@synsci/cli-darwin-arm64 1.1.76 → 1.1.78
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/bin/skills/adaptyv/SKILL.md +114 -0
- package/bin/skills/adaptyv/reference/api_reference.md +308 -0
- package/bin/skills/adaptyv/reference/examples.md +913 -0
- package/bin/skills/adaptyv/reference/experiments.md +360 -0
- package/bin/skills/adaptyv/reference/protein_optimization.md +637 -0
- package/bin/skills/aeon/SKILL.md +374 -0
- package/bin/skills/aeon/references/anomaly_detection.md +154 -0
- package/bin/skills/aeon/references/classification.md +144 -0
- package/bin/skills/aeon/references/clustering.md +123 -0
- package/bin/skills/aeon/references/datasets_benchmarking.md +387 -0
- package/bin/skills/aeon/references/distances.md +256 -0
- package/bin/skills/aeon/references/forecasting.md +140 -0
- package/bin/skills/aeon/references/networks.md +289 -0
- package/bin/skills/aeon/references/regression.md +118 -0
- package/bin/skills/aeon/references/segmentation.md +163 -0
- package/bin/skills/aeon/references/similarity_search.md +187 -0
- package/bin/skills/aeon/references/transformations.md +246 -0
- package/bin/skills/alphafold-database/SKILL.md +513 -0
- package/bin/skills/alphafold-database/references/api_reference.md +423 -0
- package/bin/skills/anndata/SKILL.md +400 -0
- package/bin/skills/anndata/references/best_practices.md +525 -0
- package/bin/skills/anndata/references/concatenation.md +396 -0
- package/bin/skills/anndata/references/data_structure.md +314 -0
- package/bin/skills/anndata/references/io_operations.md +404 -0
- package/bin/skills/anndata/references/manipulation.md +516 -0
- package/bin/skills/arboreto/SKILL.md +243 -0
- package/bin/skills/arboreto/references/algorithms.md +138 -0
- package/bin/skills/arboreto/references/basic_inference.md +151 -0
- package/bin/skills/arboreto/references/distributed_computing.md +242 -0
- package/bin/skills/arboreto/scripts/basic_grn_inference.py +97 -0
- package/bin/skills/astropy/SKILL.md +331 -0
- package/bin/skills/astropy/references/coordinates.md +273 -0
- package/bin/skills/astropy/references/cosmology.md +307 -0
- package/bin/skills/astropy/references/fits.md +396 -0
- package/bin/skills/astropy/references/tables.md +489 -0
- package/bin/skills/astropy/references/time.md +404 -0
- package/bin/skills/astropy/references/units.md +178 -0
- package/bin/skills/astropy/references/wcs_and_other_modules.md +373 -0
- package/bin/skills/benchling-integration/SKILL.md +480 -0
- package/bin/skills/benchling-integration/references/api_endpoints.md +883 -0
- package/bin/skills/benchling-integration/references/authentication.md +379 -0
- package/bin/skills/benchling-integration/references/sdk_reference.md +774 -0
- package/bin/skills/biopython/SKILL.md +443 -0
- package/bin/skills/biopython/references/advanced.md +577 -0
- package/bin/skills/biopython/references/alignment.md +362 -0
- package/bin/skills/biopython/references/blast.md +455 -0
- package/bin/skills/biopython/references/databases.md +484 -0
- package/bin/skills/biopython/references/phylogenetics.md +566 -0
- package/bin/skills/biopython/references/sequence_io.md +285 -0
- package/bin/skills/biopython/references/structure.md +564 -0
- package/bin/skills/biorxiv-database/SKILL.md +483 -0
- package/bin/skills/biorxiv-database/references/api_reference.md +280 -0
- package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
- package/bin/skills/bioservices/SKILL.md +361 -0
- package/bin/skills/bioservices/references/identifier_mapping.md +685 -0
- package/bin/skills/bioservices/references/services_reference.md +636 -0
- package/bin/skills/bioservices/references/workflow_patterns.md +811 -0
- package/bin/skills/bioservices/scripts/batch_id_converter.py +347 -0
- package/bin/skills/bioservices/scripts/compound_cross_reference.py +378 -0
- package/bin/skills/bioservices/scripts/pathway_analysis.py +309 -0
- package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
- package/bin/skills/brenda-database/SKILL.md +719 -0
- package/bin/skills/brenda-database/references/api_reference.md +537 -0
- package/bin/skills/brenda-database/scripts/brenda_queries.py +844 -0
- package/bin/skills/brenda-database/scripts/brenda_visualization.py +772 -0
- package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
- package/bin/skills/cellxgene-census/SKILL.md +511 -0
- package/bin/skills/cellxgene-census/references/census_schema.md +182 -0
