@synsci/cli-darwin-x64-baseline 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
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# Qiskit Patterns: The Four-Step Workflow
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Translate classical problems into quantum circuits and operators
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Transform domain-specific problems into quantum representations (circuits, operators, Hamiltonians).
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**Design Circuit Structure:**
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```python
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|
+
params = []
|
|
48
|
+
|
|
49
|
+
for d in range(depth):
|
|
50
|
+
# Rotation layer
|
|
51
|
+
for i in range(num_qubits):
|
|
52
|
+
theta = Parameter(f'θ_{d}_{i}')
|
|
53
|
+
params.append(theta)
|
|
54
|
+
qc.ry(theta, i)
|
|
55
|
+
|
|
56
|
+
# Entanglement layer
|
|
57
|
+
for i in range(num_qubits - 1):
|
|
58
|
+
qc.cx(i, i + 1)
|
|
59
|
+
|
|
60
|
+
return qc, params
|
|
61
|
+
|
|
62
|
+
ansatz, params = create_ansatz(num_qubits=4, depth=2)
|
|
63
|
+
```
|
|
64
|
+
|
|
65
|
+
### Considerations
|
|
66
|
+
|
|
67
|
+
- **Hardware topology**: Design with backend coupling map in mind
|
|
68
|
+
- **Gate efficiency**: Minimize two-qubit gates
|
|
69
|
+
- **Measurement basis**: Determine required measurements
|
|
70
|
+
|
|
71
|
+
### Domain-Specific Examples
|
|
72
|
+
|
|
73
|
+
**Chemistry: Molecular Hamiltonian**
|
|
74
|
+
```python
|
|
75
|
+
from qiskit_nature.second_q.drivers import PySCFDriver
|
|
76
|
+
from qiskit_nature.second_q.mappers import JordanWignerMapper
|
|
77
|
+
|
|
78
|
+
# Define molecule
|
|
79
|
+
driver = PySCFDriver(atom='H 0 0 0; H 0 0 0.735', basis='sto3g')
|
|
80
|
+
problem = driver.run()
|
|
81
|
+
|
|
82
|
+
# Map to qubit Hamiltonian
|
|
83
|
+
mapper = JordanWignerMapper()
|
|
84
|
+
hamiltonian = mapper.map(problem.hamiltonian)
|
|
85
|
+
```
|
|
86
|
+
|
|
87
|
+
**Optimization: QAOA Circuit**
|
|
88
|
+
```python
|
|
89
|
+
from qiskit.circuit import QuantumCircuit, Parameter
|
|
90
|
+
|
|
91
|
+
def qaoa_circuit(graph, p):
|
|
92
|
+
"""Create QAOA circuit for MaxCut problem"""
|
|
93
|
+
num_qubits = len(graph.nodes())
|
|
94
|
+
qc = QuantumCircuit(num_qubits)
|
|
95
|
+
|
|
96
|
+
# Initial superposition
|
|
97
|
+
qc.h(range(num_qubits))
|
|
98
|
+
|
|
99
|
+
# Alternating layers
|
|
100
|
+
betas = [Parameter(f'β_{i}') for i in range(p)]
|
|
101
|
+
gammas = [Parameter(f'γ_{i}') for i in range(p)]
|
|
102
|
+
|
|
103
|
+
for i in range(p):
|
|
104
|
+
# Problem Hamiltonian
|
|
105
|
+
for edge in graph.edges():
|
|
106
|
+
qc.cx(edge[0], edge[1])
|
|
107
|
+
qc.rz(2 * gammas[i], edge[1])
|
|
108
|
+
qc.cx(edge[0], edge[1])
|
|
109
|
+
|
|
110
|
+
# Mixer Hamiltonian
|
|
111
|
+
qc.rx(2 * betas[i], range(num_qubits))
|
|
112
|
+
|
|
113
|
+
return qc
|
|
114
|
+
```
|
|
115
|
+
|
|
116
|
+
## Step 2: Optimize
|
|
117
|
+
|
|
118
|
+
### Goal
|
|
119
|
+
Transform abstract circuits to hardware-compatible ISA (Instruction Set Architecture) circuits.
