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"visibility": null, "width": null } }, "bc572326b7544adca040359d77dfdba9": { "model_module": "@jupyter-widgets/controls", "model_name": "DescriptionStyleModel", "model_module_version": "1.5.0", "state": { "_model_module": "@jupyter-widgets/controls", "_model_module_version": "1.5.0", "_model_name": "DescriptionStyleModel", "_view_count": null, "_view_module": "@jupyter-widgets/base", "_view_module_version": "1.2.0", "_view_name": "StyleView", "description_width": "" } } } } }, "cells": [ { "cell_type": "markdown", "source": [ "### Clone BiomedCLIP repo\n", "\n", "Will be merged to the open_clip main later" ], "metadata": { "id": "e4ymt2jdGuPx" } }, { "cell_type": "code", "execution_count": 1, "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "J4N1Au3wz10u", "outputId": "bb6ddaa6-3733-43f2-9d4f-9f8f003a1a62" }, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "fatal: destination path 'open_clip' already exists and is not an empty directory.\n" ] } ], "source": [ "!git clone -b naotous/biomed_clip_224px https://github.com/usuyama/open_clip.git" ] }, { "cell_type": "markdown", "source": [ "### Install libraries\n", "**Make sure to restart the Colab runtime after installation**\n", "\n", "Colab Menu -> Runtime -> Restart runtime" ], "metadata": { "id": "t8BYG2CFF6wD" } }, { "cell_type": "code", "source": [ "!pip install -e ./open_clip transformers" ], "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "nUAkSVJ90DQs", "outputId": "f0196a2a-a631-46b9-f52c-0c2032af7c6f" }, "execution_count": 2, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "Looking in indexes: https://pypi.org/simple, https://us-python.pkg.dev/colab-wheels/public/simple/\n", "Obtaining file:///content/open_clip\n", " Preparing metadata (setup.py) ... \u001b[?25l\u001b[?25hdone\n", "Requirement already satisfied: transformers in /usr/local/lib/python3.9/dist-packages (4.27.4)\n", "Requirement already satisfied: requests in /usr/local/lib/python3.9/dist-packages (from transformers) (2.27.1)\n", "Requirement already satisfied: huggingface-hub<1.0,>=0.11.0 in /usr/local/lib/python3.9/dist-packages (from transformers) (0.13.4)\n", "Requirement already satisfied: numpy>=1.17 in /usr/local/lib/python3.9/dist-packages (from transformers) (1.22.4)\n", "Requirement already satisfied: tqdm>=4.27 in /usr/local/lib/python3.9/dist-packages (from transformers) (4.65.0)\n", "Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.9/dist-packages (from transformers) (23.0)\n", "Requirement already satisfied: filelock in /usr/local/lib/python3.9/dist-packages (from transformers) (3.10.7)\n", "Requirement already satisfied: regex!=2019.12.17 in /usr/local/lib/python3.9/dist-packages (from transformers) (2022.10.31)\n", "Requirement already satisfied: pyyaml>=5.1 in /usr/local/lib/python3.9/dist-packages (from transformers) (6.0)\n", "Requirement already satisfied: tokenizers!=0.11.3,<0.14,>=0.11.1 in /usr/local/lib/python3.9/dist-packages (from transformers) (0.13.3)\n", "Requirement already satisfied: torch>=1.9.0 in /usr/local/lib/python3.9/dist-packages (from open-clip-torch==2.16.0) (2.0.0+cu118)\n", "Requirement already satisfied: torchvision in /usr/local/lib/python3.9/dist-packages (from open-clip-torch==2.16.0) (0.15.1+cu118)\n", "Requirement already satisfied: ftfy in /usr/local/lib/python3.9/dist-packages (from open-clip-torch==2.16.0) (6.1.1)\n", "Requirement already satisfied: sentencepiece in /usr/local/lib/python3.9/dist-packages (from