- package/bin/skills/cellxgene-census/references/common_patterns.md +351 -0
- package/bin/skills/chembl-database/SKILL.md +389 -0
- package/bin/skills/chembl-database/references/api_reference.md +272 -0
- package/bin/skills/chembl-database/scripts/example_queries.py +278 -0
- package/bin/skills/cirq/SKILL.md +346 -0
- package/bin/skills/cirq/references/building.md +307 -0
- package/bin/skills/cirq/references/experiments.md +572 -0
- package/bin/skills/cirq/references/hardware.md +515 -0
- package/bin/skills/cirq/references/noise.md +515 -0
- package/bin/skills/cirq/references/simulation.md +350 -0
- package/bin/skills/cirq/references/transformation.md +416 -0
- package/bin/skills/clinicaltrials-database/SKILL.md +507 -0
- package/bin/skills/clinicaltrials-database/references/api_reference.md +358 -0
- package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
- package/bin/skills/clinpgx-database/SKILL.md +638 -0
- package/bin/skills/clinpgx-database/references/api_reference.md +757 -0
- package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
- package/bin/skills/clinvar-database/SKILL.md +362 -0
- package/bin/skills/clinvar-database/references/api_reference.md +227 -0
- package/bin/skills/clinvar-database/references/clinical_significance.md +218 -0
- package/bin/skills/clinvar-database/references/data_formats.md +358 -0
- package/bin/skills/cobrapy/SKILL.md +463 -0
- package/bin/skills/cobrapy/references/api_quick_reference.md +655 -0
- package/bin/skills/cobrapy/references/workflows.md +593 -0
- package/bin/skills/cosmic-database/SKILL.md +336 -0
- package/bin/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
- package/bin/skills/cosmic-database/scripts/download_cosmic.py +231 -0
- package/bin/skills/dask/SKILL.md +456 -0
- package/bin/skills/dask/references/arrays.md +497 -0
- package/bin/skills/dask/references/bags.md +468 -0
- package/bin/skills/dask/references/best-practices.md +277 -0
- package/bin/skills/dask/references/dataframes.md +368 -0
- package/bin/skills/dask/references/futures.md +541 -0
- package/bin/skills/dask/references/schedulers.md +504 -0
- package/bin/skills/datacommons-client/SKILL.md +255 -0
- package/bin/skills/datacommons-client/references/getting_started.md +417 -0
- package/bin/skills/datacommons-client/references/node.md +250 -0
- package/bin/skills/datacommons-client/references/observation.md +185 -0
- package/bin/skills/datacommons-client/references/resolve.md +246 -0
- package/bin/skills/datamol/SKILL.md +706 -0
- package/bin/skills/datamol/references/conformers_module.md +131 -0
- package/bin/skills/datamol/references/core_api.md +130 -0
- package/bin/skills/datamol/references/descriptors_viz.md +195 -0
- package/bin/skills/datamol/references/fragments_scaffolds.md +174 -0
- package/bin/skills/datamol/references/io_module.md +109 -0
- package/bin/skills/datamol/references/reactions_data.md +218 -0
- package/bin/skills/deepchem/SKILL.md +597 -0
- package/bin/skills/deepchem/references/api_reference.md +303 -0
- package/bin/skills/deepchem/references/workflows.md +491 -0
- package/bin/skills/deepchem/scripts/graph_neural_network.py +338 -0
- package/bin/skills/deepchem/scripts/predict_solubility.py +224 -0
- package/bin/skills/deepchem/scripts/transfer_learning.py +375 -0
- package/bin/skills/deeptools/SKILL.md +531 -0
- package/bin/skills/deeptools/assets/quick_reference.md +58 -0
- package/bin/skills/deeptools/references/effective_genome_sizes.md +116 -0
- package/bin/skills/deeptools/references/normalization_methods.md +410 -0
- package/bin/skills/deeptools/references/tools_reference.md +533 -0
- package/bin/skills/deeptools/references/workflows.md +474 -0
- package/bin/skills/deeptools/scripts/validate_files.py +195 -0
- package/bin/skills/deeptools/scripts/workflow_generator.py +454 -0
- package/bin/skills/denario/SKILL.md +215 -0
- package/bin/skills/denario/references/examples.md +494 -0
- package/bin/skills/denario/references/installation.md +213 -0
- package/bin/skills/denario/references/llm_configuration.md +265 -0
- package/bin/skills/denario/references/research_pipeline.md +471 -0
- package/bin/skills/diffdock/SKILL.md +483 -0
- package/bin/skills/diffdock/assets/batch_template.csv +4 -0
- package/bin/skills/diffdock/assets/custom_inference_config.yaml +90 -0
- package/bin/skills/diffdock/references/confidence_and_limitations.md +182 -0
