.zenodo.json
CHANGELOG.md
CITATION.cff
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
SECURITY.md
SUPPORT.md
pyproject.toml
requirements.txt
setup.py
docs/source/api_overview.rst
docs/source/apps.rst
docs/source/background.md
docs/source/citing.rst
docs/source/conf.py
docs/source/index.rst
docs/source/installation.md
docs/source/overview.md
docs/source/tutorials.md
docs/source/_static/ArtificialDatatypes.png
docs/source/_static/IEComplexity.png
docs/source/_static/KernelDensityGaussianAnimation.gif
docs/source/_static/MutualInformation.png
docs/source/_static/NoiseLevels.png
docs/source/_static/QBioCode_logo.png
docs/source/_static/QProfiler.png
docs/source/_static/QSage.png
docs/source/_static/Sierpinski_triangle.png
docs/source/_static/kurt.jpg
docs/source/_static/quantum_feature_m_data_display.png
docs/source/_static/quantum_feature_maps.png
docs/source/_static/skew.png
docs/source/_static/tutorial_data_thumb.png
docs/source/_static/workshops/ISMB26banner.png
docs/source/api/modules.rst
docs/source/api/qbiocode.apps.qprofiler.cli.rst
docs/source/api/qbiocode.apps.qprofiler.configs.rst
docs/source/api/qbiocode.apps.qprofiler.qprofiler.rst
docs/source/api/qbiocode.apps.qprofiler.qprofiler_batchmode.rst
docs/source/api/qbiocode.apps.qprofiler.rst
docs/source/api/qbiocode.apps.quvine.analysis.analyze.rst
docs/source/api/qbiocode.apps.quvine.analysis.compare.rst
docs/source/api/qbiocode.apps.quvine.analysis.rst
docs/source/api/qbiocode.apps.quvine.api.aliases.rst
docs/source/api/qbiocode.apps.quvine.api.config.rst
docs/source/api/qbiocode.apps.quvine.api.core.rst
docs/source/api/qbiocode.apps.quvine.api.rst
docs/source/api/qbiocode.apps.quvine.api.sgns.rst
docs/source/api/qbiocode.apps.quvine.api.targets.rst
docs/source/api/qbiocode.apps.quvine.baselines.adapters.rst
docs/source/api/qbiocode.apps.quvine.baselines.appnp.rst
docs/source/api/qbiocode.apps.quvine.baselines.configs.rst
docs/source/api/qbiocode.apps.quvine.baselines.gat.rst
docs/source/api/qbiocode.apps.quvine.baselines.gcn_mf.rst
docs/source/api/qbiocode.apps.quvine.baselines.graphgps.rst
docs/source/api/qbiocode.apps.quvine.baselines.graphsage.rst
docs/source/api/qbiocode.apps.quvine.baselines.hyperparameter_loader.rst
docs/source/api/qbiocode.apps.quvine.baselines.netmf.rst
docs/source/api/qbiocode.apps.quvine.baselines.node2vec.rst
docs/source/api/qbiocode.apps.quvine.baselines.registration.rst
docs/source/api/qbiocode.apps.quvine.baselines.registry.rst
docs/source/api/qbiocode.apps.quvine.baselines.rst
docs/source/api/qbiocode.apps.quvine.cli.rst
docs/source/api/qbiocode.apps.quvine.configs.rst
docs/source/api/qbiocode.apps.quvine.corpus.builder.rst
docs/source/api/qbiocode.apps.quvine.corpus.operations.rst
docs/source/api/qbiocode.apps.quvine.corpus.rst
docs/source/api/qbiocode.apps.quvine.data.data_loader.rst
docs/source/api/qbiocode.apps.quvine.data.prepare.rst
docs/source/api/qbiocode.apps.quvine.data.random_graphs.rst
