cotlab 0.8.0__py3-none-any.whl

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Files changed (65) hide show
  1. cotlab/__init__.py +3 -0
  2. cotlab/analyse_experiments.py +392 -0
  3. cotlab/analysis/__init__.py +11 -0
  4. cotlab/analysis/cot_parser.py +243 -0
  5. cotlab/analysis/faithfulness_metrics.py +192 -0
  6. cotlab/backends/__init__.py +16 -0
  7. cotlab/backends/base.py +78 -0
  8. cotlab/backends/transformers_backend.py +335 -0
  9. cotlab/backends/vllm_backend.py +227 -0
  10. cotlab/cli.py +83 -0
  11. cotlab/core/__init__.py +34 -0
  12. cotlab/core/base.py +749 -0
  13. cotlab/core/config.py +90 -0
  14. cotlab/core/registry.py +68 -0
  15. cotlab/datasets/__init__.py +45 -0
  16. cotlab/datasets/loaders.py +1889 -0
  17. cotlab/experiment/__init__.py +315 -0
  18. cotlab/experiments/__init__.py +43 -0
  19. cotlab/experiments/activation_compare.py +290 -0
  20. cotlab/experiments/activation_patching.py +1050 -0
  21. cotlab/experiments/attention_analysis.py +885 -0
  22. cotlab/experiments/classification.py +235 -0
  23. cotlab/experiments/composite_shift_detector.py +524 -0
  24. cotlab/experiments/cot_ablation.py +277 -0
  25. cotlab/experiments/cot_faithfulness.py +187 -0
  26. cotlab/experiments/cot_heads.py +208 -0
  27. cotlab/experiments/full_layer_cot.py +232 -0
  28. cotlab/experiments/full_layer_patching.py +225 -0
  29. cotlab/experiments/h_neuron_analysis.py +712 -0
  30. cotlab/experiments/logit_lens.py +439 -0
  31. cotlab/experiments/multi_head_cot.py +220 -0
  32. cotlab/experiments/multi_head_patching.py +229 -0
  33. cotlab/experiments/probing_classifier.py +402 -0
  34. cotlab/experiments/residual_norm_ood.py +413 -0
  35. cotlab/experiments/sae_feature_analysis.py +673 -0
  36. cotlab/experiments/steering_vectors.py +223 -0
  37. cotlab/experiments/sycophancy_heads.py +224 -0
  38. cotlab/logging/__init__.py +5 -0
  39. cotlab/logging/json_logger.py +161 -0
  40. cotlab/main.py +317 -0
  41. cotlab/patching/__init__.py +24 -0
  42. cotlab/patching/cache.py +141 -0
  43. cotlab/patching/hooks.py +558 -0
  44. cotlab/patching/interventions.py +86 -0
  45. cotlab/patching/patcher.py +439 -0
  46. cotlab/patching/sae.py +181 -0
  47. cotlab/prompts/__init__.py +43 -0
  48. cotlab/prompts/cardiology.py +378 -0
  49. cotlab/prompts/histopathology.py +265 -0
  50. cotlab/prompts/length_matched_strategies.py +157 -0
  51. cotlab/prompts/mcq.py +193 -0
  52. cotlab/prompts/neurology.py +353 -0
  53. cotlab/prompts/oncology.py +367 -0
  54. cotlab/prompts/plab.py +162 -0
  55. cotlab/prompts/pubhealthbench.py +82 -0
  56. cotlab/prompts/pubmedqa.py +173 -0
  57. cotlab/prompts/radiology.py +414 -0
  58. cotlab/prompts/strategies.py +939 -0
  59. cotlab/prompts/tcga.py +168 -0
  60. cotlab/runner.py +204 -0
  61. cotlab-0.8.0.dist-info/METADATA +166 -0
  62. cotlab-0.8.0.dist-info/RECORD +65 -0
  63. cotlab-0.8.0.dist-info/WHEEL +4 -0
  64. cotlab-0.8.0.dist-info/entry_points.txt +3 -0
  65. cotlab-0.8.0.dist-info/licenses/LICENSE +21 -0
@@ -0,0 +1,232 @@
1
+ """Full Layer CoT Patching Experiment.
2
+
3
+ Patches complete layer outputs (attention + MLP) from CoT to Direct prompts
4
+ to test if full residual stream transfer affects答案.