open-clip-torch==2.16.0) (0.1.97)\n", "Requirement already satisfied: protobuf<4 in /usr/local/lib/python3.9/dist-packages (from open-clip-torch==2.16.0) (3.20.3)\n", "Requirement already satisfied: timm in /usr/local/lib/python3.9/dist-packages (from open-clip-torch==2.16.0) (0.6.13)\n", "Requirement already satisfied: typing-extensions>=3.7.4.3 in /usr/local/lib/python3.9/dist-packages (from huggingface-hub<1.0,>=0.11.0->transformers) (4.5.0)\n", "Requirement already satisfied: jinja2 in /usr/local/lib/python3.9/dist-packages (from torch>=1.9.0->open-clip-torch==2.16.0) (3.1.2)\n", "Requirement already satisfied: networkx in /usr/local/lib/python3.9/dist-packages (from torch>=1.9.0->open-clip-torch==2.16.0) (3.0)\n", "Requirement already satisfied: sympy in /usr/local/lib/python3.9/dist-packages (from torch>=1.9.0->open-clip-torch==2.16.0) (1.11.1)\n", "Requirement already satisfied: triton==2.0.0 in /usr/local/lib/python3.9/dist-packages (from torch>=1.9.0->open-clip-torch==2.16.0) (2.0.0)\n", "Requirement already satisfied: lit in /usr/local/lib/python3.9/dist-packages (from triton==2.0.0->torch>=1.9.0->open-clip-torch==2.16.0) (16.0.0)\n", "Requirement already satisfied: cmake in /usr/local/lib/python3.9/dist-packages (from triton==2.0.0->torch>=1.9.0->open-clip-torch==2.16.0) (3.25.2)\n", "Requirement already satisfied: wcwidth>=0.2.5 in /usr/local/lib/python3.9/dist-packages (from ftfy->open-clip-torch==2.16.0) (0.2.6)\n", "Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/local/lib/python3.9/dist-packages (from requests->transformers) (1.26.15)\n", "Requirement already satisfied: charset-normalizer~=2.0.0 in /usr/local/lib/python3.9/dist-packages (from requests->transformers) (2.0.12)\n", "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.9/dist-packages (from requests->transformers) (2022.12.7)\n", "Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.9/dist-packages (from requests->transformers) (3.4)\n", "Requirement already satisfied: pillow!=8.3.*,>=5.3.0 in /usr/local/lib/python3.9/dist-packages (from torchvision->open-clip-torch==2.16.0) (8.4.0)\n", "Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.9/dist-packages (from jinja2->torch>=1.9.0->open-clip-torch==2.16.0) (2.1.2)\n", "Requirement already satisfied: mpmath>=0.19 in /usr/local/lib/python3.9/dist-packages (from sympy->torch>=1.9.0->open-clip-torch==2.16.0) (1.3.0)\n", "Installing collected packages: open-clip-torch\n", " Attempting uninstall: open-clip-torch\n", " Found existing installation: open-clip-torch 2.16.0\n", " Can't uninstall 'open-clip-torch'. No files were found to uninstall.\n", " Running setup.py develop for open-clip-torch\n", "Successfully installed open-clip-torch-2.16.0\n" ] } ] }, { "cell_type": "markdown", "source": [ "### Download the model checkpoint and example images" ], "metadata": { "id": "G4FRMeHQHW3c" } }, { "cell_type": "code", "source": [ "from huggingface_hub import snapshot_download\n", "snapshot_download(\"microsoft/BiomedCLIP-PubMedBERT_256-vit_base_patch16_224\", local_dir=\"biomed-clip-share\")" ], "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 67, "referenced_widgets": [ "dd364294fe024a3faff862df014abdcd", "eca221cae70445409181610afdef0e5f", "c43dae56ac244d4a9d97b39cf9d2c239", "4d234f8b73394113af464b91cbc78dbe", "56c3e17b6cdc46f888ea61128435a326", "21d52e2249eb495ebd0a52c954e8da00", "47df4590b09b4982bb189b705a10c388", "2ec4c1279d23484dbc5349e52bad13cc", "81f57d4f33d74947b78b3361ded13e60", "47839e629e6f4b078f0469351b86467b", "d7685e5180544cccb0510f7fb7a55df6" ] }, "id": "ScBC4GSiP1ya", "outputId": "70fc6620-4c67-4f39-cb0b-0d8266fb8c7e" }, "execution_count": 