AICUP2023_Pythia_70m_Phase3_Dataset.ipynb

{"cells":[{"cell_type":"markdown","metadata":{"id":"VpG6xj5zPV8U"},"source":["# Dataset"]},{"cell_type":"code","source":["!pip install transformers"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"Serh5gwQa9qq","executionInfo":{"status":"ok","timestamp":1698891046170,"user_tz":-480,"elapsed":15878,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}},"outputId":"3c550c4c-f5c7-41db-ccd1-bd10523a179f"},"execution_count":1,"outputs":[{"output_type":"stream","name":"stdout","text":["Collecting transformers\n","  Downloading transformers-4.34.1-py3-none-any.whl (7.7 MB)\n","\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m7.7/7.7 MB\u001b[0m \u001b[31m45.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n","\u001b[?25hRequirement already satisfied: filelock in /usr/local/lib/python3.10/dist-packages (from transformers) (3.12.4)\n","Collecting huggingface-hub<1.0,>=0.16.4 (from transformers)\n","  Downloading 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tokenizers-0.14.1 transformers-4.34.1\n"]}]},{"cell_type":"code","execution_count":2,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"0DMccN-wNdlQ","outputId":"b3b114e3-4a3f-4b06-90c6-f2062fd0484d","executionInfo":{"status":"ok","timestamp":1698891053345,"user_tz":-480,"elapsed":7193,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"stream","name":"stdout","text":["Collecting datasets\n","  Downloading datasets-2.14.6-py3-none-any.whl (493 kB)\n","\u001b[2K     \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m493.7/493.7 kB\u001b[0m \u001b[31m8.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n","\u001b[?25hRequirement already satisfied: numpy>=1.17 in /usr/local/lib/python3.10/dist-packages (from datasets) (1.23.5)\n","Requirement already satisfied: pyarrow>=8.0.0 in /usr/local/lib/python3.10/dist-packages (from datasets) (9.0.0)\n","Collecting dill<0.3.8,>=0.3.0 (from datasets)\n","  Downloading 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drive\n","drive.mount('/content/drive')"],"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"mAlaCxSEaqz0","executionInfo":{"status":"ok","timestamp":1698891107686,"user_tz":-480,"elapsed":54358,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}},"outputId":"ca5dbe70-3892-4df3-84a4-ea04a0388e0a"},"execution_count":3,"outputs":[{"output_type":"stream","name":"stdout","text":["Mounted at /content/drive\n"]}]},{"cell_type":"code","execution_count":4,"metadata":{"id":"32hufRYzHDTg","executionInfo":{"status":"ok","timestamp":1698891189149,"user_tz":-480,"elapsed":2878,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}},"colab":{"base_uri":"https://localhost:8080/","height":113,"referenced_widgets":["7c157013a5644771a22d3348ae6730cd","3eb08b67c5e04d62a3db7e7eb479455c","e78004c827a1464887c58a66a6d576a0","9c8a8f41ea554cd4b6cc5523f7298443","46c877a350bd45a0813ea59f9f9d9e01","420553b2ef8f41d990981410f5c9cdbf","d7c55750c39e4c1082a6f54a0080ab94","d9e40f11fd094504919e4d777982043e","e3ea6d138eba49619bbc0ce5278d3091","7678ab905a1348ff91eff23e5db942b5","b4305edba5b54e1aa5684ab58beafeeb","d843ea31787c42e8965542263d7187c4","3f96b511be66464489bd877a5ed8e4ad","de5983588b0d4dc7add1c5951d3af065","59aad6ac4e144a0e80d02314eafd1b5b","90ed0d9de1c64d64b76d254a7b14fcb8","19cde3351c274d23ad0ba02915c68fdd","8dc2710c6a3849b7bae7b42eb3369687","d0d1fe6b70b64680824d4804eb8206a9","8317675b5c0e4e529fe6242834bedf6d","9adf2cfe725b4948962d09a83073cbff","4cf2a487a9c8413f845db6db65f2c1da","9065b257c3cd4e0a870c28a6301dcf35","0cd508128ce4436d8d4bd8e6782d19d4","be23912a697747258668d3e3cdb1ead6","f60a326ff58547588ff386e911e83763","cc90c4131e7848b692322f1359101dc9","65bf5f29577c4ad4a0fc163d491a736d","6c57e2842af34cfa919d530040d27131","f8399fbe570c4bdf98b759b0130f3993","b6b65243b2bc421ab525c8cf62f005fd","ce02266decfb47c4acaa3045e05dd1b0","e6d00e99e8a340aaaac131eedd9470bb"]},"outputId":"e82f6912-e239-4d11-abfe-7086da5d52dc"},"outputs":[{"output_type":"display_data","data":{"text/plain":["Downloading data files:   0%|          | 0/1 [00:00<?, ?it/s]"],"application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":0,"model_id":"7c157013a5644771a22d3348ae6730cd"}},"metadata":{}},{"output_type":"display_data","data":{"text/plain":["Extracting data files:   0%|          | 0/1 [00:00<?, ?it/s]"],"application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":0,"model_id":"d843ea31787c42e8965542263d7187c4"}},"metadata":{}},{"output_type":"display_data","data":{"text/plain":["Generating train split: 0 examples [00:00, ? examples/s]"],"application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":0,"model_id":"9065b257c3cd4e0a870c28a6301dcf35"}},"metadata":{}}],"source":["from datasets import load_dataset, Features, Value\n","\n","dataset = load_dataset(\"csv\", data_files=\"/content/drive/MyDrive/aicup/PublicDataset_phase3/opendid_set1.tsv\", delimiter='\\t',\n","                       features = Features({\n","                              'fid': Value('string'), 'idx': Value('int64'),\n","                              'content': Value('string'), 'label': Value('string')}),\n","                              column_names=['fid', 'idx', 'content', 'label'], keep_default_na=False)"]},{"cell_type":"code","execution_count":5,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"x19syEzAM_ga","outputId":"55a9fabc-dbc0-4710-cd56-96179a5a7932","executionInfo":{"status":"ok","timestamp":1698891189150,"user_tz":-480,"elapsed":20,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"execute_result","data":{"text/plain":["DatasetDict({\n","    train: Dataset({\n","        features: ['fid', 'idx', 'content', 'label'],\n","        num_rows: 85736\n","    })\n","})"]},"metadata":{},"execution_count":5}],"source":["dataset"]},{"cell_type":"code","execution_count":6,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"0Tz7NyPCOwm7","outputId":"e551ec18-0227-4f61-8332-ac6355bc5bb6","executionInfo":{"status":"ok","timestamp":1698891189151,"user_tz":-480,"elapsed":14,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"execute_result","data":{"text/plain":["{'fid': '10',\n"," 'idx': 1,\n"," 'content': 'Episode No:  09F016547J',\n"," 'label': 'IDNUM: 09F016547J'}"]},"metadata":{},"execution_count":6}],"source":["dataset['train'][0]"]},{"cell_type":"code","execution_count":7,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"Ce_BRKKRO6EH","outputId":"a5ad7680-56aa-43e1-dc02-3248ac941d99","executionInfo":{"status":"ok","timestamp":1698891198799,"user_tz":-480,"elapsed":473,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"execute_result","data":{"text/plain":["{'fid': '10',\n"," 'idx': 25,\n"," 'content': '091016.NMT',\n"," 'label': 'MEDICALRECORD: 091016.NMT'}"]},"metadata":{},"execution_count":7}],"source":["dataset['train'][1]"]},{"cell_type":"code","execution_count":8,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"avSHt6RRO_kK","outputId":"5506311d-fa76-4cbe-ebf9-f6a5d9e02944","executionInfo":{"status":"ok","timestamp":1698891199236,"user_tz":-480,"elapsed":8,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"execute_result","data":{"text/plain":["{'fid': '10',\n"," 'idx': 114,\n"," 'content': 'D.O.B:  24/8/1993',\n"," 'label': 'DATE: 24/8/1993=>1993-08-24'}"]},"metadata":{},"execution_count":8}],"source":["dataset['train'][7]"]},{"cell_type":"markdown","metadata":{"id":"rMbLkY-sRo5W"},"source":["For demonstration purpose, we only use the randomly sampled 20000 instances."]},{"cell_type":"code","execution_count":9,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"WPySWonGPnom","outputId":"dac1fd1a-f9b2-415e-bb9f-5b57fb7b8f58","executionInfo":{"status":"ok","timestamp":1698891205268,"user_tz":-480,"elapsed":3632,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"stream","name":"stdout","text":["20000\n","{'fid': 'file26009', 'idx': 3243, 'content': 'All pancreatic blocks have been examined at multiple levels.', 'label': 'PHI: NULL'}\n","{'fid': 'file12198', 'idx': 8769, 'content': '- Tumour tissue is retained if testing for other biomarkers is required.', 'label': 'PHI: NULL'}\n","{'fid': '31', 'idx': 334, 'content': 'Left breast sentinel nodebiopsy - in print cytology.', 'label': 'PHI: NULL'}\n","{'fid': '603', 'idx': 4082, 'content': 'A.', 'label': 'PHI: NULL'}\n"]}],"source":["import torch\n","sub_datasets = torch.utils.data.random_split(dataset['train'], [20000, 65736])\n","print(len(sub_datasets[0]))\n","for i in range(4): print(sub_datasets[0][i])"]},{"cell_type":"markdown","metadata":{"id":"lAyCHpUPWPCk"},"source":["# Data loader"]},{"cell_type":"code","execution_count":10,"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":130,"referenced_widgets":["261119a8d79044e2bcefc4f0203ff133","14deaca0324b494b83812cfe7f9ef375","2eedc0cec0e640cebb2d761f1c4b958e","505f0c328af949ae93adfa7781df3e8b","b61ec5528ed84276805b6950ae765d8b","c7b88246d55a48908c3805d25b8d89ba","36b037a861b04021bc19ff2696c1e4e1","33fc2e11a3a7453abdac0d09d6ea5b06","21e120d265e54315bd144616815415a7","bb06a57b76bc4840b99ef010d1e95686","531203b03d7d4aa790fb1c6dc071eeec","28d74732fe8e446e983884936f53e6a2","dfe01cd70be74bfcba4c459e3b622771","a9fa3dbc606e4ed489ed376eb569d0a9","72b2fded181d46429cc7f1c3b1a21054","3241cc5911fb4a2ea38d45448a4ec8f3","b87d5e1db12248df84958e0a4bda8a63","60521dd89fca48f6aaff86d0c5b44825","a59832bd6b714d2c8359d0a0b538b5e6","968a1431564a42b9aacb4e60b458534c","2682ce23a38f42d0aa6bf07d2d10c36d","232dedadad0a46a898f34d2e299b4d5c","864481a70b994f319f860b2cb78500c5","d12fa6ac8aa3470b9e12791a101e18fb","10d59ae5b77b4c96ab1e675b1fdeb215","3912eef89643413fb08247c7e9dec945","023040c841e54360ae72147aea30be42","cba3ee5d80054c27ac9e1b4c240fdead","3910ce88bf2748779afe904da79c2bf6","d9b9dfd5c4d34d58bbc878f3bedb446f","d542556d229749809a9c12d21a717346","51bd44a84d364a6eb69aab211f54331a","bd81b5ce25584deb9996dd8d41251254"]},"id":"INzPxxcID4_g","outputId":"6eb044c7-1b4d-41cf-a3a5-6830b39e2755","executionInfo":{"status":"ok","timestamp":1698891238777,"user_tz":-480,"elapsed":2144,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"display_data","data":{"text/plain":["Downloading (…)okenizer_config.json:   0%|          | 0.00/396 [00:00<?, ?B/s]"],"application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":0,"model_id":"261119a8d79044e2bcefc4f0203ff133"}},"metadata":{}},{"output_type":"display_data","data":{"text/plain":["Downloading (…)p3000/tokenizer.json:   0%|          | 0.00/2.11M [00:00<?, ?B/s]"],"application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":0,"model_id":"28d74732fe8e446e983884936f53e6a2"}},"metadata":{}},{"output_type":"display_data","data":{"text/plain":["Downloading (…)cial_tokens_map.json:   0%|          | 0.00/99.0 [00:00<?, ?B/s]"],"application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":0,"model_id":"864481a70b994f319f860b2cb78500c5"}},"metadata":{}},{"output_type":"stream","name":"stdout","text":["<|pad|>: 50278\n"]}],"source":["from transformers import AutoTokenizer, AutoModelForCausalLM\n","from transformers import AutoModelForSeq2SeqLM, AutoTokenizer\n","\n","plm = \"EleutherAI/pythia-70m\" #\"EleutherAI/pythia-70m-deduped\"\n","\n","bos = '<|endoftext|>'\n","eos = '<|END|>'\n","pad = '<|pad|>'\n","sep ='\\n\\n####\\n\\n'\n","\n","special_tokens_dict = {'eos_token': eos, 'bos_token': bos, 'pad_token': pad, 'sep_token': sep}\n","\n","tokenizer = AutoTokenizer.from_pretrained(plm, revision=\"step3000\")\n","tokenizer.padding_side = 'left'\n","num_added_toks = tokenizer.add_special_tokens(special_tokens_dict)\n","print(f\"{tokenizer.pad_token}: {tokenizer.pad_token_id}\")"]},{"cell_type":"code","execution_count":11,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"vv99S2d7RUGX","outputId":"9a7c3db3-463f-484c-b29c-5c196d999055","executionInfo":{"status":"ok","timestamp":1698891243767,"user_tz":-480,"elapsed":5002,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"stream","name":"stdout","text":["Collecting islab-opendeid\n","  Downloading islab_opendeid-0.0.1.1-py3-none-any.whl (3.0 kB)\n","Installing collected packages: islab-opendeid\n","Successfully installed islab-opendeid-0.0.1.1\n"]}],"source":["!pip install islab-opendeid"]},{"cell_type":"code","execution_count":12,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"JJravn1EWQui","outputId":"f152017f-bf48-4127-f0e3-5a13eaaf0b20","executionInfo":{"status":"ok","timestamp":1698891245219,"user_tz":-480,"elapsed":1463,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"stream","name":"stdout","text":["torch.Size([3, 22])\n"]},{"output_type":"execute_result","data":{"text/plain":["(tensor([[50278, 50278, 50278, 50278, 50278, 50278, 50278, 50278, 50278, 50278,\n","          50278, 50278, 50278, 50278, 50278, 50278, 50278, 50278, 50278, 50278,\n","              0,   329,    15, 50279,  6663,    42,    27,  5812,   209, 50277],\n","         [    0,   313,  7058,    27, 25840,    16,   886,   608,    15,   805,\n","             15,  2082,    10, 50279, 33762,    27,   608,    15,   805,    15,\n","           2082, 14490,   938,  2082,    14,  1762,    14,   805,   209, 50277],\n","         [50278, 50278, 50278, 50278, 50278, 50278, 50278, 50278, 50278, 50278,\n","          50278, 50278, 50278,     0, 19954,    14,  2251,  3605,    27,   608,\n","            428,   884,     6, 50279,  6663,    42,    27,  5812,   209, 50277]]),\n"," tensor([[ -100,  -100,  -100,  -100,  -100,  -100,  -100,  -100,  -100,  -100,\n","           -100,  -100,  -100,  -100,  -100,  -100,  -100,  -100,  -100,  -100,\n","              0,   329,    15, 50279,  6663,    42,    27,  5812,   209, 50277],\n","         [    0,   313,  7058,    27, 25840,    16,   886,   608,    15,   805,\n","             15,  2082,    10, 50279, 33762,    27,   608,    15,   805,    15,\n","           2082, 14490,   938,  2082,    14,  1762,    14,   805,   209, 50277],\n","         [ -100,  -100,  -100,  -100,  -100,  -100,  -100,  -100,  -100,  -100,\n","           -100,  -100,  -100,     0, 19954,    14,  2251,  3605,    27,   608,\n","            428,   884,     6, 50279,  6663,    42,    27,  5812,   209, 50277]]),\n"," tensor([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1,\n","          1, 1, 1, 1, 1, 1],\n","         [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,\n","          1, 1, 1, 1, 1, 1],\n","         [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,\n","          1, 1, 1, 1, 1, 1]]))"]},"metadata":{},"execution_count":12}],"source":["from torch.utils.data import DataLoader\n","from islab.aicup import collate_batch_with_prompt_template\n","\n","train_data = list(sub_datasets[0])\n","train_dataloader = DataLoader(train_data, batch_size=3, shuffle=False, collate_fn=lambda batch: collate_batch_with_prompt_template(batch, tokenizer))\n","titer = iter(train_dataloader)\n","tks, labels, masks= next(titer)\n","print(tks.shape)\n","next(iter(titer))"]},{"cell_type":"code","execution_count":13,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"bwjOO5LqEKGU","outputId":"85be3ae2-cc6f-420d-fd0e-b81f52ca73cf","executionInfo":{"status":"ok","timestamp":1698891248196,"user_tz":-480,"elapsed":2987,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"stream","name":"stdout","text":["[[50278, 50278, 50278, 50278, 50278, 50278, 21663, 1621, 27, 1638, 41, 16604, 1438], [1628, 1267, 9466, 37, 23502, 668, 721, 3357, 33995, 2696, 41, 1539, 28613]]\n","\n","[50278, 50278, 50278, 50278, 50278, 50278, 21663, 1621, 27, 1638, 41, 16604, 1438]\n","<|pad|><|pad|><|pad|><|pad|><|pad|><|pad|>Lab No: 14H02780\n","[1628, 1267, 9466, 37, 23502, 668, 721, 3357, 33995, 2696, 41, 1539, 28613]\n","“STOCKDALE” 653 MONAGHAN RD\n"]}],"source":["results = tokenizer([\"Lab No: 14H02780\", \"“STOCKDALE” 653 MONAGHAN RD\"], padding=True)\n","print(results['input_ids'])\n","print()\n","print(results['input_ids'][0])\n","print(tokenizer.decode(results['input_ids'][0]))\n","print(results['input_ids'][1])\n","print(tokenizer.decode(results['input_ids'][1]))"]},{"cell_type":"code","execution_count":14,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"Usb9U7DwExrG","outputId":"0c576b7f-796a-4d8c-e10c-4f97d235d3e5","executionInfo":{"status":"ok","timestamp":1698891248197,"user_tz":-480,"elapsed":18,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"stream","name":"stdout","text":["[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]\n","[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]\n","<|endoftext|> 9364819.RAN\\nMINTANIA, JEFFRY \n","\n","####\n","\n"," ID: 9364819.RAN\\nNAME: MINTANIA, JEFFRY <|END|>\n","<|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|pad|><|endoftext|> This is a sentence \n","\n","####\n","\n"," PHI: NULL <|END|>\n"]}],"source":["results = tokenizer(\n","    [f\"{bos} 9364819.RAN\\\\nMINTANIA, JEFFRY {sep} ID: 9364819.RAN\\\\nNAME: MINTANIA, JEFFRY {eos}\",\n","     f\"{bos} This is a sentence {sep} PHI: NULL {eos}\"],\n","    padding=True\n",")\n","print(results['attention_mask'][0])\n","print(results['attention_mask'][1])\n","print(tokenizer.decode(results['input_ids'][0]))\n","print(tokenizer.decode(results['input_ids'][1]))"]},{"cell_type":"code","execution_count":15,"metadata":{"id":"whAVJPzlPGRw","executionInfo":{"status":"ok","timestamp":1698891248197,"user_tz":-480,"elapsed":14,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[],"source":["from islab.aicup import OpenDeidBatchSampler\n","\n","BATCH_SIZE = 8\n","bucket_train_dataloader = DataLoader(train_data,\n","                                     batch_sampler=OpenDeidBatchSampler(train_data, BATCH_SIZE),\n","                                     collate_fn=lambda batch: collate_batch_with_prompt_template(batch, tokenizer),\n","                                     pin_memory=True)\n","\n","# for idx, batch in enumerate(bucket_train_dataloader):\n","#     print(batch)\n","#     print(batch[0].shape)\n","#     print(batch[1].shape)\n","#     break"]},{"cell_type":"markdown","metadata":{"id":"YsaJmjzhuyv0"},"source":["# Model"]},{"cell_type":"code","execution_count":16,"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":550,"referenced_widgets":["6889a2527b80481387045aa412829b97","7dd29221bd0841f98d49eec71edd6b8d","01350020df7c471d8d93ae39f2f54fd0","5c1cc7579a8342888fb5dabb36be8cc6","05dd81ec64614198934f74cc69c489e5","5b5f86738c244c189554265515d4c7bb","a63c37dadb3948a0985156a03f9d3964","12f53a1a232945e9b022666b14e3aa21","f92b468514724e2a91867f5f27883788","90fe692f514f4d70bb902b15aa591b2b","6ba099ce5420469d8c0f5f20be2deda3","35c13767783e41eaa99f5eb12507d30e","609741f8d2f6492493a5053dba2557a6","c7849c31a00d4c32bdf113b57dbc21fa","92fbec09c3d749779a2ce21471fa5cf7","b0b9b899a04940028891c0ebf8d616b5","ee4d29a990874fdb8e3e37db2e5c83d5","c441c3e5eac1454db7a46aa1c54f1945","f3065ee4501145d49776f68e230481bd","7fa546104a21439f82b34d0fbd502117","6746ce9974844597b5d803ec5e1f473b","57fe7d5aabff4ce4b382ce878b0a3833"]},"id":"zSahXrvNqu8z","outputId":"c8401592-67fc-4736-cc93-9078a3146b86","executionInfo":{"status":"ok","timestamp":1698891255368,"user_tz":-480,"elapsed":7183,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"display_data","data":{"text/plain":["Downloading (…)lve/main/config.json:   0%|          | 0.00/567 [00:00<?, ?B/s]"],"application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":0,"model_id":"6889a2527b80481387045aa412829b97"}},"metadata":{}},{"output_type":"display_data","data":{"text/plain":["Downloading pytorch_model.bin:   0%|          | 0.00/166M [00:00<?, ?B/s]"],"application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":0,"model_id":"35c13767783e41eaa99f5eb12507d30e"}},"metadata":{}},{"output_type":"execute_result","data":{"text/plain":["GPTNeoXForCausalLM(\n","  (gpt_neox): GPTNeoXModel(\n","    (embed_in): Embedding(50304, 512)\n","    (emb_dropout): Dropout(p=0.0, inplace=False)\n","    (layers): ModuleList(\n","      (0-5): 6 x GPTNeoXLayer(\n","        (input_layernorm): LayerNorm((512,), eps=1e-05, elementwise_affine=True)\n","        (post_attention_layernorm): LayerNorm((512,), eps=1e-05, elementwise_affine=True)\n","        (post_attention_dropout): Dropout(p=0.0, inplace=False)\n","        (post_mlp_dropout): Dropout(p=0.0, inplace=False)\n","        (attention): GPTNeoXAttention(\n","          (rotary_emb): GPTNeoXRotaryEmbedding()\n","          (query_key_value): Linear(in_features=512, out_features=1536, bias=True)\n","          (dense): Linear(in_features=512, out_features=512, bias=True)\n","          (attention_dropout): Dropout(p=0.0, inplace=False)\n","        )\n","        (mlp): GPTNeoXMLP(\n","          (dense_h_to_4h): Linear(in_features=512, out_features=2048, bias=True)\n","          (dense_4h_to_h): Linear(in_features=2048, out_features=512, bias=True)\n","          (act): GELUActivation()\n","        )\n","      )\n","    )\n","    (final_layer_norm): LayerNorm((512,), eps=1e-05, elementwise_affine=True)\n","  )\n","  (embed_out): Linear(in_features=512, out_features=50304, bias=False)\n",")"]},"metadata":{},"execution_count":16}],"source":["from transformers import AutoConfig\n","# the model config to which we add the special tokens\n","config = AutoConfig.from_pretrained(plm,\n","                                    bos_token_id=tokenizer.bos_token_id,\n","                                    eos_token_id=tokenizer.eos_token_id,\n","                                    pad_token_id=tokenizer.pad_token_id,\n","                                    sep_token_id=tokenizer.sep_token_id,\n","                                    output_hidden_states=False)\n","\n","model = AutoModelForCausalLM.from_pretrained(plm, revision=\"step3000\", config=config)\n","model"]},{"cell_type":"code","execution_count":17,"metadata":{"id":"o_pJEiRyv4gH","executionInfo":{"status":"ok","timestamp":1698891255370,"user_tz":-480,"elapsed":66,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[],"source":["device = torch.device(\"cuda\" if torch.cuda.is_available() else \"cpu\")"]},{"cell_type":"code","execution_count":18,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"aw6Q6yNjwMIc","outputId":"960b032f-5c1e-48be-8ab9-535872e29023","executionInfo":{"status":"ok","timestamp":1698891269498,"user_tz":-480,"elapsed":14189,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"execute_result","data":{"text/plain":["GPTNeoXForCausalLM(\n","  (gpt_neox): GPTNeoXModel(\n","    (embed_in): Embedding(50280, 512)\n","    (emb_dropout): Dropout(p=0.0, inplace=False)\n","    (layers): ModuleList(\n","      (0-5): 6 x GPTNeoXLayer(\n","        (input_layernorm): LayerNorm((512,), eps=1e-05, elementwise_affine=True)\n","        (post_attention_layernorm): LayerNorm((512,), eps=1e-05, elementwise_affine=True)\n","        (post_attention_dropout): Dropout(p=0.0, inplace=False)\n","        (post_mlp_dropout): Dropout(p=0.0, inplace=False)\n","        (attention): GPTNeoXAttention(\n","          (rotary_emb): GPTNeoXRotaryEmbedding()\n","          (query_key_value): Linear(in_features=512, out_features=1536, bias=True)\n","          (dense): Linear(in_features=512, out_features=512, bias=True)\n","          (attention_dropout): Dropout(p=0.0, inplace=False)\n","        )\n","        (mlp): GPTNeoXMLP(\n","          (dense_h_to_4h): Linear(in_features=512, out_features=2048, bias=True)\n","          (dense_4h_to_h): Linear(in_features=2048, out_features=512, bias=True)\n","          (act): GELUActivation()\n","        )\n","      )\n","    )\n","    (final_layer_norm): LayerNorm((512,), eps=1e-05, elementwise_affine=True)\n","  )\n","  (embed_out): Linear(in_features=512, out_features=50280, bias=False)\n",")"]},"metadata":{},"execution_count":18}],"source":["from transformers import get_linear_schedule_with_warmup\n","from torch.optim import AdamW\n","\n","EPOCHS = 3 # CHANGE TO THE NUMBER OF EPOCHS YOU WANT\n","optimizer = AdamW(model.parameters(),lr=3e-5) # YOU CAN ADJUST LEARNING RATE\n","\n","model.resize_token_embeddings(len(tokenizer))\n","model.to(device)"]},{"cell_type":"code","execution_count":19,"metadata":{"colab":{"base_uri":"https://localhost:8080/"},"id":"lztz58pSwQkn","outputId":"3768044e-e51c-4311-96a8-c789f680f939","executionInfo":{"status":"ok","timestamp":1698891582529,"user_tz":-480,"elapsed":313085,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"stream","name":"stderr","text":["Epoch:  33%|███▎      | 1/3 [01:45<03:30, 105.16s/it]"]},{"output_type":"stream","name":"stdout","text":["Average train loss: 1.863233209180832\n"]},{"output_type":"stream","name":"stderr","text":["\rEpoch:  67%|██████▋   | 2/3 [03:28<01:44, 104.30s/it]"]},{"output_type":"stream","name":"stdout","text":["Average train loss: 1.4270867498278619\n"]},{"output_type":"stream","name":"stderr","text":["Epoch: 100%|██████████| 3/3 [05:12<00:00, 104.33s/it]"]},{"output_type":"stream","name":"stdout","text":["Average train loss: 1.2469054220557212\n"]},{"output_type":"stream","name":"stderr","text":["\n"]}],"source":["from tqdm import tqdm,trange\n","\n","global_step = 0\n","total_loss = 0\n","\n","model.train()\n","for _ in trange(EPOCHS, desc=\"Epoch\"):\n","    model.train()\n","    total_loss = 0\n","\n","    # Training loop\n","    predictions , true_labels = [], []\n","\n","    for step, (seqs, labels, masks) in enumerate(bucket_train_dataloader):\n","        seqs = seqs.to(device)\n","        labels = labels.to(device)\n","        masks = masks.to(device)\n","        model.zero_grad()\n","        outputs = model(seqs, labels=labels, attention_mask=masks)\n","        logits = outputs.logits\n","        loss = outputs.loss\n","        loss = loss.mean()\n","\n","        total_loss += loss.item()\n","        loss.backward()\n","        optimizer.step()\n","    avg_train_loss = total_loss / len(bucket_train_dataloader)\n","    print(\"Average train loss: {}\".format(avg_train_loss))"]},{"cell_type":"code","execution_count":20,"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":1000,"referenced_widgets":["d608d198d6394f1fb33d65011ac5b386","56f6f7877ae34e98a18fd3c1ddc661d7","7833303031394722a0bcae300619d9b3","3fa9750869594147a1d809e814497659","be28af9f0c4c48eaaebc28c18a69746f","e2a8da76b11842dd81b381a47326fcdc","d909e1eb343f40d3bb4a248cd07aa437","91eb7c34a60b4325bfefdede34440a55","750776f39370488c934e78bc5ac9e3c4","c64ce5f41f284479904afb69983a8fda","4ada0cb8a4cc496dab69288fbf56a1da","1e09c709cfe44db9ba401a9b3b01f54f","c87acf04ae274dc3962358bac337e3e6","2db97d64a299471ca628fcd13fe249ad","8fbdb1c771e04f54aaaff2a51ce76e9f","a386594b381b4ce482a4129a061c96c1","0e3ba2e58a004f9d9d55c863a3d07778","4c4b96b6e3ff4362afb8058f3cb8198a","352088f10b9e4623b126cc096afdb32b","f26d6c96b214410e9776eaeb37f0a15f","008bfaf6a0df4808993b941db3464ebe","474667495f914d639642e807bf5a3c0a","c95c02ac28784888954f0e76dda0e6a3","5bb5cffed3bb45dc99ea2cc2b309690f","24b6542a30b345b2a2ced1e81c84e89a","a4823a75655f4c2281c5b00527364f41","8d57f35a58f944eaa2fa2e61c90211ad","8d85f2835a814bd892f8782d59a8215d","cc75d432da334e43a6b4e1629e7b5583","c5939207d76544fa9505513322f297b7","448fbd3e6ced43debf839b89c109f29b","46abd52dafe6492981b5ed144f33e44e","ef8e4f0456ea44dcbb636eea7839e342"]},"id":"65hmv62Pw9Y7","outputId":"d7dabf4e-08ad-44c8-8374-a1e1b4dc3527","executionInfo":{"status":"ok","timestamp":1698892159462,"user_tz":-480,"elapsed":3457,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"display_data","data":{"text/plain":["Downloading data files:   0%|          | 0/1 [00:00<?, ?it/s]"],"application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":0,"model_id":"d608d198d6394f1fb33d65011ac5b386"}},"metadata":{}},{"output_type":"display_data","data":{"text/plain":["Extracting data files:   0%|          | 0/1 [00:00<?, ?it/s]"],"application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":0,"model_id":"1e09c709cfe44db9ba401a9b3b01f54f"}},"metadata":{}},{"output_type":"display_data","data":{"text/plain":["Generating train split: 0 examples [00:00, ? examples/s]"],"application/vnd.jupyter.widget-view+json":{"version_major":2,"version_minor":0,"model_id":"c95c02ac28784888954f0e76dda0e6a3"}},"metadata":{}},{"output_type":"execute_result","data":{"text/plain":["[{'fid': '1001',\n","  'idx': 0,\n","  'content': 'Episode No:  88Y206206L',\n","  'label': None},\n"," {'fid': '1001', 'idx': 24, 'content': '8892062.BPL', 'label': None},\n"," {'fid': '1001',\n","  'idx': 37,\n","  'content': 'Vatterott, Jerrie CLARENCE',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 65,\n","  'content': 'Lab No:  88Y20620,88Y20620',\n","  'label': None},\n"," {'fid': '1001', 'idx': 92, 'content': 'Exeter', 'label': None},\n"," {'fid': '1001',\n","  'idx': 99,\n","  'content': 'DECEPTION BAY  Northern Territory  6845',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 139,\n","  'content': 'Specimen: Fluid,Tissue',\n","  'label': None},\n"," {'fid': '1001', 'idx': 162, 'content': 'D.O.B:  15/11/2004', 'label': None},\n"," {'fid': '1001', 'idx': 181, 'content': 'Sex:  F', 'label': None},\n"," {'fid': '1001',\n","  'idx': 189,\n","  'content': 'Collected: 20/5/2064 at :',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 215,\n","  'content': 'Location:  PARKES 8 - GUNNEDAH DISTRICT HOSPITAL',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 264,\n","  'content': 'DR Edison Clay GOLDHIRSH',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 289,\n","  'content': 'Distribution:   FILE-COPY,   NSW-CANCER-REGISTRY',\n","  'label': None},\n"," {'fid': '1001', 'idx': 338, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1001',\n","  'idx': 348,\n","  'content': 'Bilateral pelvic masses.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 374,\n","  'content': 'Phx lobular breast cancer 2059, 33 positive nodes, chemo.',\n","  'label': None},\n"," {'fid': '1001', 'idx': 433, 'content': '1', 'label': None},\n"," {'fid': '1001', 'idx': 437, 'content': 'Ascites.', 'label': None},\n"," {'fid': '1001', 'idx': 448, 'content': '2', 'label': None},\n"," {'fid': '1001',\n","  'idx': 452,\n","  'content': 'Right tube and ovary (frozen section)',\n","  'label': None},\n"," {'fid': '1001', 'idx': 490, 'content': '3', 'label': None},\n"," {'fid': '1001', 'idx': 494, 'content': 'Left tube and ovary.', 'label': None},\n"," {'fid': '1001', 'idx': 515, 'content': '4', 'label': None},\n"," {'fid': '1001', 'idx': 519, 'content': 'Omental biopsy.', 'label': None},\n"," {'fid': '1001', 'idx': 537, 'content': 'PR, ER and HER2.', 'label': None},\n"," {'fid': '1001', 'idx': 554, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1001', 'idx': 567, 'content': 'A.', 'label': None},\n"," {'fid': '1001',\n","  'idx': 571,\n","  'content': 'Specimen labelled \"Right tube and ovary\" consists of an enlarged solid ovary measuring 90 x 60 x 40mm with attached tubes 60mm in length.