ ├── downloads.rst │ ├── gallery.rst │ └── tutorials.rst │ └── under-dev.rst ├── examples ├── AMBIENT │ ├── conda │ │ └── ambient_env.yml │ ├── evaluate │ │ ├── AMBER_analyze_third_search.ipynb │ │ ├── ZS_AMBER_TestFeat.ipynb │ │ ├── amber_single_run.py │ │ ├── model_space.pkl │ │ ├── plot_traj.py │ │ ├── run_metrics.py │ │ └── sbatch_single_run.sh │ ├── real_deepsea │ │ ├── ambient_nas.py │ │ ├── call_ofl_train.sh │ │ ├── read_ambient_hist.py │ │ ├── sbatch_real_deepsea.sh │ │ ├── train_from_history.py │ │ ├── zero_shot_nas.real_deepsea.py │ │ └── zs_config.py │ └── sim_data │ │ ├── sbatch_grid.sh │ │ ├── simulate_dna.sh │ │ ├── zero_shot_nas.sim_data.py │ │ └── zeroshot_grid_searcher.py ├── CROTON │ ├── amber_croton.py │ └── sbatch_croton.sh ├── DeepSEA │ ├── amber_deepsea.py │ ├── amber_env.yml │ ├── amber_tf2_env.yml │ └── conda_amber.linux_env.yml ├── MockSampling │ ├── mock_nas.py │ └── zero_shot_nas.sim_data.py └── digits_sklearn │ ├── conv2d_specs.pkl │ └── digits_sklearn.py ├── pyproject.toml ├── readthedocs.yaml ├── resources └── amber-illustrations.pptx ├── rtd.sh ├── setup.cfg ├── setup.py └── tests ├── cov_report.txt ├── coverage.svg ├── essentials ├── test_architect_controller_env.py ├── test_architect_controller_optimize.py ├── test_architect_pmbga_optimize.py └── test_modeler_sequential.py ├── helpers ├── test_architect_helper.py ├── test_architect_reward.py └── test_parallel_env.py ├── integration ├── mock_black_box │ ├── tmp_1 │ │ └── train_history.csv.gz │ ├── tmp_10 │ │ └── train_history.csv.gz │ ├── tmp_11 │ │ └── train_history.csv.gz │ ├── tmp_12 │ │ └── train_history.csv.gz │ ├── tmp_13 │ │ └── train_history.csv.gz │ ├── tmp_14 │ │ └── train_history.csv.gz │ ├── tmp_15 │ │ └── train_history.csv.gz │ ├── tmp_16 │ │ └── train_history.csv.gz │ ├── tmp_17 │ │ └── train_history.csv.gz │ ├── tmp_18 │ │ └── train_history.csv.gz │ ├── tmp_19 │ │ └── train_history.csv.gz │ ├── tmp_2 │ │ └── train_history.csv.gz │ ├── tmp_20 │ │ └── train_history.csv.gz │ ├── tmp_3 │ │ └── train_history.csv.gz │ ├── tmp_4 │ │ └── train_history.csv.gz │ ├── tmp_5 │ │ └── train_history.csv.gz │ ├── tmp_6 │ │ └── train_history.csv.gz │ ├── tmp_7 │ │ └── train_history.csv.gz │ ├── tmp_8 │ │ └── train_history.csv.gz │ └── tmp_9 │ │ └── train_history.csv.gz └── test_integration_bionas.py ├── modelers ├── modeler_pytorch │ └── test_modeler_pytorch.py ├── modeler_tf1 │ ├── test_modeler_keras.py │ ├── test_modeler_tensorflow_supercnn.py │ ├── test_modeler_tensorflow_superffnn.py │ └── test_supernet_featmodel.py └── modeler_tf2 │ └── .keep ├── run_test_pytorch.sh ├── run_test_tf1.sh └── ui ├── test_conv2d_specs.pkl ├── test_getter.py └── test_wrapper.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/README.md -------------------------------------------------------------------------------- /amber/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/__init__.py -------------------------------------------------------------------------------- /amber/_deprecated/bootstrap/analyze.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/bootstrap/analyze.py -------------------------------------------------------------------------------- /amber/_deprecated/bootstrap/dense_skipcon_space.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/bootstrap/dense_skipcon_space.py -------------------------------------------------------------------------------- /amber/_deprecated/bootstrap/explore_lambda.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/bootstrap/explore_lambda.py -------------------------------------------------------------------------------- /amber/_deprecated/bootstrap/gold_standard.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/bootstrap/gold_standard.py -------------------------------------------------------------------------------- /amber/_deprecated/bootstrap/grid_search.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/bootstrap/grid_search.py -------------------------------------------------------------------------------- /amber/_deprecated/bootstrap/simple_conv1d_space.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/bootstrap/simple_conv1d_space.py -------------------------------------------------------------------------------- /amber/_deprecated/convert_fasta_to_encoded_h5py.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/convert_fasta_to_encoded_h5py.py -------------------------------------------------------------------------------- /amber/_deprecated/convert_fasta_to_h5py.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/convert_fasta_to_h5py.py -------------------------------------------------------------------------------- /amber/_deprecated/draw_samples.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/draw_samples.py -------------------------------------------------------------------------------- /amber/_deprecated/interpret/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/interpret/__init__.py -------------------------------------------------------------------------------- /amber/_deprecated/interpret/heritability.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/interpret/heritability.py -------------------------------------------------------------------------------- /amber/_deprecated/interpret/interpret.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/interpret/interpret.py -------------------------------------------------------------------------------- /amber/_deprecated/interpret/scores.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/interpret/scores.py -------------------------------------------------------------------------------- /amber/_deprecated/interpret/sequenceModel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/interpret/sequenceModel.py -------------------------------------------------------------------------------- /amber/_deprecated/objective/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/objective/__init__.py -------------------------------------------------------------------------------- /amber/_deprecated/objective/generalObjFunc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/objective/generalObjFunc.py -------------------------------------------------------------------------------- /amber/_deprecated/objective/generalObjMath.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/objective/generalObjMath.py -------------------------------------------------------------------------------- /amber/_deprecated/objective/graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/objective/graph.py -------------------------------------------------------------------------------- /amber/_deprecated/objective/motif.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/objective/motif.py -------------------------------------------------------------------------------- /amber/_deprecated/objective/motifUtils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/objective/motifUtils.py -------------------------------------------------------------------------------- /amber/_deprecated/plots/plot_all_stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/plots/plot_all_stats.py -------------------------------------------------------------------------------- /amber/_deprecated/plots/plotsV1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/plots/plotsV1.py -------------------------------------------------------------------------------- /amber/_deprecated/split_samples.