- package/bin/skills/diffdock/references/parameters_reference.md +163 -0
- package/bin/skills/diffdock/references/workflows_examples.md +392 -0
- package/bin/skills/diffdock/scripts/analyze_results.py +334 -0
- package/bin/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
- package/bin/skills/diffdock/scripts/setup_check.py +278 -0
- package/bin/skills/dnanexus-integration/SKILL.md +383 -0
- package/bin/skills/dnanexus-integration/references/app-development.md +247 -0
- package/bin/skills/dnanexus-integration/references/configuration.md +646 -0
- package/bin/skills/dnanexus-integration/references/data-operations.md +400 -0
- package/bin/skills/dnanexus-integration/references/job-execution.md +412 -0
- package/bin/skills/dnanexus-integration/references/python-sdk.md +523 -0
- package/bin/skills/document-skills/docx/LICENSE.txt +30 -0
- package/bin/skills/document-skills/docx/SKILL.md +233 -0
- package/bin/skills/document-skills/docx/docx-js.md +350 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
- package/bin/skills/document-skills/docx/ooxml.md +610 -0
- package/bin/skills/document-skills/docx/scripts/__init__.py +1 -0
- package/bin/skills/document-skills/docx/scripts/document.py +1276 -0
- package/bin/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/people.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/utilities.py +374 -0
- package/bin/skills/document-skills/pdf/LICENSE.txt +30 -0
- package/bin/skills/document-skills/pdf/SKILL.md +330 -0
- package/bin/skills/document-skills/pdf/forms.md +205 -0
- package/bin/skills/document-skills/pdf/reference.md +612 -0
- package/bin/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
- package/bin/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
- package/bin/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
- package/bin/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
- package/bin/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
- package/bin/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
- package/bin/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
- package/bin/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
- package/bin/skills/document-skills/pptx/LICENSE.txt +30 -0
- package/bin/skills/document-skills/pptx/SKILL.md +520 -0
- package/bin/skills/document-skills/pptx/html2pptx.md +625 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
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- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
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- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
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- package/package.json +1 -1
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# Noise Modeling and Mitigation
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This guide covers noise models, noisy simulation, characterization, and error mitigation in Cirq.
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## Noise Channels
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### Depolarizing Noise
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```python
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import cirq
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import numpy as np
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# Single-qubit depolarizing channel
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depol_channel = cirq.depolarize(p=0.01)
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# Apply to qubit
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q = cirq.LineQubit(0)
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noisy_op = depol_channel(q)
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# Add to circuit
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circuit = cirq.Circuit(
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depol_channel(q),
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cirq.measure(q, key='m')
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```
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```python
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# Amplitude damping (T1 decay)
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# Apply after gate
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circuit = cirq.Circuit(
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cirq.X(q),
