@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.
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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  193. package/bin/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  194. package/bin/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
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@@ -0,0 +1,653 @@
1
+ # PufferLib Policies Guide
2
+
3
+ ## Overview
4
+
5
+ PufferLib policies are standard PyTorch modules with optional utilities for observation processing and LSTM integration. The framework provides default architectures and tools while allowing full flexibility in policy design.
6
+
7
+ ## Policy Architecture
8
+
9
+ ### Basic Policy Structure
10
+
11
+ ```python
12
+ import torch
13
+ import torch.nn as nn
14
+ from pufferlib.pytorch import layer_init
15
+
16
+ class BasicPolicy(nn.Module):
17
+ def __init__(self, observation_space, action_space):
18
+ super().__init__()
19
+
20
+ self.observation_space = observation_space
21
+ self.action_space = action_space
22
+
23
+ # Encoder network
24
+ self.encoder = nn.Sequential(
25
+ layer_init(nn.Linear(observation_space.shape[0], 256)),
26
+ nn.ReLU(),
27
+ layer_init(nn.Linear(256, 256)),
28
+ nn.ReLU()
29
+ )
30
+
31
+ # Policy head (actor)
32
+ self.actor = layer_init(nn.Linear(256, action_space.n), std=0.01)
33
+
34
+ # Value head (critic)
35
+ self.critic = layer_init(nn.Linear(256, 1), std=1.0)
36
+
37
+ def forward(self, observations):
38
+ """Forward pass through policy."""
39
+ # Encode observations
40
+ features = self.encoder(observations)
41
+
42
+ # Get action logits and value
43
+ logits = self.actor(features)
44
+ value = self.critic(features)
45
+
46
+ return logits, value
47
+
48
+ def get_action(self, observations, deterministic=False):
49
+ """Sample action from policy."""
50
+ logits, value = self.forward(observations)
51
+
52
+ if deterministic:
53
+ action = logits.argmax(dim=-1)
54
+ else:
55
+ dist = torch.distributions.Categorical(logits=logits)
56
+ action = dist.sample()
57
+
58
+ return action, value
59
+ ```
60
+
61
+ ### Layer Initialization
62
+
63
+ PufferLib provides `layer_init` for proper weight initialization:
64
+
65
+ ```python
66
+ from pufferlib.pytorch import layer_init
67
+
68
+ # Default orthogonal initialization
69
+ layer = layer_init(nn.Linear(256, 256))
70
+
71
+ # Custom standard deviation
72
+ actor_head = layer_init(nn.Linear(256, num_actions), std=0.01)
73
+ critic_head = layer_init(nn.Linear(256, 1), std=1.0)
74
+
75
+ # Works with any layer type
76
+ conv = layer_init(nn.Conv2d(3, 32, kernel_size=8, stride=4))
77
+ ```
78
+
79
+ ## CNN Policies
80
+
81
+ For image-based observations:
82
+
83
+ ```python
84
+ class CNNPolicy(nn.Module):
85
+ def __init__(self, observation_space, action_space):
86
+ super().__init__()
87
+
88
+ # CNN encoder for images
89
+ self.encoder = nn.Sequential(
90
+ layer_init(nn.Conv2d(3, 32, kernel_size=8, stride=4)),
91
+ nn.ReLU(),
92
+ layer_init(nn.Conv2d(32, 64, kernel_size=4, stride=2)),
93
+ nn.ReLU(),
94
+ layer_init(nn.Conv2d(64, 64, kernel_size=3, stride=1)),
95
+ nn.ReLU(),
96
+ nn.Flatten(),
97
+ layer_init(nn.Linear(64 * 7 * 7, 512)),
98
+ nn.ReLU()
99
+ )
100
+
101
+ self.actor = layer_init(nn.Linear(512, action_space.n), std=0.01)
102
+ self.critic = layer_init(nn.Linear(512, 1), std=1.0)
103
+
104
+ def forward(self, observations):
105
+ # Normalize pixel values
106
+ x = observations.float() / 255.0
107
+
108
+ features = self.encoder(x)
109
+ logits = self.actor(features)
110
+ value = self.critic(features)
111
+
112
+ return logits, value
113
+ ```
114
+
115
+ ### Efficient CNN Architecture
116
+
117
+ ```python
118
+ class EfficientCNN(nn.Module):
119
+ """Optimized CNN for Atari-style games."""
