@synsci/cli-darwin-x64-baseline 1.1.77 → 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.
Files changed (830) hide show
  1. package/bin/skills/adaptyv/SKILL.md +114 -0
  2. package/bin/skills/adaptyv/reference/api_reference.md +308 -0
  3. package/bin/skills/adaptyv/reference/examples.md +913 -0
  4. package/bin/skills/adaptyv/reference/experiments.md +360 -0
  5. package/bin/skills/adaptyv/reference/protein_optimization.md +637 -0
  6. package/bin/skills/aeon/SKILL.md +374 -0
  7. package/bin/skills/aeon/references/anomaly_detection.md +154 -0
  8. package/bin/skills/aeon/references/classification.md +144 -0
  9. package/bin/skills/aeon/references/clustering.md +123 -0
  10. package/bin/skills/aeon/references/datasets_benchmarking.md +387 -0
  11. package/bin/skills/aeon/references/distances.md +256 -0
  12. package/bin/skills/aeon/references/forecasting.md +140 -0
  13. package/bin/skills/aeon/references/networks.md +289 -0
  14. package/bin/skills/aeon/references/regression.md +118 -0
  15. package/bin/skills/aeon/references/segmentation.md +163 -0
  16. package/bin/skills/aeon/references/similarity_search.md +187 -0
  17. package/bin/skills/aeon/references/transformations.md +246 -0
  18. package/bin/skills/alphafold-database/SKILL.md +513 -0
  19. package/bin/skills/alphafold-database/references/api_reference.md +423 -0
  20. package/bin/skills/anndata/SKILL.md +400 -0
  21. package/bin/skills/anndata/references/best_practices.md +525 -0
  22. package/bin/skills/anndata/references/concatenation.md +396 -0
  23. package/bin/skills/anndata/references/data_structure.md +314 -0
  24. package/bin/skills/anndata/references/io_operations.md +404 -0
  25. package/bin/skills/anndata/references/manipulation.md +516 -0
  26. package/bin/skills/arboreto/SKILL.md +243 -0
  27. package/bin/skills/arboreto/references/algorithms.md +138 -0
  28. package/bin/skills/arboreto/references/basic_inference.md +151 -0
  29. package/bin/skills/arboreto/references/distributed_computing.md +242 -0
  30. package/bin/skills/arboreto/scripts/basic_grn_inference.py +97 -0
  31. package/bin/skills/astropy/SKILL.md +331 -0
  32. package/bin/skills/astropy/references/coordinates.md +273 -0
  33. package/bin/skills/astropy/references/cosmology.md +307 -0
  34. package/bin/skills/astropy/references/fits.md +396 -0
  35. package/bin/skills/astropy/references/tables.md +489 -0
  36. package/bin/skills/astropy/references/time.md +404 -0
  37. package/bin/skills/astropy/references/units.md +178 -0
  38. package/bin/skills/astropy/references/wcs_and_other_modules.md +373 -0
  39. package/bin/skills/benchling-integration/SKILL.md +480 -0
  40. package/bin/skills/benchling-integration/references/api_endpoints.md +883 -0
  41. package/bin/skills/benchling-integration/references/authentication.md +379 -0
  42. package/bin/skills/benchling-integration/references/sdk_reference.md +774 -0
  43. package/bin/skills/biopython/SKILL.md +443 -0
  44. package/bin/skills/biopython/references/advanced.md +577 -0
  45. package/bin/skills/biopython/references/alignment.md +362 -0
  46. package/bin/skills/biopython/references/blast.md +455 -0
  47. package/bin/skills/biopython/references/databases.md +484 -0
  48. package/bin/skills/biopython/references/phylogenetics.md +566 -0
  49. package/bin/skills/biopython/references/sequence_io.md +285 -0
  50. package/bin/skills/biopython/references/structure.md +564 -0
  51. package/bin/skills/biorxiv-database/SKILL.md +483 -0
  52. package/bin/skills/biorxiv-database/references/api_reference.md +280 -0
  53. package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
  54. package/bin/skills/bioservices/SKILL.md +361 -0
  55. package/bin/skills/bioservices/references/identifier_mapping.md +685 -0
  56. package/bin/skills/bioservices/references/services_reference.md +636 -0
  57. package/bin/skills/bioservices/references/workflow_patterns.md +811 -0
  58. package/bin/skills/bioservices/scripts/batch_id_converter.py +347 -0
  59. package/bin/skills/bioservices/scripts/compound_cross_reference.py +378 -0
  60. package/bin/skills/bioservices/scripts/pathway_analysis.py +309 -0
  61. package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