|
|
120
|
+
|
|
121
|
+
### Transpilation
|
|
122
|
+
|
|
123
|
+
```python
|
|
124
|
+
from qiskit import transpile
|
|
125
|
+
|
|
126
|
+
# Basic transpilation
|
|
127
|
+
qc_isa = transpile(qc, backend=backend, optimization_level=3)
|
|
128
|
+
|
|
129
|
+
# With specific initial layout
|
|
130
|
+
qc_isa = transpile(
|
|
131
|
+
qc,
|
|
132
|
+
backend=backend,
|
|
133
|
+
optimization_level=3,
|
|
134
|
+
initial_layout=[0, 2, 4, 6], # Map to specific physical qubits
|
|
135
|
+
seed_transpiler=42 # Reproducibility
|
|
136
|
+
)
|
|
137
|
+
```
|
|
138
|
+
|
|
139
|
+
### Pre-optimization Tips
|
|
140
|
+
|
|
141
|
+
1. **Test with simulators first**:
|
|
142
|
+
```python
|
|
143
|
+
from qiskit_aer import AerSimulator
|
|
144
|
+
|
|
145
|
+
sim = AerSimulator.from_backend(backend)
|
|
146
|
+
qc_test = transpile(qc, sim, optimization_level=3)
|
|
147
|
+
print(f"Estimated depth: {qc_test.depth()}")
|
|
148
|
+
```
|
|
149
|
+
|
|
150
|
+
2. **Analyze transpilation results**:
|
|
151
|
+
```python
|
|
152
|
+
print(f"Original gates: {qc.size()}")
|
|
153
|
+
print(f"Transpiled gates: {qc_isa.size()}")
|
|
154
|
+
print(f"Two-qubit gates: {qc_isa.count_ops().get('cx', 0)}")
|
|
155
|
+
```
|
|
156
|
+
|
|
157
|
+
3. **Consider circuit cutting** for large circuits:
|
|
158
|
+
```python
|
|
159
|
+
# For circuits too large for available hardware
|
|
160
|
+
# Use circuit cutting techniques to split into smaller subcircuits
|
|
161
|
+
```
|
|
162
|
+
|
|
163
|
+
## Step 3: Execute
|
|
164
|
+
|
|
165
|
+
### Goal
|
|
166
|
+
Run ISA circuits on quantum hardware using primitives.
|
|
167
|
+
|
|
168
|
+
### Using Sampler
|
|
169
|
+
|
|
170
|
+
```python
|
|
171
|
+
from qiskit_ibm_runtime import QiskitRuntimeService, SamplerV2 as Sampler
|
|
172
|
+
|
|
173
|
+
service = QiskitRuntimeService()
|
|
174
|
+
backend = service.backend("ibm_brisbane")
|
|
175
|
+
|
|
176
|
+
# Transpile first
|
|
177
|
+
qc_isa = transpile(qc, backend=backend, optimization_level=3)
|
|
178
|
+
|
|
179
|
+
# Execute
|
|
180
|
+
sampler = Sampler(backend)
|
|
181
|
+
job = sampler.run([qc_isa], shots=10000)
|
|
182
|
+
result = job.result()
|
|
183
|
+
counts = result[0].data.meas.get_counts()
|
|
184
|
+
```
|
|
185
|
+
|
|
186
|
+
### Using Estimator
|
|
187
|
+
|
|
188
|
+
```python
|
|
189
|
+
from qiskit_ibm_runtime import EstimatorV2 as Estimator
|
|
190
|
+
from qiskit.quantum_info import SparsePauliOp
|
|
191
|
+
|
|
192
|
+
service = QiskitRuntimeService()
|
|
193
|
+
backend = service.backend("ibm_brisbane")
|
|
194
|
+
|
|
195
|
+
# Transpile
|
|
196
|
+
qc_isa = transpile(qc, backend=backend, optimization_level=3)
|
|
197
|
+
|
|
198
|
+
# Define observable
|
|
199
|
+
observable = SparsePauliOp(["ZZZZ", "XXXX"])
|
|
200
|
+
|
|
201
|
+
# Execute
|
|
202
|
+
estimator = Estimator(backend)