120
+
121
+ def __init__(self, observation_space, action_space):
122
+ super().__init__()
123
+
124
+ in_channels = observation_space.shape[0] # Typically 4 for framestack
125
+
126
+ self.network = nn.Sequential(
127
+ layer_init(nn.Conv2d(in_channels, 32, 8, stride=4)),
128
+ nn.ReLU(),
129
+ layer_init(nn.Conv2d(32, 64, 4, stride=2)),
130
+ nn.ReLU(),
131
+ layer_init(nn.Conv2d(64, 64, 3, stride=1)),
132
+ nn.ReLU(),
133
+ nn.Flatten()
134
+ )
135
+
136
+ # Calculate feature size
137
+ with torch.no_grad():
138
+ sample = torch.zeros(1, *observation_space.shape)
139
+ n_features = self.network(sample).shape[1]
140
+
141
+ self.fc = layer_init(nn.Linear(n_features, 512))
142
+ self.actor = layer_init(nn.Linear(512, action_space.n), std=0.01)
143
+ self.critic = layer_init(nn.Linear(512, 1), std=1.0)
144
+
145
+ def forward(self, x):
146
+ x = x.float() / 255.0
147
+ x = self.network(x)
148
+ x = torch.relu(self.fc(x))
149
+
150
+ return self.actor(x), self.critic(x)
151
+ ```
152
+
153
+ ## Recurrent Policies (LSTM)
154
+
155
+ PufferLib provides optimized LSTM integration with automatic recurrence handling:
156
+
157
+ ```python
158
+ from pufferlib.pytorch import LSTMWrapper
159
+
160
+ class RecurrentPolicy(nn.Module):
161
+ def __init__(self, observation_space, action_space, hidden_size=256):
162
+ super().__init__()
163
+
164
+ # Observation encoder
165
+ self.encoder = nn.Sequential(
166
+ layer_init(nn.Linear(observation_space.shape[0], 128)),
167
+ nn.ReLU()
168
+ )
169
+
170
+ # LSTM layer
171
+ self.lstm = nn.LSTM(128, hidden_size, num_layers=1)
172
+
173
+ # Policy and value heads
174
+ self.actor = layer_init(nn.Linear(hidden_size, action_space.n), std=0.01)
175
+ self.critic = layer_init(nn.Linear(hidden_size, 1), std=1.0)
176
+
177
+ # Hidden state
178
+ self.hidden_size = hidden_size
179
+
180
+ def forward(self, observations, state=None):
181
+ """
182
+ Args:
183
+ observations: (batch, obs_dim)
184
+ state: Optional (h, c) tuple for LSTM
185
+
186
+ Returns:
187
+ logits, value, new_state
188
+ """
189
+ batch_size = observations.shape[0]
190
+
191
+ # Encode observations
192
+ features = self.encoder(observations)
193
+
194
+ # Initialize hidden state if needed
195
+ if state is None:
196
+ h = torch.zeros(1, batch_size, self.hidden_size, device=features.device)
197
+ c = torch.zeros(1, batch_size, self.hidden_size, device=features.device)
198
+ state = (h, c)
199
+
200
+ # LSTM forward
201
+ features = features.unsqueeze(0) # Add sequence dimension
202
+ lstm_out, new_state = self.lstm(features, state)
203
+ lstm_out = lstm_out.squeeze(0)
204
+
205
+ # Get outputs
206
+ logits = self.actor(lstm_out)
207
+ value = self.critic(lstm_out)
208
+
209
+ return logits, value, new_state
210
+ ```
211
+
212
+ ### LSTM Optimization
213
+
214
+ PufferLib's LSTM optimization uses LSTMCell during rollouts and LSTM during training for up to 3x faster inference:
215
+
216
+ ```python
217
+ class OptimizedLSTMPolicy(nn.Module):
218
+ def __init__(self, observation_space, action_space, hidden_size=256):
219
+ super().__init__()
220
+
221
+ self.encoder = nn.Sequential(
222
+ layer_init(nn.Linear(observation_space.shape[0], 128)),
223
+ nn.ReLU()
224
+ )
225
+
226
+ # Use LSTMCell for step-by-step inference
227
+ self.lstm_cell = nn.LSTMCell(128, hidden_size)
228
+
229
+ # Use LSTM for batch training
230
+ self.lstm = nn.LSTM(128, hidden_size, num_layers=1)
231
+
232
+ self.actor = layer_init(nn.Linear(hidden_size, action_space.n), std=0.01)
233
+ self.critic = layer_init(nn.Linear(hidden_size, 1), std=1.0)
234
+
235
+ self.hidden_size = hidden_size
236
+
237
+ def encode_observations(self, observations, state):
238
+ """Fast inference using LSTMCell."""
