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semantic search inference - ml4hc.ipynb
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}, | |
"cells": [ | |
{ | |
"cell_type": "markdown", | |
"metadata": { | |
"id": "view-in-github", | |
"colab_type": "text" | |
}, | |
"source": [ | |
"<a href=\"https://colab.research.google.com/gist/pszemraj/f1168c3afc8f0a9166af27939546fd3e/semantic-search-inference-ml4hc.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"source": [ | |
"# <center> asymmetric semantic search inference on pre-embedded data\n", | |
"\n", | |
"> this is a notebook to demo/use generated embeddings on course data as text (slides, lecture audio, etc) via **asymmetric search** sort of like google.\n", | |
"\n", | |
"\n", | |
"- this is largely based on SBERT docs found [here](https://www.sbert.net/examples/applications/semantic-search/README.html#python)\n", | |
"\n", | |
"by [Peter](https://peterszemraj.ch/)\n", | |
"\n", | |
"\n", | |
"---\n" | |
], | |
"metadata": { | |
"id": "Ej0_4M8vbaFx" | |
} | |
}, | |
{ | |
"cell_type": "markdown", | |
"source": [ | |
"# setup\n" | |
], | |
"metadata": { | |
"id": "sX1pA0zk0sqA" | |
} | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 1, | |
"metadata": { | |
"cellView": "form", | |
"id": "LrDWdEzv3LaX" | |
}, | |
"outputs": [], | |
"source": [ | |
"#@markdown add auto-Colab formatting with `IPython.display`\n", | |
"from IPython.display import HTML, display\n", | |
"# colab formatting\n", | |
"def set_css():\n", | |
" display(\n", | |
" HTML(\n", | |
" \"\"\"\n", | |
" <style>\n", | |
" pre {\n", | |
" white-space: pre-wrap;\n", | |
" }\n", | |
" </style>\n", | |
" \"\"\"\n", | |
" )\n", | |
" )\n", | |
"\n", | |
"get_ipython().events.register(\"pre_run_cell\", set_css)" | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"source": [ | |
"this notebook works perfectly fine without GPU, but if you want to use a GPU the below will tell you what it is\n" | |
], | |
"metadata": { | |
"id": "SzGHfgzizNoL" | |
} | |
}, | |
{ | |
"cell_type": "code", | |
"source": [ | |
"!nvidia-smi" | |
], | |
"metadata": { | |
"id": "DJdHy1sSdbBj", | |
"outputId": "dbf2ddf5-f9d3-49a9-be20-6560f3cb5fb7", | |
"colab": { | |
"base_uri": "https://localhost:8080/", | |
"height": 0 | |
} | |
}, | |
"execution_count": 2, | |
"outputs": [ | |
{ | |
"output_type": "display_data", | |
"data": { | |
"text/plain": [ | |
"<IPython.core.display.HTML object>" | |
], | |
"text/html": [ | |
"\n", | |
" <style>\n", | |
" pre {\n", | |
" white-space: pre-wrap;\n", | |
" }\n", | |
" </style>\n", | |
" " | |
] | |
}, | |
"metadata": {} | |
}, | |
{ | |
"output_type": "stream", | |
"name": "stdout", | |
"text": [ | |
"NVIDIA-SMI has failed because it couldn't communicate with the NVIDIA driver. Make sure that the latest NVIDIA driver is installed and running.\n", | |
"\n" | |
] | |
} | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 3, | |
"metadata": { | |
"id": "vH8Re5UelYAc", | |
"cellView": "form", | |
"outputId": "e3cdbac4-06b2-4d86-c8b6-2ae2a3c6b28b", | |
"colab": { | |
"base_uri": "https://localhost:8080/", | |
"height": 0 | |
} | |
}, | |
"outputs": [ | |
{ | |
"output_type": "display_data", | |
"data": { | |
"text/plain": [ | |
"<IPython.core.display.HTML object>" | |
], | |
"text/html": [ | |
"\n", | |
" <style>\n", | |
" pre {\n", | |
" white-space: pre-wrap;\n", | |
" }\n", | |
" </style>\n", | |
" " | |
] | |
}, | |
"metadata": {} | |
