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updated cache, minor formatting edits
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60 files changed

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‎NMA_2023_v0.1.cache

175 KB
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‎chatify/background.md

+1-1
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@@ -1,4 +1,4 @@
1-
### ⚠ Experimental LLM-enhanced tutorial ⚠
1+
**⚠ Experimental LLM-enhanced tutorial ⚠**
22

33
This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based "coding tutor" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.
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‎chatify/cache.pkl

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‎chatify/failed_queries.pkl

+1
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@@ -0,0 +1 @@
1+
�]�.

‎chatify/process_notebooks.py

+67-4
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,5 @@
11
import os
2+
import yaml
23
from glob import glob as lsdir
34

45
import nbformat as nbf
@@ -8,9 +9,15 @@
89
import numpy as np
910
import pickle
1011

12+
from langchain.prompts import PromptTemplate
13+
from gptcache import Cache
14+
from gptcache.processor.pre import get_prompt
15+
from gptcache.manager import get_data_manager
16+
from gptcache.similarity_evaluation.exact_match import ExactMatchEvaluation
17+
1118
source_repo = 'NeuromatchAcademy'
1219
mod_repo = 'ContextLab'
13-
CACHE = False
20+
CACHE = True
1421

1522

1623
def get_tutorial_notebooks(basedir):
@@ -82,10 +89,49 @@ def get_code_cells(fname):
8289
return [compress_code(cell['source']) for cell in notebook['cells'] if cell['cell_type'] == 'code']
8390

8491

92+
def convert_pickle_file_to_cache(pickle_file, config):
93+
cache_db_version = config['cache_config']['cache_db_version']
94+
file_name = f'NMA_2023_v{cache_db_version}.cache'
95+
96+
# Remove file before creating a new one
97+
if os.path.exists(file_name):
98+
os.remove(file_name)
99+
100+
llm_cache = Cache()
101+
llm_cache.set_openai_key()
102+
data_manager = get_data_manager(data_path=file_name)
103+
104+
llm_cache.init(
105+
pre_embedding_func=get_prompt,
106+
data_manager=data_manager,
107+
similarity_evaluation=ExactMatchEvaluation(),
108+
)
109+
110+
chatify = Chatify()
111+
prompts = chatify._read_prompt_dir()['tutor']
112+
113+
with open(pickle_file, 'rb') as f:
114+
cache = pickle.load(f)
115+
116+
for key, value in cache.items():
117+
for prompt_name, prompt in prompts.items():
118+
prompt = PromptTemplate(
119+
template=prompt['content'],
120+
input_variables=prompt['input_variables'],
121+
)
122+
question = prompt.format(text=compress_code(key))
123+
try:
124+
answer = value[prompt_name]
125+
data_manager.save(question, answer, embedding_data=question)
126+
except KeyError:
127+
pass
128+
129+
85130
tutorials = get_tutorial_notebooks(os.getcwd())
86131
tutor = Chatify()
87132
prompts = tutor._read_prompt_dir()['tutor']
88133
code_cells = []
134+
failed_queries = []
89135

90136
for notebook in tqdm(tutorials):
91137
inject_chatify(notebook)
@@ -94,28 +140,45 @@ def get_code_cells(fname):
94140

95141
if CACHE:
96142
savefile = os.path.join(os.getcwd(), 'chatify', 'cache.pkl')
143+
failed_queries_file = os.path.join(os.getcwd(), 'chatify', 'failed_queries.pkl')
144+
97145
if os.path.exists(savefile):
98146
with open(savefile, 'rb') as f:
99147
cache = pickle.load(f)
100148
else:
101149
cache = {}
150+
151+
failed_queries = []
102152

103153
tmpfile = os.path.join(os.getcwd(), 'chatify', 'tmp.pkl')
104154
for cell in tqdm(np.unique(code_cells)):
105155
if cell not in cache:
106156
cache[cell] = {}
107157

108158
for name, content in prompts.items():
109-
if name not in cache[cell]:
159+
if name not in cache[cell] or len(cache[cell][name]) == 0:
110160
try:
111161
cache[cell][name] = tutor._cache(cell, content)
112162

113163
with open(tmpfile, 'wb') as f:
114164
pickle.dump(cache, f)
165+
166+
if cache[cell][name] is None or len(cache[cell][name]) == 0:
167+
failed_queries.append((cell, name, 'null response'))
168+
print('Response failed for cell (null response):\n', cell)
115169
except:
116-
print('Response failed for cell:\n', cell)
170+
failed_queries.append((cell, name, 'exception raised'))
171+
print('Response failed for cell (exception raised):\n', cell)
117172

118173
with open(savefile, 'wb') as f:
119174
pickle.dump(cache, f)
175+
176+
with open(failed_queries_file, 'wb') as f:
177+
pickle.dump(failed_queries, f)
178+
179+
if os.path.exists(tmpfile):
180+
os.remove(tmpfile)
120181

121-
os.remove(tmpfile)
182+
# build cache
183+
config = yaml.load(open('config.yaml', 'r'), Loader=yaml.SafeLoader)
184+
convert_pickle_file_to_cache(savefile, config)

‎tutorials/Bonus_Autoencoders/student/Bonus_Tutorial1.ipynb

+1-1
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@@ -86,7 +86,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
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"\n",
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"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

‎tutorials/Bonus_Autoencoders/student/Bonus_Tutorial2.ipynb

+1-1
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@@ -75,7 +75,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
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"\n",
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"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