239
+ features = self.encoder(observations)
240
+
241
+ if state is None:
242
+ h = torch.zeros(observations.shape[0], self.hidden_size, device=features.device)
243
+ c = torch.zeros(observations.shape[0], self.hidden_size, device=features.device)
244
+ else:
245
+ h, c = state
246
+
247
+ # Step-by-step with LSTMCell (faster for inference)
248
+ h, c = self.lstm_cell(features, (h, c))
249
+
250
+ logits = self.actor(h)
251
+ value = self.critic(h)
252
+
253
+ return logits, value, (h, c)
254
+
255
+ def decode_actions(self, observations, actions, state):
256
+ """Batch training using LSTM."""
257
+ seq_len, batch_size = observations.shape[:2]
258
+
259
+ # Reshape for LSTM
260
+ obs_flat = observations.reshape(seq_len * batch_size, -1)
261
+ features = self.encoder(obs_flat)
262
+ features = features.reshape(seq_len, batch_size, -1)
263
+
264
+ if state is None:
265
+ h = torch.zeros(1, batch_size, self.hidden_size, device=features.device)
266
+ c = torch.zeros(1, batch_size, self.hidden_size, device=features.device)
267
+ state = (h, c)
268
+
269
+ # Batch processing with LSTM (faster for training)
270
+ lstm_out, new_state = self.lstm(features, state)
271
+
272
+ # Flatten back
273
+ lstm_out = lstm_out.reshape(seq_len * batch_size, -1)
274
+
275
+ logits = self.actor(lstm_out)
276
+ value = self.critic(lstm_out)
277
+
278
+ return logits, value, new_state
279
+ ```
280
+
281
+ ## Multi-Input Policies
282
+
283
+ For environments with multiple observation types:
284
+
285
+ ```python
286
+ class MultiInputPolicy(nn.Module):
287
+ def __init__(self, observation_space, action_space):
288
+ super().__init__()
289
+
290
+ # Separate encoders for different observation types
291
+ self.image_encoder = nn.Sequential(
292
+ layer_init(nn.Conv2d(3, 32, 8, stride=4)),
293
+ nn.ReLU(),
294
+ layer_init(nn.Conv2d(32, 64, 4, stride=2)),
295
+ nn.ReLU(),
296
+ nn.Flatten()
297
+ )
298
+
299
+ self.vector_encoder = nn.Sequential(
300
+ layer_init(nn.Linear(observation_space['vector'].shape[0], 128)),
301
+ nn.ReLU()
302
+ )
303
+
304
+ # Combine features
305
+ combined_size = 64 * 9 * 9 + 128 # Image features + vector features
306
+ self.combiner = nn.Sequential(
307
+ layer_init(nn.Linear(combined_size, 512)),
308
+ nn.ReLU()
309
+ )
310
+
311
+ self.actor = layer_init(nn.Linear(512, action_space.n), std=0.01)
312
+ self.critic = layer_init(nn.Linear(512, 1), std=1.0)
313
+
314
+ def forward(self, observations):
315
+ # Process each observation type
316
+ image_features = self.image_encoder(observations['image'].float() / 255.0)
317
+ vector_features = self.vector_encoder(observations['vector'])
318
+
319
