@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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# Quantum Machine Learning with PennyLane
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## Table of Contents
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1. [Hybrid Quantum-Classical Models](#hybrid-quantum-classical-models)
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2. [Framework Integration](#framework-integration)
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3. [Quantum Neural Networks](#quantum-neural-networks)
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4. [Variational Classifiers](#variational-classifiers)
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## Hybrid Quantum-Classical Models
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### Basic Hybrid Model
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```python
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import pennylane as qml
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import numpy as np
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dev = qml.device('default.qubit', wires=4)
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@qml.qnode(dev)
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def quantum_layer(inputs, weights):
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# Encode classical data
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qml.CNOT(wires=[wire, wire+1])
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# Measure
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return [qml.expval(qml.PauliZ(i)) for i in range(4)]
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# Use in classical workflow
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inputs = np.array([0.1, 0.2, 0.3, 0.4])
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weights = np.random.random(4)
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output = quantum_layer(inputs, weights)
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```
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### Quantum-Classical Pipeline
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|
45
|
+
|
|
46
|
+
```python
|
|
47
|
+
def hybrid_model(x, quantum_weights, classical_weights):
|
|
48
|
+
# Classical preprocessing
|
|
49
|
+
x_preprocessed = np.tanh(classical_weights['pre'] @ x)
|
|
50
|
+
|
|
51
|
+
# Quantum layer
|
|
52
|
+
quantum_out = quantum_layer(x_preprocessed, quantum_weights)
|
|
53
|
+
|
|
54
|
+
# Classical postprocessing
|
|
55
|
+
output = classical_weights['post'] @ quantum_out
|
|
56
|
+
|
|
57
|
+
return output
|
|
58
|
+
```
|
|
59
|
+
|
|
60
|
+
## Framework Integration
|
|
61
|
+
|
|
62
|
+
### PyTorch Integration
|
|
63
|
+
|
|
64
|
+
```python
|
|
65
|
+
import torch
|
|
66
|
+
import pennylane as qml
|
|
67
|
+
|
|
68
|
+
dev = qml.device('default.qubit', wires=2)
|
|
69
|
+
|
|
70
|
+
@qml.qnode(dev, interface='torch')
|
|
71
|
+
def quantum_circuit(inputs, weights):
|
|
72
|
+
qml.RY(inputs[0], wires=0)
|
|
73
|
+
qml.RY(inputs[1], wires=1)
|
|