  62. package/bin/skills/brenda-database/SKILL.md +719 -0
  63. package/bin/skills/brenda-database/references/api_reference.md +537 -0
  64. package/bin/skills/brenda-database/scripts/brenda_queries.py +844 -0
  65. package/bin/skills/brenda-database/scripts/brenda_visualization.py +772 -0
  66. package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
  67. package/bin/skills/cellxgene-census/SKILL.md +511 -0
  68. package/bin/skills/cellxgene-census/references/census_schema.md +182 -0
  69. package/bin/skills/cellxgene-census/references/common_patterns.md +351 -0
  70. package/bin/skills/chembl-database/SKILL.md +389 -0
  71. package/bin/skills/chembl-database/references/api_reference.md +272 -0
  72. package/bin/skills/chembl-database/scripts/example_queries.py +278 -0
  73. package/bin/skills/cirq/SKILL.md +346 -0
  74. package/bin/skills/cirq/references/building.md +307 -0
  75. package/bin/skills/cirq/references/experiments.md +572 -0
  76. package/bin/skills/cirq/references/hardware.md +515 -0
  77. package/bin/skills/cirq/references/noise.md +515 -0
  78. package/bin/skills/cirq/references/simulation.md +350 -0
  79. package/bin/skills/cirq/references/transformation.md +416 -0
  80. package/bin/skills/clinicaltrials-database/SKILL.md +507 -0
  81. package/bin/skills/clinicaltrials-database/references/api_reference.md +358 -0
  82. package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
  83. package/bin/skills/clinpgx-database/SKILL.md +638 -0
  84. package/bin/skills/clinpgx-database/references/api_reference.md +757 -0
  85. package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
  86. package/bin/skills/clinvar-database/SKILL.md +362 -0
  87. package/bin/skills/clinvar-database/references/api_reference.md +227 -0
  88. package/bin/skills/clinvar-database/references/clinical_significance.md +218 -0
  89. package/bin/skills/clinvar-database/references/data_formats.md +358 -0
  90. package/bin/skills/cobrapy/SKILL.md +463 -0
  91. package/bin/skills/cobrapy/references/api_quick_reference.md +655 -0
  92. package/bin/skills/cobrapy/references/workflows.md +593 -0
  93. package/bin/skills/cosmic-database/SKILL.md +336 -0
  94. package/bin/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
  95. package/bin/skills/cosmic-database/scripts/download_cosmic.py +231 -0
  96. package/bin/skills/dask/SKILL.md +456 -0
  97. package/bin/skills/dask/references/arrays.md +497 -0
  98. package/bin/skills/dask/references/bags.md +468 -0
  99. package/bin/skills/dask/references/best-practices.md +277 -0
  100. package/bin/skills/dask/references/dataframes.md +368 -0
  101. package/bin/skills/dask/references/futures.md +541 -0
  102. package/bin/skills/dask/references/schedulers.md +504 -0
  103. package/bin/skills/datacommons-client/SKILL.md +255 -0
  104. package/bin/skills/datacommons-client/references/getting_started.md +417 -0
  105. package/bin/skills/datacommons-client/references/node.md +250 -0
  106. package/bin/skills/datacommons-client/references/observation.md +185 -0
  107. package/bin/skills/datacommons-client/references/resolve.md +246 -0
  108. package/bin/skills/datamol/SKILL.md +706 -0
  109. package/bin/skills/datamol/references/conformers_module.md +131 -0
  110. package/bin/skills/datamol/references/core_api.md +130 -0
  111. package/bin/skills/datamol/references/descriptors_viz.md +195 -0
  112. package/bin/skills/datamol/references/fragments_scaffolds.md +174 -0
  113. package/bin/skills/datamol/references/io_module.md +109 -0
  114. package/bin/skills/datamol/references/reactions_data.md +218 -0
  115. package/bin/skills/deepchem/SKILL.md +597 -0
  116. package/bin/skills/deepchem/references/api_reference.md +303 -0
  117. package/bin/skills/deepchem/references/workflows.md +491 -0
  118. package/bin/skills/deepchem/scripts/graph_neural_network.py +338 -0
  119. package/bin/skills/deepchem/scripts/predict_solubility.py +224 -0
  120. package/bin/skills/deepchem/scripts/transfer_learning.py +375 -0
  121. package/bin/skills/deeptools/SKILL.md +531 -0
  122. package/bin/skills/deeptools/assets/quick_reference.md +58 -0
  123. package/bin/skills/deeptools/references/effective_genome_sizes.md +116 -0