+ # Combine
320
+ combined = torch.cat([image_features, vector_features], dim=-1)
321
+ features = self.combiner(combined)
322
+
323
+ return self.actor(features), self.critic(features)
324
+ ```
325
+
326
+ ## Continuous Action Policies
327
+
328
+ For continuous control tasks:
329
+
330
+ ```python
331
+ class ContinuousPolicy(nn.Module):
332
+ def __init__(self, observation_space, action_space):
333
+ super().__init__()
334
+
335
+ self.encoder = nn.Sequential(
336
+ layer_init(nn.Linear(observation_space.shape[0], 256)),
337
+ nn.ReLU(),
338
+ layer_init(nn.Linear(256, 256)),
339
+ nn.ReLU()
340
+ )
341
+
342
+ # Mean of action distribution
343
+ self.actor_mean = layer_init(nn.Linear(256, action_space.shape[0]), std=0.01)
344
+
345
+ # Log std of action distribution
346
+ self.actor_logstd = nn.Parameter(torch.zeros(1, action_space.shape[0]))
347
+
348
+ # Value head
349
+ self.critic = layer_init(nn.Linear(256, 1), std=1.0)
350
+
351
+ def forward(self, observations):
352
+ features = self.encoder(observations)
353
+
354
+ action_mean = self.actor_mean(features)
355
+ action_std = torch.exp(self.actor_logstd)
356
+
357
+ value = self.critic(features)
358
+
359
+ return action_mean, action_std, value
360
+
361
+ def get_action(self, observations, deterministic=False):
362
+ action_mean, action_std, value = self.forward(observations)
363
+
364
+ if deterministic:
365
+ return action_mean, value
366
+ else:
367
+ dist = torch.distributions.Normal(action_mean, action_std)
368
+ action = dist.sample()
369
+ return torch.tanh(action), value # Bound actions to [-1, 1]
370
+ ```
371
+
372
+ ## Observation Processing
373
+
374
+ PufferLib provides utilities for unflattening observations:
375
+
376
+ ```python
377
+ from pufferlib.pytorch import unflatten_observations
378
+
379
+ class PolicyWithUnflatten(nn.Module):
380
+ def __init__(self, observation_space, action_space):
381
+ super().__init__()
382
+
383
+ self.observation_space = observation_space
384
+
385
+ # Define encoders for each observation component
386
+ self.encoders = nn.ModuleDict({
387
+ 'image': self._make_image_encoder(),
388
+ 'vector': self._make_vector_encoder()
389
+ })
390
+
391
+ # ... rest of policy ...
392
+
393
+ def forward(self, flat_observations):
394
+ # Unflatten observations into structured format
395
+ observations = unflatten_observations(
396
+ flat_observations,
397
+ self.observation_space
398
+ )
399
+
400
+ # Process each component
401
+ image_features = self.encoders['image'](observations['image'])
402
+ vector_features = self.encoders['vector'](observations['vector'])
403
+
404
+ # Combine and continue...
