D_Treatment_Topic_Identification_Word2Vec_Roberta_Self_Report.ipynb

{"cells":[{"cell_type":"markdown","metadata":{},"source":["[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/swati-rajwal/BreastCancer_tweets_project/blob/main/D_Treatment_Topic_Identification_Word2Vec_Roberta_Self_Report.ipynb)"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"executionInfo":{"elapsed":956,"status":"ok","timestamp":1711899465802,"user":{"displayName":"Avinash kumar Pandey","userId":"07918242858559780186"},"user_tz":240},"id":"t8LS8_-Xrfor","outputId":"837b0dbe-2279-43bc-85db-42f16cf70e08"},"outputs":[{"name":"stdout","output_type":"stream","text":["Drive already mounted at /content/drive; to attempt to forcibly remount, call drive.mount(\"/content/drive\", force_remount=True).\n"]}],"source":["from google.colab import drive\n","drive.mount('/content/drive')"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"executionInfo":{"elapsed":6478,"status":"ok","timestamp":1711899473951,"user":{"displayName":"Avinash kumar Pandey","userId":"07918242858559780186"},"user_tz":240},"id":"8Emb7AaUtO0D","outputId":"a0741470-397d-48cd-bcb3-0f002f4b7da5"},"outputs":[{"name":"stdout","output_type":"stream","text":["Requirement already satisfied: bertopic in /usr/local/lib/python3.10/dist-packages (0.16.0)\n","Requirement already satisfied: numpy>=1.20.0 in /usr/local/lib/python3.10/dist-packages (from bertopic) (1.25.2)\n","Requirement already satisfied: hdbscan>=0.8.29 in /usr/local/lib/python3.10/dist-packages (from bertopic) (0.8.33)\n","Requirement already satisfied: umap-learn>=0.5.0 in /usr/local/lib/python3.10/dist-packages (from bertopic) (0.5.5)\n","Requirement already satisfied: pandas>=1.1.5 in /usr/local/lib/python3.10/dist-packages (from bertopic) (1.5.3)\n","Requirement already satisfied: scikit-learn>=0.22.2.post1 in /usr/local/lib/python3.10/dist-packages (from bertopic) (1.2.2)\n","Requirement already satisfied: tqdm>=4.41.1 in /usr/local/lib/python3.10/dist-packages (from bertopic) (4.66.2)\n","Requirement already satisfied: sentence-transformers>=0.4.1 in /usr/local/lib/python3.10/dist-packages (from bertopic) (2.6.1)\n","Requirement already satisfied: plotly>=4.7.0 in /usr/local/lib/python3.10/dist-packages (from bertopic) (5.15.0)\n","Requirement already satisfied: cython<3,>=0.27 in /usr/local/lib/python3.10/dist-packages (from hdbscan>=0.8.29->bertopic) (0.29.37)\n","Requirement already satisfied: scipy>=1.0 in /usr/local/lib/python3.10/dist-packages (from hdbscan>=0.8.29->bertopic) (1.11.4)\n","Requirement already satisfied: joblib>=1.0 in /usr/local/lib/python3.10/dist-packages (from hdbscan>=0.8.29->bertopic) (1.3.2)\n","Requirement already satisfied: python-dateutil>=2.8.1 in /usr/local/lib/python3.10/dist-packages (from pandas>=1.1.5->bertopic) (2.8.2)\n","Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas>=1.1.5->bertopic) (2023.4)\n","Requirement already satisfied: tenacity>=6.2.0 in /usr/local/lib/python3.10/dist-packages (from plotly>=4.7.0->bertopic) (8.2.3)\n","Requirement already satisfied: packaging in /usr/local/lib/python3.10/dist-packages (from plotly>=4.7.0->bertopic) (24.0)\n","Requirement