74
|
+
qml.RX(weights[0], wires=0)
|
|
75
|
+
qml.RX(weights[1], wires=1)
|
|
76
|
+
qml.CNOT(wires=[0, 1])
|
|
77
|
+
return qml.expval(qml.PauliZ(0))
|
|
78
|
+
|
|
79
|
+
# Create PyTorch layer
|
|
80
|
+
class QuantumLayer(torch.nn.Module):
|
|
81
|
+
def __init__(self, n_qubits):
|
|
82
|
+
super().__init__()
|
|
83
|
+
self.n_qubits = n_qubits
|
|
84
|
+
self.weights = torch.nn.Parameter(torch.randn(n_qubits))
|
|
85
|
+
|
|
86
|
+
def forward(self, x):
|
|
87
|
+
return torch.stack([quantum_circuit(xi, self.weights) for xi in x])
|
|
88
|
+
|
|
89
|
+
# Use in PyTorch model
|
|
90
|
+
class HybridModel(torch.nn.Module):
|
|
91
|
+
def __init__(self):
|
|
92
|
+
super().__init__()
|
|
93
|
+
self.classical_1 = torch.nn.Linear(10, 2)
|
|
94
|
+
self.quantum = QuantumLayer(2)
|
|
95
|
+
self.classical_2 = torch.nn.Linear(1, 2)
|
|
96
|
+
|
|
97
|
+
def forward(self, x):
|
|
98
|
+
x = torch.relu(self.classical_1(x))
|
|
99
|
+
x = self.quantum(x)
|
|
100
|
+
x = self.classical_2(x.unsqueeze(1))
|
|
101
|
+
return x
|
|
102
|
+
|
|
103
|
+
# Training loop
|
|
104
|
+
model = HybridModel()
|
|
105
|
+
optimizer = torch.optim.Adam(model.parameters(), lr=0.01)
|
|
106
|
+
criterion = torch.nn.CrossEntropyLoss()
|
|
107
|
+
|
|
108
|
+
for epoch in range(100):
|
|
109
|
+
optimizer.zero_grad()
|
|
110
|
+
outputs = model(inputs)
|
|
111
|
+
loss = criterion(outputs, labels)
|
|
112
|
+
loss.backward()
|
|
113
|
+
optimizer.step()
|
|
114
|
+
```
|
|
115
|
+
|
|
116
|
+
### JAX Integration
|
|
117
|
+
|
|
118
|
+
```python
|
|
119
|
+
import jax
|
|
120
|
+
import jax.numpy as jnp
|
|
121
|
+
import pennylane as qml
|
|
122
|
+
|
|
123
|
+
dev = qml.device('default.qubit', wires=2)
|
|
124
|
+
|
|
125
|
+
@qml.qnode(dev, interface='jax')
|
|
126
|
+
def quantum_circuit(inputs, weights):
|
|
127
|
+
qml.RY(inputs[0], wires=0)
|
|
128
|
+
qml.RY(inputs[1], wires=1)
|
|
129
|
+
qml.RX(weights[0], wires=0)
|
|
130
|
+
qml.RX(weights[1], wires=1)
|
|
131
|
+
qml.CNOT(wires=[0, 1])
|
|
132
|
+
return qml.expval(qml.PauliZ(0))
|
|
133
|
+
|
|
134
|
+
# JAX-compatible training
|
|
135
|
+
@jax.jit
|
|
136
|
+
def loss_fn(weights, x, y):
|
|
137
|
+
predictions = quantum_circuit(x, weights)
|
|
138
|
+
return jnp.mean((predictions - y) ** 2)
|
|
139
|
+
|
|
140
|
+
# Compute gradients with JAX
|
|
141
|
+
grad_fn = jax.grad(loss_fn)
|
|
142
|
+
|
|
143
|
+
# Training
|
|
144
|
+
weights = jnp.array([0.1, 0.2])
|
|
145
|
+
for i in range(100):
|
|
146
|
+
grads = grad_fn(weights, x_train, y_train)
|
|
147
|
+
weights = weights - 0.01 * grads
|
|
148
|
+
```
|
|
149
|
+
|
|
150
|
+
### TensorFlow Integration
|
|
151
|
+
|
|
152
|
+
```python
|
|
153
|
+
import tensorflow as tf
|
|
154
|
+
import pennylane as qml
|
|
155
|
+
|
|
156
|
+
dev = qml.device('default.qubit', wires=2)
|
|
157
|
+
|
|
158
|
+
@qml.qnode(dev, interface='tf')
|
|
159
|
+
def quantum_circuit(inputs, weights):
|
|
160
|
+
qml.RY(inputs[0], wires=0)
|
|
161
|
+
qml.RY(inputs[1], wires=1)
|
|
162
|
+
qml.RX(weights[0], wires=0)
|
|
163
|
+
qml.RX(weights[1], wires=1)
