diff --git "a/Code_for_training.ipynb" "b/Code_for_training.ipynb" deleted file mode 100644--- "a/Code_for_training.ipynb" +++ /dev/null @@ -1,5135 +0,0 @@ -{ - "cells": [ - { - "cell_type": "markdown", - "metadata": { - "id": "te5uCzPlhBWx" - }, - "source": [ - "# Processing the data (PyTorch)" - ] - }, - { - "cell_type": "markdown", - "metadata": { - "id": "eiQ3FKJDhBW0" - }, - "source": [ - "Install the Transformers, Datasets, and Evaluate libraries to run this notebook." - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "id": "HedrkDuchBW2" - }, - "outputs": [], - "source": [ - "#let's install the necessary libraries from Hugging Face\n", - "!pip install datasets evaluate transformers[sentencepiece] transformers[torch]" - ] - }, - { - "cell_type": "code", - "source": [ - "from huggingface_hub import notebook_login\n", - "#authenticate into the huggin face\n", - "notebook_login()" - ], - "metadata": { - "colab": { - "base_uri": "https://localhost:8080/", - "height": 145, - "referenced_widgets": [ - "2459586b900d4972893416101cf66518", - "bb63af0e6e2d44d39dea0c7fb50f2675", - "b84acaf57645444a93e8344e62b02f37", - "0adacec9605245e8813c1eb6c375f97c", - "3556f7c20dd942d9845a172d2fb3a308", - "c9c4f33186b34af5bfe4b23f5a94cd92", - "d9fce65fdc0f4f4e99511a95049b0627", - "1dfa79c17ca34ccb8a15887162536305", - "20b45c6e63d94306a2cd368e6dfc0719", - "7853cc389609486e9774a6327cbc6d7f", - "0bfa8f38be0c4d5e8b1a8f2a21623e2f", - "f363053a53f442379a9be069597c70dc", - "1c90fe7a114140a9b32d8107c2af011c", - "b45e9bbed2c34078813f4d8be11ba856", - "784ba2ebff4d451485ba312e0dd065e7", - "74757608b6d945b186ce03761a04a067", - "6f292a0a27234aaebaa90c47edbaa6bd", - "d35e9d78443840a6af111a3e3245184d", - "589080843ecd489488d86c10bc3c3d67", - "404e6261b69646be85dd78a0fb1dc3cc", - "adafd48f91e54326a4a5b2bb297e3d47", - "56a61a4c28de4eb9833e571d4067c4c4", - "954f23b0ee9249df81dd30725c9954b0", - "ec75914e1c264260a9f573728880474a", - "e998f2b2d75d4f3887c59669603793df", - "eea3bf1ec05c4ba28cd5f1baa44bcfd8", - "1b22a95ee6ff4fdca56a966d35c46ddf", - "83c197270ac54969af02fa998fec28f1", - "21453473c9f04ef992fe35419f6afff9", - "3980e52353a14d538c1dc4b1b45d1396", - "1fa7b92f0588403bb146f602942baea6", - "20169140dbe04320b1a7d090d738f273" - ] - }, - "id": "Z4IolwVzaQQh", - "outputId": "7f4c4beb-0cdf-4549-cfb9-6496f50c7118" - }, - "execution_count": 137, - "outputs": [ - { - "output_type": "display_data", - "data": { - "text/plain": [ - "VBox(children=(HTML(value='
] 41.00M 40.1MB/s in 1.0s \n", - "\n", - "2024-04-28 15:34:18 (40.1 MB/s) - ‘drugsCom_raw.zip.1’ saved [42989872]\n", - "\n", - "Archive: drugsCom_raw.zip\n", - "replace drugsComTest_raw.tsv? [y]es, [n]o, [A]ll, [N]one, [r]ename: y\n", - " inflating: drugsComTest_raw.tsv \n", - "replace drugsComTrain_raw.tsv? [y]es, [n]o, [A]ll, [N]one, [r]ename: y\n", - " inflating: drugsComTrain_raw.tsv \n" - ] - } - ] - }, - { - "cell_type": "code", - "source": [ - "from datasets import load_dataset\n", - "\n", - "#save the data into a csv file with both splits\n", - "data_files = {\"train\": \"drugsComTrain_raw.tsv\", \"test\": \"drugsComTest_raw.tsv\"}\n", - "# \\t is the tab character in Python\n", - "drug_dataset = load_dataset(\"csv\", data_files=data_files, delimiter=\"\\t\")\n", - "\n", - "drug_dataset" - ], - "metadata": { - "id": "yifIkdVzj1kS", - "colab": { - "base_uri": "https://localhost:8080/" - }, - "outputId": "a0b787f7-ed71-4825-d638-378c0b198dac" - }, - "execution_count": 108, - "outputs": [ - { - "output_type": "execute_result", - "data": { - "text/plain": [ - "DatasetDict({\n", - " train: Dataset({\n", - " features: ['Unnamed: 0', 'drugName', 'condition', 'review', 'rating', 'date', 'usefulCount'],\n", - " num_rows: 161297\n", - " })\n", - " test: Dataset({\n", - " features: ['Unnamed: 0', 'drugName', 'condition', 'review', 'rating', 'date', 'usefulCount'],\n", - " num_rows: 53766\n", - " })\n", - "})" - ] - }, - "metadata": {}, - "execution_count": 108 - } - ] - }, - { - "cell_type": "code", - "source": [ - "#rename columns\n", - "drug_dataset = drug_dataset.rename_column(\n", - " original_column_name=\"Unnamed: 0\", new_column_name=\"patient_id\"\n", - ")\n", - "drug_dataset" - ], - "metadata": { - "colab": { - "base_uri": "https://localhost:8080/" - }, - "id": "EOOatck3rwmY", - "outputId": "a2443b2e-db62-45a0-87d5-320d69b08404" - }, - "execution_count": 109, - "outputs": [ - { - "output_type": "execute_result", - "data": { - "text/plain": [ - "DatasetDict({\n", - " train: Dataset({\n", - " features: ['patient_id', 'drugName', 'condition', 'review', 'rating', 'date', 'usefulCount'],\n", - " num_rows: 161297\n", - " })\n", - " test: Dataset({\n", - " features: ['patient_id', 'drugName', 'condition', 'review', 'rating', 'date', 'usefulCount'],\n", - " num_rows: 53766\n", - " })\n", - "})" - ] - }, - "metadata": {}, - "execution_count": 109 - } - ] - }, - { - "cell_type": "code", - "source": [ - "#remove rows where the condition feature has no data\n", - "drug_dataset = drug_dataset.filter(lambda x: x[\"condition\"] is not None)" - ], - "metadata": { - "id": "cZzYLJphrw6W" - }, - "execution_count": 110, - "outputs": [] - }, - { - "cell_type": "code", - "source": [ - "#turn it into lowercase text\n", - "def lowercase_condition(example):\n", - " return {\"condition\": example[\"condition\"].lower()}\n", - "\n", - "drug_dataset = drug_dataset.map(lowercase_condition)" - ], - "metadata": { - "id": "MVsier2fsGr8" - }, - "execution_count": 111, - "outputs": [] - }, - { - "cell_type": "code", - "source": [ - "#create a feature called 'review length' because we will later remove reviews that are too short\n", - "def compute_review_length(example):\n", - " return {\"review_length\": len(example[\"review\"].split())}\n", - "\n", - "drug_dataset = drug_dataset.map(compute_review_length)" - ], - "metadata": { - "id": "1YS2yrZgsGgK" - }, - "execution_count": 112, - "outputs": [] - }, - { - "cell_type": "code", - "source": [ - "#keep only reviews with at least 16 letters\n", - "drug_dataset = drug_dataset.filter(lambda x: x[\"review_length\"] > 15)\n", - "print(drug_dataset.num_rows)" - ], - "metadata": { - "colab": { - "base_uri": "https://localhost:8080/" - }, - "id": "qQk-ReJssefI", - "outputId": "e1587a33-b6e4-4a7b-fcd7-2c9b8f2fb6f4" - }, - "execution_count": 113, - "outputs": [ - { - "output_type": "stream", - "name": "stdout", - "text": [ - "{'train': 151236, 'test': 50396}\n" - ] - } - ] - }, - { - "cell_type": "code", - "source": [ - "drug_dataset" - ], - "metadata": { - "colab": { - "base_uri": "https://localhost:8080/" - }, - "id": "DyNIhmXc6GQg", - "outputId": "e1807a4e-66c0-419d-c7da-e5eaeab995f5" - }, - "execution_count": 114, - "outputs": [ - { - "output_type": "execute_result", - "data": { - "text/plain": [ - "DatasetDict({\n", - " train: Dataset({\n", - " features: ['patient_id', 'drugName', 'condition', 'review', 'rating', 'date', 'usefulCount', 'review_length'],\n", - " num_rows: 151236\n", - " })\n", - " test: Dataset({\n", - " features: ['patient_id', 'drugName', 'condition', 'review', 'rating', 'date', 'usefulCount', 'review_length'],\n", - " num_rows: 50396\n", - " })\n", - "})" - ] - }, - "metadata": {}, - "execution_count": 114 - } - ] - }, - { - "cell_type": "code", - "source": [ - "import html\n", - "\n", - "#remove html characters from the review feature\n", - "new_drug_dataset = drug_dataset.map(\n", - " lambda x: {\"review\": [html.unescape(o) for o in x[\"review\"]]}, batched=True)" - ], - "metadata": { - "id": "Hzu-0TCCs7tr" - }, - "execution_count": 115, - "outputs": [] - }, - { - "cell_type": "code", - "source": [ - "#create three splits (train, validation and test) with what we have\n", - "drug_clean = new_drug_dataset[\"train\"].train_test_split(train_size=0.8, seed=42)\n", - "\n", - "# Rename the default \"test\" split to \"validation\"\n", - "drug_clean[\"validation\"] = drug_clean.pop(\"test\")\n", - "\n", - "# Add the \"test\" set to our `DatasetDict`\n", - "drug_clean[\"test\"] = new_drug_dataset[\"test\"]\n", - "\n", - "drug_clean" - ], - "metadata": { - "colab": { - "base_uri": "https://localhost:8080/" - }, - "id": "_YpST6_3yBCA", - "outputId": "21252016-7685-44b0-8c29-79031b276811" - }, - "execution_count": 116, - "outputs": [ - { - "output_type": "execute_result", - "data": { - "text/plain": [ - "DatasetDict({\n", - " train: Dataset({\n", - " features: ['patient_id', 'drugName', 'condition', 'review', 'rating', 'date', 'usefulCount', 'review_length'],\n", - " num_rows: 120988\n", - " })\n", - " validation: Dataset({\n", - " features: ['patient_id', 'drugName', 'condition', 'review', 'rating', 'date', 'usefulCount', 'review_length'],\n", - " num_rows: 30248\n", - " })\n", - " test: Dataset({\n", - " features: ['patient_id', 'drugName', 'condition', 'review', 'rating', 'date', 'usefulCount', 'review_length'],\n", - " num_rows: 50396\n", - " })\n", - "})" - ] - }, - "metadata": {}, - "execution_count": 116 - } - ] - }, - { - "cell_type": "code", - "source": [ - "drug_clean['train'].features" - ], - "metadata": { - "id": "92I1TbyMs7-_", - "colab": { - "base_uri": "https://localhost:8080/" - }, - "outputId": "8c7fbcb9-cc0d-4831-af30-5b7e6c18905c" - }, - "execution_count": 117, - "outputs": [ - { - "output_type": "execute_result", - "data": { - "text/plain": [ - "{'patient_id': Value(dtype='int64', id=None),\n", - " 'drugName': Value(dtype='string', id=None),\n", - " 'condition': Value(dtype='string', id=None),\n", - " 'review': Value(dtype='string', id=None),\n", - " 'rating': Value(dtype='float64', id=None),\n", - " 