405
+ ```
406
+
407
+ ## Multi-Agent Policies
408
+
409
+ ### Shared Parameters
410
+
411
+ All agents use the same policy:
412
+
413
+ ```python
414
+ class SharedMultiAgentPolicy(nn.Module):
415
+ def __init__(self, observation_space, action_space, num_agents):
416
+ super().__init__()
417
+
418
+ self.num_agents = num_agents
419
+
420
+ # Single policy shared across all agents
421
+ self.encoder = nn.Sequential(
422
+ layer_init(nn.Linear(observation_space.shape[0], 256)),
423
+ nn.ReLU()
424
+ )
425
+
426
+ self.actor = layer_init(nn.Linear(256, action_space.n), std=0.01)
427
+ self.critic = layer_init(nn.Linear(256, 1), std=1.0)
428
+
429
+ def forward(self, observations):
430
+ """
431
+ Args:
432
+ observations: (batch * num_agents, obs_dim)
433
+ Returns:
434
+ logits: (batch * num_agents, num_actions)
435
+ values: (batch * num_agents, 1)
436
+ """
437
+ features = self.encoder(observations)
438
+ return self.actor(features), self.critic(features)
439
+ ```
440
+
441
+ ### Independent Parameters
442
+
443
+ Each agent has its own policy:
444
+
445
+ ```python
446
+ class IndependentMultiAgentPolicy(nn.Module):
447
+ def __init__(self, observation_space, action_space, num_agents):
448
+ super().__init__()
449
+
450
+ self.num_agents = num_agents
451
+
452
+ # Separate policy for each agent
453
+ self.policies = nn.ModuleList([
454
+ self._make_policy(observation_space, action_space)
455
+ for _ in range(num_agents)
456
+ ])
457
+
458
+ def _make_policy(self, observation_space, action_space):
459
+ return nn.Sequential(
460
+ layer_init(nn.Linear(observation_space.shape[0], 256)),
461
+ nn.ReLU(),
462
+ layer_init(nn.Linear(256, 256)),
463
+ nn.ReLU()
464
+ )
465
+
466
+ def forward(self, observations, agent_ids):
467
+ """
468
+ Args:
469
+ observations: (batch, obs_dim)
470
+ agent_ids: (batch,) which agent each obs belongs to
471
+ """
472
+ outputs = []
473
+ for agent_id in range(self.num_agents):
474
+ mask = agent_ids == agent_id
475
+ if mask.any():
476
+ agent_obs = observations[mask]
477
+ agent_out = self.policies[agent_id](agent_obs)
478
+ outputs.append(agent_out)
479
+
480
+ return torch.cat(outputs, dim=0)
481
+ ```
482
+
483
+ ## Advanced Architectures
484
+
485
+ ### Attention-Based Policy
486
+
487
+ ```python
488
+ class AttentionPolicy(nn.Module):
489
+ def __init__(self, observation_space, action_space, d_model=256, nhead=8):
490
+ super().__init__()
491
+
492
+ self.encoder = layer_init(nn.Linear(observation_space.shape[0], d_model))
493
+
494
+ self.attention = nn.MultiheadAttention(d_model, nhead, batch_first=True)
495
+
496
+ self.actor = layer_init(nn.Linear(d_model, action_space.n), std=0.01)
497
+ self.critic = layer_init(nn.Linear(d_model, 1), std=1.0)
498
+
499
+ def forward(self, observations):
500
+ # Encode
501
+ features = self.encoder(observations)
502
+
503
+ # Self-attention
504
+ features = features.unsqueeze(1) # Add sequence dimension
505
+ attn_out, _ = self.attention(features, features, features)
506
+ attn_out = attn_out.squeeze(1)
507
+
508
+ return self.actor(attn_out), self.critic(attn_out)
509
+ ```
510
+
511
+ ### Residual Policy
512
+
513
+ ```python
514
+ class ResidualBlock(nn.Module):
515
+ def __init__(self, dim):
516
+ super().__init__()
517
+ self.block = nn.Sequential(
518
+ layer_init(nn.Linear(dim, dim)),
519
+ nn.ReLU(),
520
+ layer_init(nn.Linear(dim, dim))
521
+ )
522
+
523
+ def forward(self, x):
524
+ return x + self.block(x)
525
+
526
+ class ResidualPolicy(nn.Module):
527
+ def __init__(self, observation_space, action_space, num_blocks=4):
528
+ super().__init__()
529
+
530
+ dim = 256
531
+
532