|
|
203
|
+
job = estimator.run([(qc_isa, observable)])
|
|
204
|
+
result = job.result()
|
|
205
|
+
expectation_value = result[0].data.evs
|
|
206
|
+
```
|
|
207
|
+
|
|
208
|
+
### Execution Modes
|
|
209
|
+
|
|
210
|
+
**Session Mode (Iterative):**
|
|
211
|
+
```python
|
|
212
|
+
from qiskit_ibm_runtime import Session
|
|
213
|
+
|
|
214
|
+
with Session(backend=backend) as session:
|
|
215
|
+
sampler = Sampler(session=session)
|
|
216
|
+
|
|
217
|
+
# Multiple iterations
|
|
218
|
+
for iteration in range(max_iterations):
|
|
219
|
+
qc_iteration = update_circuit(params[iteration])
|
|
220
|
+
qc_isa = transpile(qc_iteration, backend=backend)
|
|
221
|
+
|
|
222
|
+
job = sampler.run([qc_isa], shots=1000)
|
|
223
|
+
result = job.result()
|
|
224
|
+
|
|
225
|
+
# Update parameters
|
|
226
|
+
params[iteration + 1] = optimize_params(result)
|
|
227
|
+
```
|
|
228
|
+
|
|
229
|
+
**Batch Mode (Parallel):**
|
|
230
|
+
```python
|
|
231
|
+
from qiskit_ibm_runtime import Batch
|
|
232
|
+
|
|
233
|
+
with Batch(backend=backend) as batch:
|
|
234
|
+
sampler = Sampler(session=batch)
|
|
235
|
+
|
|
236
|
+
# Submit all jobs at once
|
|
237
|
+
jobs = []
|
|
238
|
+
for qc in circuit_list:
|
|
239
|
+
qc_isa = transpile(qc, backend=backend)
|
|
240
|
+
job = sampler.run([qc_isa], shots=1000)
|
|
241
|
+
jobs.append(job)
|
|
242
|
+
|
|
243
|
+
# Collect results
|
|
244
|
+
results = [job.result() for job in jobs]
|
|
245
|
+
```
|
|
246
|
+
|
|
247
|
+
### Error Mitigation
|
|
248
|
+
|
|
249
|
+
```python
|
|
250
|
+
from qiskit_ibm_runtime import Options
|
|
251
|
+
|
|
252
|
+
options = Options()
|
|
253
|
+
options.resilience_level = 2 # 0=none, 1=light, 2=moderate, 3=heavy
|
|
254
|
+
options.optimization_level = 3
|
|
255
|
+
|
|
256
|
+
sampler = Sampler(backend, options=options)
|
|
257
|
+
```
|
|
258
|
+
|
|
259
|
+
## Step 4: Post-process
|
|
260
|
+
|
|
261
|
+
### Goal
|
|
262
|
+
Extract meaningful results from quantum measurements using classical computation.
|
|
263
|
+
|
|
264
|
+
### Result Processing
|
|
265
|
+
|
|
266
|
+
**For Sampler (Bitstrings):**
|
|
267
|
+
```python
|
|
268
|
+
counts = result[0].data.meas.get_counts()
|
|
269
|
+
|
|
270
|
+
# Convert to probabilities
|
|
271
|
+
total_shots = sum(counts.values())
|
|
272
|
+
probabilities = {state: count/total_shots for state, count in counts.items()}
|
|
273
|
+
|
|
274
|
+
# Find most probable state
|
|
275
|
+
max_state = max(counts, key=counts.get)
|
|
276
|
+
print(f"Most probable state: {max_state} ({counts[max_state]}/{total_shots})")
|
|
277
|
+
```
|
|
278
|
+
|
|
279
|
+
**For Estimator (Expectation Values):**
|
|
280
|
+
```python
|
|
281
|
+
expectation_value = result[0].data.evs
|
|
282
|
+
std_dev = result[0].data.stds # Standard deviation
|
|
283
|
+
|
|
284
|
+