'date': Value(dtype='string', id=None),\n", - " 'usefulCount': Value(dtype='int64', id=None),\n", - " 'review_length': Value(dtype='int64', id=None)}" - ] - }, - "metadata": {}, - "execution_count": 117 - } - ] - }, - { - "cell_type": "code", - "source": [ - "from transformers import AutoTokenizer, DataCollatorWithPadding\n", - "\n", - "#let's tokenize the review feature, which is the one we'll use as predictive feature\n", - "raw_datasets = drug_clean\n", - "checkpoint = \"bert-base-uncased\"\n", - "tokenizer = AutoTokenizer.from_pretrained(checkpoint)\n", - "\n", - "def tokenize_function(example):\n", - " return tokenizer(example[\"review\"], truncation=True)\n", - "\n", - "tokenized_datasets = raw_datasets.map(tokenize_function, batched=True)\n", - "data_collator = DataCollatorWithPadding(tokenizer=tokenizer)" - ], - "metadata": { - "id": "6z0WrmVrV5Fw", - "colab": { - "base_uri": "https://localhost:8080/", - "height": 113, - "referenced_widgets": [ - "8815bc4f84334c66a72bef825a716be6", - "12347ee2672b4b4ba3c8671c725352f5", - "6e1cf29ae5b54b6f87366ab6e66f905b", - "dcf16678502b4a19901aa56d8a16a9f4", - "0606e216d28149feb818c8e7919cf987", - "664a737eea6847c4acc62c2169b13675", - "56304f48a0de4c45b940828de823a749", - "56eb06a4ce794bc68310219e8c8891ec", - "fa7119d5141a4856a0369d42cc8c0846", - "3642d8ebdf0a4a649b2ebe309bad02a5", - "6c4c1bb481eb40639f92efeb694dc8d1", - "e87b26d89be642348040ae7e03c75fec", - "2c6bf5514fe74289954d26b01753ba08", - "5aa9a0f8dd4a4296a2e14011aecaa1c8", - "d6f72b92b863462ba31f65439c385fb0", - "a82d0e6bb393410ca7325d94f05c1dc5", - "13a407daf96e49e5b4ddd51712e33644", - "5faa4e2f8598445ebdebb2138d1db076", - "0485a3579d5544a9a36cbd81e34a3f6c", - "aa13c976a702422ea532a766810d6e2c", - "4a078d05cee54316acc4d7bd27481369", - "927ce83ff4b04b6c977e6b5c32295b8b", - "5ba5166459f24d09ae9d2474ea6d6731", - "dbd8c86d43654b48a7ec0842dbc3b9bc", - "a32fdfb0ff0b429688f24195008b61be", - "ae8bc40b6c3a427eafba8236e83e4b5c", - "e0da74ab9e214156a3b6bad7165a1475", - "33637cc35432432db50363a247cc9b0a", - "fb54e06787714635bafdc9b7f941d64d", - "fef842e408574a4998ee140a0907b2b3", - "25d1e01786ed47188e3caa184130dbd0", - "0fb40e51d1c7484b9478e3dae9134e82", - "b30c7d2540f945ebaa37ee75e7373cf1" - ] - }, - "outputId": "233d5e71-1fce-4968-f654-b05192d26de2" - }, - "execution_count": 118, - "outputs": [ - { - "output_type": "display_data", - "data": { - "text/plain": [ - "Map: 0%| | 0/120988 [00:00" - ], - "text/html": [] - }, - "metadata": {} - }, - { - "output_type": "stream", - "name": "stderr", - "text": [ - "/usr/local/lib/python3.10/dist-packages/sklearn/metrics/_classification.py:1344: UndefinedMetricWarning: Precision is ill-defined and being set to 0.0 in labels with no predicted samples. Use `zero_division` parameter to control this behavior.\n", - " _warn_prf(average, modifier, msg_start, len(result))\n", - "/usr/local/lib/python3.10/dist-packages/sklearn/metrics/_classification.py:1344: UndefinedMetricWarning: Recall is ill-defined and being set to 0.0 in labels with no true samples. Use `zero_division` parameter to control this behavior.