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 710,\n","  'content': 'The total weight is 123g.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 737,\n","  'content': 'The ovary has a solid yellow and haemorrhagic appearance with small microcysts in one area.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 831,\n","  'content': '(Blocks: 1 - one TS through solid yellow area; 2 - one TS through cystic area.)',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 913,\n","  'content': 'Blocks: 1 & 2 - frozen sections; 3 & 4 - representative (ER,PR, HER2, Ki-67 requested on block 3); 5 - representative fallopian tube.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 1049,\n","  'content': 'FROZEN SECTION REPORT:',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 1072,\n","  'content': 'Signet ring carcinoma consistent with lobular carcinoma from breast (pt has past history of lobular Ca with 33 pos LN in 2059)',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 1199,\n","  'content': 'Result to Dr Sek via anaesthetist by A/Prof X Standrew at 9:30am on 18/3/14.',\n","  'label': None},\n"," {'fid': '1001', 'idx': 1281, 'content': 'B.', 'label': None},\n"," {'fid': '1001',\n","  'idx': 1285,\n","  'content': 'Specimen labelled \"Left tube and ovary\" consists of an ovary measuring 45 x 30 x 15mm with attached fallopian tube 40mm in length and up to 12mm in diameter.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 1445,\n","  'content': 'Slicing the ovary reveals a lobular, solid cut surface with pale yellow and haemorrhagic areas.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 1543,\n","  'content': 'Blocks: 1 & 2 - representative sections of the ovary; 3 - representative sections of the fallopian tube.',\n","  'label': None},\n"," {'fid': '1001', 'idx': 1648, 'content': 'C.', 'label': None},\n"," {'fid': '1001',\n","  'idx': 1652,\n","  'content': 'Specimen labelled \"Omental biopsy\" consists of a piece of fibrofatty tissue measuring 55 x 35 x 4mm.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 1754,\n","  'content': 'No nodules are identified.',\n","  'label': None},\n"," {'fid': '1001', 'idx': 1782, 'content': 'AE 3 blocks.', 'label': None},\n"," {'fid': '1001', 'idx': 1797, 'content': '(TO: KH/ta 21/5/64)', 'label': None},\n"," {'fid': '1001',\n","  'idx': 1818,\n","  'content': 'MICROSCOPIC (Reported by Dr X Karma):',\n","  'label': None},\n"," {'fid': '1001', 'idx': 1857, 'content': 'A & B.', 'label': None},\n"," {'fid': '1001',\n","  'idx': 1865,\n","  'content': 'Sections show metastatic lobular carcinoma widely involving both ovaries and tubes.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 1950,\n","  'content': 'The malignant cells are arranged in sheets, nodules and cords.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2014,\n","  'content': \"Prominent intracytoplasmic mucin vacuoles giving a 'signet ring' appearance are present.\",\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2103,\n","  'content': 'The tumour is strongly positive for ER, negative for PR and shows 2+ Her2 staining.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2188,\n","  'content': '(Material has been sent to HALLS CREEK HOSPITAL Hospital for further Her2 studies).',\n","  'label': None},\n"," {'fid': '1001', 'idx': 2272, 'content': 'C.', 'label': None},\n"," {'fid': '1001',\n","  'idx': 2276,\n","  'content': 'The omentum shows no evidence of malignancy.',\n","  'label': None},\n"," {'fid': '1001', 'idx': 2321, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1001',\n","  'idx': 2332,\n","  'content': 'Metastatic lobular breast carcinoma involving both ovaries and tubes.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2402,\n","  'content': '(Please see recent cervical biopsy report 88Y20620).',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2455,\n","  'content': 'ADDITIONAL REPORT:  (30.5.64)',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2485,\n","  'content': 'Blocks were sent to TRANGIE MULTI PURPOSE HEALTH SERVICE Hospital for Her2 IHC analysis, Dr X Spittler reports:',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2597,\n","  'content': 'HER2 IHC Result:   2+ at POW.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2627,\n","  'content': 'Signal Detection has been performed for the Her2 gene (17q21) and chromosome 17 centromeric enumeration probe (CEP17) control using the Ventanta INFORM Her2 Dual ISH DNA Probe Cocktail Assay (Roche).',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2828,\n","  'content': 'Her2 Dual ISH result: NEGATIVE (non-amplified, polysomy).',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2887,\n","  'content': 'Mean Her2 copy number per cell: 4.9.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2924,\n","  'content': 'Mean CEP17 copy number per cell:  3.4.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2963,\n","  'content': 'HER2/CEP17 ratio:  1.44',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 2987,\n","  'content': 'SCORING CRITERIA (ASCO/CAP recommendations):',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 3032,\n","  'content': 'Negative:  HER2/CEP17 <1.8.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 3060,\n","  'content': 'Equivocal:  HER2/CEP17 = 1.8-2.2.',\n","  'label': None},\n"," {'fid': '1001',\n","  'idx': 3094,\n","  'content': 'Positive:  HER2/CEP17 >2.2.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 1,\n","  'content': 'Episode No:  46U2273647',\n","  'label': None},\n"," {'fid': '1002', 'idx': 25, 'content': '4672273.RKT', 'label': None},\n"," {'fid': '1002', 'idx': 38, 'content': 'Parmar, Gregorio', 'label': None},\n"," {'fid': '1002', 'idx': 56, 'content': 'Lab No:  46U22736', 'label': None},\n"," {'fid': '1002', 'idx': 74, 'content': 'Underdale', 'label': None},\n"," {'fid': '1002', 'idx': 84, 'content': 'TRAFALGAR  NT  3660', 'label': None},\n"," {'fid': '1002', 'idx': 104, 'content': 'Specimen: Tissue', 'label': None},\n"," {'fid': '1002', 'idx': 121, 'content': 'D.O.B:  7/12/1999', 'label': None},\n"," {'fid': '1002', 'idx': 139, 'content': 'Sex:  M', 'label': None},\n"," {'fid': '1002',\n","  'idx': 147,\n","  'content': 'Collected: 21/03/2014 at 13:26',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 178,\n","  'content': 'Location:  3HR STAY SURGICALUNIT-ROBINVALE DISTRICT HEALTH SERVICES - ROBINVALE CAMPUS',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 265,\n","  'content': 'PRO GENARO ARMAND Forcht',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 290,\n","  'content': 'Distribution:   FILE-COPY',\n","  'label': None},\n"," {'fid': '1002', 'idx': 316, 'content': 'HISTORY:', 'label': None},\n"," {'fid': '1002',\n","  'idx': 327,\n","  'content': 'Recurrent pseudomyxoma peritonei.',\n","  'label': None},\n"," {'fid': '1002', 'idx': 363, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1002', 'idx': 378, 'content': 'A.', 'label': None},\n"," {'fid': '1002',\n","  'idx': 382,\n","  'content': 'PERITONEAL DISEASE AND SMALL BOWEL.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 421,\n","  'content': 'Two segments of bowel and numerous strips of omentum and grey membranous tissue.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 503,\n","  'content': 'The largest segment of bowel measures 410mm in length x 35x35mm in maximum dimension.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 589,\n","  'content': 'Theserosal surface is dull with areas of adherent omentum and brown grey fibrinous material.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 683,\n","  'content': 'The wall thickness is 4mm.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 710,\n","  'content': 'The bowel mucosa appears unremarkable.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 750,\n","  'content': 'No diverticulae or polyps are identified in the longer specimen.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 816,\n","  'content': 'There are small areas of sclerotic nodules within the omental fat ranging from 2-5mm.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 902,\n","  'content': 'The second segment of bowel measures 98mm in length x 35x35mm in maximum dimension.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 987,\n","  'content': 'The serosal surface is dull and covered with fibrin and adherent mesocolon.This mesocolon has gelatinous substances adherent on the surface.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 1129,\n","  'content': 'On opening the bowel wall is 3mm.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 1163,\n","  'content': 'There is a pedunculated polyp within the bowel measuring 8mm in maximum dimension, otherwise the bowel mucosa is unremarkable.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 1291,\n","  'content': 'Included with the specimen are multiple fragments of adipose tissue and grey tan membranous tissue measuring from 10-40mm in maximum dimension.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 1436,\n","  'content': 'The smaller segment of bowel has diverticulae within the mucosa.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 1502,\n","  'content': '(1-8 largest segmentof bowel [1&2 surgical margins, 3&4 representative normal bowel, 5 gelatinous substance on surface of mesocolon, 6-8 representative mesocolon with areas of firm nodules within]; 9-13 smaller segment of bowel [9&10 surgical margins, 11 polyp bisected, 12 diverticulae, 13 representative nodule from mesocolon]; 14&15 representative gelatinous areas adherent to adipose tissue within separate fragments).',\n","  'label': None},\n"," {'fid': '1002', 'idx': 1926, 'content': 'RS (M-15)', 'label': None},\n"," {'fid': '1002', 'idx': 1936, 'content': 'B.', 'label': None},\n"," {'fid': '1002',\n","  'idx': 1940,\n","  'content': 'PAR-AORTIC LYMPH NODE.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 1965,\n","  'content': 'A lymph node measuring 20mm in maximum dimension.