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amp_damp(q)
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)
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```
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```python
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# Phase damping (T2 dephasing)
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gamma = 0.1
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phase_damp = cirq.phase_damp(gamma)
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+
circuit = cirq.Circuit(
|
|
50
|
+
cirq.H(q),
|
|
51
|
+
phase_damp(q)
|
|
52
|
+
)
|
|
53
|
+
```
|
|
54
|
+
|
|
55
|
+
### Bit Flip Noise
|
|
56
|
+
|
|
57
|
+
```python
|
|
58
|
+
# Bit flip channel
|
|
59
|
+
bit_flip_prob = 0.01
|
|
60
|
+
bit_flip = cirq.bit_flip(bit_flip_prob)
|
|
61
|
+
|
|
62
|
+
circuit = cirq.Circuit(
|
|
63
|
+
cirq.H(q),
|
|
64
|
+
bit_flip(q)
|
|
65
|
+
)
|
|
66
|
+
```
|
|
67
|
+
|
|
68
|
+
### Phase Flip Noise
|
|
69
|
+
|
|
70
|
+
```python
|
|
71
|
+
# Phase flip channel
|
|
72
|
+
phase_flip_prob = 0.01
|
|
73
|
+
phase_flip = cirq.phase_flip(phase_flip_prob)
|
|
74
|
+
|
|
75
|
+
circuit = cirq.Circuit(
|
|
76
|
+
cirq.H(q),
|
|
77
|
+
phase_flip(q)
|
|
78
|
+
)
|
|
79
|
+
```
|
|
80
|
+
|
|
81
|
+
### Generalized Amplitude Damping
|
|
82
|
+
|
|
83
|
+
```python
|
|
84
|
+
# Generalized amplitude damping
|
|
85
|
+
p = 0.1 # Damping probability
|
|
86
|
+
gamma = 0.2 # Excitation probability
|
|
87
|
+
gen_amp_damp = cirq.generalized_amplitude_damp(p=p, gamma=gamma)
|
|
88
|
+
```
|
|
89
|
+
|
|
90
|
+
### Reset Channel
|
|
91
|
+
|
|
92
|
+
```python
|
|
93
|
+
# Reset to |0⟩ or |1⟩
|
|
94
|
+
reset_to_zero = cirq.reset(q)
|
|
95
|
+
|
|
96
|
+
# Reset appears as measurement followed by conditional flip
|
|
97
|
+
circuit = cirq.Circuit(
|
|
98
|
+
cirq.H(q),
|
|
99
|
+
reset_to_zero
|
|
100
|
+
)
|
|
101
|
+
```
|
|
102
|
+
|
|
103
|
+
## Noise Models
|
|
104
|
+
|
|
105
|
+
### Constant Noise Model
|
|
106
|
+
|
|
107
|
+
```python
|
|
108
|
+
# Apply same noise to all qubits
|
|
109
|
+
noise = cirq.ConstantQubitNoiseModel(
|
|
110
|
+
qubit_noise_gate=cirq.depolarize(0.01)
|
|
111
|
+
)
|
|
112
|
+
|
|
113
|
+
# Simulate with noise
|
|
114
|
+
simulator = cirq.DensityMatrixSimulator(noise=noise)
|
|
115
|
+
result = simulator.run(circuit, repetitions=1000)
|
|
116
|
+
```
|
|
117
|
+
|
|
118
|
+
### Gate-Specific Noise
|
|
119
|
+
|
|
120
|
+
```python
|
|
121
|
+
class CustomNoiseModel(cirq.NoiseModel):
|
|
122
|
+
"""Apply different noise to different gate types."""
|
|
123
|
+
|
|
124
|
+
def noisy_operation(self, op):
|
|
125
|
+
# Single-qubit gates: depolarizing noise
|
|
126
|
+
if len(op.qubits) == 1:
|
|
127
|
+
return [op, cirq.depolarize(0.001)(op.qubits[0])]
|
|
128
|
+
|
|
129
|
+
# Two-qubit gates: higher depolarizing noise
|
|
130
|
+
elif len(op.qubits) == 2:
|
|
131
|
+
return [
|
|
132
|
+
op,
|
|
133
|
+
cirq.depolarize(0.01)(op.qubits[0]),
|
|
134
|
+
cirq.depolarize(0.01)(op.qubits[1])
|
|
135
|
+
]
|
|
136
|
+
|
|
137
|
+
return op
|
|
138
|
+
|
|
139
|
+
# Use custom noise model
|
|
140
|
+
noise_model = CustomNoiseModel()
|
|
141
|
+
simulator = cirq.DensityMatrixSimulator(noise=noise_model)
|
|
142
|
+
```
|
|
143
|
+
|
|
144
|
+
### Qubit-Specific Noise
|
|
145
|
+
|
|
146
|
+
```python
|
|
147
|
+
class QubitSpecificNoise(cirq.NoiseModel):
|
|
148
|
+
"""Different noise for different qubits."""
|
|
149
|
+
|
|
150
|
+
def __init__(self, qubit_noise_map):
|
|
151
|
+
self.qubit_noise_map = qubit_noise_map
|
|
152
|
+
|
|
153
|
+
def noisy_operation(self, op):
|
|
154
|
+
noise_ops = [op]
|
|
155
|
+
for qubit in op.qubits:
|
|
156
|
+
if qubit in self.qubit_noise_map:
|
|
157
|
+
noise = self.qubit_noise_map[qubit]
|
|
158
|
+
noise_ops.append(noise(qubit))
|
|
159
|
+
return noise_ops
|
|
160
|
+
|
|
161
|
+
# Define per-qubit noise
|
|
162
|
+
q0, q1, q2 = cirq.LineQubit.range(3)
|
|
163
|
+
noise_map = {
|
|
164
|
+
q0: cirq.depolarize(0.001),
|
|
165
|
+
q1: cirq.depolarize(0.005),
|
|
166
|
+
q2: cirq.depolarize(0.002)
|
|
167
|
+
}
|
|
168
|
+
|
|
169
|
+
noise_model = QubitSpecificNoise(noise_map)
|
|
170
|
+
```
|
|
171
|
+
|
|
172
|
+
### Thermal Noise
|
|
173
|
+
|
|
174
|
+
```python
|
|
175
|
+
class ThermalNoise(cirq.NoiseModel):
|
|
176
|
+
"""Thermal relaxation noise."""