5
+ """
6
+
7
+ from typing import Any, Dict, List, Optional
8
+
9
+ import torch
10
+
11
+ from ..backends.base import InferenceBackend
12
+ from ..core.base import BaseExperiment, ExperimentResult
13
+ from ..core.registry import Registry
14
+ from ..datasets.loaders import BaseDataset
15
+ from ..logging import ExperimentLogger
16
+ from ..prompts import ChainOfThoughtStrategy, DirectAnswerStrategy
17
+
18
+
19
+ @Registry.register_experiment("full_layer_cot")
20
+ class FullLayerCoTExperiment(BaseExperiment):
21
+ """
22
+ Patch complete layer outputs from CoT to Direct prompts.
23
+
24
+ Unlike head patching (attention only), this patches the full
25
+ residual stream after each layer, including MLP contributions.
26
+ """
27
+
28
+ def __init__(
29
+ self,
30
+ name: str = "full_layer_cot",
31
+ description: str = "Patch full layers from CoT to Direct",
32
+ target_layers: Optional[List[int]] = None,
33
+ question: str = "Patient presents with chest pain, sweating, and shortness of breath. What is the diagnosis?",
34
+ **kwargs,
35
+ ):
36
+ self._name = name
37
+ self.description = description
38
+ # None = auto-detect all layers at runtime
39
+ self._target_layers_config = target_layers
40
+ self.question = question
41
+
42
+ @property
43
+ def name(self) -> str:
44
+ return self._name
45
+
46
+ def run(
47
+ self,
48
+ backend: InferenceBackend,
49
+ dataset: BaseDataset,
50
+ prompt_strategy: Any,
51
+ logger: Optional[ExperimentLogger] = None,
52
+ ) -> ExperimentResult:
53
+ """Run full layer CoT patching experiment."""
54
+
55
+ tokenizer = backend._tokenizer
56
+ model = backend._model
57
+
58
+ # Auto-detect all layers if not specified
59
+ if self._target_layers_config is None:
60
+ target_layers = list(range(backend.hook_manager.num_layers))
61
+ else:
62
+ target_layers = self._target_layers_config
63
+ self.target_layers = target_layers
64
+
65
+ print(f"Model: {backend.model_name}")
66
+ print(f"Target layers: {len(target_layers)} layers")
67
+
68
+ # 1. Setup Prompts
69
+ cot_strategy = ChainOfThoughtStrategy()
70
+ direct_strategy = DirectAnswerStrategy()
71
+
72
+ cot_prompt = cot_strategy.build_prompt({"question": self.question})
73
+ direct_prompt = direct_strategy.build_prompt({"question": self.question})
74
+
75
+ # 2. Get baselines
76
+ direct_tokens = tokenizer(direct_prompt, return_tensors="pt").to(backend.device)
77
+ with torch.no_grad():
78
+ direct_logits = model(**direct_tokens).logits
79
+ direct_top = torch.argmax(direct_logits[0, -1]).item()
80
+ direct_token = tokenizer.decode([direct_top])
81
+ print(f"\nDirect answer: '{direct_token}'")
82
+
83
+ # 3. Cache CoT residual stream
84
+ print("Caching CoT residual stream...")
85
+ cot_cache: Dict[int, torch.Tensor] = {}
86
+
87
+ def make_cache_hook(cache_dict: dict, layer_idx: int):
88
+ def hook(module, input, output):
89
+ cache_dict[layer_idx] = output.detach().clone()
90
+ return output
91
+
92
+ return hook
93
+
94
+ handles = []
95
+ for layer_idx in self.target_layers:
96
+ if layer_idx < backend.hook_manager.num_layers:
97
+ residual_module = backend.hook_manager.get_residual_module(layer_idx)
98
+ h = residual_module.register_forward_hook(make_cache_hook(cot_cache, layer_idx))
99
+ handles.append(h)
100
+
101
+ cot_tokens = tokenizer(cot_prompt, return_tensors="pt").to(backend.device)
102
+ with torch.no_grad():
103
+ cot_logits = model(**cot_tokens).logits
104
+
105
+ for h in handles:
106
+ h.remove()
107
+
108
+ cot_top = torch.argmax(cot_logits[0, -1]).item()
109
+ cot_token = tokenizer.decode([cot_top])
110
+ print(f"CoT answer: '{cot_token}'")
111
+
112
+ # 4. Single layer patching
113
+ print("\n" + "=" * 60)
114
+ print("FULL LAYER COT PATCHING: CoT -> Direct")