\n", - " _warn_prf(average, modifier, msg_start, len(result))\n" - ] - } - ] - }, - { - "cell_type": "code", - "source": [ - "import numpy as np\n", - "#given that we get all the logs from the trainer, we'll select the label with the highest likelihood with an argmax function\n", - "preds = np.argmax(predictions.predictions, axis=-1)" - ], - "metadata": { - "id": "DgBVUDfQzZSM" - }, - "execution_count": 140, - "outputs": [] - }, - { - "cell_type": "code", - "source": [ - "from evaluate import load\n", - "#let's define a comput_metrics function that will return accuracy, precision, recall and f1 for our training\n", - "def compute_metrics(eval_preds):\n", - " logits, labels = eval_preds\n", - " preds = np.argmax(logits, axis=-1)\n", - "\n", - " # Load metrics with zero_division parameter set to 1\n", - " metrics = {\n", - " 'accuracy': load('accuracy'),\n", - " 'precision': load('precision', config={'zero_division': 1}),\n", - " 'recall': load('recall', config={'zero_division': 1}),\n", - " 'f1': load('f1', config={'zero_division': 1})\n", - " }\n", - "\n", - " # Compute each metric, omitting the 'average' argument for accuracy\n", - " results = {}\n", - " for metric_name, metric in metrics.items():\n", - " if metric_name == 'accuracy':\n", - " result = metric.compute(predictions=preds, references=labels)\n", - " results[metric_name] = result['accuracy']\n", - " else:\n", - " result = metric.compute(predictions=preds, references=labels, average='weighted')\n", - " results[metric_name] = result[metric_name]\n", - "\n", - " return results" - ], - "metadata": { - "id": "6x4ETEv1Fr_2" - }, - "execution_count": 141, - "outputs": [] - }, - { - "cell_type": "code", - "source": [ - "#let's train the model right away\n", - "trainer.train()" - ], - "metadata": { - "colab": { - "base_uri": "https://localhost:8080/", - "height": 348 - }, - "id": "7WZ77bmbG5Zt", - "outputId": "b8100baf-99fc-425c-9a5b-e74ab3562d29" - }, - "execution_count": 142, - "outputs": [ - { - "output_type": "display_data", - "data": { - "text/plain": [ - "" - ], - "text/html": [ - "\n", - "
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EpochTraining LossValidation LossAccuracyPrecisionRecallF1
1No log1.1375110.7747040.7301480.7747040.744985
2No log0.5595480.8853750.8674840.8853750.872829
3No log0.4307890.9209490.9060860.9209490.910576

" - ] - }, - "metadata": {} - }, - { - "output_type": "stream", - "name": "stderr", - "text": [ - "/usr/local/lib/python3.10/dist-packages/sklearn/metrics/_classification.py:1344: UndefinedMetricWarning: Precision is ill-defined and being set to 0.0 in labels with no predicted samples. Use `zero_division` parameter to control this behavior.\n", - " _warn_prf(average, modifier, msg_start, len(result))\n", - "/usr/local/lib/python3.10/dist-packages/sklearn/metrics/_classification.py:1344: UndefinedMetricWarning: Precision is ill-defined and being set to 0.0 in labels with no predicted samples. Use `zero_division` parameter to control this behavior.\n", - " _warn_prf(average, modifier, msg_start, len(result))\n", - "/usr/local/lib/python3.10/dist-packages/sklearn/metrics/_classification.py:1344: UndefinedMetricWarning: Precision is ill-defined and being set to 0.0 in labels with no predicted samples. Use `zero_division` parameter to control this behavior.