|
|
177
|
+
|
|
178
|
+
def __init__(self, T1, T2, gate_time):
|
|
179
|
+
self.T1 = T1 # Amplitude damping time
|
|
180
|
+
self.T2 = T2 # Dephasing time
|
|
181
|
+
self.gate_time = gate_time
|
|
182
|
+
|
|
183
|
+
def noisy_operation(self, op):
|
|
184
|
+
# Calculate probabilities
|
|
185
|
+
p_amp = 1 - np.exp(-self.gate_time / self.T1)
|
|
186
|
+
p_phase = 1 - np.exp(-self.gate_time / self.T2)
|
|
187
|
+
|
|
188
|
+
noise_ops = [op]
|
|
189
|
+
for qubit in op.qubits:
|
|
190
|
+
noise_ops.append(cirq.amplitude_damp(p_amp)(qubit))
|
|
191
|
+
noise_ops.append(cirq.phase_damp(p_phase)(qubit))
|
|
192
|
+
|
|
193
|
+
return noise_ops
|
|
194
|
+
|
|
195
|
+
# Typical superconducting qubit parameters
|
|
196
|
+
T1 = 50e-6 # 50 μs
|
|
197
|
+
T2 = 30e-6 # 30 μs
|
|
198
|
+
gate_time = 25e-9 # 25 ns
|
|
199
|
+
|
|
200
|
+
noise_model = ThermalNoise(T1, T2, gate_time)
|
|
201
|
+
```
|
|
202
|
+
|
|
203
|
+
## Adding Noise to Circuits
|
|
204
|
+
|
|
205
|
+
### with_noise Method
|
|
206
|
+
|
|
207
|
+
```python
|
|
208
|
+
# Add noise to all operations
|
|
209
|
+
noisy_circuit = circuit.with_noise(cirq.depolarize(p=0.01))
|
|
210
|
+
|
|
211
|
+
# Simulate noisy circuit
|
|
212
|
+
simulator = cirq.DensityMatrixSimulator()
|
|
213
|
+
result = simulator.run(noisy_circuit, repetitions=1000)
|
|
214
|
+
```
|
|
215
|
+
|
|
216
|
+
### insert_into_circuit Method
|
|
217
|
+
|
|
218
|
+
```python
|
|
219
|
+
# Manual noise insertion
|
|
220
|
+
def add_noise_to_circuit(circuit, noise_model):
|
|
221
|
+
noisy_moments = []
|
|
222
|
+
for moment in circuit:
|
|
223
|
+
ops = []
|
|
224
|
+
for op in moment:
|
|
225
|
+
ops.extend(noise_model.noisy_operation(op))
|
|
226
|
+
noisy_moments.append(cirq.Moment(ops))
|
|
227
|
+
return cirq.Circuit(noisy_moments)
|
|
228
|
+
```
|
|
229
|
+
|
|
230
|
+
## Readout Noise
|
|
231
|
+
|
|
232
|
+
### Measurement Error Model
|
|
233
|
+
|
|
234
|
+
```python
|
|
235
|
+
class ReadoutNoiseModel(cirq.NoiseModel):
|
|
236
|
+
"""Model readout/measurement errors."""
|
|
237
|
+
|
|
238
|
+
def __init__(self, p0_given_1, p1_given_0):
|
|
239
|
+
# p0_given_1: Probability of measuring 0 when state is 1
|
|
240
|
+
# p1_given_0: Probability of measuring 1 when state is 0
|
|
241
|
+
self.p0_given_1 = p0_given_1
|
|
242
|
+
self.p1_given_0 = p1_given_0
|
|
243
|
+
|
|
244
|
+
def noisy_operation(self, op):
|
|
245
|
+
if isinstance(op.gate, cirq.MeasurementGate):
|
|
246
|
+
# Apply bit flip before measurement
|
|
247
|
+
noise_ops = []
|
|
248
|
+
for qubit in op.qubits:
|
|
249
|
+
# Average readout error
|
|
250
|
+
p_error = (self.p0_given_1 + self.p1_given_0) / 2
|
|
251
|
+
noise_ops.append(cirq.bit_flip(p_error)(qubit))
|
|
252
|
+
noise_ops.append(op)
|
|
253
|
+
return noise_ops
|
|
254
|
+
return op
|
|
255
|
+
|
|
256
|
+
# Typical readout errors
|
|
257
|
+
readout_noise = ReadoutNoiseModel(p0_given_1=0.02, p1_given_0=0.01)
|
|
258
|
+
```
|
|
259
|
+
|
|
260
|
+
## Noise Characterization
|
|
261
|
+
|
|
262
|
+
### Randomized Benchmarking
|
|
263
|
+
|
|
264
|
+
```python
|
|
265
|
+
import cirq
|
|
266
|
+
|
|
267
|
+
def generate_rb_circuit(qubits, depth):
|
|
268
|
+
"""Generate randomized benchmarking circuit."""