3, "outputs": [ { "output_type": "display_data", "data": { "text/plain": [ "Fetching 15 files: 0%| | 0/15 [00:00, ?it/s]" ], "application/vnd.jupyter.widget-view+json": { "version_major": 2, "version_minor": 0, "model_id": "dd364294fe024a3faff862df014abdcd" } }, "metadata": {} }, { "output_type": "execute_result", "data": { "text/plain": [ "'/content/biomed-clip-share'" ], "application/vnd.google.colaboratory.intrinsic+json": { "type": "string" } }, "metadata": {}, "execution_count": 3 } ] }, { "cell_type": "code", "source": [ "!ls biomed-clip-share" ], "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "4WOxBdKr0e_m", "outputId": "8decdbf2-fb53-40c4-c5f4-22d1cc4f224c" }, "execution_count": 4, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "biomed_clip_example_20230323.ipynb example_data models\n", "biomed-vlp-eval.svg\t\t LICENSE.md\t README.md\n" ] } ] }, { "cell_type": "markdown", "source": [ "### Load BiomedCLIP model" ], "metadata": { "id": "ZQ7D3zXKGcaM" } }, { "cell_type": "code", "source": [ "import glob\n", "from collections import OrderedDict\n", "\n", "import torch\n", "from PIL import Image\n", "import open_clip\n", "\n", "# Timm contiual pretraining\n", "model_name = 'PubMedBERT_256-timm-vit_base_patch16_224'\n", "checkpoint = 'biomed-clip-share/models/2022_11_08-07_39_28-model_timm-vit_base_patch16_224-lr_0.0005-b_1024-j_8-p_amp/checkpoints/epoch_32.pt'\n", "\n", "model, transform_train, transform_val = open_clip.create_model_and_transforms(model_name)\n", "checkpoint = torch.load(checkpoint, map_location=\"cpu\")\n", "\n", "tokenizer = open_clip.get_tokenizer(model_name)\n", "context_length = 256\n", "\n", "new_state_dict = OrderedDict()\n", "for k,v in checkpoint['state_dict'].items():\n", " new_k = k.replace('module.', '')\n", " new_state_dict[new_k] = v\n", "model.load_state_dict(new_state_dict, strict=False) # can set this to be true except for timm models" ], "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 286, "referenced_widgets": [ "567f7218c19e423094943bcc1e2d949b", "1dacb2bd8efe494b9af0f14bd00de103", "3da95a498ce5481ebf6cdee3845556e3", "effd51f491da420dbd2189b71ec45bc2", "e80a18da678c4a2b966a5916f59973c7", "5869689db6bc478e9e1fc882f4940395", "b884bf53904d4decaeb82b13d750222f", "6a09cd03963c49118c7b3b09069affcf", "9d97118639af417398ec047fce465ad4", "5fce92dd68734554a72770c5956e20ac", "1dede12557ae4d08be0d02f626793f9b", "977698fe79d7438da30291edc33f1fcd", "01a9180d588a40d8aec90d04f706b396", "a53a3834d6e44bf182f4445ddf58b891", "2999b53117744ea596ac33bd6c2f5369", "f355ec466eb14e648cd7c83069fb4728", "48cb79b41ca84241aecfc31e7aedef01", "3fb54fb6e23a49cb94e71626cc8d210b", "50fa00bf7fe04a71b5b65fe4e633663e", "583c48826b6e470abccfbaa2f0f7277b", "502c43bb126e40d597f08b531ec0d8b5", "58c105a5cece403fa753051a32bfa680", "bcb369cde62c4b57850166e739f70cb4", "6a103517d1154760a574493bf45037a3", "1991167f95644ca3afd5a0fee31e6c9f", "165098b5aaf64e378eea9620dcf8c80e", "27d672359bb5483a826f671b65c28d23", "563c7194bb884b52a35d3e60080fca59", "d48f091a22d844af8eb4d41093722c7f", "183c0ab8e9f94e16999501a95e2e0430", "d01b5d6098b649a692920f300c968c4f", "f4ebab0dfb4c48f987a91359e139f272", "1e297107c9374160970da511c195be59", "04c1bccf173248f8833c48cac89a9da1", "4982661c09844b7294563e375e850c14", "67c8c149a6e544879e797161baf89d95", "fd6accc637f447a4875a696912c3cae2", "239c9bc740f54fad88ab04e24b70ac7e", "dc1655a283ba40c5b041514549b0dfe5", "b6e29f8c6a684d72b5a3064b124bef0a", "f20dcdc727de45