}, | |
{ | |
"output_type": "stream", | |
"name": "stdout", | |
"text": [ | |
"\u001b[K |████████████████████████████████| 85 kB 2.7 MB/s \n", | |
"\u001b[K |████████████████████████████████| 35.3 MB 137 kB/s \n", | |
"\u001b[K |████████████████████████████████| 4.7 MB 48.2 MB/s \n", | |
"\u001b[K |████████████████████████████████| 1.3 MB 32.9 MB/s \n", | |
"\u001b[K |████████████████████████████████| 120 kB 42.2 MB/s \n", | |
"\u001b[K |████████████████████████████████| 6.6 MB 30.2 MB/s \n", | |
"\u001b[?25h Building wheel for sentence-transformers (setup.py) ... \u001b[?25l\u001b[?25hdone\n" | |
] | |
} | |
], | |
"source": [ | |
"#@title installs\n", | |
"\n", | |
"!pip install -U sentence-transformers pyarrow -q\n", | |
"\n", | |
"import torch\n", | |
"from pathlib import Path\n", | |
"\n", | |
"from sentence_transformers import SentenceTransformer, util\n", | |
"import logging\n", | |
"logging.basicConfig(\n", | |
" level=logging.INFO, \n", | |
" format=\"%(asctime)s - %(levelname)s - %(message)s\",\n", | |
" filename=\"embed_coursedata.log\",\n", | |
"\n", | |
")" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"source": [ | |
"hf_tag = \"sentence-transformers/msmarco-distilbert-cos-v5\" #@param {type:\"string\"}\n", | |
"\n", | |
"use_gpu = torch.cuda.is_available()\n", | |
"print(f\"using GPU = {use_gpu}\")\n", | |
"model = SentenceTransformer(\n", | |
" hf_tag,\n", | |
" device='cuda' if use_gpu else 'cpu',\n", | |
" )\n", | |
"# model = SentenceTransformer('sentence-transformers/msmarco-MiniLM-L12-cos-v5')\n", | |
"\n" | |
], | |
"metadata": { | |
"cellView": "form", | |
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"height": 0, | |
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] | |
} | |
}, | |
"execution_count": 4, | |
"outputs": [ | |
{ | |
"output_type": "display_data", | |
"data": { | |
"text/plain": [ | |
"<IPython.core.display.HTML object>" | |
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" " | |
] | |
}, | |
"metadata": {} | |
}, | |
{ | |
"output_type": "stream", | |
"name": "stdout", | |
"text": [ | |
"using GPU = False\n" | |
] | |
}, | |
{ | |
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} | |
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"metadata": {} | |
} | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"source": [ | |
"## load data\n" | |
], | |
"metadata": { | |
"id": "t_17L9_H0vE1" | |
} | |
}, | |
{ | |
"cell_type": "code", | |
"source": [ | |
"#@markdown Embeddings on documents are pre-computed :)\n", | |
"\n", | |
"url = \"https://www.dropbox.com/s/847egxwysc75g2p/embedded_course_data.pkl?dl=1\" #@param {type:\"string\"}\n" | |
], | |
"metadata": { | |
"cellView": "form", | |
"id": "WzlEqQ9PxLRe", | |
"outputId": "44246f24-f2fd-4053-cf04-4eb4a7c8f30d", | |
"colab": { | |
"base_uri": "https://localhost:8080/", | |
"height": 0 | |
} | |
}, | |
"execution_count": 5, | |
"outputs": [ | |
{ | |
"output_type": "display_data", | |
"data": { | |
"text/plain": [ | |
"<IPython.core.display.HTML object>" | |
], | |
"text/html": [ | |
"\n", | |
" <style>\n", | |
" pre {\n", | |
" white-space: pre-wrap;\n", | |
" }\n", | |
" </style>\n", | |
" " | |
] | |
}, | |
"metadata": {} | |
} | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"source": [ | |
"data_path = \"embedded_course_data.pkl\"\n", | |
"!wget -O $data_path $url" | |
], | |
"metadata": { | |
"id": "fMkGkeGbxWYw", | |