docs/source/api/qbiocode.apps.quvine.data.random_graphs_extended.rst
docs/source/api/qbiocode.apps.quvine.data.rst
docs/source/api/qbiocode.apps.quvine.data.sparsify.rst
docs/source/api/qbiocode.apps.quvine.data.subgraph.rst
docs/source/api/qbiocode.apps.quvine.embedding.quantum_filters.rst
docs/source/api/qbiocode.apps.quvine.embedding.registry.rst
docs/source/api/qbiocode.apps.quvine.embedding.rst
docs/source/api/qbiocode.apps.quvine.embedding.word2vec.rst
docs/source/api/qbiocode.apps.quvine.evaluation.classification.rst
docs/source/api/qbiocode.apps.quvine.evaluation.link_prediction.rst
docs/source/api/qbiocode.apps.quvine.evaluation.ranking.rst
docs/source/api/qbiocode.apps.quvine.evaluation.rst
docs/source/api/qbiocode.apps.quvine.fusion.fuse.rst
docs/source/api/qbiocode.apps.quvine.fusion.fuse_fixes.rst
docs/source/api/qbiocode.apps.quvine.fusion.rst
docs/source/api/qbiocode.apps.quvine.main.rst
docs/source/api/qbiocode.apps.quvine.pipeline.rst
docs/source/api/qbiocode.apps.quvine.reproducibility.dataset_registry.rst
docs/source/api/qbiocode.apps.quvine.reproducibility.graph_generator.rst
docs/source/api/qbiocode.apps.quvine.reproducibility.method_adapters.rst
docs/source/api/qbiocode.apps.quvine.reproducibility.method_runner.rst
docs/source/api/qbiocode.apps.quvine.reproducibility.ppi_workflow.rst
docs/source/api/qbiocode.apps.quvine.reproducibility.rst
docs/source/api/qbiocode.apps.quvine.reproducibility.seed_manager.rst
docs/source/api/qbiocode.apps.quvine.reproducibility.split_generator.rst
docs/source/api/qbiocode.apps.quvine.reproducibility.validator.rst
docs/source/api/qbiocode.apps.quvine.rst
docs/source/api/qbiocode.apps.quvine.utils.io.rst
docs/source/api/qbiocode.apps.quvine.utils.logging.rst
docs/source/api/qbiocode.apps.quvine.utils.rst
docs/source/api/qbiocode.apps.quvine.utils.seed.rst
docs/source/api/qbiocode.apps.quvine.utils.torch_utils.rst
docs/source/api/qbiocode.apps.quvine.utils.utilities.rst
docs/source/api/qbiocode.apps.quvine.views.generator.rst
docs/source/api/qbiocode.apps.quvine.views.rst
docs/source/api/qbiocode.apps.quvine.views.views.rst
docs/source/api/qbiocode.apps.quvine.walks.base.rst
docs/source/api/qbiocode.apps.quvine.walks.ctqw.rst
docs/source/api/qbiocode.apps.quvine.walks.dtqw.rst
docs/source/api/qbiocode.apps.quvine.walks.rst
docs/source/api/qbiocode.apps.quvine.walks.rwr.rst
docs/source/api/qbiocode.apps.rst
docs/source/api/qbiocode.apps.sage.rst
docs/source/api/qbiocode.apps.sage.sage.rst
docs/source/api/qbiocode.data_generation.generator.rst
docs/source/api/qbiocode.data_generation.make_blobs.rst
docs/source/api/qbiocode.data_generation.make_circles.rst
docs/source/api/qbiocode.data_generation.make_class.rst
docs/source/api/qbiocode.data_generation.make_moons.rst
docs/source/api/qbiocode.data_generation.make_s_curve.rst
docs/source/api/qbiocode.data_generation.make_spheres.rst
docs/source/api/qbiocode.data_generation.make_spirals.rst