|
|
269
|
+
# Random Clifford gates
|
|
270
|
+
clifford_gates = [cirq.X, cirq.Y, cirq.Z, cirq.H, cirq.S]
|
|
271
|
+
|
|
272
|
+
circuit = cirq.Circuit()
|
|
273
|
+
for _ in range(depth):
|
|
274
|
+
for qubit in qubits:
|
|
275
|
+
gate = np.random.choice(clifford_gates)
|
|
276
|
+
circuit.append(gate(qubit))
|
|
277
|
+
|
|
278
|
+
# Add inverse to return to initial state (ideally)
|
|
279
|
+
# (simplified - proper RB requires tracking full sequence)
|
|
280
|
+
|
|
281
|
+
circuit.append(cirq.measure(*qubits, key='result'))
|
|
282
|
+
return circuit
|
|
283
|
+
|
|
284
|
+
# Run RB experiment
|
|
285
|
+
def run_rb_experiment(qubits, depths, repetitions=1000):
|
|
286
|
+
"""Run randomized benchmarking at various depths."""
|
|
287
|
+
simulator = cirq.DensityMatrixSimulator(
|
|
288
|
+
noise=cirq.ConstantQubitNoiseModel(cirq.depolarize(0.01))
|
|
289
|
+
)
|
|
290
|
+
|
|
291
|
+
survival_probs = []
|
|
292
|
+
for depth in depths:
|
|
293
|
+
circuits = [generate_rb_circuit(qubits, depth) for _ in range(20)]
|
|
294
|
+
|
|
295
|
+
total_survival = 0
|
|
296
|
+
for circuit in circuits:
|
|
297
|
+
result = simulator.run(circuit, repetitions=repetitions)
|
|
298
|
+
# Calculate survival probability (returned to |0⟩)
|
|
299
|
+
counts = result.histogram(key='result')
|
|
300
|
+
survival = counts.get(0, 0) / repetitions
|
|
301
|
+
total_survival += survival
|
|
302
|
+
|
|
303
|
+
avg_survival = total_survival / len(circuits)
|
|
304
|
+
survival_probs.append(avg_survival)
|
|
305
|
+
|
|
306
|
+
return survival_probs
|
|
307
|
+
|
|
308
|
+
# Fit to extract error rate
|
|
309
|
+
# p_survival = A * p^depth + B
|
|
310
|
+
# Error per gate ≈ (1 - p) / 2
|
|
311
|
+
```
|
|
312
|
+
|
|
313
|
+
### Cross-Entropy Benchmarking (XEB)
|
|
314
|
+
|
|
315
|
+
```python
|
|
316
|
+
def xeb_fidelity(circuit, simulator, ideal_probs, repetitions=10000):
|
|
317
|
+
"""Calculate XEB fidelity."""
|
|
318
|
+
|
|
319
|
+
# Run noisy simulation
|
|
320
|
+
result = simulator.run(circuit, repetitions=repetitions)
|
|
321
|
+
measured_probs = result.histogram(key='result')
|
|
322
|
+
|
|
323
|
+
# Normalize
|
|
324
|
+
for key in measured_probs:
|
|
325
|
+
measured_probs[key] /= repetitions
|
|
326
|
+
|
|
327
|
+
# Calculate cross-entropy
|
|
328
|
+
cross_entropy = 0
|
|
329
|
+
for bitstring, prob in measured_probs.items():
|
|
330
|
+
if bitstring in ideal_probs:
|
|
331
|
+
cross_entropy += prob * np.log2(ideal_probs[bitstring])
|
|
332
|
+
|
|
333
|
+
# Convert to fidelity
|
|
334
|
+
n_qubits = len(circuit.all_qubits())
|
|
335
|
+
fidelity = (2**n_qubits * cross_entropy + 1) / (2**n_qubits - 1)
|
|
336
|
+
|
|
337
|
+
return fidelity
|
|
338
|
+
```
|
|
339
|
+
|
|
340
|
+
## Noise Visualization
|
|
341
|
+
|
|
342
|
+
### Heatmap Visualization
|
|
343
|
+
|
|
344
|
+
```python
|
|
345
|
+
import matplotlib.pyplot as plt
|
|
346
|
+
|
|
347
|
+
def plot_noise_heatmap(device, noise_metric):
|
|
348
|
+
"""Plot noise characteristics across 2D grid device."""