already satisfied: threadpoolctl>=2.0.0 in /usr/local/lib/python3.10/dist-packages (from scikit-learn>=0.22.2.post1->bertopic) (3.4.0)\n","Requirement already satisfied: transformers<5.0.0,>=4.32.0 in /usr/local/lib/python3.10/dist-packages (from sentence-transformers>=0.4.1->bertopic) (4.38.2)\n","Requirement already satisfied: torch>=1.11.0 in /usr/local/lib/python3.10/dist-packages (from sentence-transformers>=0.4.1->bertopic) (2.2.1+cu121)\n","Requirement already satisfied: huggingface-hub>=0.15.1 in /usr/local/lib/python3.10/dist-packages (from sentence-transformers>=0.4.1->bertopic) (0.20.3)\n","Requirement already satisfied: Pillow in /usr/local/lib/python3.10/dist-packages (from sentence-transformers>=0.4.1->bertopic) (9.4.0)\n","Requirement already satisfied: numba>=0.51.2 in /usr/local/lib/python3.10/dist-packages (from umap-learn>=0.5.0->bertopic) (0.58.1)\n","Requirement already satisfied: pynndescent>=0.5 in /usr/local/lib/python3.10/dist-packages (from umap-learn>=0.5.0->bertopic) (0.5.12)\n","Requirement already satisfied: filelock in /usr/local/lib/python3.10/dist-packages (from huggingface-hub>=0.15.1->sentence-transformers>=0.4.1->bertopic) (3.13.3)\n","Requirement already satisfied: fsspec>=2023.5.0 in /usr/local/lib/python3.10/dist-packages (from huggingface-hub>=0.15.1->sentence-transformers>=0.4.1->bertopic) (2023.6.0)\n","Requirement already satisfied: requests in /usr/local/lib/python3.10/dist-packages (from huggingface-hub>=0.15.1->sentence-transformers>=0.4.1->bertopic) (2.31.0)\n","Requirement already satisfied: pyyaml>=5.1 in /usr/local/lib/python3.10/dist-packages (from huggingface-hub>=0.15.1->sentence-transformers>=0.4.1->bertopic) (6.0.1)\n","Requirement already satisfied: typing-extensions>=3.7.4.3 in /usr/local/lib/python3.10/dist-packages (from huggingface-hub>=0.15.1->sentence-transformers>=0.4.1->bertopic) (4.10.0)\n","Requirement already satisfied: llvmlite<0.42,>=0.41.0dev0 in /usr/local/lib/python3.10/dist-packages (from numba>=0.51.2->umap-learn>=0.5.0->bertopic) (0.41.1)\n","Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-dateutil>=2.8.1->pandas>=1.1.5->bertopic) (1.16.0)\n","Requirement already satisfied: sympy in /usr/local/lib/python3.10/dist-packages (from torch>=1.11.0->sentence-transformers>=0.4.1->bertopic) (1.12)\n","Requirement already satisfied: networkx in /usr/local/lib/python3.10/dist-packages (from torch>=1.11.0->sentence-transformers>=0.4.1->bertopic) (3.2.1)\n","Requirement already satisfied: jinja2 in 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satisfied: nvidia-nvtx-cu12==12.1.105 in /usr/local/lib/python3.10/dist-packages (from torch>=1.11.0->sentence-transformers>=0.4.1->bertopic) (12.1.105)\n","Requirement already satisfied: triton==2.2.0 in /usr/local/lib/python3.10/dist-packages (from torch>=1.11.0->sentence-transformers>=0.4.1->bertopic) (2.2.0)\n","Requirement already satisfied: nvidia-nvjitlink-cu12 in /usr/local/lib/python3.10/dist-packages (from nvidia-cusolver-cu12==11.4.5.107->torch>=1.11.0->sentence-transformers>=0.4.1->bertopic) (12.4.99)\n","Requirement already satisfied: regex!