+ self.encoder = layer_init(nn.Linear(observation_space.shape[0], dim))
533
+
534
+ self.blocks = nn.Sequential(
535
+ *[ResidualBlock(dim) for _ in range(num_blocks)]
536
+ )
537
+
538
+ self.actor = layer_init(nn.Linear(dim, action_space.n), std=0.01)
539
+ self.critic = layer_init(nn.Linear(dim, 1), std=1.0)
540
+
541
+ def forward(self, observations):
542
+ x = torch.relu(self.encoder(observations))
543
+ x = self.blocks(x)
544
+ return self.actor(x), self.critic(x)
545
+ ```
546
+
547
+ ## Policy Best Practices
548
+
549
+ ### Initialization
550
+
551
+ ```python
552
+ # Always use layer_init for proper initialization
553
+ good_layer = layer_init(nn.Linear(256, 256))
554
+
555
+ # Use small std for actor head (more stable early training)
556
+ actor = layer_init(nn.Linear(256, num_actions), std=0.01)
557
+
558
+ # Use std=1.0 for critic head
559
+ critic = layer_init(nn.Linear(256, 1), std=1.0)
560
+ ```
561
+
562
+ ### Observation Normalization
563
+
564
+ ```python
565
+ class NormalizedPolicy(nn.Module):
566
+ def __init__(self, observation_space, action_space):
567
+ super().__init__()
568
+
569
+ # Running statistics for normalization
570
+ self.obs_mean = nn.Parameter(torch.zeros(observation_space.shape[0]), requires_grad=False)
571
+ self.obs_std = nn.Parameter(torch.ones(observation_space.shape[0]), requires_grad=False)
572
+
573
+ # ... rest of policy ...
574
+
575
+ def forward(self, observations):
576
+ # Normalize observations
577
+ normalized_obs = (observations - self.obs_mean) / (self.obs_std + 1e-8)
578
+
579
+ # Continue with normalized observations
580
+ return self.policy(normalized_obs)
581
+
582
+ def update_normalization(self, observations):
583
+ """Update running statistics."""
584
+ self.obs_mean.data = observations.mean(dim=0)
585
+ self.obs_std.data = observations.std(dim=0)
586
+ ```
587
+
588
+ ### Gradient Clipping
589
+
590
+ ```python
591
+ # PufferLib trainer handles gradient clipping automatically
592
+ trainer = PuffeRL(
593
+ env=env,
594
+ policy=policy,
595
+ max_grad_norm=0.5 # Clip gradients to this norm
596
+ )
597
+ ```
598
+
599
+ ### Model Compilation
600
+
601
+ ```python
602
+ # Enable torch.compile for faster training (PyTorch 2.0+)
603
+ policy = MyPolicy(observation_space, action_space)
604
+
605
+ # Compile the model
606
+ policy = torch.compile(policy, mode='reduce-overhead')
607
+
608
+ # Use with trainer
609
+ trainer = PuffeRL(env=env, policy=policy, compile=True)
610
+ ```
611
+
612
+ ## Debugging Policies
613
+
614
+ ### Check Output Shapes
615
+
616
+ ```python
617
+ def test_policy_shapes(policy, observation_space, batch_size=32):
618
+ """Verify policy output shapes."""
619
+ # Create dummy observations
620
+ obs = torch.randn(batch_size, *observation_space.shape)
621
+
622
+ # Forward pass
623
+ logits, value = policy(obs)
624
+
625
+ # Check shapes
626
+ assert logits.shape == (batch_size, policy.action_space.n)
627
+ assert value.shape == (batch_size, 1)
628
+
629
+ print("✓ Policy shapes correct")
630
+ ```
631
+
632
+ ### Verify Gradients
633
+
634
+ ```python
635
+ def check_gradients(policy, observation_space):
636
+ """Check that gradients flow properly."""
637
+ obs = torch.randn(1, *observation_space.shape, requires_grad=True)
638
+
639
+ logits, value = policy(obs)
640
+
641
+ # Backward pass
642
+ loss = logits.sum() + value.sum()
643
+ loss.backward()
644
+
645
+ # Check gradients exist
646
+ for name, param in policy.named_parameters():
647
+ if param.grad is None:
648
+ print(f"⚠ No gradient for {name}")
649
+ elif torch.isnan(param.grad).any():
650
+ print(f"⚠ NaN gradient for {name}")
651
+ else:
652
+ print(f"✓ Gradient OK for {name}")
653
+ ```