From 2ae6855f9924f19f1569836589050e73ff468d85 Mon Sep 17 00:00:00 2001 From: Neeraja Krishnakumar Date: Sun, 5 May 2024 18:48:47 +0530 Subject: [PATCH] Internship Application --- .../IndividualRound.ipynb | 5632 +++++++++++++++++ .../Internship Letter.pdf | Bin 0 -> 31822 bytes 2 files changed, 5632 insertions(+) create mode 100644 Internship Project/Neeraja Krishnakumar/IndividualRound.ipynb create mode 100644 Internship Project/Neeraja Krishnakumar/Internship Letter.pdf diff --git a/Internship Project/Neeraja Krishnakumar/IndividualRound.ipynb b/Internship Project/Neeraja Krishnakumar/IndividualRound.ipynb new file mode 100644 index 0000000..ae559c4 --- /dev/null +++ b/Internship Project/Neeraja Krishnakumar/IndividualRound.ipynb @@ -0,0 +1,5632 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": { + "id": "DiFsNuEplzXv" + }, + "source": [ + "# **Document Title, Author(s) Extraction and Alternative Title Generation**\n", + "\n", + "\n", + "# Introduction\n", + "\n", + "This project aims to automatically extract document details" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "ZvEkxNQMmPRe" + }, + "source": [ + "# Setup\n", + "\n", + "Install pytesseract for OCR.\n", + "\n", + "Install tesseract-ocr for text recognition." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "NYJeTs71FMdz", + "outputId": "3eebb4e1-8eb1-4eed-ec95-b978719980f3" + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Collecting pytesseract\n", + " Downloading pytesseract-0.3.10-py3-none-any.whl (14 kB)\n", + "Requirement already satisfied: packaging>=21.3 in /usr/local/lib/python3.10/dist-packages (from pytesseract) (24.0)\n", + "Requirement already satisfied: Pillow>=8.0.0 in /usr/local/lib/python3.10/dist-packages (from pytesseract) (9.4.0)\n", + "Installing collected packages: pytesseract\n", + "Successfully installed pytesseract-0.3.10\n", + "Reading package lists... Done\n", + "Building dependency tree... Done\n", + "Reading state information... Done\n", + "The following additional packages will be installed:\n", + " tesseract-ocr-eng tesseract-ocr-osd\n", + "The following NEW packages will be installed:\n", + " tesseract-ocr tesseract-ocr-eng tesseract-ocr-osd\n", + "0 upgraded, 3 newly installed, 0 to remove and 45 not upgraded.\n", + "Need to get 4,816 kB of archives.\n", + "After this operation, 15.6 MB of additional disk space will be used.\n", + "Get:1 http://archive.ubuntu.com/ubuntu jammy/universe amd64 tesseract-ocr-eng all 1:4.00~git30-7274cfa-1.1 [1,591 kB]\n", + "Get:2 http://archive.ubuntu.com/ubuntu jammy/universe amd64 tesseract-ocr-osd all 1:4.00~git30-7274cfa-1.1 [2,990 kB]\n", + "Get:3 http://archive.ubuntu.com/ubuntu jammy/universe amd64 tesseract-ocr amd64 4.1.1-2.1build1 [236 kB]\n", + "Fetched 4,816 kB in 1s (4,124 kB/s)\n", + "debconf: unable to initialize frontend: Dialog\n", + "debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 78, <> line 3.)\n", + "debconf: falling back to frontend: Readline\n", + "debconf: unable to initialize frontend: Readline\n", + "debconf: (This frontend requires a controlling tty.)\n", + "debconf: falling back to frontend: Teletype\n", + "dpkg-preconfigure: unable to re-open stdin: \n", + "Selecting previously unselected package tesseract-ocr-eng.\n", + "(Reading database ... 121920 files and directories currently installed.)\n", + "Preparing to unpack .../tesseract-ocr-eng_1%3a4.00~git30-7274cfa-1.1_all.deb ...\n", + "Unpacking tesseract-ocr-eng (1:4.00~git30-7274cfa-1.1) ...\n", + "Selecting previously unselected package tesseract-ocr-osd.\n", + "Preparing to unpack .../tesseract-ocr-osd_1%3a4.00~git30-7274cfa-1.1_all.deb ...\n", + "Unpacking tesseract-ocr-osd (1:4.00~git30-7274cfa-1.1) ...\n", + "Selecting previously unselected package tesseract-ocr.\n", + "Preparing to unpack .../tesseract-ocr_4.1.1-2.1build1_amd64.deb ...\n", + "Unpacking tesseract-ocr (4.1.1-2.1build1) ...\n", + "Setting up tesseract-ocr-eng (1:4.00~git30-7274cfa-1.1) ...\n", + "Setting up tesseract-ocr-osd (1:4.00~git30-7274cfa-1.1) ...\n", + "Setting up tesseract-ocr (4.1.1-2.1build1) ...\n", + "Processing triggers for man-db (2.10.2-1) ...