\n", - " _warn_prf(average, modifier, msg_start, len(result))\n" - ] - }, - { - "output_type": "execute_result", - "data": { - "text/plain": [ - "TrainOutput(global_step=339, training_loss=1.01418788313514, metrics={'train_runtime': 138.9845, 'train_samples_per_second': 19.513, 'train_steps_per_second': 2.439, 'total_flos': 245512156913712.0, 'train_loss': 1.01418788313514, 'epoch': 3.0})" - ] - }, - "metadata": {}, - "execution_count": 142 - } - ] - }, - { - "cell_type": "code", - "source": [ - "#it's good. Let's push the model to the hugging face hub\n", - "trainer.push_to_hub()" - ], - "metadata": { - "colab": { - "base_uri": "https://localhost:8080/", - "height": 70 - }, - "id": "DxFz2gWSMUI6", - "outputId": "9e83f368-3084-4168-c828-1665b934e769" - }, - "execution_count": 143, - "outputs": [ - { - "output_type": "execute_result", - "data": { - "text/plain": [ - "CommitInfo(commit_url='https://huggingface.co/Marcuswas/bert-drug-review-to-condition/commit/d6f99808a6fad08574389e154a44694bbd24ad5d', commit_message='End of training', commit_description='', oid='d6f99808a6fad08574389e154a44694bbd24ad5d', pr_url=None, pr_revision=None, pr_num=None)" - ], - "application/vnd.google.colaboratory.intrinsic+json": { - "type": "string" - } - }, - "metadata": {}, - "execution_count": 143 - } - ] - } - ], - "metadata": { - "colab": { - "provenance": [], - "gpuType": "T4" - }, - "language_info": { - "name": "python" - }, - "kernelspec": { - "name": "python3", - "display_name": "Python 3" - }, - "widgets": { - "application/vnd.jupyter.widget-state+json": { - "2459586b900d4972893416101cf66518": { - "model_module": "@jupyter-widgets/controls", - "model_name": "VBoxModel", - "model_module_version": "1.5.0", - "state": { - "_dom_classes": [], - "_model_module": "@jupyter-widgets/controls", - "_model_module_version": "1.5.0", - "_model_name": "VBoxModel", - "_view_count": null, - "_view_module": "@jupyter-widgets/controls", - "_view_module_version": "1.5.0", - "_view_name": "VBoxView", - "box_style": "", - "children": [ - "IPY_MODEL_adafd48f91e54326a4a5b2bb297e3d47", - "IPY_MODEL_56a61a4c28de4eb9833e571d4067c4c4", - "IPY_MODEL_954f23b0ee9249df81dd30725c9954b0", - "IPY_MODEL_ec75914e1c264260a9f573728880474a" - ], - "layout": "IPY_MODEL_d9fce65fdc0f4f4e99511a95049b0627" - } - }, - "bb63af0e6e2d44d39dea0c7fb50f2675": { - "model_module": "@jupyter-widgets/controls", - "model_name": "HTMLModel", - "model_module_version": "1.5.0", - "state": { - "_dom_classes": [], - "_model_module": "@jupyter-widgets/controls", - "_model_module_version": "1.5.0", - "_model_name": "HTMLModel", - "_view_count": null, - "_view_module": "@jupyter-widgets/controls", - "_view_module_version": "1.5.0", - "_view_name": "HTMLView", - "description": "", - "description_tooltip": null, - "layout": "IPY_MODEL_1dfa79c17ca34ccb8a15887162536305", - "placeholder": "​", - "style": "IPY_MODEL_20b45c6e63d94306a2cd368e6dfc0719", - "value": "


Copy a token from your Hugging Face\ntokens page and paste it below.
Immediately click login after copying\nyour token or it might be stored in plain text in this notebook file.
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