‎tutorials/Bonus_Autoencoders/student/Bonus_Tutorial3.ipynb

+1-1
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@@ -77,7 +77,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
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"\n",
8282
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

‎tutorials/W1D1_ModelTypes/student/W1D1_Tutorial1.ipynb

+1-1
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@@ -88,7 +88,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
9292
"\n",
9393
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
9494
"\n",

‎tutorials/W1D1_ModelTypes/student/W1D1_Tutorial2.ipynb

+1-1
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@@ -82,7 +82,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8686
"\n",
8787
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

‎tutorials/W1D1_ModelTypes/student/W1D1_Tutorial3.ipynb

+1-1
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@@ -140,7 +140,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
144144
"\n",
145145
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

‎tutorials/W1D1_ModelTypes/student/W1D1_Tutorial4.ipynb

+1-1
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@@ -76,7 +76,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8080
"\n",
8181
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

‎tutorials/W1D2_ModelFitting/student/W1D2_Tutorial1.ipynb

+1-1
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
91+
"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
9292
"\n",
9393
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

‎tutorials/W1D2_ModelFitting/student/W1D2_Tutorial2.ipynb

+1-1
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@@ -84,7 +84,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
87+
"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8888
"\n",
8989
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
9090
"\n",

‎tutorials/W1D2_ModelFitting/student/W1D2_Tutorial3.ipynb

+1-1
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@@ -82,7 +82,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
85+
"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8686
"\n",
8787
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

‎tutorials/W1D2_ModelFitting/student/W1D2_Tutorial4.ipynb

+1-1
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
87+
"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8888
"\n",
8989
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
9090
"\n",

‎tutorials/W1D2_ModelFitting/student/W1D2_Tutorial5.ipynb

+1-1
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
88+
"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8989
"\n",
9090
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
9191
"\n",

‎tutorials/W1D2_ModelFitting/student/W1D2_Tutorial6.ipynb

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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
83+
"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8484
"\n",
8585
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
8686
"\n",

‎tutorials/W1D3_GeneralizedLinearModels/student/W1D3_Tutorial1.ipynb

+1-1
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
90+
"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
9191
"\n",
9292
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
9393
"\n",

‎tutorials/W1D3_GeneralizedLinearModels/student/W1D3_Tutorial2.ipynb

+1-1
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8989
"\n",
9090
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
9191
"\n",

‎tutorials/W1D4_DimensionalityReduction/student/W1D4_Tutorial1.ipynb

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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
86+
"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8787
"\n",
8888
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
8989
"\n",

‎tutorials/W1D4_DimensionalityReduction/student/W1D4_Tutorial2.ipynb

+1-1
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@@ -85,7 +85,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
88+
"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8989
"\n",
9090
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
9191
"\n",

‎tutorials/W1D4_DimensionalityReduction/student/W1D4_Tutorial3.ipynb

+1-1
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@@ -141,7 +141,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
145145
"\n",
146146
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
147147
"\n",

‎tutorials/W1D4_DimensionalityReduction/student/W1D4_Tutorial4.ipynb

+1-1
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@@ -136,7 +136,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
140140
"\n",
141141
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
142142
"\n",

‎tutorials/W1D5_DeepLearning/student/W1D5_Tutorial1.ipynb

+1-1
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@@ -87,7 +87,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
90+
"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
9191
"\n",
9292
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
9393
"\n",

‎tutorials/W1D5_DeepLearning/student/W1D5_Tutorial2.ipynb

+1-1
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@@ -82,7 +82,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
85+
"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8686
"\n",
8787
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

‎tutorials/W1D5_DeepLearning/student/W1D5_Tutorial3.ipynb

+1-1
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@@ -85,7 +85,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8989
"\n",
9090
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
9191
"\n",

‎tutorials/W1D5_DeepLearning/student/W1D5_Tutorial4.ipynb

+1-1
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@@ -57,7 +57,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
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"\n",
6262
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
6363
"\n",

‎tutorials/W2D1_ModelingPractice/student/W2D1_Tutorial1.ipynb

+1-1
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@@ -79,7 +79,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
8383
"\n",
8484
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

‎tutorials/W2D2_LinearSystems/student/W2D2_Tutorial1.ipynb

+1-1
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
93+
"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
9494
"\n",
9595
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

‎tutorials/W2D2_LinearSystems/student/W2D2_Tutorial2.ipynb

+1-1
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@@ -89,7 +89,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
9393
"\n",
9494
"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

‎tutorials/W2D2_LinearSystems/student/W2D2_Tutorial3.ipynb

+1-1
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@@ -85,7 +85,7 @@
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"execution": {}
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},
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"source": [
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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
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"\n",
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"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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‎tutorials/W2D2_LinearSystems/student/W2D2_Tutorial4.ipynb

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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
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"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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‎tutorials/W2D3_BiologicalNeuronModels/student/W2D3_Tutorial1.ipynb

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"### ⚠ Experimental LLM-enhanced tutorial ⚠\n",
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"**⚠ Experimental LLM-enhanced tutorial ⚠**\n",
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"\n",
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"This notebook includes Neuromatch's experimental [Chatify](https://github.com/ContextLab/chatify) 🤖 functionality. The Chatify notebook extension adds support for a large language model-based \"coding tutor\" to the materials. The tutor provides automatically generated text to help explain any code cell in this notebook.\n",
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"\n",

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