  124. package/bin/skills/deeptools/references/normalization_methods.md +410 -0
  125. package/bin/skills/deeptools/references/tools_reference.md +533 -0
  126. package/bin/skills/deeptools/references/workflows.md +474 -0
  127. package/bin/skills/deeptools/scripts/validate_files.py +195 -0
  128. package/bin/skills/deeptools/scripts/workflow_generator.py +454 -0
  129. package/bin/skills/denario/SKILL.md +215 -0
  130. package/bin/skills/denario/references/examples.md +494 -0
  131. package/bin/skills/denario/references/installation.md +213 -0
  132. package/bin/skills/denario/references/llm_configuration.md +265 -0
  133. package/bin/skills/denario/references/research_pipeline.md +471 -0
  134. package/bin/skills/diffdock/SKILL.md +483 -0
  135. package/bin/skills/diffdock/assets/batch_template.csv +4 -0
  136. package/bin/skills/diffdock/assets/custom_inference_config.yaml +90 -0
  137. package/bin/skills/diffdock/references/confidence_and_limitations.md +182 -0
  138. package/bin/skills/diffdock/references/parameters_reference.md +163 -0
  139. package/bin/skills/diffdock/references/workflows_examples.md +392 -0
  140. package/bin/skills/diffdock/scripts/analyze_results.py +334 -0
  141. package/bin/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
  142. package/bin/skills/diffdock/scripts/setup_check.py +278 -0
  143. package/bin/skills/dnanexus-integration/SKILL.md +383 -0
  144. package/bin/skills/dnanexus-integration/references/app-development.md +247 -0
  145. package/bin/skills/dnanexus-integration/references/configuration.md +646 -0
  146. package/bin/skills/dnanexus-integration/references/data-operations.md +400 -0
  147. package/bin/skills/dnanexus-integration/references/job-execution.md +412 -0
  148. package/bin/skills/dnanexus-integration/references/python-sdk.md +523 -0
  149. package/bin/skills/document-skills/docx/LICENSE.txt +30 -0
  150. package/bin/skills/document-skills/docx/SKILL.md +233 -0
  151. package/bin/skills/document-skills/docx/docx-js.md +350 -0
  152. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  153. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  154. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  155. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  156. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  157. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  158. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
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  160. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  161. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  162. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
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@@ -0,0 +1,671 @@
1
+ # Optimization in PennyLane
2
+
3
+ ## Table of Contents
4
+ 1. [Built-in Optimizers](#built-in-optimizers)
5
+ 2. [Gradient Computation](#gradient-computation)
6
+ 3. [Variational Algorithms](#variational-algorithms)
7
+ 4. [QAOA](#qaoa-quantum-approximate-optimization-algorithm)
8
+ 5. [Training Strategies](#training-strategies)
9
+ 6. [Optimization Challenges](#optimization-challenges)
10
+
11
+ ## Built-in Optimizers
12
+
13
+ ### Gradient Descent Optimizer
14
+
15
+ ```python
16
+ import pennylane as qml
17
+ from pennylane import numpy as np
18
+
19
+ dev = qml.device('default.qubit', wires=2)
20
+
21
+ @qml.qnode(dev)
22
+ def cost_function(params):
23
+ qml.RX(params[0], wires=0)
24
+ qml.RY(params[1], wires=1)
25
+ qml.CNOT(wires=[0, 1])
26
+ return qml.expval(qml.PauliZ(0) @ qml.PauliZ(1))
27
+
28
+ # Initialize optimizer
29
+ opt = qml.GradientDescentOptimizer(stepsize=0.1)
30
+
31
+ # Initialize parameters
32
+ params = np.array([0.1, 0.2], requires_grad=True)
33
+
34
+ # Training loop
35
+ for i in range(100):
36
+ params = opt.step(cost_function, params)
37
+
38
+ if i % 10 == 0:
39
+ print(f"Step {i}: Cost = {cost_function(params):.6f}")
40
+ ```
41
+
42
+ ### Adam Optimizer
43
+
44
+ ```python
45
+ # Adaptive learning rate optimizer
46
+ opt = qml.AdamOptimizer(stepsize=0.01, beta1=0.9, beta2=0.999)
47
+
48
+ params = np.random.random(10, requires_grad=True)
49
+
50
+ for i in range(100):
51