"outputId": "cd672bf0-8680-43d2-ae67-5cf8b3efa6aa", | |
"colab": { | |
"base_uri": "https://localhost:8080/", | |
"height": 0 | |
} | |
}, | |
"execution_count": 6, | |
"outputs": [ | |
{ | |
"output_type": "display_data", | |
"data": { | |
"text/plain": [ | |
"<IPython.core.display.HTML object>" | |
], | |
"text/html": [ | |
"\n", | |
" <style>\n", | |
" pre {\n", | |
" white-space: pre-wrap;\n", | |
" }\n", | |
" </style>\n", | |
" " | |
] | |
}, | |
"metadata": {} | |
}, | |
{ | |
"output_type": "stream", | |
"name": "stdout", | |
"text": [ | |
"--2022-09-02 14:17:49-- https://www.dropbox.com/s/847egxwysc75g2p/embedded_course_data.pkl?dl=1\n", | |
"Resolving www.dropbox.com (www.dropbox.com)... 162.125.80.18, 2620:100:6017:18::a27d:212\n", | |
"Connecting to www.dropbox.com (www.dropbox.com)|162.125.80.18|:443... connected.\n", | |
"HTTP request sent, awaiting response... 302 Found\n", | |
"Location: /s/dl/847egxwysc75g2p/embedded_course_data.pkl [following]\n", | |
"--2022-09-02 14:17:49-- https://www.dropbox.com/s/dl/847egxwysc75g2p/embedded_course_data.pkl\n", | |
"Reusing existing connection to www.dropbox.com:443.\n", | |
"HTTP request sent, awaiting response... 302 Found\n", | |
"Location: https://uc9beaf85f78916abdebe9585e3d.dl.dropboxusercontent.com/cd/0/get/BsIRAYwDMKVONRsCzI0qk9lNvvuf-vYWyYk_mn9k6EqT6rxl0HtiKS4Skb59YlKY2TnVh8eLDmnV8TaPyYJFoGXBJiwLukj8b_614HCrhQ9ueSVssBGVkNCqfSFAJZetdg_r-lIVvocuePiA9uUXpMaGtMjyBcUMp1wRg3GYw0T6ag/file?dl=1# [following]\n", | |
"--2022-09-02 14:17:50-- https://uc9beaf85f78916abdebe9585e3d.dl.dropboxusercontent.com/cd/0/get/BsIRAYwDMKVONRsCzI0qk9lNvvuf-vYWyYk_mn9k6EqT6rxl0HtiKS4Skb59YlKY2TnVh8eLDmnV8TaPyYJFoGXBJiwLukj8b_614HCrhQ9ueSVssBGVkNCqfSFAJZetdg_r-lIVvocuePiA9uUXpMaGtMjyBcUMp1wRg3GYw0T6ag/file?dl=1\n", | |
"Resolving uc9beaf85f78916abdebe9585e3d.dl.dropboxusercontent.com (uc9beaf85f78916abdebe9585e3d.dl.dropboxusercontent.com)... 162.125.80.15, 2620:100:6030:15::a27d:500f\n", | |
"Connecting to uc9beaf85f78916abdebe9585e3d.dl.dropboxusercontent.com (uc9beaf85f78916abdebe9585e3d.dl.dropboxusercontent.com)|162.125.80.15|:443... connected.\n", | |
"HTTP request sent, awaiting response... 200 OK\n", | |
"Length: 5685949 (5.4M) [application/binary]\n", | |
"Saving to: ‘embedded_course_data.pkl’\n", | |
"\n", | |
"embedded_course_dat 100%[===================>] 5.42M 11.8MB/s in 0.5s \n", | |
"\n", | |
"2022-09-02 14:17:55 (11.8 MB/s) - ‘embedded_course_data.pkl’ saved [5685949/5685949]\n", | |
"\n" | |
] | |
} | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"source": [ | |
"import joblib\n", | |
"data_path = Path(data_path).resolve()\n", | |
"embedded_course = joblib.load(data_path)\n", | |
"embedded_course.head()" | |
], | |
"metadata": { | |
"colab": { | |
"base_uri": "https://localhost:8080/", | |
"height": 0 | |
}, | |
"id": "cBGRPiPKxv-k", | |
"outputId": "25c06f15-0dae-4100-81ef-915c4beb8cb9" | |
}, | |
"execution_count": 7, | |
"outputs": [ | |
{ | |
"output_type": "display_data", | |
"data": { | |
"text/plain": [ | |
"<IPython.core.display.HTML object>" | |
], | |
"text/html": [ | |
"\n", | |
" <style>\n", | |
" pre {\n", | |
" white-space: pre-wrap;\n", | |
" }\n", | |
" </style>\n", | |
" " | |
] | |
}, | |
"metadata": {} | |
}, | |
{ | |
"output_type": "execute_result", | |
"data": { | |
"text/plain": [ | |
" id_within_doc doc_text \\\n", | |
"0 0 zurich natural language processing project 2 a... \n", | |
"1 1 alizee pace 29. 03. 2021 pain exposure physica... \n", | |