print(f"Energy: {expectation_value} ± {std_dev}")
|
|
285
|
+
```
|
|
286
|
+
|
|
287
|
+
### Domain-Specific Post-Processing
|
|
288
|
+
|
|
289
|
+
**Chemistry: Ground State Energy**
|
|
290
|
+
```python
|
|
291
|
+
def post_process_chemistry(result, nuclear_repulsion):
|
|
292
|
+
"""Extract ground state energy"""
|
|
293
|
+
electronic_energy = result[0].data.evs
|
|
294
|
+
total_energy = electronic_energy + nuclear_repulsion
|
|
295
|
+
return total_energy
|
|
296
|
+
```
|
|
297
|
+
|
|
298
|
+
**Optimization: MaxCut Solution**
|
|
299
|
+
```python
|
|
300
|
+
def post_process_maxcut(counts, graph):
|
|
301
|
+
"""Find best cut from measurement results"""
|
|
302
|
+
def compute_cut_value(bitstring, graph):
|
|
303
|
+
cut_value = 0
|
|
304
|
+
for edge in graph.edges():
|
|
305
|
+
if bitstring[edge[0]] != bitstring[edge[1]]:
|
|
306
|
+
cut_value += 1
|
|
307
|
+
return cut_value
|
|
308
|
+
|
|
309
|
+
# Find bitstring with maximum cut
|
|
310
|
+
best_cut = 0
|
|
311
|
+
best_string = None
|
|
312
|
+
|
|
313
|
+
for bitstring, count in counts.items():
|
|
314
|
+
cut = compute_cut_value(bitstring, graph)
|
|
315
|
+
if cut > best_cut:
|
|
316
|
+
best_cut = cut
|
|
317
|
+
best_string = bitstring
|
|
318
|
+
|
|
319
|
+
return best_string, best_cut
|
|
320
|
+
```
|
|
321
|
+
|
|
322
|
+
### Advanced Post-Processing
|
|
323
|
+
|
|
324
|
+
**Error Mitigation Post-Processing:**
|
|
325
|
+
```python
|
|
326
|
+
# Apply additional classical error mitigation
|
|
327
|
+
from qiskit.result import marginal_counts
|
|
328
|
+
|
|
329
|
+
# Marginalize to relevant qubits
|
|
330
|
+
relevant_qubits = [0, 1, 2]
|
|
331
|
+
marginal = marginal_counts(counts, indices=relevant_qubits)
|
|
332
|
+
```
|
|
333
|
+
|
|
334
|
+
**Statistical Analysis:**
|
|
335
|
+
```python
|
|
336
|
+
import numpy as np
|
|
337
|
+
|
|
338
|
+
def analyze_results(results_list):
|
|
339
|
+
"""Analyze multiple runs for statistics"""
|
|
340
|
+
energies = [r[0].data.evs for r in results_list]
|
|
341
|
+
|
|
342
|
+
mean_energy = np.mean(energies)
|
|
343
|
+
std_energy = np.std(energies)
|
|
344
|
+
confidence_interval = 1.96 * std_energy / np.sqrt(len(energies))
|
|
345
|
+
|
|
346
|
+
return {
|
|
347
|
+
'mean': mean_energy,
|
|
348
|
+
'std': std_energy,
|
|
349
|
+
'95% CI': (mean_energy - confidence_interval, mean_energy + confidence_interval)
|
|
350
|
+
}
|
|
351
|
+
```
|
|
352
|
+
|
|
353
|
+
**Visualization:**
|
|
354
|
+
```python
|
|
355
|
+
from qiskit.visualization import plot_histogram
|
|
356
|
+
import matplotlib.pyplot as plt
|
|
357
|
+
|
|
358
|
+
# Visualize results
|
|
359
|
+
plot_histogram(counts, figsize=(12, 6))
|
|
360
|
+
plt.title("Measurement Results")
|
|
361
|
+
plt.show()
|
|
362
|
+
```
|
|
363
|
+
|
|
364
|
+
## Complete Example: VQE for Chemistry
|
|
365
|
+
|
|
366
|
+
```python
|