+ params, cost = opt.step_and_cost(cost_function, params)
52
+
53
+ if i % 10 == 0:
54
+ print(f"Step {i}: Cost = {cost:.6f}")
55
+ ```
56
+
57
+ ### Momentum Optimizer
58
+
59
+ ```python
60
+ # Gradient descent with momentum
61
+ opt = qml.MomentumOptimizer(stepsize=0.01, momentum=0.9)
62
+
63
+ params = np.random.random(5, requires_grad=True)
64
+
65
+ for i in range(100):
66
+ params = opt.step(cost_function, params)
67
+ ```
68
+
69
+ ### AdaGrad Optimizer
70
+
71
+ ```python
72
+ # Adaptive gradient algorithm
73
+ opt = qml.AdagradOptimizer(stepsize=0.1)
74
+
75
+ params = np.random.random(8, requires_grad=True)
76
+
77
+ for i in range(100):
78
+ params = opt.step(cost_function, params)
79
+ ```
80
+
81
+ ### RMSProp Optimizer
82
+
83
+ ```python
84
+ # Root mean square propagation
85
+ opt = qml.RMSPropOptimizer(stepsize=0.01, decay=0.9, eps=1e-8)
86
+
87
+ params = np.random.random(6, requires_grad=True)
88
+
89
+ for i in range(100):
90
+ params = opt.step(cost_function, params)
91
+ ```
92
+
93
+ ### Nesterov Momentum Optimizer
94
+
95
+ ```python
96
+ # Nesterov accelerated gradient
97
+ opt = qml.NesterovMomentumOptimizer(stepsize=0.01, momentum=0.9)
98
+
99
+ params = np.random.random(4, requires_grad=True)
100
+
101
+ for i in range(100):
102
+ params = opt.step(cost_function, params)
103
+ ```
104
+
105
+ ## Gradient Computation
106
+
107
+ ### Automatic Differentiation
108
+
109
+ ```python
110
+ # Backpropagation (for simulators)
111
+ @qml.qnode(dev, diff_method='backprop')
112
+ def circuit_backprop(params):
113
+ qml.RX(params[0], wires=0)
114
+ qml.RY(params[1], wires=1)
115
+ return qml.expval(qml.PauliZ(0))
116
+
117
+ # Compute gradient
118
+ grad_fn = qml.grad(circuit_backprop)
119
+ params = np.array([0.1, 0.2], requires_grad=True)
120
+ gradients = grad_fn(params)
121
+ ```
122
+
123
+ ### Parameter-Shift Rule
124
+
125
+ ```python
126
+ # Hardware-compatible gradient method
127
+ @qml.qnode(dev, diff_method='parameter-shift')
128
+ def circuit_param_shift(params):
129
+ qml.RX(params[0], wires=0)
130
+ qml.RY(params[1], wires=1)
131
+ qml.CNOT(wires=[0, 1])
132
+ return qml.expval(qml.PauliZ(0))
133
+
134
+ # Works on quantum hardware
135
+ grad_fn = qml.grad(circuit_param_shift)
136
+ gradients = grad_fn(params)
137
+ ```
138
+
139
+ ### Finite Differences
140
+
141
+ ```python
142
+ # Numerical gradient approximation
143
+ @qml.qnode(dev, diff_method='finite-diff')
144
+ def circuit_finite_diff(params):
145
+ qml.RX(params[0], wires=0)
146
+ return qml.expval(qml.PauliZ(0))
147
+
148
+ grad_fn = qml.grad(circuit_finite_diff)
149
+ gradients = grad_fn(params)
150
+ ```
151
+
152
+ ### Adjoint Method
153
+
154
+ ```python
155
+ # Efficient gradient for state vector simulators
156
+ @qml.qnode(dev, diff_method='adjoint')
157
+ def circuit_adjoint(params):
158
+ qml.RX(params[0], wires=0)
159
+ qml.RY(params[1], wires=1)
160
+ return qml.expval(qml.PauliZ(0))
161
+
162
+ grad_fn = qml.grad(circuit_adjoint)
163
+ gradients = grad_fn(params)
164
+ ```
165
+
166
+ ### Custom Gradients
167
+
168
+ ```python
169
+ @qml.qnode(dev, diff_method='parameter-shift')
170
+ def circuit(params):
171
+ qml.RX(params[0], wires=0)
172
+ qml.RY(params[1], wires=1)
173
+ return qml.expval(qml.PauliZ(0))
174
+
175
+ # Compute Hessian
176
+ hessian_fn = qml.jacobian(qml.grad(circuit))
177
+ hessian = hessian_fn(params)
178
+ ```
179
+
180
+ ### Stochastic Parameter-Shift
181
+
182
+ ```python
183
+ # For circuits with many parameters
184
+ @qml.qnode(dev, diff_method='spsa') # Simultaneous Perturbation Stochastic Approximation
185
+ def large_circuit(params):
186
+ for i, param in enumerate(params):
187
+ qml.RY(param, wires=i % 4)
188
+ return qml.expval(qml.PauliZ(0))
189
+
190
+ # Efficient for high-dimensional parameter spaces
191
+ opt = qml.SPSAOptimizer(maxiter=100)
192
+ params = np.random.random(100, requires_grad=True)
193
+ params = opt.minimize(large_circuit, params)
194
+ ```
195
+
196
+ ## Variational Algorithms
197
+
198
+ ### Variational Quantum Eigensolver (VQE)
199
+
200
+ ```python
201
+ # Ground state energy calculation
202
+ def vqe(hamiltonian, ansatz, n_qubits):
203
+ """VQE implementation."""