"2 2 ##359 doi : 10. 1007 / s00432 - 004 - 0552 mas... \n", | |
"3 3 history of chronic hepatitis in urban shanghai... \n", | |
"4 4 phase 3 trial in 3 ascending, orvolvement of a... \n", | |
"\n", | |
" doc_name doc_dir doc_relative_loc \\\n", | |
"0 OCR_Project2ML4HNLP_ coursedocsJune22-ml4hc 0.0 \n", | |
"1 OCR_Project2ML4HNLP_ coursedocsJune22-ml4hc 7.143 \n", | |
"2 OCR_Project2ML4HNLP_ coursedocsJune22-ml4hc 14.286 \n", | |
"3 OCR_Project2ML4HNLP_ coursedocsJune22-ml4hc 21.429 \n", | |
"4 OCR_Project2ML4HNLP_ coursedocsJune22-ml4hc 28.571 \n", | |
"\n", | |
" doc_embeddings \n", | |
"0 [-0.0071430462, -0.035852537, 0.06472769, -0.0... \n", | |
"1 [-0.054871712, 0.0041954266, 0.035234813, 0.00... \n", | |
"2 [0.012789174, 0.014841921, -0.01317768, -0.021... \n", | |
"3 [-0.042795025, -0.038891725, 0.023976067, -0.0... \n", | |
"4 [-0.05967743, -0.0730482, 0.05493018, -0.02719... " | |
], | |
"text/html": [ | |
"\n", | |
" <div id=\"df-73f5c187-1032-4cee-b227-fe2847e21236\">\n", | |
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} | |
] | |
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{ | |
"cell_type": "code", | |
"source": [ | |
"#@markdown `embedded_course` is a pandas df can be used for\n", | |
"#@markdown whatever pandas things you need.\n", | |
"\n", | |
"print(f\"type is {type(embedded_course)}\")\n", | |
"embedded_course.info()" | |
], | |
"metadata": { | |
"colab": { | |
"base_uri": "https://localhost:8080/", | |
"height": 0 | |
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"cellView": "form", | |
"id": "p7YL1KGPxZsz", | |
"outputId": "ee9f5b8a-da58-4447-b459-0285026ec87c" | |
}, | |
"execution_count": 8, | |
"outputs": [ | |
{ | |
"output_type": "display_data", | |
"data": { | |
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"metadata": {} | |
}, | |
{ | |
"output_type": "stream", | |
"name": "stdout", | |
"text": [ | |
"type is <class 'pandas.core.frame.DataFrame'>\n", | |
"<class 'pandas.core.frame.DataFrame'>\n", | |
"RangeIndex: 1471 entries, 0 to 1470\n", | |
"Data columns (total 6 columns):\n", | |
" # Column Non-Null Count Dtype \n", | |
"--- ------ -------------- ----- \n", | |
" 0 id_within_doc 1471 non-null Int64 \n", | |
" 1 doc_text 1471 non-null string \n", | |
" 2 doc_name 1471 non-null string \n", | |
" 3 doc_dir 1471 non-null string \n", | |
" 4 doc_relative_loc 1471 non-null Float64\n", | |
" 5 doc_embeddings 1471 non-null object \n", | |
"dtypes: Float64(1), Int64(1), object(1), string(3)\n", | |
"memory usage: 72.0+ KB\n" | |
] | |
} | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"source": [ | |
"# Query the embeddings\n" | |
], | |
"metadata": { | |
"id": "5kzc-FgIeiiZ" | |
} | |
}, | |
{ | |
"cell_type": "code", | |
"source": [ | |
"\n", | |
"import pprint as pp\n", | |
"import time\n", | |
"from pathlib import Path\n", | |
"\n", | |
"import joblib\n", | |
"import numpy as np\n", | |
"import pandas as pd\n", | |
"import torch\n", | |
"from sentence_transformers import SentenceTransformer, util\n", | |
"#@markdown define `semantic_search`\n", | |
"import pandas as pd\n", | |
"def semantic_search(\n", | |
" query: str,\n", | |
" sbert_model,\n", | |
" emdf: pd.DataFrame,\n", | |
" embedding_col: str = \"doc_embeddings\",\n", | |
" top_n=5,\n", | |
" unique_col=\"doc_name\",\n", | |
" return_unique=True,\n", | |
"):\n", | |
" \"\"\"\n", | |
" semantic_search - core semantic search function using cosine similarity\n", | |