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/_deprecated/split_samples.py -------------------------------------------------------------------------------- /amber/architect/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/__init__.py -------------------------------------------------------------------------------- /amber/architect/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/base.py -------------------------------------------------------------------------------- /amber/architect/buffer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/buffer.py -------------------------------------------------------------------------------- /amber/architect/commonOps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/commonOps.py -------------------------------------------------------------------------------- /amber/architect/manager.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/manager.py -------------------------------------------------------------------------------- /amber/architect/modelSpace.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/modelSpace.py -------------------------------------------------------------------------------- /amber/architect/optim/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /amber/architect/optim/controller/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/controller/__init__.py -------------------------------------------------------------------------------- /amber/architect/optim/controller/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/controller/base.py -------------------------------------------------------------------------------- /amber/architect/optim/controller/controllerTrainEnv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/controller/controllerTrainEnv.py -------------------------------------------------------------------------------- /amber/architect/optim/controller/pytorch/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/controller/pytorch/__init__.py -------------------------------------------------------------------------------- /amber/architect/optim/controller/pytorch/generalController.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/controller/pytorch/generalController.py -------------------------------------------------------------------------------- /amber/architect/optim/controller/tf1/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/controller/tf1/__init__.py -------------------------------------------------------------------------------- /amber/architect/optim/controller/tf1/generalController.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/controller/tf1/generalController.py -------------------------------------------------------------------------------- /amber/architect/optim/controller/tf1/multiioController.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/controller/tf1/multiioController.py -------------------------------------------------------------------------------- /amber/architect/optim/controller/tf1/operationController.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/controller/tf1/operationController.py -------------------------------------------------------------------------------- /amber/architect/optim/controller/tf1/zeroShotController.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/controller/tf1/zeroShotController.py -------------------------------------------------------------------------------- /amber/architect/optim/controller/tf2/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/controller/tf2/__init__.py -------------------------------------------------------------------------------- /amber/architect/optim/controller/tf2/generalController.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/controller/tf2/generalController.py -------------------------------------------------------------------------------- /amber/architect/optim/pmbga/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/pmbga/__init__.py -------------------------------------------------------------------------------- /amber/architect/optim/pmbga/bayes_prob.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/pmbga/bayes_prob.py -------------------------------------------------------------------------------- /amber/architect/optim/pmbga/genetic_algo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/optim/pmbga/genetic_algo.py -------------------------------------------------------------------------------- /amber/architect/reward.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/reward.py -------------------------------------------------------------------------------- /amber/architect/store.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/store.py -------------------------------------------------------------------------------- /amber/architect/trainEnv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/architect/trainEnv.py -------------------------------------------------------------------------------- /amber/backend/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/__init__.py -------------------------------------------------------------------------------- /amber/backend/amber_ops.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/amber_ops.py -------------------------------------------------------------------------------- /amber/backend/backend.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/backend.py -------------------------------------------------------------------------------- /amber/backend/pytorch/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/pytorch/__init__.py -------------------------------------------------------------------------------- /amber/backend/pytorch/cache.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/pytorch/cache.py -------------------------------------------------------------------------------- /amber/backend/pytorch/layer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/pytorch/layer.py -------------------------------------------------------------------------------- /amber/backend/pytorch/math.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/pytorch/math.py -------------------------------------------------------------------------------- /amber/backend/pytorch/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/pytorch/model.py -------------------------------------------------------------------------------- /amber/backend/pytorch/session.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/pytorch/session.py -------------------------------------------------------------------------------- /amber/backend/pytorch/tensor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/pytorch/tensor.py -------------------------------------------------------------------------------- /amber/backend/pytorch/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/pytorch/utils.py -------------------------------------------------------------------------------- /amber/backend/set_default_backend.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/set_default_backend.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_1/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_1/__init__.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_1/_operators/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_1/_operators/__init__.