204
+
205
+ dev = qml.device('default.qubit', wires=n_qubits)
206
+
207
+ @qml.qnode(dev)
208
+ def cost_fn(params):
209
+ ansatz(params, wires=range(n_qubits))
210
+ return qml.expval(hamiltonian)
211
+
212
+ # Initialize parameters
213
+ n_params = 10 # Depends on ansatz
214
+ params = np.random.random(n_params, requires_grad=True)
215
+
216
+ # Optimize
217
+ opt = qml.AdamOptimizer(stepsize=0.1)
218
+
219
+ energies = []
220
+ for i in range(100):
221
+ params, energy = opt.step_and_cost(cost_fn, params)
222
+ energies.append(energy)
223
+
224
+ if i % 10 == 0:
225
+ print(f"Step {i}: Energy = {energy:.6f}")
226
+
227
+ return params, energy, energies
228
+
229
+ # Example usage
230
+ from pennylane import qchem
231
+
232
+ symbols = ['H', 'H']
233
+ coords = np.array([0.0, 0.0, 0.0, 0.0, 0.0, 0.74])
234
+ H, n_qubits = qchem.molecular_hamiltonian(symbols, coords)
235
+
236
+ def simple_ansatz(params, wires):
237
+ qml.BasisState(qchem.hf_state(2, n_qubits), wires=wires)
238
+ for i, param in enumerate(params):
239
+ qml.RY(param, wires=i % len(wires))
240
+ for i in range(len(wires)-1):
241
+ qml.CNOT(wires=[i, i+1])
242
+
243
+ params, energy, history = vqe(H, simple_ansatz, n_qubits)
244
+ ```
245
+
246
+ ### Quantum Natural Gradient
247
+
248
+ ```python
249
+ # More efficient optimization for variational circuits
250
+ @qml.qnode(dev)
251
+ def circuit(params):
252
+ for i, param in enumerate(params):
253
+ qml.RY(param, wires=i)
254
+ return qml.expval(qml.PauliZ(0))
255
+
256
+ # Use quantum natural gradient
257
+ opt = qml.QNGOptimizer(stepsize=0.01)
258
+ params = np.random.random(4, requires_grad=True)
259
+
260
+ for i in range(100):
261
+ params, cost = opt.step_and_cost(circuit, params)
262
+ ```
263
+
264
+ ### Rotosolve
265
+
266
+ ```python
267
+ # Analytical parameter update
268
+ opt = qml.RotosolveOptimizer()
269
+
270
+ @qml.qnode(dev)
271
+ def cost_fn(params):
272
+ qml.RX(params[0], wires=0)
273
+ qml.RY(params[1], wires=1)
274
+ return qml.expval(qml.PauliZ(0))
275
+
276
+ params = np.array([0.1, 0.2], requires_grad=True)
277
+
278
+ for i in range(20): # Converges quickly
279
+ params = opt.step(cost_fn, params)
280
+ ```
281
+
282
+ ### Quantum Analytic Descent
283
+
284
+ ```python
285
+ # Hybrid quantum-classical optimization
286
+ opt = qml.QNSPSAOptimizer(stepsize=0.01)
287
+
288
+ params = np.random.random(10, requires_grad=True)
289
+
290
+ for i in range(100):
291
+ params = opt.step(cost_function, params)
292
+ ```
293
+
294
+ ## QAOA (Quantum Approximate Optimization Algorithm)
295
+
296
+ ### Basic QAOA
297
+
298
+ ```python
299
+ from pennylane import qaoa
300
+
301
+ # Define problem: MaxCut on a graph
302
+ edges = [(0, 1), (1, 2), (2, 0)]
303
+ graph = [(edge[0], edge[1], 1.0) for edge in edges]
304
+
305
+ # Cost Hamiltonian
306
+ cost_h = qaoa.maxcut(graph)
307
+
308
+ # Mixer Hamiltonian
309
+ mixer_h = qaoa.x_mixer(range(3))
310
+
311
+ # QAOA circuit
312
+ def qaoa_layer(gamma, alpha):
313
+ """Single QAOA layer."""