|
|
349
|
+
|
|
350
|
+
# Get device qubits (assuming GridQubit)
|
|
351
|
+
qubits = sorted(device.metadata.qubit_set)
|
|
352
|
+
rows = max(q.row for q in qubits) + 1
|
|
353
|
+
cols = max(q.col for q in qubits) + 1
|
|
354
|
+
|
|
355
|
+
# Create heatmap data
|
|
356
|
+
heatmap = np.full((rows, cols), np.nan)
|
|
357
|
+
|
|
358
|
+
for qubit in qubits:
|
|
359
|
+
if isinstance(qubit, cirq.GridQubit):
|
|
360
|
+
value = noise_metric.get(qubit, 0)
|
|
361
|
+
heatmap[qubit.row, qubit.col] = value
|
|
362
|
+
|
|
363
|
+
# Plot
|
|
364
|
+
plt.figure(figsize=(10, 8))
|
|
365
|
+
plt.imshow(heatmap, cmap='RdYlGn_r', interpolation='nearest')
|
|
366
|
+
plt.colorbar(label='Error Rate')
|
|
367
|
+
plt.title('Qubit Error Rates')
|
|
368
|
+
plt.xlabel('Column')
|
|
369
|
+
plt.ylabel('Row')
|
|
370
|
+
plt.show()
|
|
371
|
+
|
|
372
|
+
# Example usage
|
|
373
|
+
noise_metric = {q: np.random.random() * 0.01 for q in device.metadata.qubit_set}
|
|
374
|
+
plot_noise_heatmap(device, noise_metric)
|
|
375
|
+
```
|
|
376
|
+
|
|
377
|
+
### Gate Fidelity Visualization
|
|
378
|
+
|
|
379
|
+
```python
|
|
380
|
+
def plot_gate_fidelities(calibration_data):
|
|
381
|
+
"""Plot single- and two-qubit gate fidelities."""
|
|
382
|
+
|
|
383
|
+
sq_fidelities = []
|
|
384
|
+
tq_fidelities = []
|
|
385
|
+
|
|
386
|
+
for qubit, metrics in calibration_data.items():
|
|
387
|
+
if 'single_qubit_rb_fidelity' in metrics:
|
|
388
|
+
sq_fidelities.append(metrics['single_qubit_rb_fidelity'])
|
|
389
|
+
if 'two_qubit_rb_fidelity' in metrics:
|
|
390
|
+
tq_fidelities.append(metrics['two_qubit_rb_fidelity'])
|
|
391
|
+
|
|
392
|
+
fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12, 5))
|
|
393
|
+
|
|
394
|
+
ax1.hist(sq_fidelities, bins=20)
|
|
395
|
+
ax1.set_xlabel('Single-Qubit Gate Fidelity')
|
|
396
|
+
ax1.set_ylabel('Count')
|
|
397
|
+
ax1.set_title('Single-Qubit Gate Fidelities')
|
|
398
|
+
|
|
399
|
+
ax2.hist(tq_fidelities, bins=20)
|
|
400
|
+
ax2.set_xlabel('Two-Qubit Gate Fidelity')
|
|
401
|
+
ax2.set_ylabel('Count')
|
|
402
|
+
ax2.set_title('Two-Qubit Gate Fidelities')
|
|
403
|
+
|
|
404
|
+
plt.tight_layout()
|
|
405
|
+
plt.show()
|
|
406
|
+
```
|
|
407
|
+
|
|
408
|
+
## Error Mitigation Techniques
|
|
409
|
+
|
|
410
|
+
### Zero-Noise Extrapolation
|
|
411
|
+
|
|
412
|
+
```python
|
|
413
|
+
def zero_noise_extrapolation(circuit, noise_levels, simulator):
|
|
414
|
+
"""Extrapolate to zero noise limit."""
|
|
415
|
+
|
|
416
|
+
expectation_values = []
|
|
417
|
+
|
|
418
|
+
for noise_level in noise_levels:
|
|
419
|
+
# Scale noise
|
|
420
|
+
noisy_circuit = circuit.with_noise(
|
|
421
|
+
cirq.depolarize(p=noise_level)
|
|
422
|
+
)
|
|
423
|
+
|
|
424
|
+
# Measure expectation
|
|
425
|
+
result = simulator.simulate(noisy_circuit)
|
|
426
|
+
# ... calculate expectation value
|
|
427
|
+
exp_val = calculate_expectation(result)
|
|
428
|
+
expectation_values.append(exp_val)
|
|
429
|
+
|
|
430
|
+
# Extrapolate to zero noise
|
|
431
|
+
from scipy.optimize import curve_fit
|
|
432
|
+
|
|
433
|
+
def exponential_fit(x, a, b, c):
|
|
434
|
+
return a * np.exp(-b * x) + c
|
|
435
|
+
|
|
436
|
+
popt, _ = curve_fit(exponential_fit, noise_levels, expectation_values)
|
|
437
|
+
zero_noise_value = popt[2]
|
|
438
|
+
|
|
439
|
+
return zero_noise_value
|
|
440
|
+
```
|
|
441
|
+
|
|
442
|
+
### Probabilistic Error Cancellation
|
|
443
|
+
|
|
444
|
+
```python
|
|
445
|
+
def quasi_probability_decomposition(noisy_gate, ideal_gate, noise_model):
|
|
446
|
+
"""Decompose noisy gate into quasi-probability distribution."""