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 2016,\n","  'content': 'Specimen serially sectioned and all embedded in two blocks.',\n","  'label': None},\n"," {'fid': '1002', 'idx': 2077, 'content': 'AE (M-2/JL/ank)', 'label': None},\n"," {'fid': '1002',\n","  'idx': 2093,\n","  'content': 'MICROSCOPIC:  (L. Lazewski)',\n","  'label': None},\n"," {'fid': '1002', 'idx': 2121, 'content': 'A.', 'label': None},\n"," {'fid': '1002',\n","  'idx': 2125,\n","  'content': 'Sections show low grade mucinous neoplasm comprising of extracellular mucin and associated with low grade mucinous epithelium involving mesentery of larger segment of colon and separatelysubmitted fibrofatty peritoneal fragments.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 2355,\n","  'content': 'One of the segments of colon also shows a tubular adenoma with mild dysplasia in its mucosa.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 2448,\n","  'content': 'Local lymph nodes recovered from both segments of bowel show no significant abnormality.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 2537,\n","  'content': 'There is no evidence of destructive tumour with desmoplastic stroma.',\n","  'label': None},\n"," {'fid': '1002', 'idx': 2607, 'content': 'B.', 'label': None},\n"," {'fid': '1002',\n","  'idx': 2611,\n","  'content': 'Sections show reactive lymph node with scattered lipogranulomas.',\n","  'label': None},\n"," {'fid': '1002',\n","  'idx': 2676,\n","  'content': 'There is no evidence ofmalignancy.',\n","  'label': None},\n"," {'fid': '1002', 'idx': 2711, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1002',\n","  'idx': 2724,\n","  'content': 'PERITONEAL DISEASE AND BOWEL:',\n","  'label': None},\n"," {'fid': '1002', 'idx': 2757, 'content': '#NAME?', 'label': None},\n"," {'fid': '1002',\n","  'idx': 2878,\n","  'content': 'PARA-AORTIC LYMPH NODE:  NO EVIDENCE OF MALIGNANCY.',\n","  'label': None},\n"," {'fid': '1002', 'idx': 2930, 'content': '27/5/64 ht', 'label': None},\n"," {'fid': '1003',\n","  'idx': 0,\n","  'content': 'Episode No:  94Q248422C',\n","  'label': None},\n"," {'fid': '1003', 'idx': 24, 'content': '9462484.GGC', 'label': None},\n"," {'fid': '1003', 'idx': 37, 'content': 'Pullon, Loren DUANE', 'label': None},\n"," {'fid': '1003', 'idx': 58, 'content': 'Lab No:  94Q24842', 'label': None},\n"," {'fid': '1003', 'idx': 76, 'content': 'Bellanca', 'label': None},\n"," {'fid': '1003', 'idx': 85, 'content': 'COOKTOWN  VIC  2739', 'label': None},\n"," {'fid': '1003', 'idx': 105, 'content': 'Specimen: Tissue', 'label': None},\n"," {'fid': '1003', 'idx': 122, 'content': 'D.O.B:  29/9/2000', 'label': None},\n"," {'fid': '1003', 'idx': 140, 'content': 'Sex:  M', 'label': None},\n"," {'fid': '1003',\n","  'idx': 148,\n","  'content': 'Collected: 18/03/2014 at 19:04',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 179,\n","  'content': 'Location:  2.PARKES 8-TULLAMORE MULTI PURPOSE HEALTH SERVICE',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 240,\n","  'content': 'PRO FELIPE Eldridge ALLCORN',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 268,\n","  'content': 'Distribution:   FILE-COPY,   NSW-CANCER-REGISTRY',\n","  'label': None},\n"," {'fid': '1003', 'idx': 317, 'content': 'HISTORY:', 'label': None},\n"," {'fid': '1003', 'idx': 328, 'content': 'PMP - appendiceal.', 'label': None},\n"," {'fid': '1003', 'idx': 348, 'content': 'Right hemicolectomy.', 'label': None},\n"," {'fid': '1003',\n","  'idx': 370,\n","  'content': 'Peritonectomy PCI-19.',\n","  'label': None},\n"," {'fid': '1003', 'idx': 392, 'content': 'Omentum.', 'label': None},\n"," {'fid': '1003',\n","  'idx': 401,\n","  'content': 'Diaphragm + pelvic strip.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 427,\n","  'content': 'Lymph node right iliac chain.right hemicolectomy.',\n","  'label': None},\n"," {'fid': '1003', 'idx': 477, 'content': 'Umbilicus.', 'label': None},\n"," {'fid': '1003',\n","  'idx': 488,\n","  'content': 'Previous pathology reports:',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 516,\n","  'content': '94-QH-48-4220673 BARALABA HOSPITAL, 2/10/2062: appendix with LAMN and acute appendicitis',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 605,\n","  'content': '94624-84GG: 16/1/2062, R hemicolectomy with peritoneum: focal mucinous neoplasm involving serosal/peritoneal surface.',\n","  'label': None},\n"," {'fid': '1003', 'idx': 723, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1003', 'idx': 738, 'content': 'A.', 'label': None},\n"," {'fid': '1003',\n","  'idx': 742,\n","  'content': \"'OMENTUM, RIGHT COLON, DIAPHRAGM, PELVIC STRIP, UMBILICUS + PERITONEAL DISEASE'.\",\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 824,\n","  'content': 'Multiple pieces of tissue including omentum, a piece of bowel within anastomosis, a further piece of bowel, strips or peritoneum or diaphragm.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 968,\n","  'content': 'Multiple pieces of fatty tissue and the umbilicus with underlying fatty tissue.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1049,\n","  'content': 'The peritoneum is approximately 300x190x20-30mm.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1099,\n","  'content': 'There is mucinous material on the surface forming numerous patches.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1168,\n","  'content': 'There are no solid nodular areas.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1203,\n","  'content': 'There are two pieces of bowel, the first is 50mm in length and 50mm in circumference.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1289,\n","  'content': 'The serosal surface is unremarkable.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1326,\n","  'content': 'The wall contains an area of haemorrhage 5mm in thickness and the mucosa is unremarkable.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1416,\n","  'content': 'The second piece of bowel is V shaped with a central anastomosis.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1482,\n","  'content': 'The two pieces of bowel are 60 and 65mm in length respectively and has a circumference of 40mm and 30mm respectively.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1601,\n","  'content': 'There are no abnormalities seen on the external surface.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1658,\n","  'content': 'The wall is 5mm in thickness and the mucosal surface is unremarkable.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1728,\n","  'content': 'The attached fatty tissue is unremarkable.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1771,\n","  'content': 'No mucin is present.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1793,\n","  'content': 'The umbilicus is 25mm in diameter and underlying it is fatty tissue 40x30x10mm.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1874,\n","  'content': 'This is unremarkable.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1897,\n","  'content': 'There is a strip of peritoneum which is irregularly shaped and is approximately 300x70x5-10mm.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 1993,\n","  'content': 'No mucin is present on the serosal surface.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 2037,\n","  'content': 'There is a strip of ? diaphragmatic tissue 50x10x203mm.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 2094,\n","  'content': 'There are no mucinous material present, however there is a white nodule 10mm in diameter.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 2185,\n","  'content': 'Also in the bucket are numerous pieces of irregularly shaped fatty tissue with an aggregate of 100x100x20-30mm.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 2298,\n","  'content': 'Mucin is not present.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 2322,\n","  'content': '(11-4 omentum; 5 small piece of bowel with anastomosis with resection margins; 6 larger piece of bowel with resection margins; 7 umbilicus; 8-11 peritoneum; 12 ? diaphragm; 13-20 sections from piece of fat in bottom of jar).',\n","  'label': None},\n"," {'fid': '1003', 'idx': 2548, 'content': 'RS (M-20)', 'label': None},\n"," {'fid': '1003', 'idx': 2558, 'content': 'B.', 'label': None},\n"," {'fid': '1003',\n","  'idx': 2562,\n","  'content': \"'LYMPH NODE RIGHT ILIAC CHAIN'.\",\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 2595,\n","  'content': 'A lymph node 10mm in diameter with a small amount of fatty tissue.',\n","  'label': None},\n"," {'fid': '1003', 'idx': 2663, 'content': 'AE (2-1/BI/ank)', 'label': None},\n"," {'fid': '1003', 'idx': 2679, 'content': 'MICROSCOPIC:', 'label': None},\n"," {'fid': '1003', 'idx': 2694, 'content': 'A.', 'label': None},\n"," {'fid': '1003',\n","  'idx': 2698,\n","  'content': 'The mucin deposits over peritoneal surfaces of omentum and peritoneum sampled show changes of low grade pseudomyxoma peritonei.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 2827,\n","  'content': 'Some of the mucin deposits are acellular and have a surrounding foreign body giant cell reaction.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 2926,\n","  'content': 'Others contain small amounts of neoplastic mucinous epithelium which is arranged in flat non-complex strips and shows low grade atypia.',\n","  'label': None},\n"," {'fid': '1003', 'idx': 3063, 'content': 'No invasion.', 'label': None},\n"," {'fid': '1003',\n","  'idx': 3077,\n","  'content': 'No signet ring cell component seen.