\n" + ] + } + ], + "source": [ + "!pip install pytesseract\n", + "!sudo apt install tesseract-ocr" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "Ym5o4WilmbeT" + }, + "source": [ + "Install unrar for extracting .rar files." + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "0REateOyIWzd", + "outputId": "003ab890-f5f9-40c9-87d4-b7a53c9e0c41" + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Reading package lists... Done\n", + "Building dependency tree... Done\n", + "Reading state information... Done\n", + "unrar is already the newest version (1:6.1.5-1).\n", + "0 upgraded, 0 newly installed, 0 to remove and 45 not upgraded.\n" + ] + } + ], + "source": [ + "!sudo apt-get install unrar" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "3EV5NBocmmTm" + }, + "source": [ + "#Data Upload\n", + "\n", + "Upload the dataset file (.rar format)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 73 + }, + "id": "EM9WD0tdKl-7", + "outputId": "9a69e9b5-abdb-4982-c98b-606a3db7dac1" + }, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + " \n", + " \n", + " Upload widget is only available when the cell has been executed in the\n", + " current browser session. Please rerun this cell to enable.\n", + " \n", + " " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Saving scientific_publication.rar to scientific_publication.rar\n" + ] + } + ], + "source": [ + "from google.colab import files\n", + "\n", + "# Upload .rar file\n", + "uploaded = files.upload()" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "sighYoeTm8ai" + }, + "source": [ + "#Extract Images\n", + "\n", + "Extract images from the uploaded .rar file" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "JbDlwjnpLsMQ", + "outputId": "e0e6a356-58e7-4c0d-afe8-e52f025d2d4a" + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\n", + "UNRAR 6.11 beta 1 freeware Copyright (c) 1993-2022 Alexander Roshal\n", + "\n", + "\n", + "Extracting from scientific_publication.rar\n", + "\n", + "Creating scientific_publication OK\n", + "Extracting scientific_publication/doc_000016.png \b\b\b\b 1%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000045.png \b\b\b\b 4%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000050.png \b\b\b\b 6%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000061.png \b\b\b\b 7%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000089.png \b\b\b\b 9%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000121.png \b\b\b\b 11%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000128.png \b\b\b\b 13%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000130.png \b\b\b\b 15%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000171.png \b\b\b\b 17%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000228.png \b\b\b\b 18%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000235.png \b\b\b\b 20%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000240.png \b\b\b\b 22%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000250.png \b\b\b\b 23%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000285.png \b\b\b\b 25%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000298.png \b\b\b\b 27%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000309.png \b\b\b\b 29%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000311.png \b\b\b\b 29%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000334.png \b\b\b\b 32%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000345.png \b\b\b\b 35%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000349.png \b\b\b\b 36%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000392.png \b\b\b\b 38%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000429.png \b\b\b\b 39%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000437.png \b\b\b\b 41%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000438.png \b\b\b\b 43%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000445.png \b\b\b\b 45%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000451.png \b\b\b\b 47%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000453.png \b\b\b\b 48%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000480.png \b\b\b\b 50%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000498.png \b\b\b\b 52%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000509.png \b\b\b\b 54%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000513.png \b\b\b\b 56%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000515.png \b\b\b\b 58%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000522.png \b\b\b\b 59%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000530.png \b\b\b\b 61%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000584.png \b\b\b\b 62%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000594.png \b\b\b\b 63%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000615.png \b\b\b\b 66%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000617.png \b\b\b\b 68%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000697.png \b\b\b\b 70%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000741.png \b\b\b\b 72%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000756.png \b\b\b\b 75%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000766.png \b\b\b\b 77%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000767.png \b\b\b\b 79%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000769.png \b\b\b\b 81%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000779.png \b\b\b\b 83%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000785.png \b\b\b\b 84%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000821.png \b\b\b\b 87%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000832.png \b\b\b\b 89%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000845.png \b\b\b\b 92%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000864.png \b\b\b\b 93%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000891.png \b\b\b\b 96%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000942.png \b\b\b\b 97%\b\b\b\b\b OK \n", + "Extracting scientific_publication/doc_000950.png \b\b\b\b 99%\b\b\b\b\b OK \n", + "All OK\n" + ] + } + ], + "source": [ + "# Extract images from the uploaded .rar folder\n", + "!unrar x \"scientific_publication.rar\"" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "pS2mNOfZnFiX" + }, + "source": [ + "#Import Libraries\n", + "\n", + "Import necessary libraries such as os, pytesseract, Image, and pandas." + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": { + "id": "YCwiznwxVh3z" + }, + "outputs": [], + "source": [ + "import os\n", + "import pytesseract\n", + "from PIL import Image\n", + "import pandas as pd" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "ie9N8z4JnM9u" + }, + "source": [ + "#Text Extraction From Images\n", + "\n", + "**OCR Function**\n", + "\n", + "Define a function to extract text from images using OCR." + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": { + "id": "4MwDeFEtagCf" + }, + "outputs": [], + "source": [ + "def extract_text_from_image(image_path):\n", + " # Open the image\n", + " img = Image.open(image_path)\n", + "\n", + " # Perform OCR to extract text\n", + " text = pytesseract.image_to_string(img)\n", + "\n", + " return text\n" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "2JPaayM_nzcM" + }, + "source": [ + "**Set Image Directory**\n", + "\n", + "Define the directory containing extracted images.\n" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "id": "rqA8XuqMalcV" + }, + "outputs": [], + "source": [ + "image_dir = '/content/scientific_publication/'" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "xdQdMmBzn2yu" + }, + "source": [ + "**List Image Files**\n", + "\n", + "List all image files in the specified directory." + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": { + "id": "Wxu7gcycbHUp" + }, + "outputs": [], + "source": [ + "image_files = [os.path.join(image_dir, f) for f in os.listdir(image_dir) if os.path.isfile(os.path.join(image_dir, f))]" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "GPs0B9u5n7zw" + }, + "source": [ + "**Extract Text from Images**\n", + "\n", + "Extract text from each image and store it in a dictionary." + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "id": "T0R5WdqoYr9b" + }, + "outputs": [], + "source": [ + "image_texts = {}\n", + "\n", + "for image_file in image_files:\n", + " text = extract_text_from_image(image_file)\n", + " image_texts[os.path.basename(image_file)] = text\n", + " break\n" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "fJXG1kPNn-ns" + }, + "source": [ + "**Display Extracted Text**\n", + "\n", + "Display the extracted text from each image." + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "GJw_2Qp9d1YN", + "outputId": "707243a8-79d6-4305-d4c1-31271b99cb84" + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Text extracted from doc_000891.png:\n", + "Reprinted from Biochemistry, 198, 27, 40\n", + "— copyright © 198 bythe American Choma! Soest and reprinted By peviniaon of copyright owner.\n", + "\n", + "Native Structure and Physical Properties of Bovine Brain Kinesin and\n", + "Identification of the ATP-Binding Subunit Polypeptide!