docs/source/api/qbiocode.data_generation.make_swiss_roll.rst
docs/source/api/qbiocode.data_generation.rst
docs/source/api/qbiocode.embeddings.compute_autoencoder.rst
docs/source/api/qbiocode.embeddings.embed.rst
docs/source/api/qbiocode.embeddings.rst
docs/source/api/qbiocode.evaluation.dataset_evaluation.rst
docs/source/api/qbiocode.evaluation.graph_evaluation.rst
docs/source/api/qbiocode.evaluation.model_evaluation.rst
docs/source/api/qbiocode.evaluation.model_run.rst
docs/source/api/qbiocode.evaluation.rst
docs/source/api/qbiocode.learning.compute_dt.rst
docs/source/api/qbiocode.learning.compute_lr.rst
docs/source/api/qbiocode.learning.compute_mlp.rst
docs/source/api/qbiocode.learning.compute_nb.rst
docs/source/api/qbiocode.learning.compute_pqk.rst
docs/source/api/qbiocode.learning.compute_qensemble.rst
docs/source/api/qbiocode.learning.compute_qnn.rst
docs/source/api/qbiocode.learning.compute_qpl.rst
docs/source/api/qbiocode.learning.compute_qsvc.rst
docs/source/api/qbiocode.learning.compute_rf.rst
docs/source/api/qbiocode.learning.compute_svc.rst
docs/source/api/qbiocode.learning.compute_vqc.rst
docs/source/api/qbiocode.learning.compute_xgb.rst
docs/source/api/qbiocode.learning.rst
docs/source/api/qbiocode.rst
docs/source/api/qbiocode.utils.combine_evals_results.rst
docs/source/api/qbiocode.utils.data_encoding.rst
docs/source/api/qbiocode.utils.dataset_checkpoint.rst
docs/source/api/qbiocode.utils.find_duplicates.rst
docs/source/api/qbiocode.utils.find_string.rst
docs/source/api/qbiocode.utils.generate_qml_configs.rst
docs/source/api/qbiocode.utils.helper_fn.rst
docs/source/api/qbiocode.utils.ibm_account.rst
docs/source/api/qbiocode.utils.qc_winner_finder.rst
docs/source/api/qbiocode.utils.qutils.rst
docs/source/api/qbiocode.utils.rst
docs/source/api/qbiocode.utils.tutorial_data.rst
docs/source/api/qbiocode.version.rst
docs/source/api/qbiocode.visualization.rst
docs/source/api/qbiocode.visualization.visualize_correlation.rst
docs/source/apps/config.md
docs/source/apps/profiler.rst
docs/source/apps/quvine.rst
docs/source/apps/quvine_config.md
docs/source/apps/sage.rst
docs/source/workshops/ISMB_2025.rst
docs/source/workshops/ISMB_2026.rst
docs/source/workshops/_tutorial.rst
docs/source/workshops/index.rst
qbiocode/__init__.py
qbiocode/version.py
qbiocode.egg-info/PKG-INFO
qbiocode.egg-info/SOURCES.txt
qbiocode.egg-info/dependency_links.txt
qbiocode.egg-info/entry_points.txt
qbiocode.egg-info/requires.txt
qbiocode.egg-info/top_level.txt
qbiocode/apps/__init__.py
qbiocode/apps/qprofiler/__init__.py
qbiocode/apps/qprofiler/cli.py
qbiocode/apps/qprofiler/qprofiler.py
qbiocode/apps/qprofiler/qprofiler_batchmode.py
qbiocode/apps/qprofiler/configs/__init__.py
qbiocode/apps/qprofiler/configs/config.yaml
qbiocode/apps/quvine/__init__.py
qbiocode/apps/quvine/_deps.py
qbiocode/apps/quvine/cli.py
qbiocode/apps/quvine/main.py
qbiocode/apps/quvine/pipeline.py
qbiocode/apps/quvine/analysis/__init__.py
qbiocode/apps/quvine/analysis/analyze.py