f8903b13dda22660a6", "8c01911ecb8b4afea7c6f29c4b5b0461", "fa8a049155f94db38e757daed40deb82", "476d555e6f584616b051ff70611e4384", "60eef94bc2cc4688ab13305ad1a1908d", "8763bcae7a424f21b926581f4cfc3f79", "1a840b729f764907a9e3eb4bc3c1c2c9", "abba5e7c32fd44a6b872690c897e9725", "48eb304451c64f2db0e565ffd2b1d218", "2e726f67f1bb4e97acd689615c97c09d", "44310507110c4492a68f38313ee95058", "4ef47128a9564e5fb88adba8c31a32ce", "6765c01450054686a94a47e24ce1d1ae", "728d7d32d78040408b839f245e7ec9ce", "bc572326b7544adca040359d77dfdba9" ] }, "id": "v88W1wY01oxB", "outputId": "14fce3aa-60bf-485d-98dd-0bd33933ce1d" }, "execution_count": 5, "outputs": [ { "output_type": "stream", "name": "stderr", "text": [ "The cache for model files in Transformers v4.22.0 has been updated. Migrating your old cache. This is a one-time only operation. You can interrupt this and resume the migration later on by calling `transformers.utils.move_cache()`.\n" ] }, { "output_type": "display_data", "data": { "text/plain": [ "0it [00:00, ?it/s]" ], "application/vnd.jupyter.widget-view+json": { "version_major": 2, "version_minor": 0, "model_id": "567f7218c19e423094943bcc1e2d949b" } }, "metadata": {} }, { "output_type": "display_data", "data": { "text/plain": [ "Downloading (…)lve/main/config.json: 0%| | 0.00/385 [00:00, ?B/s]" ], "application/vnd.jupyter.widget-view+json": { "version_major": 2, "version_minor": 0, "model_id": "977698fe79d7438da30291edc33f1fcd" } }, "metadata": {} }, { "output_type": "display_data", "data": { "text/plain": [ "Downloading pytorch_model.bin: 0%| | 0.00/440M [00:00, ?B/s]" ], "application/vnd.jupyter.widget-view+json": { "version_major": 2, "version_minor": 0, "model_id": "bcb369cde62c4b57850166e739f70cb4" } }, "metadata": {} }, { "output_type": "stream", "name": "stderr", "text": [ "Some weights of the model checkpoint at microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract were not used when initializing BertModel: ['cls.seq_relationship.weight', 'cls.predictions.decoder.weight', 'cls.seq_relationship.bias', 'cls.predictions.transform.dense.bias', 'cls.predictions.transform.dense.weight', 'cls.predictions.bias', 'cls.predictions.transform.LayerNorm.weight', 'cls.predictions.transform.LayerNorm.bias', 'cls.predictions.decoder.bias']\n", "- This IS expected if you are initializing BertModel 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 BertModel from the checkpoint of a model that you expect to be exactly identical (initializing a BertForSequenceClassification model from a BertForSequenceClassification model).\n" ] }, { "output_type": "display_data", "data": { "text/plain": [ "Downloading (…)okenizer_config.json: 0%| | 0.00/28.0 [00:00, ?B/s]" ], "application/vnd.jupyter.widget-view+json": { "version_major": 2, "version_minor": 0, "model_id": "04c1bccf173248f8833c48cac89a9da1" } }, "metadata": {} }, { "output_type": "display_data", "data": { "text/plain": [ "Downloading (…)solve/main/vocab.txt: 0%| | 0.00/225k [00:00, ?B/s]" ], "application/vnd.jupyter.widget-view+json": { "version_major": 2, "version_minor": 0, "model_id": "60eef94bc2cc4688ab13305ad1a1908d" } }, "metadata": {} }, { "output_type": "execute_result", "data": { "text/plain": [ "_IncompatibleKeys(missing_keys=['text.transformer.pooler.dense.weight', 'text.transformer.pooler.dense.bias'], unexpected_keys=[])" ] }, "metadata": {}, "execution_count": 5 } ] }, { "cell_type": "markdown", "source": [ "### Example: Zero-shot classifications" ], "metadata": { "id": "_11A5zFuGfkG" } }, { "cell_type": "code", "source": [ "dataset_path = 'biomed-clip-share/example_data/biomed_image_classification_example_data'\n", "template = 'this is a photo of '\n", "labels = [\n", " 'adenocarcinoma histopathology',\n", " 'brain MRI',\n", " 'covid line chart',\n", " 'squamous cell carcinoma histopathology',\n", " 'immunohistochemistry histopathology',\n", " 'bone X-ray',\n", " 'chest X-ray',\n", " 'pie chart',\n", " 'hematoxylin and eosin histopathology'\n", "]\n", "\n", "import glob\n", "test_imgs = glob.glob(dataset_path + '/*')\n", "\n", "device = torch.device('cuda') if torch.cuda.is_available() else torch.device('cpu')\n", "model.to(device)\n", "model.eval()\n", "\n", "images = torch.stack([transform_val(Image.open(img)) for img in test_imgs]).to(device)\n", "texts = tokenizer([template + l for l in labels], context_length=context_length).to(device)\n", "with torch.no_grad():\n", " image_features, text_features, logit_scale = model(images, texts)\n", "\n", " logits = (logit_scale * image_features @ text_features.t()).detach().softmax(dim=-1)\n", " sorted_indices = torch.argsort(logits, dim=-1, descending=True)\n", "\n", " logits = logits.cpu().numpy()\n", " sorted_indices = sorted_indices.cpu().numpy()\n", "\n", "top_k = -1\n", "\n", "for i, img in enumerate(test_imgs):\n", " pred = labels[sorted_indices[i][0]]\n", "\n", " top_k = len(labels) if top_k == -1 else top_k\n", " print(img.split('/')[-1] + ':')\n", " for j in range(top_k):\n", " jth_index = sorted_indices[i][j]\n", " print(f'{labels[jth_index]}: {logits[i][jth_index]}')\n", " print('\\n')" ], "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "XSJw7Qpm1w-f", "outputId": "c2998da1-d12e-4d9c-8aa0-a730f9191eb1" }, "execution_count": 6, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "chest_X-ray.jpg:\n", "chest X-ray: 0.9998347759246826\n", "hematoxylin and eosin histopathology: 0.00012055984552716836\n", "bone X-ray: 4.112849273951724e-05\n", "immunohistochemistry histopathology: 1.048634430844686e-06\n", "adenocarcinoma histopathology: 9.666315463618957e-07\n", "covid line chart: 9.508923426437832e-07\n", "brain MRI: 3.2323802656719636e-07\n", "squamous cell carcinoma histopathology: 2.533681140448607e-07\n", "pie chart: 3.698396922047209e-09\n", "\n", "\n", "IHC_histopathology.jpg:\n", "immunohistochemistry histopathology: 0.9465932250022888\n", "hematoxylin and eosin histopathology: 0.032324664294719696\n", "brain MRI: 0.020657304674386978\n", "adenocarcinoma histopathology: 0.0003047357895411551\n", "bone X-ray: 4.5735243475064635e-05\n", "squamous cell carcinoma histopathology: 3.150888369418681e-05\n", "covid line chart: 2.0559631593641825e-05\n", "chest X-ray: 1.271547625947278e-05\n", "pie chart: 9.552859410177916e-06\n", "\n", "\n", "covid_line_chart.png:\n", "covid line chart: 0.9493206143379211\n", "adenocarcinoma histopathology: 0.018982239067554474\n", "squamous cell carcinoma histopathology: 0.017550276592373848\n", "immunohistochemistry histopathology: 0.0067917839623987675\n", "hematoxylin and eosin histopathology: 0.0034173389431089163\n", "brain MRI: 0.0026299129240214825\n", "chest X-ray: 0.001004116260446608\n", "bone X-ray: 0.00024685877724550664\n", "pie chart: 5.681261609424837e-05\n", "\n", "\n", "bone_X-ray.jpg:\n", "bone X-ray: 0.9037957191467285\n", "hematoxylin and eosin histopathology: 0.07279353588819504\n", "brain MRI: 0.01353507675230503\n", "chest X-ray: 0.008212101645767689\n", "immunohistochemistry histopathology: 0.001647883327677846\n", "squamous cell carcinoma histopathology: 1.4188161912898067e-05\n", "covid