\n", + "\n", + "George S. Bloom,\" Mark C. Wagner, K. Kevin Pfister, and Soot T- Brady\n", + "\n", + "Department of Cell Biology ond Anatomy, Unversity of Texas Souwen, “Medical Center at Dallas, $323 Harry Hines\n", + "‘Boulevard, Dallas, Texas 75235\n", + "\n", + "‘Received June 2, 1987; Revised Manuscript Received October 29, 1987\n", + "\n", + " \n", + "\n", + " \n", + "\n", + "anstract: Kinesin was extensively purified from bovine brain cytosol by 8 ricrotubule-binding step in\n", + "{fe presence of 5-adenylylimidodipbosphate (AMP-PNP),folowat by gel filtration chromatography and\n", + "the present on ultracentrifugation. The prodets consistently contained 12400 (124K) and 64000 (64K)\n", + "aaa rides, These tw popes appear to represent heat and BN chains of kinesin, respectively,\n", + "Galton Po aiid on suerose gradients toa constant and equimolar stoichonery ‘and bound stably\n", + "area ae cain the presence of AMP-PNP bat sot ATP. ‘The mobilities Of 124K and 64K in sodium\n", + "‘Paseo sulfate-polyacrylamide gels under reducing conditions were te S06 ‘under nonreducing conditions.\n", + "\n", + "gosGifusion coefficient of (2.24 + 0.21) X 107 ems” and 2 sedimentation coefficient of (9.56 + 0.34)\n", + "A ais oe ined for native Knesn by gl filtration and sucrose prion’ ultracentrifugation,\n", + "apectvely These values were used to eaeulate a native malerlae ight of about 379 000 an suggest\n", + "eee axial rato of approximately 20, Extensively purified Kine exhibited microtubule-\n", + "a a esti, and only the 124K subunit incorporated ATP in photoanty labeling experiments\n", + "sine DEPIATP. Collectively, these data favor the interpretation hat bovine brain kinesin is 2 highly\n", + "wane ted snicrotubuleactivated ATPase comprising wo subunits cach of 124000 and 64000 daltons, that\n", + "nea eee pt inked to one another by dsaide Bonds, and thatthe heawy chains are the ATP-binding\n", + "subunits.\n", + "\n", + " \n", + "\n", + " \n", + " \n", + "\n", + "Beene the sor cts the mer mutiney tyne mp raed hat hae epion P\n", + "Bocuse tence se re Team impor Mile or ee\n", + "se i he faye ae NE a a\n", + "FE eC itomperty a) a outaly\n", + "Te ee re ee\n", + "Hk as mcctond, sal ml antesof he aon een on\n", + "segs at ne ae ee nace HSM ee PN\n", + "2S Sami Ge rt oman oR\n", + "Bh PO pega (60) Ee oe\n", + "an rim onmncii 8 and o\n", + "\n", + " \n", + "\n", + " \n", + "\n", + "sees) \"Together, the anterograde and retrograde or S-adensyh inidodiphosphate (AMP-PNP), was found t0 in-\n", + "fancile movements ate known as “fast axonal transport hibit this process (Brady et al, 1983, 1985; Lasek & Brady.\n", + "Bem Seganle motity has been observed inte cytoplasm 1985), EAS the presence of nearly stoichiometric levels\n", + "\n", + "Sree types as diverse as HeLa ces (Freed & Lebowitz, OEATP, AMP-PNP blocks organelle movements completely,\n", + "Soo), frog Keratocytes (Hayden et al, 1983: Hayden & Allen, while promeite the formation of stable complexes of orgs:\n", + "\n", + "1984), and giant amoebae (Koonce & Schliva, 1985), im- nee Microtubule, and, apparently, the motors for organelle\n", + "iyi that che proses of widespread biological signifieance, ans (Lasek & Brady, 1985). By contast, in other motility\n", + "Bone ee we of dso enhanced ight microscopy in cou» systems Sao) as the exoneme (Satir et al, 1981; Penningrath\n", + "\n", + "Jpnriion wth correlative immunoflurescence or electron 1982) and actomyosin (Greene & Eisenberg, 1980;\n", + "junction nas established that mirotubules serve as tracks Bicsca 6 1986), AMP-PNP promotes dissociation of the\n", + "rept orgenllesravel an that individual microtubules motes yaein ‘myosin) from the structure it moves (mi-\n", + "aon vat biectine! vse anspor (Hayden tal, 1983: crotubsies of filaments). The effects of AMP-PNP on\n", + "Haydon & Allen, 1983; Koonce & Sehliva, 1985;Schnapp organ ‘motility in the axon indicated, therefore, that fast\n", + "et al., 1983) sronal transport is driven by a new class of mechnochemica}\n", + "\n", + "aia uth leading challenges to emerge from these Findings protein tha is ‘biochemically and pharmacologically distinet\n", + "aan aeatife mechandchemiea proteins responsible for from dynein and yet (Lasek & Brady, 1985).