" Parameters\n", | |
" ----------\n", | |
" query : str, text to search for\n", | |
" sbert_model : sentence-transformers model to use for encoding\n", | |
" emdf : dataframe with the encoded document embeddings\n", | |
" embedding_col : str, column name of the embedding column in the emdf, by default \"doc_embeddings\"\n", | |
" top_n : int, optional, by default 5, number of most-similar results to return\n", | |
" Returns\n", | |
" -------\n", | |
" dict - a dictionary with the aggregated search result text as key, cosine similarity score as value\n", | |
" \"\"\"\n", | |
" top_n_loop = top_n + 30 if return_unique else top_n\n", | |
" top_k = min(top_n_loop, len(emdf))\n", | |
" _data = [np.array(a, dtype=np.float32) for a in emdf[embedding_col].values]\n", | |
"\n", | |
" use_gpu = torch.cuda.is_available()\n", | |
"\n", | |
" corpus_embeddings = torch.FloatTensor(_data)\n", | |
" query_embedding = sbert_model.encode(query, convert_to_tensor=True)\n", | |
"\n", | |
" if use_gpu:\n", | |
" corpus_embeddings = corpus_embeddings.to(\"cuda\")\n", | |
" query_embedding = query_embedding.to(\"cuda\")\n", | |
" else:\n", | |
" corpus_embeddings = corpus_embeddings.cpu()\n", | |
" query_embedding = query_embedding.cpu()\n", | |
" cos_scores = util.cos_sim(query_embedding, corpus_embeddings)[0]\n", | |
" top_results = torch.topk(cos_scores, k=top_k)\n", | |
"\n", | |
" results = []\n", | |
" docs_found = []\n", | |
" result_rank = 0\n", | |
" for score, idx in zip(top_results[0], top_results[1]):\n", | |
"\n", | |
" result_rank += 1\n", | |
" idx = int(idx)\n", | |
" _result = {}\n", | |
" _result[\"Rank\"] = result_rank\n", | |
" _result[\"Score (0-1)\"] = round(float(score.cpu().numpy()), 4)\n", | |
"\n", | |
" for c in emdf.columns:\n", | |
" if c == embedding_col:\n", | |
" continue\n", | |
" _result[c] = emdf.loc[idx, c]\n", | |
"\n", | |
" if return_unique:\n", | |
" # check if the result is already in the results list\n", | |
" if _result[unique_col] in docs_found:\n", | |
" continue\n", | |
" else:\n", | |
" results.append(_result)\n", | |
" docs_found.append(_result[unique_col])\n", | |
"\n", | |
" else:\n", | |
" results.append(_result)\n", | |
"\n", | |
" if len(results) >= top_n:\n", | |
" break\n", | |
" return results" | |
], | |
"metadata": { | |
"colab": { | |
"base_uri": "https://localhost:8080/", | |
"height": 17 | |
}, | |
"cellView": "form", | |
"id": "bxMKbeijejch", | |
"outputId": "bf701bf8-886d-4a3e-fd0f-c224f870e219" | |
}, | |
"execution_count": 9, | |
"outputs": [ | |
{ | |
"output_type": "display_data", | |
"data": { | |
"text/plain": [ | |
"<IPython.core.display.HTML object>" | |
], | |
"text/html": [ | |
"\n", | |
" <style>\n", | |
" pre {\n", | |
" white-space: pre-wrap;\n", | |
" }\n", | |
" </style>\n", | |
" " | |
] | |
}, | |
"metadata": {} | |
} | |
] | |
}, | |
{ | |
"cell_type": "markdown", | |
"source": [ | |
"\n", | |
"## <font color=\"DodgerBlue\"> _**Your Query Goes Here**_\n", | |
"\n", | |
"Enter the term/phrase you want to find results for (_think Google search_) into `query`, and adjust params. Then run the cell! Should only take a couple seconds max.\n", | |
"\n", | |
"- `return_unique`: whether or not you want the search results to be unique with respect to what text file (lecture1 audio, tecture 3 slides, etc) they are from\n", | |
"- `number_results`: how many results to return\n", | |
"\n", | |