line chart: 1.1351595503583667e-06\n", "adenocarcinoma histopathology: 2.3802178361620463e-07\n", "pie chart: 9.43324423019476e-08\n", "\n", "\n", "H_and_E_histopathology.jpg:\n", "hematoxylin and eosin histopathology: 0.7953248620033264\n", "immunohistochemistry histopathology: 0.19780027866363525\n", "chest X-ray: 0.005973882507532835\n", "bone X-ray: 0.0008049227762967348\n", "adenocarcinoma histopathology: 9.133952698903158e-05\n", "squamous cell carcinoma histopathology: 3.642378715085215e-06\n", "brain MRI: 6.688669031973404e-07\n", "pie chart: 4.2787809206856764e-07\n", "covid line chart: 3.051618335803141e-08\n", "\n", "\n", "brain_MRI.jpg:\n", "brain MRI: 0.9565798044204712\n", "hematoxylin and eosin histopathology: 0.041418008506298065\n", "immunohistochemistry histopathology: 0.0019450504332780838\n", "pie chart: 2.7151156245963648e-05\n", "squamous cell carcinoma histopathology: 1.0223747267446015e-05\n", "bone X-ray: 8.662519576319028e-06\n", "chest X-ray: 7.967662895680405e-06\n", "adenocarcinoma histopathology: 2.769203774732887e-06\n", "covid line chart: 3.420072687276843e-07\n", "\n", "\n", "squamous_cell_carcinoma_histopathology.jpeg:\n", "squamous cell carcinoma histopathology: 0.946948766708374\n", "adenocarcinoma histopathology: 0.05259053036570549\n", "hematoxylin and eosin histopathology: 0.0003988392127212137\n", "immunohistochemistry histopathology: 6.187905091792345e-05\n", "chest X-ray: 1.4099564182856739e-08\n", "pie chart: 3.522493408070204e-10\n", "bone X-ray: 2.9633698273023867e-10\n", "brain MRI: 1.2720474673599824e-10\n", "covid line chart: 1.8425671145100297e-12\n", "\n", "\n", "adenocarcinoma_histopathology.jpg:\n", "adenocarcinoma histopathology: 0.7818866968154907\n", "hematoxylin and eosin histopathology: 0.1551772654056549\n", "immunohistochemistry histopathology: 0.061494577676057816\n", "squamous cell carcinoma histopathology: 0.001418206375092268\n", "chest X-ray: 2.017212136706803e-05\n", "brain MRI: 1.2181552619949798e-06\n", "pie chart: 7.932691801215697e-07\n", "bone X-ray: 7.436469786625821e-07\n", "covid line chart: 4.4826077783000073e-07\n", "\n", "\n", "pie_chart.png:\n", "pie chart: 0.999992847442627\n", "covid line chart: 6.0569645938812755e-06\n", "brain MRI: 6.212229095581279e-07\n", "bone X-ray: 1.8702795046010579e-07\n", "chest X-ray: 1.4315868668290932e-07\n", "immunohistochemistry histopathology: 7.397999013392109e-08\n", "hematoxylin and eosin histopathology: 1.3329846559884118e-08\n", "adenocarcinoma histopathology: 7.695412307384686e-09\n", "squamous cell carcinoma histopathology: 4.512859419492088e-09\n", "\n", "\n" ] } ] }, { "cell_type": "markdown", "source": [ "
\n", "adenocarcinoma_histopathology.jpg:\n", "adenocarcinoma histopathology: 0.7818863987922668\n", "hematoxylin and eosin histopathology: 0.15517690777778625\n", "immunohistochemistry histopathology: 0.06149514392018318\n", "squamous cell carcinoma histopathology: 0.0014182085869833827\n", "chest X-ray: 2.017213228100445e-05\n", "brain MRI: 1.2181524198240368e-06\n", "pie chart: 7.932688959044754e-07\n", "bone X-ray: 7.436410101036017e-07\n", "covid line chart: 4.482610052036762e-07\n", "\n", "\n", "covid_line_chart.png:\n", "covid line chart: 0.9493210315704346\n", "adenocarcinoma histopathology: 0.01898195780813694\n", "squamous cell carcinoma histopathology: 0.0175501499325037\n", "immunohistochemistry histopathology: 0.006791787222027779\n", "hematoxylin and eosin histopathology: 0.003417333820834756\n", "brain MRI: 0.002629919210448861\n", "chest X-ray: 