|
|
164
|
+
qml.CNOT(wires=[0, 1])
|
|
165
|
+
return qml.expval(qml.PauliZ(0))
|
|
166
|
+
|
|
167
|
+
# Keras layer
|
|
168
|
+
class QuantumLayer(tf.keras.layers.Layer):
|
|
169
|
+
def __init__(self, n_qubits):
|
|
170
|
+
super().__init__()
|
|
171
|
+
self.n_qubits = n_qubits
|
|
172
|
+
weight_init = tf.random_uniform_initializer()
|
|
173
|
+
self.weights = tf.Variable(
|
|
174
|
+
initial_value=weight_init(shape=(n_qubits,), dtype=tf.float32),
|
|
175
|
+
trainable=True
|
|
176
|
+
)
|
|
177
|
+
|
|
178
|
+
def call(self, inputs):
|
|
179
|
+
return tf.stack([quantum_circuit(x, self.weights) for x in inputs])
|
|
180
|
+
|
|
181
|
+
# Keras model
|
|
182
|
+
model = tf.keras.Sequential([
|
|
183
|
+
tf.keras.layers.Dense(2, activation='relu'),
|
|
184
|
+
QuantumLayer(2),
|
|
185
|
+
tf.keras.layers.Dense(2, activation='softmax')
|
|
186
|
+
])
|
|
187
|
+
|
|
188
|
+
model.compile(
|
|
189
|
+
optimizer=tf.keras.optimizers.Adam(0.01),
|
|
190
|
+
loss='sparse_categorical_crossentropy',
|
|
191
|
+
metrics=['accuracy']
|
|
192
|
+
)
|
|
193
|
+
|
|
194
|
+
model.fit(x_train, y_train, epochs=100, batch_size=32)
|
|
195
|
+
```
|
|
196
|
+
|
|
197
|
+
## Quantum Neural Networks
|
|
198
|
+
|
|
199
|
+
### Variational Quantum Circuit (VQC)
|
|
200
|
+
|
|
201
|
+
```python
|
|
202
|
+
from pennylane import numpy as np
|
|
203
|
+
|
|
204
|
+
dev = qml.device('default.qubit', wires=4)
|
|
205
|
+
|
|
206
|
+
def variational_block(weights, wires):
|
|
207
|
+
"""Single layer of variational circuit."""
|
|
208
|
+
for i, wire in enumerate(wires):
|
|
209
|
+
qml.RY(weights[i, 0], wires=wire)
|
|
210
|
+
qml.RZ(weights[i, 1], wires=wire)
|
|
211
|
+
|
|
212
|
+
for i in range(len(wires)-1):
|
|
213
|
+
qml.CNOT(wires=[wires[i], wires[i+1]])
|
|
214
|
+
|
|
215
|
+
@qml.qnode(dev)
|
|
216
|
+
def quantum_neural_network(inputs, weights):
|
|
217
|
+
# Encode inputs
|
|
218
|
+
for i, inp in enumerate(inputs):
|
|
219
|
+
qml.RY(inp, wires=i)
|
|
220
|
+
|
|
221
|
+
# Apply variational layers
|
|
222
|
+
n_layers = len(weights)
|
|
223
|
+
for layer_weights in weights:
|
|
224
|
+
variational_block(layer_weights, wires=range(4))
|
|
225
|
+
|
|
226
|
+
return qml.expval(qml.PauliZ(0))
|
|
227
|
+
|
|
228
|
+
# Initialize weights
|
|
229
|
+
n_layers = 3
|
|
230
|
+
n_wires = 4
|
|
231
|
+
weights_shape = (n_layers, n_wires, 2)
|
|
232
|
+
weights = np.random.random(weights_shape, requires_grad=True)
|
|
233
|
+
```
|
|
234
|
+
|
|
235
|
+
### Quantum Convolutional Neural Network
|
|
236
|
+
|
|
237
|
+
```python
|
|
238
|
+
def conv_layer(weights, wires):
|
|
239
|
+
"""Quantum convolutional layer."""
|
|
240
|
+
n_wires = len(wires)
|
|
241
|
+
|
|
242
|
+
# Apply local unitaries
|
|
243
|
+
for i in range(n_wires):
|
|
244
|
+
qml.RY(weights[i], wires=wires[i])
|
|
245
|
+
|
|
246
|
+
# Nearest-neighbor entanglement
|
|
247
|
+
for i in range(0, n_wires-1, 2):
|
|
248
|
+
qml.CNOT(wires=[wires[i], wires[i+1]])
|
|
249
|
+
|
|
250
|
+
def pooling_layer(wires):
|
|
251
|
+
"""Quantum pooling (measure and discard)."""