314
+ qaoa.cost_layer(gamma, cost_h)
315
+ qaoa.mixer_layer(alpha, mixer_h)
316
+
317
+ @qml.qnode(dev)
318
+ def qaoa_circuit(params, depth):
319
+ """Full QAOA circuit."""
320
+ # Initialize in superposition
321
+ for wire in range(3):
322
+ qml.Hadamard(wires=wire)
323
+
324
+ # Apply QAOA layers
325
+ for i in range(depth):
326
+ gamma = params[i]
327
+ alpha = params[depth + i]
328
+ qaoa_layer(gamma, alpha)
329
+
330
+ # Measure in computational basis
331
+ return qml.expval(cost_h)
332
+
333
+ # Optimize
334
+ depth = 3
335
+ params = np.random.uniform(0, 2*np.pi, 2*depth, requires_grad=True)
336
+
337
+ opt = qml.AdamOptimizer(stepsize=0.1)
338
+
339
+ for i in range(100):
340
+ params = opt.step(lambda p: -qaoa_circuit(p, depth), params) # Minimize negative = maximize
341
+
342
+ if i % 10 == 0:
343
+ print(f"Step {i}: Cost = {-qaoa_circuit(params, depth):.4f}")
344
+ ```
345
+
346
+ ### QAOA for MaxCut
347
+
348
+ ```python
349
+ import networkx as nx
350
+
351
+ # Create graph
352
+ G = nx.cycle_graph(4)
353
+
354
+ # Generate cost Hamiltonian
355
+ cost_h, mixer_h = qaoa.maxcut(G, constrained=False)
356
+
357
+ n_wires = len(G.nodes)
358
+ dev = qml.device('default.qubit', wires=n_wires)
359
+
360
+ def qaoa_maxcut(params, depth):
361
+ """QAOA for MaxCut problem."""
362
+
363
+ @qml.qnode(dev)
364
+ def circuit(gammas, betas):
365
+ # Initialize
366
+ for wire in range(n_wires):
367
+ qml.Hadamard(wires=wire)
368
+
369
+ # QAOA layers
370
+ for gamma, beta in zip(gammas, betas):
371
+ # Cost layer
372
+ for edge in G.edges:
373
+ wire1, wire2 = edge
374
+ qml.CNOT(wires=[wire1, wire2])
375
+ qml.RZ(gamma, wires=wire2)
376
+ qml.CNOT(wires=[wire1, wire2])
377
+
378
+ # Mixer layer
379
+ for wire in range(n_wires):
380
+ qml.RX(2 * beta, wires=wire)
381
+
382
+ return qml.expval(cost_h)
383
+
384
+ gammas = params[:depth]
385
+ betas = params[depth:]
386
+ return circuit(gammas, betas)
387
+
388
+ # Optimize
389
+ depth = 3
390
+ params = np.random.uniform(0, 2*np.pi, 2*depth, requires_grad=True)
391
+
392
+ opt = qml.AdamOptimizer(0.1)
393
+ for i in range(100):
394
+ params = opt.step(lambda p: -qaoa_maxcut(p, depth), params)
395
+ ```
396
+
397
+ ### QAOA for QUBO
398
+
399
+ ```python
400
+ def qaoa_qubo(Q, depth):
401
+ """QAOA for Quadratic Unconstrained Binary Optimization."""