\n", + "\n", + " \n", + "\n", + " \n", + "\n", + " \n", + "\n", + " \n", + "\n", + "ransiocating memorane-bounded organelles along microtu- “The evidence that AMP-PNP stabilizes binding of @ fast\n", + "rrpartant clues to the identity of « motor for fast axonal anspor AN to microtubules in situ suggested that\n", + "bales ener! were gained from studies of axopasm exr tis raleaide ibe able to serve as a selective probe for\n", + "\n", + "anon anspor, =1.17 in /usr/local/lib/python3.10/dist-packages (from datasets) (1.25.2)\n", + 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"execution_count": 12, + "metadata": { + "id": "iUWpILF15Ngt" + }, + "outputs": [], + "source": [ + "from transformers import pipeline" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "gg4-AnIOpGZd" + }, + "source": [ + "**Title and Author Extraction**\n", + "\n", + "Define a function to extract title and author using question answering.\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": { + "id": "gafnMn3ix9Ct" + }, + "outputs": [], + "source": [ + "# Function to extract title and author using question answering\n", + "def extract_title_and_author(text):\n", + " # Initialize QA pipeline\n", + " qa_pipeline = pipeline(\"question-answering\", model=\"bert-large-uncased-whole-word-masking-finetuned-squad\")\n", + "\n", + " # Define questions\n", + " title_question = \"What is the title of this document?\"\n", + " author_question = \"Who are the authors of this document?\"\n", + "\n", + " # Extract title\n", + " title_result = qa_pipeline(question=title_question, context=text)\n", + " title = title_result['answer']\n", + "\n", + " # Extract author\n", + " author_result = qa_pipeline(question=author_question, context=text)\n", + " author = author_result['answer']\n", + "\n", + " return title, author\n" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "4VD0MKI_pMFQ" + }, + "source": [ + "**Alternative Title Generation**\n", + "\n", + "Define a function to generate alternative titles using BART models.\n", + "\n" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 375, + "referenced_widgets": [ + "96324af20bd342cb84492e302c609bc5", + "89568f4673d5433e9d73386d4952fc6f", + "34a7ddf2ef494b0f82927650726ff43c", + "f72970f0dca042a8b05f5a82435fa3bd", + "57b176d87b244a61919c54bc1cc0b31e", + "cf79e6976d8545a381c1ec4c9769669d", + "3a3d380fe40a4f30b9f81bc4b32577ad", + "ba2ba32fb7d84a24b3dee3e8ebc4a198", + 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"ca8f0c8b1e7e48b3a83f821462cb2f53", + "71c7eca8bdee43ff95df67be5ea65110", + "f62909ca755c429e9e2b8fec8d0ccd70", + "e0d03ace23f1488bbea90b1743905052", + "8f9359786d244d31b41f9c874775fd05", + "a0021ac9ca67490094ca4eb3683afc7f" + ] + }, + "id": "Z6IJ1aOCPhTg", + "outputId": "1dfa9211-bc77-4e09-906c-650e3d23ad55" + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/usr/local/lib/python3.10/dist-packages/huggingface_hub/file_download.py:1132: FutureWarning: `resume_download` is deprecated and will be removed in version 1.0.0. Downloads always resume when possible. If you want to force a new download, use `force_download=True`.\n", + " warnings.warn(\n", + "/usr/local/lib/python3.10/dist-packages/huggingface_hub/utils/_token.py:89: UserWarning: \n", + "The secret `HF_TOKEN` does not exist in your Colab secrets.\n", + "To authenticate with the Hugging Face Hub, create a token in your settings tab (https://huggingface.co/settings/tokens), set it as secret in your Google Colab and restart your session.\n", + "You will be able to reuse this secret in all of your notebooks.\n", + "Please note that authentication is recommended but still optional to access public models or datasets.\n", + " warnings.warn(\n" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "96324af20bd342cb84492e302c609bc5", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "vocab.json: 0%| | 0.00/899k [00:00\n", + "
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Document TitleAuthor(s)Generated Title
doc_000891.pngclectopharesisAmerican Chemical SocietyKinesin was extensively purified from bovine b...