|
|
252
|
+
measurements = []
|
|
253
|
+
for i in range(0, len(wires), 2):
|
|
254
|
+
measurements.append(qml.measure(wires[i]))
|
|
255
|
+
return measurements
|
|
256
|
+
|
|
257
|
+
@qml.qnode(dev)
|
|
258
|
+
def qcnn(inputs, weights):
|
|
259
|
+
# Encode image data
|
|
260
|
+
for i, pixel in enumerate(inputs):
|
|
261
|
+
qml.RY(pixel, wires=i)
|
|
262
|
+
|
|
263
|
+
# Convolutional layers
|
|
264
|
+
conv_layer(weights[0], wires=range(8))
|
|
265
|
+
pooling_layer(wires=range(0, 8, 2))
|
|
266
|
+
|
|
267
|
+
conv_layer(weights[1], wires=range(1, 8, 2))
|
|
268
|
+
pooling_layer(wires=range(1, 8, 4))
|
|
269
|
+
|
|
270
|
+
return qml.expval(qml.PauliZ(1))
|
|
271
|
+
```
|
|
272
|
+
|
|
273
|
+
### Quantum Recurrent Neural Network
|
|
274
|
+
|
|
275
|
+
```python
|
|
276
|
+
def qrnn_cell(x, hidden, weights):
|
|
277
|
+
"""Single QRNN cell."""
|
|
278
|
+
@qml.qnode(dev)
|
|
279
|
+
def cell(x, h, w):
|
|
280
|
+
# Encode input and hidden state
|
|
281
|
+
qml.RY(x, wires=0)
|
|
282
|
+
qml.RY(h, wires=1)
|
|
283
|
+
|
|
284
|
+
# Apply recurrent transformation
|
|
285
|
+
qml.RX(w[0], wires=0)
|
|
286
|
+
qml.RX(w[1], wires=1)
|
|
287
|
+
qml.CNOT(wires=[0, 1])
|
|
288
|
+
qml.RY(w[2], wires=1)
|
|
289
|
+
|
|
290
|
+
return qml.expval(qml.PauliZ(1))
|
|
291
|
+
|
|
292
|
+
return cell(x, hidden, weights)
|
|
293
|
+
|
|
294
|
+
def qrnn_sequence(sequence, weights):
|
|
295
|
+
"""Process sequence with QRNN."""
|
|
296
|
+
hidden = 0.0
|
|
297
|
+
outputs = []
|
|
298
|
+
|
|
299
|
+
for x in sequence:
|
|
300
|
+
hidden = qrnn_cell(x, hidden, weights)
|
|
301
|
+
outputs.append(hidden)
|
|
302
|
+
|
|
303
|
+
return outputs
|
|
304
|
+
```
|
|
305
|
+
|
|
306
|
+
## Variational Classifiers
|
|
307
|
+
|
|
308
|
+
### Binary Classification
|
|
309
|
+
|
|
310
|
+
```python
|
|
311
|
+
dev = qml.device('default.qubit', wires=2)
|
|
312
|
+
|
|
313
|
+
@qml.qnode(dev)
|
|
314
|
+
def variational_classifier(x, weights):
|
|
315
|
+
# Feature map
|
|
316
|
+
qml.RY(x[0], wires=0)
|
|
317
|
+
qml.RY(x[1], wires=1)
|
|
318
|
+
|
|
319
|
+
# Variational layers
|
|
320
|
+
for w in weights:
|
|
321
|
+
qml.RX(w[0], wires=0)
|
|
322
|
+
qml.RX(w[1], wires=1)
|
|
323
|
+
qml.CNOT(wires=[0, 1])
|
|
324
|
+
qml.RY(w[2], wires=0)
|
|
325
|
+
qml.RY(w[3], wires=1)
|
|
326
|
+
|
|
327
|
+
return qml.expval(qml.PauliZ(0))
|
|
328
|
+
|
|
329
|
+
def cost_function(weights, X, y):
|
|
330
|
+
"""Binary cross-entropy loss."""