0.0010041205678135157\n", "bone X-ray: 0.00024685842799954116\n", "pie chart: 5.6812208640621975e-05\n", "\n", "\n", "bone_X-ray.jpg:\n", "bone X-ray: 0.9037961959838867\n", "hematoxylin and eosin histopathology: 0.07279316335916519\n", "brain MRI: 0.013534954749047756\n", "chest X-ray: 0.00821212213486433\n", "immunohistochemistry histopathology: 0.001647887285798788\n", "squamous cell carcinoma histopathology: 1.418814281350933e-05\n", "covid line chart: 1.1351590956110158e-06\n", "adenocarcinoma histopathology: 2.3802124360372545e-07\n", "pie chart: 9.433303205241828e-08\n", "\n", "\n", "pie_chart.png:\n", "pie chart: 0.999992847442627\n", "covid line chart: 6.056906840967713e-06\n", "brain MRI: 6.212158041307703e-07\n", "bone X-ray: 1.870277799298492e-07\n", "chest X-ray: 1.4315827456812258e-07\n", "immunohistochemistry histopathology: 7.397970591682679e-08\n", "hematoxylin and eosin histopathology: 1.3329795045535775e-08\n", "adenocarcinoma histopathology: 7.695367898463701e-09\n", "squamous cell carcinoma histopathology: 4.512833662317917e-09\n", "\n", "\n", "H_and_E_histopathology.jpg:\n", "hematoxylin and eosin histopathology: 0.7953251600265503\n", "immunohistochemistry histopathology: 0.19779996573925018\n", "chest X-ray: 0.005973907187581062\n", "bone X-ray: 0.0008049230673350394\n", "adenocarcinoma histopathology: 9.133991261478513e-05\n", "squamous cell carcinoma histopathology: 3.6423973597266013e-06\n", "brain MRI: 6.688684948130685e-07\n", "pie chart: 4.278819574210502e-07\n", "covid line chart: 3.051619401617245e-08\n", "\n", "\n", "brain_MRI.jpg:\n", "brain MRI: 0.9565795660018921\n", "hematoxylin and eosin histopathology: 0.041418157517910004\n", "immunohistochemistry histopathology: 0.0019450499676167965\n", "pie chart: 2.7151252652402036e-05\n", "squamous cell carcinoma histopathology: 1.0223812751064543e-05\n", "bone X-ray: 8.662499567435589e-06\n", "chest X-ray: 7.96773747424595e-06\n", "adenocarcinoma histopathology: 2.7692055937222904e-06\n", "covid line chart: 3.420084908611898e-07\n", "\n", "\n", "chest_X-ray.jpg:\n", "chest X-ray: 0.9998347759246826\n", "hematoxylin and eosin histopathology: 0.0001205605294671841\n", "bone X-ray: 4.112880560569465e-05\n", "immunohistochemistry histopathology: 1.0486423889233265e-06\n", "adenocarcinoma histopathology: 9.66637117016944e-07\n", "covid line chart: 9.508977996119938e-07\n", "brain MRI: 3.232386518448038e-07\n", "squamous cell carcinoma histopathology: 2.53368597213921e-07\n", "pie chart: 3.6984038054299617e-09\n", "\n", "\n", "squamous_cell_carcinoma_histopathology.jpeg:\n", "squamous cell carcinoma histopathology: 0.9469489455223083\n", "adenocarcinoma histopathology: 0.05259034037590027\n", "hematoxylin and eosin histopathology: 0.0003988408425357193\n", "immunohistochemistry histopathology: 6.187965482240543e-05\n", "chest X-ray: 1.4099594380923008e-08\n", "pie chart: 3.522500624519864e-10\n", "bone X-ray: 2.9633814846441453e-10\n", "brain MRI: 1.2720452469139332e-10\n", "covid line chart: 1.8425603924565603e-12\n", "\n", "\n", "IHC_histopathology.jpg:\n", "immunohistochemistry histopathology: 0.9465934634208679\n", "hematoxylin and eosin histopathology: 0.03232448548078537\n", "brain MRI: 0.020657211542129517\n", "adenocarcinoma histopathology: 0.000304735847748816\n", "bone X-ray: 4.5735167077509686e-05\n", "squamous cell carcinoma histopathology: 3.150868360535242e-05\n", "covid line chart: 2.0559578842949122e-05\n", "chest X-ray: 1.2715442608168814e-05\n", "pie chart: 9.55282575887395e-06\n", "\n", "