qbiocode/apps/quvine/analysis/compare.py
qbiocode/apps/quvine/api/__init__.py
qbiocode/apps/quvine/api/aliases.py
qbiocode/apps/quvine/api/config.py
qbiocode/apps/quvine/api/core.py
qbiocode/apps/quvine/api/sgns.py
qbiocode/apps/quvine/api/targets.py
qbiocode/apps/quvine/baselines/__init__.py
qbiocode/apps/quvine/baselines/adapters.py
qbiocode/apps/quvine/baselines/appnp.py
qbiocode/apps/quvine/baselines/configs.py
qbiocode/apps/quvine/baselines/gat.py
qbiocode/apps/quvine/baselines/gcn_mf.py
qbiocode/apps/quvine/baselines/graphgps.py
qbiocode/apps/quvine/baselines/graphsage.py
qbiocode/apps/quvine/baselines/hyperparameter_loader.py
qbiocode/apps/quvine/baselines/netmf.py
qbiocode/apps/quvine/baselines/node2vec.py
qbiocode/apps/quvine/baselines/registration.py
qbiocode/apps/quvine/baselines/registry.py
qbiocode/apps/quvine/configs/__init__.py
qbiocode/apps/quvine/configs/config.yaml
qbiocode/apps/quvine/corpus/__init__.py
qbiocode/apps/quvine/corpus/builder.py
qbiocode/apps/quvine/corpus/operations.py
qbiocode/apps/quvine/data/README_random_graphs.md
qbiocode/apps/quvine/data/__init__.py
qbiocode/apps/quvine/data/data_loader.py
qbiocode/apps/quvine/data/prepare.py
qbiocode/apps/quvine/data/random_graphs.py
qbiocode/apps/quvine/data/random_graphs_extended.py
qbiocode/apps/quvine/data/sparsify.py
qbiocode/apps/quvine/data/subgraph.py
qbiocode/apps/quvine/embedding/__init__.py
qbiocode/apps/quvine/embedding/quantum_filters.py
qbiocode/apps/quvine/embedding/registry.py
qbiocode/apps/quvine/embedding/word2vec.py
qbiocode/apps/quvine/evaluation/__init__.py
qbiocode/apps/quvine/evaluation/classification.py
qbiocode/apps/quvine/evaluation/link_prediction.py
qbiocode/apps/quvine/evaluation/ranking.py
qbiocode/apps/quvine/fusion/__init__.py
qbiocode/apps/quvine/fusion/fuse.py
qbiocode/apps/quvine/fusion/fuse_fixes.py
qbiocode/apps/quvine/reproducibility/__init__.py
qbiocode/apps/quvine/reproducibility/dataset_registry.py
qbiocode/apps/quvine/reproducibility/graph_generator.py
qbiocode/apps/quvine/reproducibility/method_adapters.py
qbiocode/apps/quvine/reproducibility/method_runner.py
qbiocode/apps/quvine/reproducibility/ppi_workflow.py
qbiocode/apps/quvine/reproducibility/seed_manager.py
qbiocode/apps/quvine/reproducibility/split_generator.py
qbiocode/apps/quvine/reproducibility/validator.py
qbiocode/apps/quvine/utils/__init__.py
qbiocode/apps/quvine/utils/io.py
qbiocode/apps/quvine/utils/logging.py
qbiocode/apps/quvine/utils/seed.py
qbiocode/apps/quvine/utils/torch_utils.py
qbiocode/apps/quvine/utils/utilities.py
qbiocode/apps/quvine/views/__init__.py
qbiocode/apps/quvine/views/generator.py
qbiocode/apps/quvine/views/views.py
qbiocode/apps/quvine/walks/__init__.py
qbiocode/apps/quvine/walks/base.py
qbiocode/apps/quvine/walks/ctqw.py
qbiocode/apps/quvine/walks/dtqw.py
qbiocode/apps/quvine/walks/rwr.py
qbiocode/apps/sage/__init__.py
qbiocode/apps/sage/sage.py
qbiocode/data_generation/__init__.py