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 3114,\n","  'content': 'Sections of the bowel ends are unremarkable.',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 3159,\n","  'content': 'There is fibrous scaring in tissue deep to umbilicus.',\n","  'label': None},\n"," {'fid': '1003', 'idx': 3213, 'content': 'B.', 'label': None},\n"," {'fid': '1003',\n","  'idx': 3217,\n","  'content': 'The lymph node is negative for tumour (0/1).',\n","  'label': None},\n"," {'fid': '1003', 'idx': 3262, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1003', 'idx': 3275, 'content': 'A.', 'label': None},\n"," {'fid': '1003',\n","  'idx': 3279,\n","  'content': 'OMENTUM, RIGHT COLON, DIAPHRAGM, PELVIC STRIP, UMBILICUS and PERITONEAL DISEASE -',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 3362,\n","  'content': '- low grade pseudomyxoma peritonei (consistent with appendix origin); equivalent to DPAM (Ronnett).',\n","  'label': None},\n"," {'fid': '1003', 'idx': 3462, 'content': 'B.', 'label': None},\n"," {'fid': '1003',\n","  'idx': 3466,\n","  'content': 'LYMPH NODE RIGHT ILIAC CHAIN -',\n","  'label': None},\n"," {'fid': '1003',\n","  'idx': 3498,\n","  'content': '- negative for tumour (0/1).',\n","  'label': None},\n"," {'fid': '1003', 'idx': 3527, 'content': '23/5/64, Z Varajas.', 'label': None},\n"," {'fid': '1004',\n","  'idx': 0,\n","  'content': 'Episode No:  52N379480L',\n","  'label': None},\n"," {'fid': '1004', 'idx': 24, 'content': '5253794.VBL', 'label': None},\n"," {'fid': '1004',\n","  'idx': 37,\n","  'content': 'KLAAMEYER, Gaye Wadjarri',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 63,\n","  'content': 'Lab No:  52N37948,52N37948',\n","  'label': None},\n"," {'fid': '1004', 'idx': 90, 'content': 'Schroeder', 'label': None},\n"," {'fid': '1004',\n","  'idx': 100,\n","  'content': 'HURSTBRIDGE  SA  2464',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 122,\n","  'content': 'Specimen: Washings,Tissue',\n","  'label': None},\n"," {'fid': '1004', 'idx': 148, 'content': 'D.O.B:  7/12/2004', 'label': None},\n"," {'fid': '1004', 'idx': 166, 'content': 'Sex:  F', 'label': None},\n"," {'fid': '1004',\n","  'idx': 174,\n","  'content': 'Collected: 26/5/2064 at:',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 199,\n","  'content': 'Location:  DAY SURGERY - RENMARK PARINGA DISTRICT HOSPITAL',\n","  'label': None},\n"," {'fid': '1004', 'idx': 258, 'content': 'DR SYBIL RIVA SMIDT', 'label': None},\n"," {'fid': '1004',\n","  'idx': 278,\n","  'content': 'Distribution:   FILE-COPY,   NSW-CANCER-REGISTRY',\n","  'label': None},\n"," {'fid': '1004', 'idx': 327, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1004', 'idx': 337, 'content': 'Endometrial cancer.', 'label': None},\n"," {'fid': '1004', 'idx': 359, 'content': '1', 'label': None},\n"," {'fid': '1004', 'idx': 363, 'content': 'Pelvic washings.', 'label': None},\n"," {'fid': '1004', 'idx': 382, 'content': '2', 'label': None},\n"," {'fid': '1004',\n","  'idx': 386,\n","  'content': 'Uterus, tubes, ovaries, cervix.',\n","  'label': None},\n"," {'fid': '1004', 'idx': 420, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1004',\n","  'idx': 433,\n","  'content': 'Specimen labelled \"Uterus tubes ovaries\" consists of a uterus, cervix with attached bilateral ovary and tubes weighing 87g in total.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 566,\n","  'content': 'The uterus measures 85 x 65 x 35mm and has a smooth shiny serosal surface.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 642,\n","  'content': 'The ectocervix measures 30 x 25mm and has unremarkable surface.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 706,\n","  'content': 'On sectioning, the endometrium is 1mm in maximum thickness and the myometrium is 50mm in maximum thickness.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 815,\n","  'content': 'There is an exophytic pale tumour located at the fundus at the right side of the uterus involving both anterior and posterior wall measuring 18 x 8 x 8mm.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 971,\n","  'content': 'There are multiple fibroids ranging from 10mm in diameter to 20mm in diameter.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 1051,\n","  'content': 'There is extensive calcification involving the fibroids.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 1110,\n","  'content': 'The right fallopian tube with fimbrial measures 65mm in length, 5mm in maximum external dimension.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 1210,\n","  'content': 'The right ovary measures 34 x 16 x 7mm and has an unremarkable surface.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 1282,\n","  'content': 'The left fallopian tube and fimbrial measures 70mm in length, 8mm in maximum dimension.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 1371,\n","  'content': 'The left ovary measures 45 x 15 x 6mm and has an unremarkable surface.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 1444,\n","  'content': 'Blocks: 1 to 3 - parasagittal section of mid portion of anterior aspect of the uterus and cervix; 4 to 14 - sections of the tumour (4 & 5 - paired, 6 & 7 - paired; 8 & 9 - paired; 10 & 11 - paired; 12 & 13 - paired); 15 - corneum ofthe right side; 16 to 18 - midline LS posterior uterus and cervix; 19 to 24 - post sagittal sections posterior uterus with tumour (19 & 20 - paired, 21 & 22 paired); 25 - right ovary and tube; 26 - left ovary and tube.',\n","  'label': None},\n"," {'fid': '1004', 'idx': 1896, 'content': '(TO: ME/ta 27/5/64)', 'label': None},\n"," {'fid': '1004',\n","  'idx': 1917,\n","  'content': 'MICROSCOPIC:  (Reported by Dr O Lenski)',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 1957,\n","  'content': 'Sections of the uterine tumour show a Grade 1 endometrioid endometrial adenocarcinoma.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 2044,\n","  'content': 'The adenocarcinoma consists predominantly of complex, crowded glands, some of which have a cribriform morphology, lined by moderately pleomorphic carcinoma cells (FIGO architecture grade 1; nuclear grade 2 = overall grade 1).',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 2270,\n","  'content': 'The carcinoma extends 2.2mm into a uterine wall 12mm thick.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 2330,\n","  'content': 'There is no evidence of lymphovascular space invasion.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 2385,\n","  'content': 'The carcinoma does not involve the sampled uterine cornua.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 2444,\n","  'content': 'The non-neoplastic endometrium shows patchy atypical complex endometrial hyperplasia.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 2530,\n","  'content': 'There is widespread adenomyosis and scattered benign leiomyomas.',\n","  'label': None},\n"," {'fid': '1004',\n","  'idx': 2595,\n","  'content': 'The uterine cervix, bilateral fallopian tubes and ovaries show no significant abnormality.',\n","  'label': None},\n"," {'fid': '1004', 'idx': 2687, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1004',\n","  'idx': 2698,\n","  'content': 'Uterus: FIGO Grade 1 endometrioid endometrial adenocarcinoma.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 1,\n","  'content': 'Episode No:  10J399538T',\n","  'label': None},\n"," {'fid': '1005', 'idx': 25, 'content': '1033995.KWT', 'label': None},\n"," {'fid': '1005',\n","  'idx': 38,\n","  'content': 'Atterberry, REGGIE YOLNGU',\n","  'label': None},\n"," {'fid': '1005', 'idx': 65, 'content': 'Lab No:  10J39953', 'label': None},\n"," {'fid': '1005', 'idx': 83, 'content': 'Shady Wood', 'label': None},\n"," {'fid': '1005', 'idx': 94, 'content': 'CESSNOCK  ACT  3700', 'label': None},\n"," {'fid': '1005', 'idx': 114, 'content': 'Specimen: Tissue', 'label': None},\n"," {'fid': '1005', 'idx': 131, 'content': 'D.O.B:  11/5/2032', 'label': None},\n"," {'fid': '1005', 'idx': 149, 'content': 'Sex:  F', 'label': None},\n"," {'fid': '1005',\n","  'idx': 157,\n","  'content': 'Collected: 21/5/2064 at :',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 183,\n","  'content': 'Location:  DICKINSON 3 NORTH - MOURA HOSPITAL',\n","  'label': None},\n"," {'fid': '1005', 'idx': 229, 'content': 'DR LEONEL MEL Branon', 'label': None},\n"," {'fid': '1005',\n","  'idx': 250,\n","  'content': 'Distribution:   FILE-COPY,   NSW-CANCER-REGISTRY',\n","  'label': None},\n"," {'fid': '1005', 'idx': 299, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1005', 'idx': 309, 'content': 'Pelvic node.', 'label': None},\n"," {'fid': '1005', 'idx': 323, 'content': 'SCC cervix.', 'label': None},\n"," {'fid': '1005', 'idx': 336, 'content': 'Cervical cancer 1b.', 'label': None},\n"," {'fid': '1005', 'idx': 358, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1005', 'idx': 371, 'content': 'A.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 375,\n","  'content': 'Specimen labelled \"(L) External iliac LN\" consists of fatty tissue 35 x 10 x 5mm.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 458,\n","  'content': 'One lymph node is identified, 25 x 9 x 5mm.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 503,\n","  'content': 'A second lymph node is identified measuring 10 x 5 x 4mm.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 563,\n","  'content': 'Blocks:  1 & 2 - frozen sections; 3 - remainder of the tissue.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 628,\n","  'content': 'FROZEN SECTION REPORT:',\n","  'label': None},\n"," {'fid': '1005', 'idx': 653, 'content': 'No tumour seen.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 671,\n","  'content': 'Phone result to anaesthetist by Dr C Nixa/C Tappendorf at 10.17 on 19.03.14.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 748, 'content': 'B.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 752,\n","  'content': 'Specimen labelled \"Uterus and cervix\" consists of a uterus with attached cervix, weighing 110g in total.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 858,\n","  'content': 'The uterus measures 110 x 70 x 50mm and has a smooth shiny serosal surface.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 935,\n","  'content': 'The ectocervix measures 31mm.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 966,\n","  'content': 'The soft tissue margin is inked blue anteriorly and black posteriorly.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 1038,\n","  'content': 'There is an ill defined pale solid mass within the cervix measuring approximately 28 x 25 x 5mm.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 1136,\n","  'content': 'The endometrium is 1mm in maximum thickness and the myometrium is 33mm in maximum thickness.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 1230,\n","  'content': 'The myometrium is unremarkable.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 1264,\n","  'content': \"Blocks:  1 to 17 - the entire cervix blocked clockwise starting from 3 o'clock; 18 to 20 - full longitudinal section of anterior body; 21 to 24 - full longitudinal section of posterior body.