=2019.12.17 in /usr/local/lib/python3.10/dist-packages (from transformers<5.0.0,>=4.32.0->sentence-transformers>=0.4.1->bertopic) (2023.12.25)\n","Requirement already satisfied: tokenizers<0.19,>=0.14 in /usr/local/lib/python3.10/dist-packages (from transformers<5.0.0,>=4.32.0->sentence-transformers>=0.4.1->bertopic) (0.15.2)\n","Requirement already satisfied: safetensors>=0.4.1 in /usr/local/lib/python3.10/dist-packages (from 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(2024.2.2)\n","Requirement already satisfied: mpmath>=0.19 in /usr/local/lib/python3.10/dist-packages (from sympy->torch>=1.11.0->sentence-transformers>=0.4.1->bertopic) (1.3.0)\n"]}],"source":["pip install bertopic"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"executionInfo":{"elapsed":131,"status":"ok","timestamp":1711899734355,"user":{"displayName":"Avinash kumar Pandey","userId":"07918242858559780186"},"user_tz":240},"id":"Ne-zjmRprVKo","outputId":"f928f72a-0f72-4a17-839e-63fe59d9b79b"},"outputs":[{"name":"stderr","output_type":"stream","text":["[nltk_data] Downloading package punkt to /root/nltk_data...\n","[nltk_data]   Package punkt is already up-to-date!\n","[nltk_data] Downloading package stopwords to /root/nltk_data...\n","[nltk_data]   Package stopwords is already up-to-date!\n","[nltk_data] Downloading package stopwords to /root/nltk_data...\n","[nltk_data]   Package stopwords is already up-to-date!\n","[nltk_data] Downloading package wordnet to /root/nltk_data...\n","[nltk_data]   Package wordnet is already up-to-date!\n","[nltk_data] Downloading package punkt to /root/nltk_data...\n","[nltk_data]   Package punkt is already up-to-date!\n","[nltk_data] Downloading package vader_lexicon to /root/nltk_data...\n","[nltk_data]   Package vader_lexicon is already up-to-date!\n"]},{"data":{"text/plain":["True"]},"execution_count":12,"metadata":{},"output_type":"execute_result"}],"source":["# Import Libraries\n","import pandas as pd\n","import nltk\n","from nltk.sentiment import SentimentIntensityAnalyzer\n","import pandas as pd\n","from bertopic import BERTopic\n","import matplotlib.pyplot as plt\n","import gensim\n","from sklearn.metrics.pairwise import cosine_similarity\n","from gensim.models import KeyedVectors\n","import nltk\n","nltk.download('punkt')\n","nltk.download('stopwords')\n","import string\n","nltk.download('stopwords')\n","nltk.download('wordnet')\n","nltk.download('punkt')\n","nltk.download('vader_lexicon')"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"executionInfo":{"elapsed":5231270,"status":"ok","timestamp":1711905010461,"user":{"displayName":"Avinash kumar Pandey","userId":"07918242858559780186"},"user_tz":240},"id":"zODRV27vKZdF","outputId":"cb402511-4d8b-4da1-c1e3-f09c20791f2a"},"outputs":[{"name":"stdout","output_type":"stream","text":["df original shape: (154571, 5)\n"]}],"source":["# Import Self Classified (Roberta Classifier : 1) tweets dataset\n","df = pd.read_csv('/content/drive/MyDrive/Emory/BMI NLP/Breast Cancer Data/CSV Files/roberta_prediction_1_only_with_sentiment.csv')\n","print(\"df original shape:\", df.shape)\n","\n","# Load pre-trained Word2Vec embeddings\n","word_vectors = KeyedVectors.load_word2vec_format('/content/drive/MyDrive/Emory/BMI NLP/Breast Cancer Data/GoogleNews-vectors-negative300.bin', binary=True)\n","\n","# Filter Tweets with negative sentiments\n","df = df[df['sentiment_on_preprocessed'] <= 0.5].copy()\n","df = df.reset_index(drop=True)\n","\n","# Filter posts that contain treatment side-effect / negative keywords\n","trestment_bc_negative_keywords = [\"treatment\",\"medication\",\"medicine\",\"med\",\"tablets\",\"side effect\",\"reaction\",\"drug\",\"tamoxifen\",\"chemo\",\"mental\",\"emotion\",\n","                     \"lump\",\"pain\",\"sleep\",\"docetaxel\",\"oncologist\",\"doc\" \"stop\"]  # Keywords based on literature review of Pub_med papers (reference in main article)\n","\n","# Function to find similar words in a text\n","def find_similar_words(text, word_vectors, uncertainty_words, threshold=0.5):\n","    similar_words = []\n","    unc_words = []\n","    for word in text.lower().split():\n","        if word in word_vectors:\n","            word_embedding = word_vectors[word]\n","            for unc_word in uncertainty_words:\n","                if unc_word in word_vectors:\n","                    unc_embedding = word_vectors[unc_word]\n","                    similarity = cosine_similarity([word_embedding], [unc_embedding])[0][0]\n","                    if similarity > threshold:\n","                        similar_words.append(word)\n","                        similar_words.append(unc_word)\n","                        break\n","    return similar_words\n","\n","# Load the dataset\n","df['similar_uncertainty_words'] = df['text'].apply(lambda x: find_similar_words(x, word_vectors, trestment_bc_negative_keywords))"]},{"cell_type":"code","execution_count":null,"metadata":{"id":"nifQecRhTUej"},"outputs":[],"source":["df.to_csv('/content/drive/MyDrive/Emory/BMI NLP/Breast Cancer Data/CSV Files/roberta_prediction_1_only_with_sentiment_similar_words.csv', index=False)"]},{"cell_type":"code","execution_count":null,"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":1000,"referenced_widgets":["7a2029a6916b44eaa72405864c3c2bd0","0869102b533c4b6e886d6cab947435f4","dc885ccf225c44b5811c06bed91eb01c","08b28a8a05d8423398d4f23cafa676ea","f054b51d2bba493db55fe9bdd3534e4c","21d10ff262e044929459e519eed975ec","b7a02d6d6458458da3b326c6584462aa","d500a0bb4ae34a10bf2bdc889ac10fe8","c9d46399719842129e20151e5b113903","08a6e621950d464582e25b02c8de7c84","ea888d27d91249228948871dccb36a3b","442e9cd33c504c6d8f8cd1cdf8419629","81eb842159464693b935e7f1cb7d46bb","45e46bcc7f8046ec9afc644d9240edfb","572e5ed8b9a74364be35c5619f54c3e1","04c75aae1bb948eeb9ea56432ff57890","6178affdde654398b9193345cc8352ec","688d1920f1b4457ca3bdffb90101a5ba","f6b02d6cc964446ca4bafa7c3d18048a","106fd3f7cbb44d0990d5aec2be3bf09c","d86190c84c454bf29c25286b5a3f2240","eed3be602c7142fd8a847cb0329782e2","f80399bae2564aa79eb33966ddc0d8d6","801bf21fedbe4111b337154017c304ea","81986b4ebf7c4c9b94b7e4aef9da5720","f7b703c5781f4c98bb72f13c81046f66","beaa443e81a743df81bd3a65b87d3d2b","6f1373d69b06457abb65f0e0b2088148","cf5376ca5b7b4a6580af44aecbabc7de","60f73cef80344b829929bb110f0b0f76","1e64bb44742b43bf90af