|
367
|
+
from qiskit import QuantumCircuit, transpile
|
|
368
|
+
from qiskit_ibm_runtime import QiskitRuntimeService, EstimatorV2 as Estimator, Session
|
|
369
|
+
from qiskit.quantum_info import SparsePauliOp
|
|
370
|
+
from scipy.optimize import minimize
|
|
371
|
+
import numpy as np
|
|
372
|
+
|
|
373
|
+
# 1. MAP: Create parameterized circuit
|
|
374
|
+
def create_ansatz(num_qubits):
|
|
375
|
+
qc = QuantumCircuit(num_qubits)
|
|
376
|
+
params = []
|
|
377
|
+
|
|
378
|
+
for i in range(num_qubits):
|
|
379
|
+
theta = f'θ_{i}'
|
|
380
|
+
params.append(theta)
|
|
381
|
+
qc.ry(theta, i)
|
|
382
|
+
|
|
383
|
+
for i in range(num_qubits - 1):
|
|
384
|
+
qc.cx(i, i + 1)
|
|
385
|
+
|
|
386
|
+
return qc, params
|
|
387
|
+
|
|
388
|
+
# Define Hamiltonian (example: H2 molecule)
|
|
389
|
+
hamiltonian = SparsePauliOp(["IIZZ", "ZZII", "XXII", "IIXX"], coeffs=[0.3, 0.3, 0.1, 0.1])
|
|
390
|
+
|
|
391
|
+
# 2. OPTIMIZE: Connect and prepare
|
|
392
|
+
service = QiskitRuntimeService()
|
|
393
|
+
backend = service.backend("ibm_brisbane")
|
|
394
|
+
|
|
395
|
+
ansatz, param_names = create_ansatz(num_qubits=4)
|
|
396
|
+
|
|
397
|
+
# 3. EXECUTE: Run VQE
|
|
398
|
+
def cost_function(params):
|
|
399
|
+
# Bind parameters
|
|
400
|
+
bound_circuit = ansatz.assign_parameters({param_names[i]: params[i] for i in range(len(params))})
|
|
401
|
+
|
|
402
|
+
# Transpile
|
|
403
|
+
qc_isa = transpile(bound_circuit, backend=backend, optimization_level=3)
|
|
404
|
+
|
|
405
|
+
# Execute
|
|
406
|
+
job = estimator.run([(qc_isa, hamiltonian)])
|
|
407
|
+
result = job.result()
|
|
408
|
+
energy = result[0].data.evs
|
|
409
|
+
|
|
410
|
+
return energy
|
|
411
|
+
|
|
412
|
+
with Session(backend=backend) as session:
|
|
413
|
+
estimator = Estimator(session=session)
|
|
414
|
+
|
|
415
|
+
# Classical optimization loop
|
|
416
|
+
initial_params = np.random.random(len(param_names)) * 2 * np.pi
|
|
417
|
+
result = minimize(cost_function, initial_params, method='COBYLA')
|
|
418
|
+
|
|
419
|
+
# 4. POST-PROCESS: Extract ground state energy
|
|
420
|
+
ground_state_energy = result.fun
|
|
421
|
+
optimized_params = result.x
|
|
422
|
+
|
|
423
|
+
print(f"Ground state energy: {ground_state_energy}")
|
|
424
|
+
print(f"Optimized parameters: {optimized_params}")
|
|
425
|
+
```
|
|
426
|
+
|
|
427
|
+
## Best Practices
|
|
428
|
+
|
|
429
|
+
### 1. Iterate Locally First
|
|
430
|
+
Test the full workflow with simulators before using hardware:
|
|
431
|
+
```python
|
|
432
|
+
from qiskit.primitives import StatevectorEstimator
|
|
433
|
+
|
|
434
|
+
estimator = StatevectorEstimator()
|
|
435
|
+
# Test workflow locally
|
|
436
|
+
```
|
|
437
|
+
|
|
438
|
+
### 2. Use Sessions for Iterative Algorithms
|
|
439
|
+
VQE, QAOA, and other variational algorithms benefit from sessions.