"If you want more details, you can use `embedded_course` as a standard dataframe to find things 👍" | |
], | |
"metadata": { | |
"id": "ZZlxdLf8zojH" | |
} | |
}, | |
{ | |
"cell_type": "code", | |
"source": [ | |
"%%time\n", | |
"query = \"jensen divergence metric downsides\" #@param {type:\"string\"}\n", | |
"return_unique = True #@param {type:\"boolean\"}\n", | |
"number_results = 5 #@param {type:\"integer\"}\n", | |
"import pprint as pp\n", | |
"result = semantic_search(\n", | |
" query=query,\n", | |
" sbert_model=model,\n", | |
" emdf=embedded_course,\n", | |
" return_unique=return_unique,\n", | |
" top_n = number_results,\n", | |
")\n", | |
"#@markdown note that `doc_relative_loc` is a _percentage_ of the way through\n", | |
"#@markdown the parent text file that the snippet is found.\n", | |
"pp.pprint(result)" | |
], | |
"metadata": { | |
"colab": { | |
"base_uri": "https://localhost:8080/", | |
"height": 1000 | |
}, | |
"cellView": "form", | |
"id": "qaAAlbqtel7e", | |
"outputId": "bfc1be3e-ce95-4be1-d26b-a7d1bdf020b4" | |
}, | |
"execution_count": 11, | |
"outputs": [ | |
{ | |
"output_type": "display_data", | |
"data": { | |
"text/plain": [ | |
"<IPython.core.display.HTML object>" | |
], | |
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"\n", | |
" <style>\n", | |
" pre {\n", | |
" white-space: pre-wrap;\n", | |
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" " | |
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{ | |
"output_type": "stream", | |
"name": "stdout", | |
"text": [ | |
"[{'Rank': 1,\n", | |
" 'Score (0-1)': 0.3537,\n", | |
" 'doc_dir': 'papers-referenced',\n", | |
" 'doc_name': 'OCR Multilevel Medical Embedding of Electronic Health Records '\n", | |
" 'for Predictive Healthcare',\n", | |
" 'doc_relative_loc': 69.565,\n", | |
" 'doc_text': 'the preferred nonlinear activation for hidden layers in many '\n", | |
" 'studies this seems due t0 the regularizing effect of sigmoid '\n", | |
" 'and tanh functions _ whereas relu can produce outputs as high '\n", | |
" 'as infinity, sigmoid and tanh have bounded outputs considering '\n", | |
" 'that sigmoid, tanh and relu all sum up the code embeddings in '\n", | |
" 'visit v ( t ) before applying the nonlinear activation, '\n", | |
" 'constraining the output of the nonlinear activation seems to '\n", | |
" 'work favorably, especially in d3 where there are more 13 codes '\n", | |
" 'per visit. this regularization benefit, however ; diminishes as '\n", | |
" 'the dataset grows, which can be confirmed by table / 7lin '\n", | |
" 'sectionf ] in addition, as can be seen by the performance of '\n", | |
" 'sigmoid, lp, sigmoid suffers from the vanishing gradient '\n", | |
" 'problem as opposed to tanh o relu that have larger gradient '\n", | |
" 'values. e roc - auc of heart failure prediction on datasets d1, '\n", | |
" 'dz, and d : table 6 : roc - auc of all models for hf prediction '\n", | |
" 'on small datasets. values in the parentheses denote standard '\n", | |
" 'deviations from 5 - fold random data splits two best values in '\n", | |
" 'each column are marked in bold : d2 d ; visit complexity 0 - '\n", | |
" '159, 5608',\n", | |
" 'id_within_doc': 48},\n", | |
" {'Rank': 2,\n", | |
" 'Score (0-1)': 0.3488,\n", | |
" 'doc_dir': 'coursedocsJune22-ml4hc',\n", | |
" 'doc_name': 'OCR_Tutorial13-Examquestions_',\n", | |
" 'doc_relative_loc': 90.476,\n", | |