11206c029cb7","c7e7992935e34139b42c11882d3ca247","4e8b5b8bb9054dd69676ea05e4388c8e","5cb05475f8854dc198a53a5b92efd6e9","7d244f4b7f8f40dfb90ebdaffc6e5be8","5e9b163216d542488818ed53e9150124","a7051234da4749779e76fed7d4bbd56b","dce83482cdb34aa8b36b99fd7cd2a327","67b750f878524eeeb21654dcf89975a4","a05984c7bdcd4b198677b59810c7f3ab","7897fadeec8343ba9a7f12e969123140","46fb56bf3f0c4fa3853000d3cd5eb084","1344b298fe5d4818a06869bd3dbd17a7","7d31643f79b64f97ac0f26aff76a868e","ff9a165d67b14b158dc2bad196cc782e","8613efab5c8446ab921c4d476eea24f4","4df9fa351c99439c8e66a0a1bb9cf486","94c2afa551d7490d84ba4c70529118d1","d6acc0993d3b4cdc9fcd7716d788b176","fccf3dea1a6f4efaa8f978fd64235ca3","43de83c2eaf34f49b55d5cffa18e5002","665ed6c381ac4f168230eb1d77295977","eb7bed63c2c642eeb369b2ff373d4eea","0fd02244678d46df81285821ee0234e5","71b7d91e87924a9a9e7792e860ea4181","fd62e8d0332245b9846ab3ade000716e","8506bac9d23f47438aea98abd8809f41","8c5d7e3c91d14349963e4693ca4f82b4","9ab2bfad38f34c638d1e65c82938261b","63015cf70fa94710b5de9320db37f28d","8f694e062bc34f19a8859fba84aee1ad","6a4466669eac4ec78d66c479548e3d2a","9d226eabc3fe44559a063e7097a99123","943cfad0887a4dc5804e7ee8a7ec2ab9","f49c059af7ed4f5b8389de4dc1d39e01","66bb202b5cc84fb899246c752a40171d","3d295b56c01549e0be0f003607f76718","37a57f5cca3c4595a414906230e945b0","e2b46908d5c04f5baa72a48db996baa0","dff738bf5edc4be4aff096b190a42c5d","6a9b9f725ab54b2fa7d0badcd0bb7ab4","980cd0a007cb4ba0a586085eb1baa9f2","f3334f484667447098e82d6a56ca6b74","978dc3fdd3a8479eaa80fccae0092dbc","300d12c59f1744bda157e754b18539f1","c95c773f67f64e7995068eab4b85ca8d","bf64d8b528334eeea7f5881b834a4af5","e3ed13a2579d49f289cc95c817433a0a","d76620e4cd914cc3893f13a6fb08bc2e","02bd3f164d0c45b2ad67671911dc601a","17ae618d6ba24c16b47447816505531d","f615fbc8fae04bd080ab124983890934","e71a910ee92148de925dfb7f536315ee","8a4b781b84954652819eb61336d0be93","c364e1601278417c9132442a73c94b1a","a3d8bb84c49e47e99e4257136ff46887","fefc2494cb854688bbed12c831a8a61b","9cac19a3c0ba4fb490a41e246f668a5f","245bb9b89d594b18b15e89fa171040f5","c775cff2ecff439f86e2e21b0a908175","4e6a337a2f3244b881b6d23c6f4a0d27","0b19cf2784f345a29459849755ea622e","213360c4a0f8412b926692ba28b55e63","d42e41462cd641cfac53a46206836125","342e667558864d068a605c956cfe9045","2b15e8316c804acc94c2a65f530046f2","d3fe39f6645f4f389bdfbc089002e2e0","b1b55758f6bc4ce8a3d95a13f1fc604a","f56205c184d442078f51a858d581174c","389f20f3c63a42ccb7c27abacf7d05ab","6fe33708c68d47aa9b48a0311bb0636b","cb8be2e43504411da7881248ad28945f","4f1f9b49e9bf475880258cb1be23e4fd","b9e3a017f5aa449b90c526828edf2d54","fb03df64d2aa40dabafb9f645cdb3044","b87c63a7623344d2b5016f8df2a85861","c734e9dda41446908ee929925d5c866f","70b577aa6a9a440ab1d3e553065967b0","4fcb1bf43e2f4ce6bffd2549303ecdb0","1a15817cdd0e426da769eb8d4795436d","615f76751eab4355b3b401a60b8c57cd","4d3b0b02099b4d31b855e585c612c967","50398cd19df2480bb2c9a19db48e880d","d6f2e9a4265f4906b47a1cfe1b82c2c2","c3548861c4ae48b391a5a512fc0cf2c8","30444b01da2a48568dd16a5aeef5ed5d","d40f789c8e7b4705b03aeeba16f79d6f","dcfb4ac4a0eb48cc970cae2e94fb70b7","5840c1ee823e47be80a832a66a9c8835","4f487fa9e02f4b328e586fe26ba5f758","9ca6002315eb495d8d73f06