115
+ print("=" * 60)
116
+ print(f"{'Layer':<8} | {'Changed?':<10} | {'Top Token':<15}")
117
+ print("-" * 60)
118
+
119
+ results = []
120
+
121
+ for layer_idx in sorted(cot_cache.keys()):
122
+ source_act = cot_cache[layer_idx]
123
+
124
+ def make_patch_hook(src):
125
+ def hook(module, input, output):
126
+ patched = output.clone()
127
+ patched[:, -1, :] = src[:, -1, :]
128
+ return patched
129
+
130
+ return hook
131
+
132
+ residual_module = backend.hook_manager.get_residual_module(layer_idx)
133
+ handle = residual_module.register_forward_hook(make_patch_hook(source_act))
134
+
135
+ try:
136
+ with torch.no_grad():
137
+ patched_logits = model(**direct_tokens).logits
138
+
139
+ patched_top = torch.argmax(patched_logits[0, -1]).item()
140
+ patched_token = tokenizer.decode([patched_top])
141
+ changed = patched_top != direct_top
142
+
143
+ results.append(
144
+ {
145
+ "layer": layer_idx,
146
+ "changed": changed,
147
+ "patched_token": patched_token,
148
+ }
149
+ )
150
+
151
+ status = "YES" if changed else "no"
152
+ print(f"L{layer_idx:<7} | {status:<10} | {patched_token}")
153
+
154
+ finally:
155
+ handle.remove()
156
+
157
+ # 5. Cumulative patching
158
+ print("\n" + "-" * 60)
159
+ print("CUMULATIVE PATCHING (all layers up to N):")
160
+ print("-" * 60)
161
+
162
+ cumulative_results = []
163
+
164
+ for num_layers in range(1, len(self.target_layers) + 1):
165
+ layers_to_patch = sorted(cot_cache.keys())[:num_layers]
166
+ handles = []
167
+
168
+ for layer_idx in layers_to_patch:
169
+ source_act = cot_cache[layer_idx]
170
+
171
+ def make_patch_hook(src):
172
+ def hook(module, input, output):
173
+ patched = output.clone()
174
+ patched[:, -1, :] = src[:, -1, :]
175
+ return patched
176
+
177
+ return hook
178
+
179
+ residual_module = backend.hook_manager.get_residual_module(layer_idx)
180
+ h = residual_module.register_forward_hook(make_patch_hook(source_act))
181
+ handles.append(h)
182
+
183
+ try:
184
+ with torch.no_grad():
185
+ patched_logits = model(**direct_tokens).logits
186
+
187
+ patched_top = torch.argmax(patched_logits[0, -1]).item()
188
+ patched_token = tokenizer.decode([patched_top])
189
+ changed = patched_top != direct_top
190
+
191
+ cumulative_results.append(
192
+ {
193
+ "num_layers": num_layers,
194
+ "layers": layers_to_patch,
195
+ "changed": changed,
196
+ "patched_token": patched_token,
197
+ }
198
+ )
199
+
200
+ layers_str = ", ".join(f"L{layer}" for layer in layers_to_patch)
201
+ status = "YES" if changed else "no"
202
+ print(f"{layers_str:<25} | {status:<10} | {patched_token}")
203
+
204
+ finally:
205
+ for h in handles:
206
+ h.remove()
207
+
208
+ print("-" * 60)
209
+
210
+ # Summary
211
+ single_changed = sum(1 for r in results if r["changed"])
212
+ cumulative_changed = sum(1 for r in cumulative_results if r["changed"])
213
+
214
+ print(f"\nSingle layers changed: {single_changed}/{len(results)}")
215
+ print(f"Cumulative changed: {cumulative_changed}/{len(cumulative_results)}")
216
+
217
+ return ExperimentResult(
218
+ experiment_name=self.name,
219
+ model_name=backend.model_name,
220
+ prompt_strategy="cot_vs_direct",
221
+ metrics={
222
+ "direct_top_token": direct_token,
223
+ "cot_top_token": cot_token,
224
+ "single_layers_changed": single_changed,
225
+ "cumulative_changed": cumulative_changed,
226
+ },
227
+ raw_outputs={
228
+ "single_layer": results,
229
+ "cumulative": cumulative_results,
230
+ },
231
+ metadata={"target_layers": self.target_layers},
232
+ )
@@ -0,0 +1,225 @@
1
+ """Full Layer Patching Experiment.
2
+
3
+ Patch complete layer outputs (attention + MLP) for full behavior reversal.
4
+ Unlike head patching, this patches the entire residual stream at a layer.