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_1/_operators/denovo_motif_conv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_1/_operators/denovo_motif_conv.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_1/_operators/sepfc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_1/_operators/sepfc.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_1/_operators/topk.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_1/_operators/topk.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_1/math.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_1/math.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_1/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_1/model.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_1/session.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_1/session.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_1/tensor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_1/tensor.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_2/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_2/__init__.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_2/_operators/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_2/_operators/__init__.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_2/_operators/denovo_motif_conv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_2/_operators/denovo_motif_conv.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_2/_operators/sepfc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_2/_operators/sepfc.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_2/_operators/topk.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_2/_operators/topk.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_2/cache.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_2/cache.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_2/math.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_2/math.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_2/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_2/model.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_2/session.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_2/session.py -------------------------------------------------------------------------------- /amber/backend/tensorflow_2/tensor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/backend/tensorflow_2/tensor.py -------------------------------------------------------------------------------- /amber/getter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/getter.py -------------------------------------------------------------------------------- /amber/modeler/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/__init__.py -------------------------------------------------------------------------------- /amber/modeler/_deprecated/child.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/_deprecated/child.py -------------------------------------------------------------------------------- /amber/modeler/_deprecated/dag.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/_deprecated/dag.py -------------------------------------------------------------------------------- /amber/modeler/_deprecated/enasModeler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/_deprecated/enasModeler.py -------------------------------------------------------------------------------- /amber/modeler/_deprecated/preprocess/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /amber/modeler/_deprecated/preprocess/cluster.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/_deprecated/preprocess/cluster.py -------------------------------------------------------------------------------- /amber/modeler/_deprecated/preprocess/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/_deprecated/preprocess/pipeline.py -------------------------------------------------------------------------------- /amber/modeler/architectureDecoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/architectureDecoder.py -------------------------------------------------------------------------------- /amber/modeler/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/base.py -------------------------------------------------------------------------------- /amber/modeler/resnet/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/resnet/__init__.py -------------------------------------------------------------------------------- /amber/modeler/resnet/keras_resnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/resnet/keras_resnet.py -------------------------------------------------------------------------------- /amber/modeler/resnet/pytorch_resnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/resnet/pytorch_resnet.py -------------------------------------------------------------------------------- /amber/modeler/sequential/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/sequential/__init__.py -------------------------------------------------------------------------------- /amber/modeler/sequential/keras_sequential.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/sequential/keras_sequential.py -------------------------------------------------------------------------------- /amber/modeler/sequential/pytorch_sequential.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/sequential/pytorch_sequential.py -------------------------------------------------------------------------------- /amber/modeler/sparse_ffnn/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/sparse_ffnn/__init__.py -------------------------------------------------------------------------------- /amber/modeler/sparse_ffnn/keras_ffnn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/sparse_ffnn/keras_ffnn.py -------------------------------------------------------------------------------- /amber/modeler/sparse_ffnn/pytorch_ffnn.py: -------------------------------------------------------------------------------- 1 | # not implemented yet -------------------------------------------------------------------------------- /amber/modeler/sparse_ffnn/tf1_featmod_ffnn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/sparse_ffnn/tf1_featmod_ffnn.py -------------------------------------------------------------------------------- /amber/modeler/supernet/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/supernet/__init__.py -------------------------------------------------------------------------------- /amber/modeler/supernet/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/supernet/base.py -------------------------------------------------------------------------------- /amber/modeler/supernet/pytorch_supernet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/supernet/pytorch_supernet.py -------------------------------------------------------------------------------- /amber/modeler/supernet/tf1_supernet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/modeler/supernet/tf1_supernet.py -------------------------------------------------------------------------------- /amber/offline_learn/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/offline_learn/__init__.py -------------------------------------------------------------------------------- /amber/offline_learn/mock_manager.