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" + ] + }, + "execution_count": 19, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.head(10)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": { + "id": "50nMC34w2Yu5" + }, + "outputs": [], + "source": [ + "Expand to include more fields" + ] + }, + { + "cell_type": "markdown", + "metadata": { + "id": "KhSjxR2z2Xzc" + }, + "source": [] + }, + { + "cell_type": "code", + "execution_count": 43, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/" + }, + "id": "KOR4UtX5tdSQ", + "outputId": "54395f2b-fc68-4b33-f925-98cb33fad954" + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Some weights of the model checkpoint at bert-large-uncased-whole-word-masking-finetuned-squad were not used when initializing BertForQuestionAnswering: ['bert.pooler.dense.bias', 'bert.pooler.dense.weight']\n", + "- This IS expected if you are initializing BertForQuestionAnswering from the checkpoint of a model trained on another task or with another architecture (e.g. initializing a BertForSequenceClassification model from a BertForPreTraining model).\n", + "- This IS NOT expected if you are initializing BertForQuestionAnswering from the checkpoint of a model that you expect to be exactly identical (initializing a BertForSequenceClassification model from a BertForSequenceClassification model).\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " Title Year Author Type \\\n", + "0 clectopharesis 1988 American Chemical Society SDS-PAGE \n", + "\n", + " Short description Focal constructs \\\n", + "0 one polypeptide ATP-binding\\nsubunits \n", + "\n", + " Theoretical perspective \\\n", + "0 selective probe for\\n\\nanon anspor \n", + "\n", + " Context Study design Level(s) \\\n", + "0 as a selective probe for\\n\\nanon anspor selective probe stoichiometric \n", + "\n", + " Methods notes \\\n", + "0 American Chemical Society \n", + "\n", + " Main study findings \\\n", + "0 Native Structure and Physical Properties of Bo... \n", + "\n", + " LLM Generated Executive Summary Insights related to my research question \\\n", + "0 SDS-PAGE microtubules from cick brain extracts \n", + "\n", + " Quotable points Potential use \\\n", + "0 0427-3409801.50/0 serve as a selective probe for\\n\\nanon anspor \n", + "\n", + " Additional Notes \n", + "0 American Chemical Society \n" + ] + } + ], + "source": [ + "import pandas as pd\n", + "\n", + "# Define a function to extract additional details using question answering\n", + "qa_pipeline = pipeline(\"question-answering\", model=\"bert-large-uncased-whole-word-masking-finetuned-squad\")\n", + "\n", + "def extract_additional_details(image_texts):\n", + " questions = {\n", + " \"Title\":\"What is the title of the paper?\",\n", + " \"Year\": \"What is the publication year?\",\n", + " \"Author\":\"Which persons are the authors of the paper?\",\n", + " \"Type\": \"What type of document is it?\",\n", + " \"Short description\": \"Can you provide a short description?\",\n", + " \"Focal constructs\": \"What are the focal constructs?\",\n", + " \"Theoretical perspective\": \"What is the theoretical perspective?\",\n", + " \"Context\": \"Can you describe the context?\",\n", + " \"Study design\": \"What study design was used?\",\n", + " \"Level(s)\": \"What are the levels?\",\n", + " \"Methods notes\": \"Do you have any methodological notes?\",\n", + " \"Main study findings\": \"What are the main findings of the study?\",\n", + " \"LLM Generated Executive Summary\": \"Can you provide a generated executive summary?\",\n", + " \"Insights related to my research question\": \"What insights are related to your research question?\",\n", + " \"Quotable points\": \"Can you provide any quotable points?\",\n", + " \"Potential use\": \"How can this document be used?\",\n", + " \"Additional Notes\": \"Do you have any additional notes?\"\n", + " }\n", + "\n", + " data = []\n", + " for _, text in image_texts.items():\n", + " details = []\n", + " for question in questions.values():\n", + " answer = qa_pipeline(question=question, context=text)\n", + " details.append(answer[\"answer\"])\n", + " data.append(details)\n", + "\n", + " return pd.DataFrame(data, columns=questions.keys())\n", + "\n", + "# Example usage:\n", + "additional_details_df = extract_additional_details(image_texts)\n", + "print(additional_details_df)" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "metadata": { + "colab": { + "base_uri": "https://localhost:8080/", + "height": 219 + }, + "id": "DSlXR2VAtzO7", + "outputId": "0e53939f-3a40-4c42-8791-c79b2b76c608" + }, + "outputs": [ + { + "data": { + "application/vnd.google.colaboratory.intrinsic+json": { + "summary": "{\n \"name\": \"additional_details_df\",\n \"rows\": 1,\n \"fields\": [\n {\n \"column\": \"Title\",\n \"properties\": {\n \"dtype\": \"string\",\n \"num_unique_values\": 1,\n \"samples\": [\n \"clectopharesis\"\n ],\n 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