" 'doc_text': 'gan and the reasons to use wgan over gan. classical gans use '\n", | |
" 'the jensen divergence metric ( not continuous ) to compare the '\n", | |
" 'true and the synthetic data distribution wasserstein gans use '\n", | |
" 'the earth - mover divergence ( continuous ) metric to compare '\n", | |
" 'the true and the synthetic data distributions wgans are more '\n", | |
" 'stable due to smoother gradients. they are preferred in '\n", | |
" 'practice 34 machine learning for health care, spring 2022 '\n", | |
" 'tutorial 13 alice bizeul 24. 05. 2022 ethics e question 1 1. '\n", | |
" 'mark below the necessary criteria for consent : a voluntariness '\n", | |
" 'b _ willfulness c capacity to understand d. trustworthiness e _ '\n", | |
" 'adequate information 35 machine learning for health care, '\n", | |
" 'spring 2022 tutorial 13 alice bizeul 24. 05. 2022 ethics e '\n", | |
" 'question 1 1. mark below the necessary criteria for consent : a '\n", | |
" 'voluntariness b willfulness c capacity to understand d _ '\n", | |
" 'trustworthiness e adequate information 36 machine learning for '\n", | |
" 'health care, spring 2022 tutorial 13 alice bizeul 24. 05. 2022 '\n", | |
" 'questions? also, on moodle ( preferred : your classmates '\n", | |
" 'probably have similar questions! ) or by email at alice bizeul '\n", | |
" '@ aiethzch machine learning for health care, spring 2022',\n", | |
" 'id_within_doc': 19},\n", | |
" {'Rank': 3,\n", | |
" 'Score (0-1)': 0.3356,\n", | |
" 'doc_dir': 'lecture-audio-full',\n", | |
" 'doc_name': 'SC_lecture_privac_transcription_15_GT',\n", | |
" 'doc_relative_loc': 76.923,\n", | |
" 'doc_text': ', and first, we tried to predict our patient readmission. it '\n", | |
" \"worked okay, and then we said as it's that imbalances we tried \"\n", | |
" 'to in, in addition, neurite the unbalanced the minority class '\n", | |
" 'and see what hips and see if you can also with '\n", | |
" 'disdegeneratedta, enrich thbbaseta to help the basil hospital '\n", | |
" \"in the end and for this, we used a model as i said before, it's \"\n", | |
" \"not viable gear. still, it's a little different, but we used a \"\n", | |
" 'different loss term and a different way to quantify the '\n", | |
" 'difference between the generated and training data instead of '\n", | |
" 'the trans and china direction. the basasteine and the '\n", | |
" 'passionate distance are different ways of measuring the '\n", | |
" \"distance between distributions. so here's an example of the \"\n", | |
" 'difference between the vassasteine distance and the sham '\n", | |
" 'divergence used in a classic grain. so the classic grain uses '\n", | |
" 'the genzenchanne divergence some compared distributions. still, '\n", | |
" 'if these distributions are completely dishonest, as you see '\n", | |
" 'here, this is a function where they are completely disjointed '\n", | |
" 'except when this distribution here is zero, so they are the '\n", | |
" \"same. and if you compute this distance here, there's a sudden\",\n", | |
" 'id_within_doc': 20},\n", | |
" {'Rank': 4,\n", | |
" 'Score (0-1)': 0.3155,\n", | |
" 'doc_dir': 'lecture-audio-full',\n", | |
" 'doc_name': 'SC_lecture_genetics_p_2_v_2_c_transcription_12_GT',\n", | |
" 'doc_relative_loc': 32.203,\n", | |
" 'doc_text': 'so instead of using conditional probabilities, we have these '\n", | |
" 'joint probabilities, which take just this systemic expression '\n", | |