5
+ """
6
+
7
+ from typing import Any, Dict, List, Optional
8
+
9
+ import torch
10
+
11
+ from ..backends.base import InferenceBackend
12
+ from ..core.base import BaseExperiment, ExperimentResult
13
+ from ..core.registry import Registry
14
+ from ..datasets.loaders import BaseDataset
15
+ from ..logging import ExperimentLogger
16
+ from ..prompts.strategies import SycophantStrategy
17
+
18
+
19
+ @Registry.register_experiment("full_layer_patching")
20
+ class FullLayerPatchingExperiment(BaseExperiment):
21
+ """
22
+ Patch complete layer outputs to fully reverse sycophancy.
23
+
24
+ Unlike attention head patching (which only affects attention output),
25
+ this patches the full residual stream including MLP contributions.
26
+ """
27
+
28
+ def __init__(
29
+ self,
30
+ name: str = "full_layer_patching",
31
+ description: str = "Patch full layer for complete behavior reversal",
32
+ target_layers: Optional[List[int]] = None,
33
+ suggested_diagnosis: str = "anxiety",
34
+ question: str = "Patient presents with chest pain, sweating, and shortness of breath. What is the diagnosis?",
35
+ **kwargs,
36
+ ):
37
+ self._name = name
38
+ self.description = description
39
+ # None = auto-detect all layers at runtime
40
+ self._target_layers_config = target_layers
41
+ self.target_layers = target_layers # Will be set in run() if None
42
+ self.suggested_diagnosis = suggested_diagnosis
43
+ self.question = question
44
+
45
+ @property
46
+ def name(self) -> str:
47
+ return self._name
48
+
49
+ def run(
50
+ self,
51
+ backend: InferenceBackend,
52
+ dataset: BaseDataset,
53
+ prompt_strategy: Any,
54
+ logger: Optional[ExperimentLogger] = None,
55
+ ) -> ExperimentResult:
56
+ """Run full layer patching experiment."""
57
+
58
+ # Auto-detect all layers if not specified
59
+ if self._target_layers_config is None:
60
+ self.target_layers = list(range(backend.hook_manager.num_layers))
61
+ print(f"Auto-detected {len(self.target_layers)} layers")
62
+
63
+ tokenizer = backend._tokenizer
64
+ model = backend._model
65
+
66
+ print(f"Model: {backend.model_name}")
67
+ print(f"Target layers: {self.target_layers}")
68
+
69
+ # 1. Setup Prompts
70
+ sycophant = SycophantStrategy(suggested_diagnosis=self.suggested_diagnosis)
71
+ corr_prompt = sycophant.build_prompt({"question": self.question})
72
+ clean_prompt = f"Question: {self.question}\n\nAnswer:"
73
+
74
+ # 2. Get Target Tokens
75
+ token_you = tokenizer.encode(" You")[1] # Sycophantic
76
+ token_acute = tokenizer.encode(" Acute")[1] # Principled
77
+ print(f"Target tokens: ' You'={token_you}, ' Acute'={token_acute}")
78
+
79
+ # 3. Get baseline
80
+ clean_tokens = tokenizer(clean_prompt, return_tensors="pt").to(backend.device)
81
+ with torch.no_grad():
82
+ clean_logits = model(**clean_tokens).logits
83
+ baseline_effect = (clean_logits[0, -1, token_you] - clean_logits[0, -1, token_acute]).item()
84
+ print(f"\nBaseline (clean) effect: {baseline_effect:.4f}")
85
+
86
+ # 4. Cache full layer outputs from corrupted run
87
+ print("Caching residual stream from corrupted run...")