\",\n","  'label': None},\n"," {'fid': '1005', 'idx': 1457, 'content': 'C.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 1461,\n","  'content': 'Specimen labelled \"Left fallopian tube\" consists of a fallopian tube 50mm in length and up to 9mm in diameter.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 1573,\n","  'content': 'The cut surface is unremarkable.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 1606,\n","  'content': 'Blocks:  1 - representatives.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 1638, 'content': 'D.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 1642,\n","  'content': 'Specimen labelled \"Right fallopian tube\" consists of a fallopian tube 50mm in length and up to 7mm in diameter.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 1755,\n","  'content': 'The cut surfaces are unremarkable.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 1792,\n","  'content': 'Blocks:  1- representative sections.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 1831, 'content': 'E.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 1835,\n","  'content': 'Specimen labelled \"Left external iliac lymph node\" consists of pieces offatty tissue 33 x 20 x 6mm in aggregate.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 1949,\n","  'content': 'One lymph node is identified 10mm in maximum dimension.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 2007,\n","  'content': 'Blocks:  1- one bisected lymph node; 2- remainder of the tissue.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 2073, 'content': 'AE.', 'label': None},\n"," {'fid': '1005', 'idx': 2077, 'content': 'F.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 2081,\n","  'content': 'Specimen labelled \"Left obturator lymph node\"consists of fragments of fibrofatty tissue and blood clots 55 x 40 x 10mm in aggregate.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 2215,\n","  'content': 'Two lymph nodes are identified 30 and 14mm in maximum dimension.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 2282,\n","  'content': 'Blocks:  1 - one lymph node; 2 - one bisected lymph node.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 2342, 'content': 'G.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 2346,\n","  'content': 'Specimen labelled \"Right external iliac lymph node\" consists of fibrofatty tissue 50 x 25 x 8mm in aggregate.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 2457,\n","  'content': 'Two likely lymph nodes are identified.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 2496,\n","  'content': 'Blocks:  1- one likely lymph node; 2- one likely lymph node; 3 & 4 - the remainder ofthe tissue.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 2594, 'content': 'AE.', 'label': None},\n"," {'fid': '1005', 'idx': 2598, 'content': 'H.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 2602,\n","  'content': 'Specimen labelled \"Right obturator lymph node\" consists of fragments of fatty tissue 45 x 35 x 5mm in aggregate.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 2716,\n","  'content': 'Two likely lymph nodes are identified.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 2756,\n","  'content': 'Blocks:  -1 - likely lymph nodes as seen; 2 &3 - remainder of the tissue.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 2831, 'content': 'AE 1 block.', 'label': None},\n"," {'fid': '1005', 'idx': 2843, 'content': 'I.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 2847,\n","  'content': 'Specimen labelled \"Left common iliac lymph node\" consists of a piece of fibrofatty tissue 27 x 8 x 3mm.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 2952,\n","  'content': 'One lymph node is identified 10 x 3 x 3mm.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 2997,\n","  'content': 'Blocks:  1- one lymph node.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 3027, 'content': 'J.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 3031,\n","  'content': 'Specimen labelled \"Right common iliac lymph node\" consists of a piece of fibrofatty tissue 25 x 7 x 2mm.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 3137,\n","  'content': 'One lymph node is identified 12mm in maximum dimension.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 3195,\n","  'content': 'Blocks:  1- one bisected lymph node.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 3233,\n","  'content': '(TO: HM:HM/mm 22.5.64)',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 3257,\n","  'content': 'MICROSCOPIC (reported by Dr C Zornes):',\n","  'label': None},\n"," {'fid': '1005', 'idx': 3297, 'content': 'A.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 3301,\n","  'content': 'Sections show two lymph nodes.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 3333,\n","  'content': 'There is focal metastatic squamous cell carcinoma involving the subcapsular sinus of one of the nodes.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 3437,\n","  'content': 'The tumour deposit measures 0.5mm in diameter and the total node measures 10mm in main diameter.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 3535,\n","  'content': 'The focal deposit is present in the paraffin section but was not present in the frozen section.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 3633, 'content': 'B.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 3637,\n","  'content': 'Sections of the cervix show an invasive moderatelydifferentiated squamous cell carcinoma.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 3728,\n","  'content': 'The tumour measures 16mm wide x 13mm long.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 3772,\n","  'content': 'Maximum depth of cervical stromal invasion is 8mm out of total cervical stromal thickness of 10mm.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 3872,\n","  'content': 'There is multifocal lymphovascular invasion.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 3918,\n","  'content': 'Tumouris 2mm from the ectocervical excision margin at the closest point.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 3992,\n","  'content': 'The tumour is ulcerated and no overlying CIN 3 is seen.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 4049,\n","  'content': 'The ectocervical margin is free of dysplasia.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 4097,\n","  'content': 'Sections of the endometrium show that this is in late menstrual phase.',\n","  'label': None},\n"," {'fid': '1005',\n","  'idx': 4169,\n","  'content': 'The myometrium is unremarkable.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4203, 'content': 'C, D.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4210,\n","  'content': 'Sections show unremarkable fallopian tubes.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4256, 'content': 'E.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4260,\n","  'content': 'Sections show two lymph nodes.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4292, 'content': 'No tumour is seen.', 'label': None},\n"," {'fid': '1005', 'idx': 4313, 'content': 'F.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4317,\n","  'content': 'Sections show two lymph nodes.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4349, 'content': 'No tumour is seen.', 'label': None},\n"," {'fid': '1005', 'idx': 4370, 'content': 'G.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4374,\n","  'content': 'Sections show four lymph nodes.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4407, 'content': 'No tumouris seen.', 'label': None},\n"," {'fid': '1005', 'idx': 4427, 'content': 'H.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4431,\n","  'content': 'Sections show six lymph nodes.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4463, 'content': 'No tumour is seen.', 'label': None},\n"," {'fid': '1005', 'idx': 4484, 'content': 'I.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4488,\n","  'content': 'Sections show one lymph node.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4519, 'content': 'No tumour is seen.', 'label': None},\n"," {'fid': '1005', 'idx': 4539, 'content': 'J.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4543,\n","  'content': 'Sections show one lymph node.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4574, 'content': 'No tumour is seen.', 'label': None},\n"," {'fid': '1005', 'idx': 4595, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4606,\n","  'content': 'A.Left external iliac lymph nodes:  Focal metastatic squamous carcinoma in subcapsular sinus of one node (1/2).',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4720, 'content': 'B.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4724,\n","  'content': 'Uterus:  Moderately differentiated squamous cell carcinoma of cervix stage 1B1.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4804, 'content': 'C.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4808,\n","  'content': 'Left fallopian tube:  No abnormality seen.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4853, 'content': 'D.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4857,\n","  'content': 'Right fallopian tube:  No abnormality seen.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4903, 'content': 'E.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4907,\n","  'content': 'Left external iliac lymph nodes:  No tumour (0/2).',\n","  'label': None},\n"," {'fid': '1005', 'idx': 4960, 'content': 'F.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 4964,\n","  'content': 'Left obturator lymph nodes:  No tumour (0/2).',\n","  'label': None},\n"," {'fid': '1005', 'idx': 5012, 'content': 'G.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 5016,\n","  'content': 'Right external iliac lymph nodes:  No tumour (0/4).',\n","  'label': None},\n"," {'fid': '1005', 'idx': 5069, 'content': 'H.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 5073,\n","  'content': 'Right obturator lymph nodes.