|
|
331
|
+
predictions = np.array([variational_classifier(x, weights) for x in X])
|
|
332
|
+
predictions = (predictions + 1) / 2 # Map [-1, 1] to [0, 1]
|
|
333
|
+
return -np.mean(y * np.log(predictions) + (1 - y) * np.log(1 - predictions))
|
|
334
|
+
|
|
335
|
+
# Training
|
|
336
|
+
n_layers = 2
|
|
337
|
+
n_params_per_layer = 4
|
|
338
|
+
weights = np.random.random((n_layers, n_params_per_layer), requires_grad=True)
|
|
339
|
+
|
|
340
|
+
opt = qml.GradientDescentOptimizer(stepsize=0.1)
|
|
341
|
+
for i in range(100):
|
|
342
|
+
weights = opt.step(lambda w: cost_function(w, X_train, y_train), weights)
|
|
343
|
+
```
|
|
344
|
+
|
|
345
|
+
### Multi-Class Classification
|
|
346
|
+
|
|
347
|
+
```python
|
|
348
|
+
@qml.qnode(dev)
|
|
349
|
+
def multiclass_circuit(x, weights):
|
|
350
|
+
# Encode input
|
|
351
|
+
for i, val in enumerate(x):
|
|
352
|
+
qml.RY(val, wires=i)
|
|
353
|
+
|
|
354
|
+
# Variational circuit
|
|
355
|
+
for layer_weights in weights:
|
|
356
|
+
for i, w in enumerate(layer_weights):
|
|
357
|
+
qml.RY(w, wires=i)
|
|
358
|
+
for i in range(len(x)-1):
|
|
359
|
+
qml.CNOT(wires=[i, i+1])
|
|
360
|
+
|
|
361
|
+
# Multiple outputs for classes
|
|
362
|
+
return [qml.expval(qml.PauliZ(i)) for i in range(3)]
|
|
363
|
+
|
|
364
|
+
def softmax(x):
|
|
365
|
+
exp_x = np.exp(x - np.max(x))
|
|
366
|
+
return exp_x / exp_x.sum()
|
|
367
|
+
|
|
368
|
+
def predict_class(x, weights):
|
|
369
|
+
logits = multiclass_circuit(x, weights)
|
|
370
|
+
return softmax(logits)
|
|
371
|
+
```
|
|
372
|
+
|
|
373
|
+
## Training and Optimization
|
|
374
|
+
|
|
375
|
+
### Gradient-Based Training
|
|
376
|
+
|
|
377
|
+
```python
|
|
378
|
+
# Automatic differentiation
|
|
379
|
+
@qml.qnode(dev, diff_method='backprop')
|
|
380
|
+
def circuit_backprop(x, weights):
|
|
381
|
+
# ... circuit definition
|
|
382
|
+
return qml.expval(qml.PauliZ(0))
|
|
383
|
+
|
|
384
|
+
# Parameter shift rule
|
|
385
|
+
@qml.qnode(dev, diff_method='parameter-shift')
|
|
386
|
+
def circuit_param_shift(x, weights):
|
|
387
|
+
# ... circuit definition
|
|
388
|
+
return qml.expval(qml.PauliZ(0))
|
|
389
|
+
|
|
390
|
+
# Finite differences
|
|
391
|
+
@qml.qnode(dev, diff_method='finite-diff')
|
|
392
|
+
def circuit_finite_diff(x, weights):
|
|
393
|
+
# ... circuit definition
|
|
394
|
+
return qml.expval(qml.PauliZ(0))
|
|
395
|
+
```
|
|
396
|
+
|
|
397
|
+
### Mini-Batch Training
|
|
398
|
+
|
|
399
|
+
```python
|
|
400
|
+
def batch_cost(weights, X_batch, y_batch):
|
|
401
|
+
predictions = np.array([variational_classifier(x, weights) for x in X_batch])
|
|
402
|
+
return np.mean((predictions - y_batch) ** 2)
|
|
403
|
+
|
|
404
|
+
# Mini-batch training
|