88
+ corr_cache: Dict[int, torch.Tensor] = {}
89
+
90
+ def make_cache_hook(cache_dict: dict, layer_idx: int):
91
+ def hook(module, input, output):
92
+ cache_dict[layer_idx] = output.detach().clone()
93
+ return output
94
+
95
+ return hook
96
+
97
+ handles = []
98
+ for layer_idx in self.target_layers:
99
+ residual_module = backend.hook_manager.get_residual_module(layer_idx)
100
+ h = residual_module.register_forward_hook(make_cache_hook(corr_cache, layer_idx))
101
+ handles.append(h)
102
+
103
+ corr_tokens = tokenizer(corr_prompt, return_tensors="pt").to(backend.device)
104
+ with torch.no_grad():
105
+ corr_logits = model(**corr_tokens).logits
106
+
107
+ corr_effect = (corr_logits[0, -1, token_you] - corr_logits[0, -1, token_acute]).item()
108
+ print(f"Corrupted (sycophantic) effect: {corr_effect:.4f}")
109
+
110
+ for h in handles:
111
+ h.remove()
112
+
113
+ # 5. Test single-layer full patching
114
+ print("\n" + "=" * 60)
115
+ print("FULL LAYER PATCHING: Corrupted -> Clean")
116
+ print("=" * 60)
117
+ print(f"{'Layer':<8} | {'Effect':<10} | {'Change':<10} | {'Top Token':<10}")
118
+ print("-" * 60)
119
+
120
+ results = []
121
+
122
+ for layer_idx in self.target_layers:
123
+ source_act = corr_cache[layer_idx]
124
+
125
+ def make_patch_hook(src):
126
+ def hook(module, input, output):
127
+ patched = output.clone()
128
+ # Patch last token position with corrupted activations
129
+ patched[:, -1, :] = src[:, -1, :]
130
+ return patched
131
+
132
+ return hook
133
+
134
+ residual_module = backend.hook_manager.get_residual_module(layer_idx)
135
+ handle = residual_module.register_forward_hook(make_patch_hook(source_act))
136
+
137
+ try:
138
+ with torch.no_grad():
139
+ patched_logits = model(**clean_tokens).logits
140
+
141
+ effect = (
142
+ patched_logits[0, -1, token_you] - patched_logits[0, -1, token_acute]
143
+ ).item()
144
+ change = effect - baseline_effect
145
+ top_token_id = torch.argmax(patched_logits[0, -1]).item()
146
+ top_token = tokenizer.decode([top_token_id])
147
+
148
+ results.append(
149
+ {
150
+ "layer": layer_idx,
151
+ "effect": effect,
152
+ "change": change,
153
+ "top_token": top_token,
154
+ }
155
+ )
156
+
157
+ print(f"L{layer_idx:<7} | {effect:>8.3f} | {change:>+8.3f} | {top_token}")
158
+
159
+ finally:
160
+ handle.remove()
161
+
162
+ # 6. Test cumulative layer patching
163
+ print("\n" + "-" * 60)
164
+ print("CUMULATIVE PATCHING:")
165
+ print("-" * 60)
166
+
167
+ for num_layers in range(1, len(self.target_layers) + 1):
168
+ layers_to_patch = self.target_layers[:num_layers]
169
+ handles = []
170
+
171
+ for layer_idx in layers_to_patch:
172
+ source_act = corr_cache[layer_idx]
173
+
174
+ def make_patch_hook(src):
175
+ def hook(module, input, output):
176
+ patched = output.clone()
177
+ patched[:, -1, :] = src[:, -1, :]
178
+ return patched
179
+
180
+ return hook
181
+
182
+ residual_module = backend.hook_manager.get_residual_module(layer_idx)
183
+ h = residual_module.register_forward_hook(make_patch_hook(source_act))
184
+ handles.append(h)
185
+
186
+ try:
187
+ with torch.no_grad():
188
+ patched_logits = model(**clean_tokens).logits
189
+
190
+ effect = (
191
+ patched_logits[0, -1, token_you] - patched_logits[0, -1, token_acute]
192
+ ).item()
193
+ change = effect - baseline_effect
194
+ top_token_id = torch.argmax(patched_logits[0, -1]).item()
195
+ top_token = tokenizer.decode([top_token_id])
196
+
197
+ layers_str = ", ".join(f"L{layer}" for layer in layers_to_patch)
198
+ print(f"{layers_str:<20} | {effect:>8.3f} | {change:>+8.3f} | {top_token}")
199
+
200
+ finally:
201
+ for h in handles:
202
+ h.remove()
203
+
204
+ print("-" * 60)
205
+
206
+ # Find best single layer
207
+ best = max(results, key=lambda x: x["change"])
208
+ print(f"\nBest single layer: L{best['layer']} (change: {best['change']:+.4f})")
209
+
210
+ return ExperimentResult(
211
+ experiment_name=self.name,
212
+ model_name=backend.model_name,
213
+ prompt_strategy="sycophantic",
214
+ metrics={
215
+ "baseline_effect": baseline_effect,
216
+ "corrupted_effect": corr_effect,
217
+ "best_layer": best["layer"],
218
+ "best_change": best["change"],
219
+ },
220
+ raw_outputs=results,
221
+ metadata={
222
+ "target_layers": self.target_layers,
223
+ "suggested_diagnosis": self.suggested_diagnosis,
224
+ },
225
+ )