402
+
403
+ n = len(Q)
404
+ dev = qml.device('default.qubit', wires=n)
405
+
406
+ # Build cost Hamiltonian from QUBO matrix
407
+ coeffs = []
408
+ obs = []
409
+
410
+ for i in range(n):
411
+ for j in range(i, n):
412
+ if Q[i][j] != 0:
413
+ if i == j:
414
+ coeffs.append(-Q[i][j] / 2)
415
+ obs.append(qml.PauliZ(i))
416
+ else:
417
+ coeffs.append(-Q[i][j] / 4)
418
+ obs.append(qml.PauliZ(i) @ qml.PauliZ(j))
419
+
420
+ cost_h = qml.Hamiltonian(coeffs, obs)
421
+
422
+ @qml.qnode(dev)
423
+ def circuit(params):
424
+ # Initialize
425
+ for wire in range(n):
426
+ qml.Hadamard(wires=wire)
427
+
428
+ # QAOA layers
429
+ for i in range(depth):
430
+ gamma = params[i]
431
+ beta = params[depth + i]
432
+
433
+ # Cost layer
434
+ for coeff, op in zip(coeffs, obs):
435
+ qml.exp(op, -1j * gamma * coeff)
436
+
437
+ # Mixer layer
438
+ for wire in range(n):
439
+ qml.RX(2 * beta, wires=wire)
440
+
441
+ return qml.expval(cost_h)
442
+
443
+ return circuit
444
+
445
+ # Example QUBO
446
+ Q = np.array([[1, -2], [-2, 1]])
447
+ circuit = qaoa_qubo(Q, depth=2)
448
+
449
+ params = np.random.random(4, requires_grad=True)
450
+ opt = qml.AdamOptimizer(0.1)
451
+
452
+ for i in range(100):
453
+ params = opt.step(circuit, params)
454
+ ```
455
+
456
+ ## Training Strategies
457
+
458
+ ### Learning Rate Scheduling
459
+
460
+ ```python
461
+ def train_with_schedule(circuit, initial_params, n_epochs):
462
+ """Train with learning rate decay."""
463
+
464
+ params = initial_params
465
+ base_lr = 0.1
466
+ decay_rate = 0.95
467
+ decay_steps = 10
468
+
469
+ for epoch in range(n_epochs):
470
+ # Update learning rate
471
+ lr = base_lr * (decay_rate ** (epoch // decay_steps))
472
+ opt = qml.GradientDescentOptimizer(stepsize=lr)
473
+
474
+ # Training step
475
+ params = opt.step(circuit, params)
476
+
477
+ if epoch % 10 == 0:
478
+ print(f"Epoch {epoch}: LR = {lr:.4f}, Cost = {circuit(params):.4f}")
479
+
480
+ return params
481
+ ```
482
+
483
+ ### Mini-Batch Training
484
+
485
+ ```python
486
+ def minibatch_train(circuit, X, y, batch_size=32, n_epochs=100):
487
+ """Mini-batch training for quantum circuits."""
488
+
489
+ params = np.random.random(10, requires_grad=True)
490
+ opt = qml.AdamOptimizer(stepsize=0.01)
491
+
492
+ n_samples = len(X)
493
+
494
+ for epoch in range(n_epochs):
495
+ # Shuffle data
496
+ indices = np.random.permutation(n_samples)
497
+ X_shuffled = X[indices]
498
+ y_shuffled = y[indices]
499
+
500
+ # Mini-batch updates
501
+ for i in range(0, n_samples, batch_size):
502
+ X_batch = X_shuffled[i:i+batch_size]
503
+ y_batch = y_shuffled[i:i+batch_size]
504
+
505
+ # Compute batch cost
506
+ def batch_cost(p):
507
+ predictions = np.array([circuit(x, p) for x in X_batch])
508
+ return np.mean((predictions - y_batch) ** 2)
509
+
510
+ params = opt.step(batch_cost, params)
511
+
512
+ if epoch % 10 == 0:
513
+ loss = batch_cost(params)
514
+ print(f"Epoch {epoch}: Loss = {loss:.4f}")
515
+
516
+ return params
517
+ ```
518
+
519
+ ### Early Stopping
520
+
521
+ ```python
522
+ def train_with_early_stopping(circuit, params, X_train, X_val, patience=10):
523
+ """Train with early stopping based on validation loss."""
524
+
525
+ opt = qml.AdamOptimizer(stepsize=0.01)
526
+
527
+ best_val_loss = float('inf')
528
+ patience_counter = 0
529
+ best_params = params.copy()
530
+
531
+ for epoch in range(1000):
532
+ # Training step
533
+ params = opt.step(lambda p: cost_fn(p, X_train), params)
534
+
535
+ # Validation
536
+ val_loss = cost_fn(params, X_val)
537
+
538
+ if val_loss < best_val_loss:
539
+ best_val_loss = val_loss
540
+ best_params = params.copy()
541
+ patience_counter = 0
542
+ else:
543
+ patience_counter += 1
544
+
545
+ if patience_counter >= patience:
546
+ print(f"Early stopping at epoch {epoch}")
547
+ break
548
+
549
+ return best_params
550
+ ```
551
+
552
+ ### Gradient Clipping
553
+
554
+ ```python
555
+ def train_with_gradient_clipping(circuit, params, max_norm=1.0):
556
+ """Train with gradient clipping to prevent exploding gradients."""