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/offline_learn/mock_manager.py -------------------------------------------------------------------------------- /amber/plots/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/plots/__init__.py -------------------------------------------------------------------------------- /amber/plots/heatmap2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/plots/heatmap2.py -------------------------------------------------------------------------------- /amber/plots/ontology.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/plots/ontology.py -------------------------------------------------------------------------------- /amber/plots/plotsV1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/plots/plotsV1.py -------------------------------------------------------------------------------- /amber/plots/sankey.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/plots/sankey.py -------------------------------------------------------------------------------- /amber/utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/__init__.py -------------------------------------------------------------------------------- /amber/utils/data_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/data_parser.py -------------------------------------------------------------------------------- /amber/utils/io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/io.py -------------------------------------------------------------------------------- /amber/utils/logging.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/logging.py -------------------------------------------------------------------------------- /amber/utils/motif.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/motif.py -------------------------------------------------------------------------------- /amber/utils/saliency.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/saliency.py -------------------------------------------------------------------------------- /amber/utils/sampler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/sampler.py -------------------------------------------------------------------------------- /amber/utils/sequences.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/sequences.py -------------------------------------------------------------------------------- /amber/utils/simulator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/simulator.py -------------------------------------------------------------------------------- /amber/utils/tensorflowMem.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/tensorflowMem.py -------------------------------------------------------------------------------- /amber/utils/testing_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/testing_utils.py -------------------------------------------------------------------------------- /amber/utils/tests/files/small_genome.encoded.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/tests/files/small_genome.encoded.h5 -------------------------------------------------------------------------------- /amber/utils/tests/files/small_genome.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/tests/files/small_genome.fa -------------------------------------------------------------------------------- /amber/utils/tests/files/small_genome.fa.fai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/tests/files/small_genome.fa.fai -------------------------------------------------------------------------------- /amber/utils/tests/files/small_genome.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/tests/files/small_genome.h5 -------------------------------------------------------------------------------- /amber/utils/tests/test_encoded_genome.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/tests/test_encoded_genome.py -------------------------------------------------------------------------------- /amber/utils/tests/test_encoded_hdf5_genome.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/tests/test_encoded_hdf5_genome.py -------------------------------------------------------------------------------- /amber/utils/tests/test_genome.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/tests/test_genome.py -------------------------------------------------------------------------------- /amber/utils/tests/test_hdf5_genome.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/utils/tests/test_hdf5_genome.py -------------------------------------------------------------------------------- /amber/wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/amber/wrapper.py -------------------------------------------------------------------------------- /bin/amber-cli: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/bin/amber-cli -------------------------------------------------------------------------------- /dev.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/dev.md -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/_config.yml -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/source/_static/img/amber-logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/_static/img/amber-logo.png -------------------------------------------------------------------------------- /docs/source/_static/img/controller.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/_static/img/controller.png -------------------------------------------------------------------------------- /docs/source/_static/img/package_layout.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/_static/img/package_layout.png -------------------------------------------------------------------------------- /docs/source/amber-cli.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/amber-cli.rst -------------------------------------------------------------------------------- /docs/source/amber.architect.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/amber.architect.rst -------------------------------------------------------------------------------- /docs/source/amber.bootstrap.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/amber.bootstrap.rst -------------------------------------------------------------------------------- /docs/source/amber.interpret.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/amber.interpret.rst -------------------------------------------------------------------------------- /docs/source/amber.modeler.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/amber.modeler.rst -------------------------------------------------------------------------------- /docs/source/amber.objective.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/amber.objective.rst -------------------------------------------------------------------------------- /docs/source/amber.plots.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/amber.plots.rst -------------------------------------------------------------------------------- /docs/source/amber.resources.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/amber.resources.rst -------------------------------------------------------------------------------- /docs/source/amber.utils.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/amber.utils.rst -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /docs/source/modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/modules.rst -------------------------------------------------------------------------------- /docs/source/overview/faq.