|
|
447
|
+
|
|
448
|
+
# Decompose noisy gate as: N = ideal + error
|
|
449
|
+
# Invert: ideal = (N - error) / (1 - error_rate)
|
|
450
|
+
|
|
451
|
+
# This creates a quasi-probability distribution
|
|
452
|
+
# (some probabilities may be negative)
|
|
453
|
+
|
|
454
|
+
# Implementation depends on specific noise model
|
|
455
|
+
pass
|
|
456
|
+
```
|
|
457
|
+
|
|
458
|
+
### Readout Error Mitigation
|
|
459
|
+
|
|
460
|
+
```python
|
|
461
|
+
def mitigate_readout_errors(results, confusion_matrix):
|
|
462
|
+
"""Apply readout error mitigation using confusion matrix."""
|
|
463
|
+
|
|
464
|
+
# Invert confusion matrix
|
|
465
|
+
inv_confusion = np.linalg.inv(confusion_matrix)
|
|
466
|
+
|
|
467
|
+
# Get measured counts
|
|
468
|
+
counts = results.histogram(key='result')
|
|
469
|
+
|
|
470
|
+
# Convert to probability vector
|
|
471
|
+
total_counts = sum(counts.values())
|
|
472
|
+
measured_probs = np.array([counts.get(i, 0) / total_counts
|
|
473
|
+
for i in range(len(confusion_matrix))])
|
|
474
|
+
|
|
475
|
+
# Apply inverse
|
|
476
|
+
corrected_probs = inv_confusion @ measured_probs
|
|
477
|
+
|
|
478
|
+
# Convert back to counts
|
|
479
|
+
corrected_counts = {i: int(p * total_counts)
|
|
480
|
+
for i, p in enumerate(corrected_probs) if p > 0}
|
|
481
|
+
|
|
482
|
+
return corrected_counts
|
|
483
|
+
```
|
|
484
|
+
|
|
485
|
+
## Hardware-Based Noise Models
|
|
486
|
+
|
|
487
|
+
### From Google Calibration
|
|
488
|
+
|
|
489
|
+
```python
|
|
490
|
+
import cirq_google
|
|
491
|
+
|
|
492
|
+
# Get calibration data
|
|
493
|
+
processor = cirq_google.get_engine().get_processor('weber')
|
|
494
|
+
noise_props = processor.get_device_specification()
|
|
495
|
+
|
|
496
|
+
# Create noise model from calibration
|
|
497
|
+
noise_model = cirq_google.NoiseModelFromGoogleNoiseProperties(noise_props)
|
|
498
|
+
|
|
499
|
+
# Simulate with realistic noise
|
|
500
|
+
simulator = cirq.DensityMatrixSimulator(noise=noise_model)
|
|
501
|
+
result = simulator.run(circuit, repetitions=1000)
|
|
502
|
+
```
|
|
503
|
+
|
|
504
|
+
## Best Practices
|
|
505
|
+
|
|
506
|
+
1. **Use density matrix simulator for noisy simulations**: State vector simulators cannot model mixed states
|
|
507
|
+
2. **Match noise model to hardware**: Use calibration data when available
|
|
508
|
+
3. **Include all error sources**: Gate errors, decoherence, readout errors
|
|
509
|
+
4. **Characterize before mitigating**: Understand noise before applying mitigation
|
|
510
|
+
5. **Consider error propagation**: Noise compounds through circuit depth
|
|
511
|
+
6. **Use appropriate benchmarking**: RB for gate errors, XEB for full circuit fidelity
|
|
512
|
+
7. **Visualize noise patterns**: Identify problematic qubits and gates
|
|
513
|
+
8. **Apply targeted mitigation**: Focus on dominant error sources
|
|
514
|
+
9. **Validate mitigation**: Verify that mitigation improves results
|
|
515
|
+
10. **Keep circuits shallow**: Minimize noise accumulation
|