qbiocode/data_generation/generator.py
qbiocode/data_generation/make_blobs.py
qbiocode/data_generation/make_circles.py
qbiocode/data_generation/make_class.py
qbiocode/data_generation/make_moons.py
qbiocode/data_generation/make_s_curve.py
qbiocode/data_generation/make_spheres.py
qbiocode/data_generation/make_spirals.py
qbiocode/data_generation/make_swiss_roll.py
qbiocode/embeddings/__init__.py
qbiocode/embeddings/compute_autoencoder.py
qbiocode/embeddings/embed.py
qbiocode/evaluation/__init__.py
qbiocode/evaluation/dataset_evaluation.py
qbiocode/evaluation/graph_evaluation.py
qbiocode/evaluation/model_evaluation.py
qbiocode/evaluation/model_run.py
qbiocode/learning/__init__.py
qbiocode/learning/_grid.py
qbiocode/learning/compute_dt.py
qbiocode/learning/compute_lr.py
qbiocode/learning/compute_mlp.py
qbiocode/learning/compute_nb.py
qbiocode/learning/compute_pqk.py
qbiocode/learning/compute_qensemble.py
qbiocode/learning/compute_qnn.py
qbiocode/learning/compute_qpl.py
qbiocode/learning/compute_qsvc.py
qbiocode/learning/compute_rf.py
qbiocode/learning/compute_svc.py
qbiocode/learning/compute_vqc.py
qbiocode/learning/compute_xgb.py
qbiocode/utils/__init__.py
qbiocode/utils/_openmp.py
qbiocode/utils/combine_evals_results.py
qbiocode/utils/data_encoding.py
qbiocode/utils/dataset_checkpoint.py
qbiocode/utils/find_duplicates.py
qbiocode/utils/find_string.py
qbiocode/utils/generate_qml_configs.py
qbiocode/utils/helper_fn.py
qbiocode/utils/ibm_account.py
qbiocode/utils/qc_winner_finder.py
qbiocode/utils/qutils.py
qbiocode/utils/tutorial_data.py
qbiocode/visualization/__init__.py
qbiocode/visualization/visualize_correlation.py
requirements/requirements-base.txt
requirements/requirements-docs.txt
requirements/requirements-quvine.txt
requirements/requirements.txt
tutorial/PQK - OV.ipynb
tutorial/Artificial_data_generation/example_data_generation.ipynb
tutorial/Preprocessing/sc-qc.ipynb
tutorial/QEnsemble/QEnsemble_example_blobs.ipynb
tutorial/QEnsemble/experiments/Blobs_best_stats.csv
tutorial/QEnsemble/experiments/datasets.pkl
tutorial/QEnsemble/experiments/predictions.pkl
tutorial/QProfiler/example_qprofiler.ipynb
tutorial/QProfiler/sc_binary_qprofiler.ipynb
tutorial/QProfiler/sc_binary_quvine_2x2_qprofiler.ipynb
tutorial/QProfiler/configs/config.yaml
tutorial/QProfiler/configs/credentials.example.json
tutorial/QProfiler/data/pbmc5k_small_cd4_vs_cd8.h5ad
tutorial/QProfiler/data/sc_binary/pbmc-cd4_vs_cd8.csv
tutorial/QProfiler/data/sc_binary/pbmc-lymphoid_vs_myeloid.csv
tutorial/QProfiler/data/sc_binary/pbmc-t_vs_mono.csv
tutorial/QSage/qsage.ipynb
tutorial/QSage/data/qprofiler_benchmarks.csv
tutorial/QuVINE/example_quvine.ipynb
tutorial/QuVINE/quvine_sc_cd4_vs_cd8.ipynb
tutorial/QuVINE/quvine_sc_t_vs_mono.ipynb
tutorial/Quantum_Projection_Learning/QPL_example.ipynb
tutorial/Quantum_Projection_Learning/configs/qpl.yaml
tutorial/Quantum_Projection_Learning/configs/rf.yaml
tutorial/Quantum_Projection_Learning/configs/xgb.yaml