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/overview/faq.rst -------------------------------------------------------------------------------- /docs/source/overview/installation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/overview/installation.rst -------------------------------------------------------------------------------- /docs/source/overview/overview.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/overview/overview.rst -------------------------------------------------------------------------------- /docs/source/overview/reference.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/overview/reference.rst -------------------------------------------------------------------------------- /docs/source/resource/downloads.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/resource/downloads.rst -------------------------------------------------------------------------------- /docs/source/resource/gallery.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/resource/gallery.rst -------------------------------------------------------------------------------- /docs/source/resource/tutorials.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/resource/tutorials.rst -------------------------------------------------------------------------------- /docs/source/under-dev.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/docs/source/under-dev.rst -------------------------------------------------------------------------------- /examples/AMBIENT/conda/ambient_env.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/conda/ambient_env.yml -------------------------------------------------------------------------------- /examples/AMBIENT/evaluate/AMBER_analyze_third_search.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/evaluate/AMBER_analyze_third_search.ipynb -------------------------------------------------------------------------------- /examples/AMBIENT/evaluate/ZS_AMBER_TestFeat.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/evaluate/ZS_AMBER_TestFeat.ipynb -------------------------------------------------------------------------------- /examples/AMBIENT/evaluate/amber_single_run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/evaluate/amber_single_run.py -------------------------------------------------------------------------------- /examples/AMBIENT/evaluate/model_space.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/evaluate/model_space.pkl -------------------------------------------------------------------------------- /examples/AMBIENT/evaluate/plot_traj.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/evaluate/plot_traj.py -------------------------------------------------------------------------------- /examples/AMBIENT/evaluate/run_metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/evaluate/run_metrics.py -------------------------------------------------------------------------------- /examples/AMBIENT/evaluate/sbatch_single_run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/evaluate/sbatch_single_run.sh -------------------------------------------------------------------------------- /examples/AMBIENT/real_deepsea/ambient_nas.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/real_deepsea/ambient_nas.py -------------------------------------------------------------------------------- /examples/AMBIENT/real_deepsea/call_ofl_train.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/real_deepsea/call_ofl_train.sh -------------------------------------------------------------------------------- /examples/AMBIENT/real_deepsea/read_ambient_hist.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/real_deepsea/read_ambient_hist.py -------------------------------------------------------------------------------- /examples/AMBIENT/real_deepsea/sbatch_real_deepsea.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/real_deepsea/sbatch_real_deepsea.sh -------------------------------------------------------------------------------- /examples/AMBIENT/real_deepsea/train_from_history.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/real_deepsea/train_from_history.py -------------------------------------------------------------------------------- /examples/AMBIENT/real_deepsea/zero_shot_nas.real_deepsea.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/real_deepsea/zero_shot_nas.real_deepsea.py -------------------------------------------------------------------------------- /examples/AMBIENT/real_deepsea/zs_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/real_deepsea/zs_config.py -------------------------------------------------------------------------------- /examples/AMBIENT/sim_data/sbatch_grid.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/sim_data/sbatch_grid.sh -------------------------------------------------------------------------------- /examples/AMBIENT/sim_data/simulate_dna.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/sim_data/simulate_dna.sh -------------------------------------------------------------------------------- /examples/AMBIENT/sim_data/zero_shot_nas.sim_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/sim_data/zero_shot_nas.sim_data.py -------------------------------------------------------------------------------- /examples/AMBIENT/sim_data/zeroshot_grid_searcher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/AMBIENT/sim_data/zeroshot_grid_searcher.py -------------------------------------------------------------------------------- /examples/CROTON/amber_croton.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/CROTON/amber_croton.py -------------------------------------------------------------------------------- /examples/CROTON/sbatch_croton.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/CROTON/sbatch_croton.sh -------------------------------------------------------------------------------- /examples/DeepSEA/amber_deepsea.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/DeepSEA/amber_deepsea.py -------------------------------------------------------------------------------- /examples/DeepSEA/amber_env.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/DeepSEA/amber_env.yml -------------------------------------------------------------------------------- /examples/DeepSEA/amber_tf2_env.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/DeepSEA/amber_tf2_env.yml -------------------------------------------------------------------------------- /examples/DeepSEA/conda_amber.linux_env.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/DeepSEA/conda_amber.linux_env.yml -------------------------------------------------------------------------------- /examples/MockSampling/mock_nas.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/MockSampling/mock_nas.py -------------------------------------------------------------------------------- /examples/MockSampling/zero_shot_nas.sim_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/MockSampling/zero_shot_nas.sim_data.py -------------------------------------------------------------------------------- /examples/digits_sklearn/conv2d_specs.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/digits_sklearn/conv2d_specs.pkl -------------------------------------------------------------------------------- /examples/digits_sklearn/digits_sklearn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/examples/digits_sklearn/digits_sklearn.py -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/pyproject.toml -------------------------------------------------------------------------------- /readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/readthedocs.yaml -------------------------------------------------------------------------------- /resources/amber-illustrations.