557
+
558
+ opt = qml.GradientDescentOptimizer(stepsize=0.1)
559
+
560
+ for i in range(100):
561
+ # Compute gradients
562
+ grad_fn = qml.grad(circuit)
563
+ grads = grad_fn(params)
564
+
565
+ # Clip gradients
566
+ grad_norm = np.linalg.norm(grads)
567
+ if grad_norm > max_norm:
568
+ grads = grads * (max_norm / grad_norm)
569
+
570
+ # Manual update with clipped gradients
571
+ params = params - opt.stepsize * grads
572
+
573
+ if i % 10 == 0:
574
+ print(f"Step {i}: Grad norm = {grad_norm:.4f}")
575
+
576
+ return params
577
+ ```
578
+
579
+ ## Optimization Challenges
580
+
581
+ ### Barren Plateaus
582
+
583
+ ```python
584
+ def detect_barren_plateau(circuit, params, n_samples=100):
585
+ """Detect barren plateau by measuring gradient variance."""
586
+
587
+ grad_fn = qml.grad(circuit)
588
+ grad_variances = []
589
+
590
+ for _ in range(n_samples):
591
+ # Random initialization
592
+ random_params = np.random.uniform(-np.pi, np.pi, len(params))
593
+
594
+ # Compute gradient
595
+ grads = grad_fn(random_params)
596
+ grad_variances.append(np.var(grads))
597
+
598
+ mean_var = np.mean(grad_variances)
599
+
600
+ print(f"Mean gradient variance: {mean_var:.6f}")
601
+
602
+ if mean_var < 1e-6:
603
+ print("Warning: Barren plateau detected!")
604
+
605
+ return mean_var
606
+ ```
607
+
608
+ ### Parameter Initialization
609
+
610
+ ```python
611
+ def initialize_params_smart(n_params, strategy='small_random'):
612
+ """Smart parameter initialization strategies."""
613
+
614
+ if strategy == 'small_random':
615
+ # Small random values
616
+ return np.random.uniform(-0.1, 0.1, n_params, requires_grad=True)
617
+
618
+ elif strategy == 'xavier':
619
+ # Xavier initialization
620
+ return np.random.normal(0, 1/np.sqrt(n_params), n_params, requires_grad=True)
621
+
622
+ elif strategy == 'identity':
623
+ # Start near identity (zeros for rotations)
624
+ return np.zeros(n_params, requires_grad=True)
625
+
626
+ elif strategy == 'layerwise':
627
+ # Layer-dependent initialization
628
+ return np.array([0.1 / (i+1) for i in range(n_params)], requires_grad=True)
629
+ ```
630
+
631
+ ### Local Minima Escape
632
+
633
+ ```python
634
+ def train_with_restarts(circuit, n_restarts=5):
635
+ """Multiple random restarts to escape local minima."""
636
+
637
+ best_cost = float('inf')
638
+ best_params = None
639
+
640
+ for restart in range(n_restarts):
641
+ # Random initialization
642
+ params = np.random.uniform(-np.pi, np.pi, 10, requires_grad=True)
643
+
644
+ # Optimize
645
+ opt = qml.AdamOptimizer(stepsize=0.1)
646
+ for i in range(100):
647
+ params = opt.step(circuit, params)
648
+
649
+ # Check if better
650
+ cost = circuit(params)
651
+ if cost < best_cost:
652
+ best_cost = cost
653
+ best_params = params
654
+
655
+ print(f"Restart {restart}: Cost = {cost:.6f}")
656
+
657
+ return best_params, best_cost
658
+ ```
659
+
660
+ ## Best Practices
661
+
662
+ 1. **Choose appropriate optimizer** - Adam for general use, QNG for variational circuits
663
+ 2. **Use parameter-shift on hardware** - Backprop only works on simulators
664
+ 3. **Initialize carefully** - Avoid barren plateaus with smart initialization
665
+ 4. **Monitor gradients** - Check for vanishing/exploding gradients
666
+ 5. **Use learning rate schedules** - Decay learning rate over time
667
+ 6. **Try multiple restarts** - Escape local minima
668
+ 7. **Validate on test set** - Prevent overfitting
669
+ 8. **Profile optimization** - Identify bottlenecks
670
+ 9. **Clip gradients** - Prevent instability
671
+ 10. **Start shallow** - Use fewer layers initially, then grow