a02eca1e2","c783be2a3479429f8e65b9d36069d3b7","a9724481a7bc410b89722c7e7f1b1869","91244ed73f2b464998b13fec2f3794b1","ae6c63f4e17d49e381edaab838000e3e","e9d3102e61df47f997de88f5d22ccf7e","91aefbb23a7f4e3d9dfd2db9794cd1c0","a1f4a6fbe178452abfdfe6f84ec704b6","b6175a8decbc4f6dbb36799483607719","5811f5059c734336b7c1b45396b9bf41","a5ee10d4db3e466ba298c4fa4abb71d4","e0452816a831468b99d9e35a0069b57a"]},"executionInfo":{"elapsed":866802,"status":"ok","timestamp":1711910334973,"user":{"displayName":"Avinash kumar Pandey","userId":"07918242858559780186"},"user_tz":240},"id":"PLPb2BOys9Sz","outputId":"603960fb-dff5-42cd-c12b-2aacd9f63fbe"},"outputs":[{"name":"stderr","output_type":"stream","text":["2024-03-31 18:24:28,207 - BERTopic - Embedding - Transforming documents to embeddings.\n"]},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"7a2029a6916b44eaa72405864c3c2bd0","version_major":2,"version_minor":0},"text/plain":["modules.json:   0%|          | 0.00/349 [00:00<?, ?B/s]"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"442e9cd33c504c6d8f8cd1cdf8419629","version_major":2,"version_minor":0},"text/plain":["config_sentence_transformers.json:   0%|          | 0.00/116 [00:00<?, ?B/s]"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"f80399bae2564aa79eb33966ddc0d8d6","version_major":2,"version_minor":0},"text/plain":["README.md:   0%|          | 0.00/10.7k [00:00<?, ?B/s]"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"5cb05475f8854dc198a53a5b92efd6e9","version_major":2,"version_minor":0},"text/plain":["sentence_bert_config.json:   0%|          | 0.00/53.0 [00:00<?, ?B/s]"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"ff9a165d67b14b158dc2bad196cc782e","version_major":2,"version_minor":0},"text/plain":["config.json:   0%|          | 0.00/612 [00:00<?, ?B/s]"]},"metadata":{},"output_type":"display_data"},{"data":{"application/vnd.jupyter.widget-view+json":{"model_id":"fd62e8d0332245b9846ab3ade000716e","version_major":2,"version_minor":0},"text/plain":["model.safetensors:   0%|          | 0.00/90.9M [00:00<?, 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18:38:44,263 - BERTopic - Cluster - Completed ✓\n","2024-03-31 18:38:44,301 - BERTopic - Representation - Extracting topics from clusters using representation models.\n","2024-03-31 18:38:50,006 - BERTopic - Representation - Completed ✓\n"]},{"data":{"text/html":["<html>\n","<head><meta charset=\"utf-8\" /></head>\n","<body>\n","    <div>            <script src=\"https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js?config=TeX-AMS-MML_SVG\"></script><script type=\"text/javascript\">if (window.MathJax && window.MathJax.Hub && window.MathJax.Hub.Config) {window.MathJax.Hub.Config({SVG: {font: \"STIX-Web\"}});}</script>                <script type=\"text/javascript\">window.PlotlyConfig = {MathJaxConfig: 'local'};</script>\n","        <script charset=\"utf-8\" src=\"https://cdn.plot.ly/plotly-2.24.1.min.js\"></script>                <div id=\"5e860942-3006-4264-b2cd-1be1d43c6f3f\" class=\"plotly-graph-div\" style=\"height:4500px; width:1000px;\"></div>            <script 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