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/resources/amber-illustrations.pptx -------------------------------------------------------------------------------- /rtd.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/rtd.sh -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/setup.cfg -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/setup.py -------------------------------------------------------------------------------- /tests/cov_report.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/cov_report.txt -------------------------------------------------------------------------------- /tests/coverage.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/coverage.svg -------------------------------------------------------------------------------- /tests/essentials/test_architect_controller_env.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/essentials/test_architect_controller_env.py -------------------------------------------------------------------------------- /tests/essentials/test_architect_controller_optimize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/essentials/test_architect_controller_optimize.py -------------------------------------------------------------------------------- /tests/essentials/test_architect_pmbga_optimize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/essentials/test_architect_pmbga_optimize.py -------------------------------------------------------------------------------- /tests/essentials/test_modeler_sequential.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/essentials/test_modeler_sequential.py -------------------------------------------------------------------------------- /tests/helpers/test_architect_helper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/helpers/test_architect_helper.py -------------------------------------------------------------------------------- /tests/helpers/test_architect_reward.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/helpers/test_architect_reward.py -------------------------------------------------------------------------------- /tests/helpers/test_parallel_env.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/helpers/test_parallel_env.py -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_1/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_1/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_10/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_10/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_11/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_11/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_12/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_12/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_13/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_13/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_14/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_14/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_15/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_15/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_16/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_16/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_17/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_17/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_18/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_18/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_19/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_19/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_2/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_2/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_20/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_20/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_3/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_3/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_4/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_4/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_5/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_5/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_6/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_6/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_7/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_7/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_8/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_8/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/mock_black_box/tmp_9/train_history.csv.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/mock_black_box/tmp_9/train_history.csv.gz -------------------------------------------------------------------------------- /tests/integration/test_integration_bionas.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/integration/test_integration_bionas.py -------------------------------------------------------------------------------- /tests/modelers/modeler_pytorch/test_modeler_pytorch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/modelers/modeler_pytorch/test_modeler_pytorch.py -------------------------------------------------------------------------------- /tests/modelers/modeler_tf1/test_modeler_keras.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/modelers/modeler_tf1/test_modeler_keras.py -------------------------------------------------------------------------------- /tests/modelers/modeler_tf1/test_modeler_tensorflow_supercnn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/modelers/modeler_tf1/test_modeler_tensorflow_supercnn.py -------------------------------------------------------------------------------- /tests/modelers/modeler_tf1/test_modeler_tensorflow_superffnn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/modelers/modeler_tf1/test_modeler_tensorflow_superffnn.py -------------------------------------------------------------------------------- /tests/modelers/modeler_tf1/test_supernet_featmodel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/modelers/modeler_tf1/test_supernet_featmodel.py -------------------------------------------------------------------------------- /tests/modelers/modeler_tf2/.keep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/run_test_pytorch.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/run_test_pytorch.sh -------------------------------------------------------------------------------- /tests/run_test_tf1.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/run_test_tf1.sh -------------------------------------------------------------------------------- /tests/ui/test_conv2d_specs.pkl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/ui/test_conv2d_specs.pkl -------------------------------------------------------------------------------- /tests/ui/test_getter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/ui/test_getter.py -------------------------------------------------------------------------------- /tests/ui/test_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zj-zhang/AMBER/HEAD/tests/ui/test_wrapper.py --------------------------------------------------------------------------------