|
|
440
|
+
|
|
441
|
+
### 3. Choose Appropriate Shots
|
|
442
|
+
- Development/testing: 100-1000 shots
|
|
443
|
+
- Production: 10,000+ shots
|
|
444
|
+
|
|
445
|
+
### 4. Monitor Convergence
|
|
446
|
+
```python
|
|
447
|
+
energies = []
|
|
448
|
+
|
|
449
|
+
def cost_function_with_tracking(params):
|
|
450
|
+
energy = cost_function(params)
|
|
451
|
+
energies.append(energy)
|
|
452
|
+
print(f"Iteration {len(energies)}: E = {energy}")
|
|
453
|
+
return energy
|
|
454
|
+
```
|
|
455
|
+
|
|
456
|
+
### 5. Save Results
|
|
457
|
+
```python
|
|
458
|
+
import json
|
|
459
|
+
|
|
460
|
+
results_data = {
|
|
461
|
+
'energy': float(ground_state_energy),
|
|
462
|
+
'parameters': optimized_params.tolist(),
|
|
463
|
+
'iterations': len(energies),
|
|
464
|
+
'backend': backend.name
|
|
465
|
+
}
|
|
466
|
+
|
|
467
|
+
with open('vqe_results.json', 'w') as f:
|
|
468
|
+
json.dump(results_data, f, indent=2)
|
|
469
|
+
```
|
|
470
|
+
|
|
471
|
+
## Qiskit Serverless
|
|
472
|
+
|
|
473
|
+
For large-scale workflows, use Qiskit Serverless for distributed computation:
|
|
474
|
+
|
|
475
|
+
```python
|
|
476
|
+
from qiskit_serverless import ServerlessClient, QiskitFunction
|
|
477
|
+
|
|
478
|
+
client = ServerlessClient()
|
|
479
|
+
|
|
480
|
+
# Define serverless function
|
|
481
|
+
@QiskitFunction()
|
|
482
|
+
def run_vqe_serverless(hamiltonian, ansatz):
|
|
483
|
+
# Your VQE implementation
|
|
484
|
+
pass
|
|
485
|
+
|
|
486
|
+
# Execute remotely
|
|
487
|
+
job = run_vqe_serverless(hamiltonian, ansatz)
|
|
488
|
+
result = job.result()
|
|
489
|
+
```
|
|
490
|
+
|
|
491
|
+
## Common Workflow Patterns
|
|
492
|
+
|
|
493
|
+
### Pattern 1: Parameter Sweep
|
|
494
|
+
```python
|
|
495
|
+
# Map → Optimize once → Execute many → Post-process
|
|
496
|
+
qc_isa = transpile(parameterized_circuit, backend=backend)
|
|
497
|
+
|
|
498
|
+
with Batch(backend=backend) as batch:
|
|
499
|
+
sampler = Sampler(session=batch)
|
|
500
|
+
results = []
|
|
501
|
+
|
|
502
|
+
for param_set in parameter_sweep:
|
|
503
|
+
bound_qc = qc_isa.assign_parameters(param_set)
|
|
504
|
+
job = sampler.run([bound_qc], shots=1000)
|
|
505
|
+
results.append(job.result())
|
|
506
|
+
```
|
|
507
|
+
|
|
508
|
+
### Pattern 2: Iterative Refinement
|
|
509
|
+
```python
|
|
510
|
+
# Map → (Optimize → Execute → Post-process) repeated
|
|
511
|
+
with Session(backend=backend) as session:
|
|
512
|
+
estimator = Estimator(session=session)
|
|
513
|
+
|
|
514
|
+
for iteration in range(max_iter):
|
|
515
|
+
qc = update_circuit(params)
|
|
516
|
+
qc_isa = transpile(qc, backend=backend)
|
|
517
|
+
|
|
518
|
+
result = estimator.run([(qc_isa, observable)]).result()
|
|
519
|
+
params = update_params(result)
|
|
520
|
+
```
|
|
521
|
+
|
|
522
|
+
### Pattern 3: Ensemble Measurement
|
|
523
|
+
```python
|
|
524
|
+
# Map → Optimize → Execute many observables → Post-process
|
|
525
|
+
qc_isa = transpile(qc, backend=backend)
|
|
526
|
+
|
|
527
|
+
observables = [obs1, obs2, obs3, obs4]
|
|
528
|
+
jobs = [(qc_isa, obs) for obs in observables]
|
|
529
|
+
|
|
530
|
+
estimator = Estimator(backend)
|
|
531
|
+
result = estimator.run(jobs).result()
|
|
532
|
+
expectation_values = [r.data.evs for r in result]
|
|
533
|
+
```
|