|
405
|
+
batch_size = 32
|
|
406
|
+
n_epochs = 100
|
|
407
|
+
|
|
408
|
+
for epoch in range(n_epochs):
|
|
409
|
+
for i in range(0, len(X_train), batch_size):
|
|
410
|
+
X_batch = X_train[i:i+batch_size]
|
|
411
|
+
y_batch = y_train[i:i+batch_size]
|
|
412
|
+
|
|
413
|
+
weights = opt.step(lambda w: batch_cost(w, X_batch, y_batch), weights)
|
|
414
|
+
```
|
|
415
|
+
|
|
416
|
+
### Learning Rate Scheduling
|
|
417
|
+
|
|
418
|
+
```python
|
|
419
|
+
def train_with_schedule(weights, X, y, n_epochs):
|
|
420
|
+
initial_lr = 0.1
|
|
421
|
+
decay = 0.95
|
|
422
|
+
|
|
423
|
+
for epoch in range(n_epochs):
|
|
424
|
+
lr = initial_lr * (decay ** epoch)
|
|
425
|
+
opt = qml.GradientDescentOptimizer(stepsize=lr)
|
|
426
|
+
|
|
427
|
+
weights = opt.step(lambda w: cost_function(w, X, y), weights)
|
|
428
|
+
|
|
429
|
+
if epoch % 10 == 0:
|
|
430
|
+
print(f"Epoch {epoch}, Loss: {cost_function(weights, X, y)}")
|
|
431
|
+
|
|
432
|
+
return weights
|
|
433
|
+
```
|
|
434
|
+
|
|
435
|
+
## Data Encoding Strategies
|
|
436
|
+
|
|
437
|
+
### Angle Encoding
|
|
438
|
+
|
|
439
|
+
```python
|
|
440
|
+
def angle_encoding(x, wires):
|
|
441
|
+
"""Encode features as rotation angles."""
|
|
442
|
+
for i, feature in enumerate(x):
|
|
443
|
+
qml.RY(feature, wires=wires[i])
|
|
444
|
+
```
|
|
445
|
+
|
|
446
|
+
### Amplitude Encoding
|
|
447
|
+
|
|
448
|
+
```python
|
|
449
|
+
def amplitude_encoding(x, wires):
|
|
450
|
+
"""Encode features as state amplitudes."""
|
|
451
|
+
# Normalize
|
|
452
|
+
x_norm = x / np.linalg.norm(x)
|
|
453
|
+
qml.MottonenStatePreparation(x_norm, wires=wires)
|
|
454
|
+
```
|
|
455
|
+
|
|
456
|
+
### Basis Encoding
|
|
457
|
+
|
|
458
|
+
```python
|
|
459
|
+
def basis_encoding(x, wires):
|
|
460
|
+
"""Encode binary features in computational basis."""
|
|
461
|
+
for i, bit in enumerate(x):
|
|
462
|
+
if bit:
|
|
463
|
+
qml.PauliX(wires=wires[i])
|
|
464
|
+
```
|
|
465
|
+
|
|
466
|
+
### IQP Encoding
|
|
467
|
+
|
|
468
|
+
```python
|
|
469
|
+
def iqp_encoding(x, wires):
|
|
470
|
+
"""Instantaneous Quantum Polynomial encoding."""
|
|
471
|
+
# Hadamard layer
|
|
472
|
+
for wire in wires:
|
|
473
|
+
qml.Hadamard(wires=wire)
|
|
474
|
+
|
|
475
|
+
# Encode features
|
|
476
|
+
for i, feature in enumerate(x):
|
|
477
|
+
qml.RZ(feature, wires=wires[i])
|
|
478
|
+
|
|
479
|
+
# Entanglement
|
|
480
|
+
for i in range(len(wires)-1):
|
|
481
|
+
qml.IsingZZ(x[i] * x[i+1], wires=[wires[i], wires[i+1]])
|
|
482
|
+
```
|
|
483
|
+
|
|
484
|
+
### Hamiltonian Encoding
|
|
485
|
+
|
|
486
|
+
```python
|
|
487
|
+
def hamiltonian_encoding(x, wires, time=1.0):
|
|
488
|
+
"""Encode via Hamiltonian evolution."""