" 'here, and then, by a miracle, it worked quite nicely. so '\n", | |
" 'instead of having this violation where everything is crowded, '\n", | |
" 'you have the beautiful civilization where we see clusters in '\n", | |
" 'our data ; the main reason for this was the properties of the '\n", | |
" 'kashit distribution here that it has heavier tails so the '\n", | |
" 'customers can kind of. they prefer to go away from one another. '\n", | |
" 'so now i wanted to show you what kind of visualization the time '\n", | |
" 'can create when we change this parameter of perplexity, which '\n", | |
" 'affects how far each observation contains other observations so '\n", | |
" 'hear the original later set was this one about two reasons to '\n", | |
" 'closure is a sample with the ocean distribution. then we apply '\n", | |
" 'themselves of different values of the perplexity parameters '\n", | |
" 'from two to one hundred, and this is what the restrictions that '\n", | |
" 'we can obtain so he would transform to do into two do, but this '\n", | |
" 'is just for an illustration purpose. what you can see here is '\n", | |
" 'only that with perplexity values about thirty and fifty. you '\n", | |
" 'see this too. beautiful questions when perplexity is too low, '\n", | |
" 'we see too many letters, so we cannot really capture the true '\n", | |
" 'structure in the data, and then the',\n", | |
" 'id_within_doc': 19},\n", | |
" {'Rank': 6,\n", | |
" 'Score (0-1)': 0.2879,\n", | |
" 'doc_dir': 'papers-referenced',\n", | |
" 'doc_name': 'OCR_3D Conditional GAN-based Super-resolution for CT Slice '\n", | |
" 'Interval',\n", | |
" 'doc_relative_loc': 28.571,\n", | |
" 'doc_text': 'adversarial model d that tries to maximize it. g and d can be '\n", | |
" 'implemented as convolutional neural networks ( cnn ). we also '\n", | |
" 'use l loss to calculate pixel - wise appearance differences '\n", | |
" 'between ground truth images and generated images, which has '\n", | |
" 'been shown to give less blurring than the lz loss in diversity '\n", | |
" 'of image - to - image translation tasks [ 7 ; therefore, the '\n", | |
" 'out final objective is expressed as arg min max lcgan ( g, d ) '\n", | |
" '+ all ( g ) ( 2 ) figure q ] illustrates the proposed '\n", | |
" 'adversarial training procedure. note that the additional '\n", | |
" 'conditions are not inputted into the generator. aj kudo et al. '\n", | |
" 'positive examples 8 negative examples discriminator '\n", | |
" 'discriminator ground truth thick image virtual thin thick image '\n", | |
" 'body part 0 - level slice ( mm ) body part 0 - level slice ( mm '\n", | |
" ') generator input ground truth condition thick image degrade 8 '\n", | |
" 'mm m conditions body part : head slice : 8 mm 1. 6 gaussian '\n", | |
" 'blurs ( 0 _ downsample spline interpolation fig. 2. adversarial '\n", | |
" 'training framework of thick - thin slice translation on ct '\n", | |
" 'images. in each training iteration, the thin slice input data '\n", | |
" 'is randomly degraded to simulate thick slice data. for the '\n", | |
" 'generator',\n", | |
" 'id_within_doc': 6}]\n", | |
"CPU times: user 167 ms, sys: 4.24 ms, total: 171 ms\n", | |
"Wall time: 166 ms\n" | |
] | |
} | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"source": [], | |
"metadata": { | |
"id": "d4KUgZo9eucn" | |
}, | |
"execution_count": 10, | |
"outputs": [] | |
} | |
] | |
} |
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