|
|
489
|
+
# Build Hamiltonian from features
|
|
490
|
+
coeffs = x
|
|
491
|
+
obs = [qml.PauliZ(i) for i in wires]
|
|
492
|
+
|
|
493
|
+
H = qml.Hamiltonian(coeffs, obs)
|
|
494
|
+
|
|
495
|
+
# Apply time evolution
|
|
496
|
+
qml.ApproxTimeEvolution(H, time, n=10)
|
|
497
|
+
```
|
|
498
|
+
|
|
499
|
+
## Transfer Learning
|
|
500
|
+
|
|
501
|
+
### Pre-trained Quantum Model
|
|
502
|
+
|
|
503
|
+
```python
|
|
504
|
+
# Train on large dataset
|
|
505
|
+
pretrained_weights = train_quantum_model(large_dataset)
|
|
506
|
+
|
|
507
|
+
# Fine-tune on specific task
|
|
508
|
+
def fine_tune(pretrained_weights, small_dataset, n_epochs=50):
|
|
509
|
+
# Freeze early layers
|
|
510
|
+
frozen_weights = pretrained_weights[:-1] # All but last layer
|
|
511
|
+
trainable_weights = pretrained_weights[-1:] # Only last layer
|
|
512
|
+
|
|
513
|
+
@qml.qnode(dev)
|
|
514
|
+
def transfer_circuit(x, trainable):
|
|
515
|
+
# Apply frozen layers
|
|
516
|
+
for layer_w in frozen_weights:
|
|
517
|
+
variational_block(layer_w, wires=range(4))
|
|
518
|
+
|
|
519
|
+
# Apply trainable layer
|
|
520
|
+
variational_block(trainable, wires=range(4))
|
|
521
|
+
|
|
522
|
+
return qml.expval(qml.PauliZ(0))
|
|
523
|
+
|
|
524
|
+
# Train only last layer
|
|
525
|
+
opt = qml.AdamOptimizer(stepsize=0.01)
|
|
526
|
+
for epoch in range(n_epochs):
|
|
527
|
+
trainable_weights = opt.step(
|
|
528
|
+
lambda w: cost_function(w, small_dataset),
|
|
529
|
+
trainable_weights
|
|
530
|
+
)
|
|
531
|
+
|
|
532
|
+
return np.concatenate([frozen_weights, trainable_weights])
|
|
533
|
+
```
|
|
534
|
+
|
|
535
|
+
### Classical-to-Quantum Transfer
|
|
536
|
+
|
|
537
|
+
```python
|
|
538
|
+
# Use classical network for feature extraction
|
|
539
|
+
import torch.nn as nn
|
|
540
|
+
|
|
541
|
+
classical_extractor = nn.Sequential(
|
|
542
|
+
nn.Conv2d(3, 16, 3),
|
|
543
|
+
nn.ReLU(),
|
|
544
|
+
nn.MaxPool2d(2),
|
|
545
|
+
nn.Flatten(),
|
|
546
|
+
nn.Linear(16*13*13, 4) # Output 4 features for quantum circuit
|
|
547
|
+
)
|
|
548
|
+
|
|
549
|
+
# Quantum classifier
|
|
550
|
+
@qml.qnode(dev)
|
|
551
|
+
def quantum_classifier(features, weights):
|
|
552
|
+
angle_encoding(features, wires=range(4))
|
|
553
|
+
variational_block(weights, wires=range(4))
|
|
554
|
+
return qml.expval(qml.PauliZ(0))
|
|
555
|
+
|
|
556
|
+
# Combined model
|
|
557
|
+
def hybrid_transfer_model(image, classical_weights, quantum_weights):
|
|
558
|
+
features = classical_extractor(image)
|
|
559
|
+
return quantum_classifier(features, quantum_weights)
|
|
560
|
+
```
|
|
561
|
+
|
|
562
|
+
## Best Practices
|
|
563
|
+
|
|
564
|
+
1. **Start simple** - Begin with small circuits and scale up
|
|
565
|
+
2. **Choose encoding wisely** - Match encoding to data structure
|
|
566
|
+
3. **Use appropriate interfaces** - Select interface matching your ML framework
|
|
567
|
+
4. **Monitor gradients** - Check for vanishing/exploding gradients (barren plateaus)
|
|
568
|
+
5. **Regularize** - Add L2 regularization to prevent overfitting
|
|
569
|
+
6. **Validate hardware compatibility** - Test on simulators before hardware
|
|
570
|
+
7. **Batch efficiently** - Use vectorization when possible
|
|
571
|
+
8. **Cache compilations** - Reuse compiled circuits for inference
|