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 5103, 'content': 'No tumour (0/6).', 'label': None},\n"," {'fid': '1005', 'idx': 5122, 'content': 'I.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 5126,\n","  'content': 'Left common iliac lymph node:  No tumour (0/1).',\n","  'label': None},\n"," {'fid': '1005', 'idx': 5174, 'content': 'J.', 'label': None},\n"," {'fid': '1005',\n","  'idx': 5178,\n","  'content': 'Right common iliac lymph node.',\n","  'label': None},\n"," {'fid': '1005', 'idx': 5210, 'content': 'No tumour (0/1).', 'label': None},\n"," {'fid': '1006', 'idx': 1, 'content': '2109904.YSE', 'label': None},\n"," {'fid': '1006',\n","  'idx': 13,\n","  'content': 'SHANSKY, Nganu Annamarie VANESA',\n","  'label': None},\n"," {'fid': '1006', 'idx': 45, 'content': '21A99049,21A99049', 'label': None},\n"," {'fid': '1006',\n","  'idx': 64,\n","  'content': 'Last edited: 30/5/2064  Page: 2',\n","  'label': None},\n"," {'fid': '1006', 'idx': 96, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1006',\n","  'idx': 106,\n","  'content': 'Grade 1 - 2 endometrial cancer.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 138,\n","  'content': 'Uterus, cervix, adnexal remnants.',\n","  'label': None},\n"," {'fid': '1006', 'idx': 174, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1006',\n","  'idx': 187,\n","  'content': 'Specimen labelled \"Uterus cervix and tubal remains\", consists of a uterus with cervix 70 x 65 x 40mm, weighing 83g.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 304,\n","  'content': 'The ectocervix is 25 x 20mm.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 334,\n","  'content': 'The anterior margin is inked blue and the posterior margin is inked black.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 410,\n","  'content': 'The endometrium is less than 1mm thick.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 451,\n","  'content': 'In the endometrial cavity arising from the anterior wall is a 6mm polyp.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 525,\n","  'content': 'In the left cornu region there is a vague area of abnormality in the endometrrium 10mm across.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 621,\n","  'content': 'There is an intramural fibroid in the posterior uterine wall, 27mm across.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 697,\n","  'content': 'There is a 12mm intramural fibroid inanterior wall.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 750,\n","  'content': 'No residual fallopian tubes are seen.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 788,\n","  'content': 'Blocks: 1 to3 - full longitudinal midline section of anterior uterine body and cervix; 4 to 9 - left anterior endometrialcavity with polyp in block 6; 10 to 12 - area of irregularity in left cornu; 13 and 14 - right anterior endometrial cavity; 15 to 19 - full longitudinal section of posterior body and cervix; 20 and 21 - left posterior endometrial cavity; 22 - remainder of right posterior endometrial cavity.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 1202,\n","  'content': 'Endometrial cavity AE.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 1226,\n","  'content': '(TO: UJ;WN/vo 29.5.64)',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 1251,\n","  'content': 'MICROSCOPIC (Reported by Dr. H Huser):',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 1290,\n","  'content': 'Sections show a small amount of residual endometrioid adenocarcinoma of the endometrium.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 1380,\n","  'content': 'Considering the tumour in the previous curette (21A99049) the tumour is best graded as grade 2.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 1477,\n","  'content': 'No myometrial or lymphvascular invasion is seen.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 1526,\n","  'content': 'The ectocervix and endocervix are uninvolved.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 1573,\n","  'content': 'The myometrium shows adenomyosis and leiomyomas.',\n","  'label': None},\n"," {'fid': '1006', 'idx': 1622, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1006',\n","  'idx': 1633,\n","  'content': 'Grade 2 endometrioid adenocarcinoma of the endometrium.',\n","  'label': None},\n"," {'fid': '1006',\n","  'idx': 1690,\n","  'content': 'No myometrial or lymphvascular invasion.',\n","  'label': None},\n"," {'fid': '1006', 'idx': 1732, 'content': 'Cervix uninvolved.', 'label': None},\n"," {'fid': '1007', 'idx': 1, 'content': '8889114.NNN', 'label': None},\n"," {'fid': '1007',\n","  'idx': 13,\n","  'content': 'Newbrough, Jerrod Deane',\n","  'label': None},\n"," {'fid': '1007', 'idx': 37, 'content': '88W91145', 'label': None},\n"," {'fid': '1007',\n","  'idx': 47,\n","  'content': 'Last edited : 29/5/2064  Page: 2',\n","  'label': None},\n"," {'fid': '1007', 'idx': 80, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1007',\n","  'idx': 90,\n","  'content': 'Left hood wire localized breast calcification, surgical wide local excision.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 168,\n","  'content': 'Deep margin close towire distally, deep margin re-excised intraoperatively and sutured to specimen.',\n","  'label': None},\n"," {'fid': '1007', 'idx': 270, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1007', 'idx': 283, 'content': 'A.', 'label': None},\n"," {'fid': '1007',\n","  'idx': 287,\n","  'content': 'Specimen labelled \"Long stitch lateral medium stitch skin superficial left breast lesion\", consists of a mass of breast tissue with two sutures.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 433,\n","  'content': 'The two sutures had  been displaced and the specimen was re-orientated following a discussion with Dr Lon GRAYDON over the phone.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 564,\n","  'content': 'The specimen weighs 56g and measures 55mm from medial to lateral, 25mm from superior to inferior, 65mm from superficial to deep.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 694,\n","  'content': 'An ellipse of skin measuring 25 x 10mm is present on the superficial surface.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 773,\n","  'content': 'Two hookwires are inserted from the superficial aspect of the specimen.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 846,\n","  'content': 'The lateral surface is inked red, the superior surface is inked blue and the inferior surface is inked black.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 957,\n","  'content': 'The specimen is serially sectioned from superficial to deep into twelve slices, slice one superficial slice twelve deep.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 1079,\n","  'content': 'On the cut surface a previous biopsy cavity is noted in slices three to eight, filled with foreign body material.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 1194,\n","  'content': 'A clip is noted on the x-ray but was displaced during slicing.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 1258,\n","  'content': 'The cut surface of the breast tissue is fatty; no mass is seen.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 1322,\n","  'content': 'Blocks: 1 and 2 - LS superficial margin; 3 and 4 - slice two; 5 and 6 - slice three; 7 and 8 - slice four; 9 and 10 - slice five; 11 and 12 - slice six; 13 and 14 - slice seven; 15 to 17 - slice eight; 18 to 20 - slice nine; 21 to 23 - slice ten; 24 and 25 - slice eleven; 26 and 27 - LS of slice 12 deep margin.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 1636,\n","  'content': 'Multiple pieces in 27 blocks.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 1666,\n","  'content': '(TO: RC;QF/vo 27.5.64)',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 1690,\n","  'content': 'MICROSCOPIC (Reported by DrW Dilts):',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 1727,\n","  'content': 'Sections show breast tissue with a previous biopsy site associated with adjacent fat necrosis.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 1823,\n","  'content': 'There is sclerosing adenosis, apocrine metaplasia, and columnar cell change without atypia associated with luminal coarse calcification, and some moderate and florid epithelial hyperplasia of usual type.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 2028,\n","  'content': 'Stromal calcification is also present.',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 2068,\n","  'content': 'There is also a single small focus of atypical ductal hyperplasia; this is in the centre of the specimen and is well away from all excision margins (block 9).',\n","  'label': None},\n"," {'fid': '1007',\n","  'idx': 2228,\n","  'content': 'There is no in-situ or invasive malignancy.',\n","  'label': None},\n"," {'fid': '1007', 'idx': 2273, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1007',\n","  'idx': 2284,\n","  'content': 'Left breast lesion:  Focal atypical ductal hyperplasia, columnar cell change without atypia, apocrine metaplasia and epithelial hyperplasia of usual type.',\n","  'label': None},\n"," {'fid': '1008', 'idx': 2, 'content': '4670325.CIW', 'label': None},\n"," {'fid': '1008', 'idx': 14, 'content': 'Bialczyk, GEOFFREY', 'label': None},\n"," {'fid': '1008', 'idx': 33, 'content': '46S03251', 'label': None},\n"," {'fid': '1008',\n","  'idx': 43,\n","  'content': 'Last edited : 27/5/2064  Page: 2',\n","  'label': None},\n"," {'fid': '1008', 'idx': 76, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1008',\n","  'idx': 86,\n","  'content': 'Left frontoparietal lesion found after simplepartial seizures.',\n","  'label': None},\n"," {'fid': '1008',\n","  'idx': 150,\n","  'content': 'Lesion also found in rectum on CT.',\n","  'label': None},\n"," {'fid': '1008',\n","  'idx': 186,\n","  'content': 'No other history of malignancy in past.',\n","  'label': None},\n"," {'fid': '1008',\n","  'idx': 227,\n","  'content': 'Previous heavy smoker.',\n","  'label': None},\n"," {'fid': '1008',\n","  'idx': 251,\n","  'content': 'Previously well, parietal tumour.',\n","  'label': None},\n"," {'fid': '1008',\n","  'idx': 286,\n","  'content': 'Left parietal tumour.  ?GBM.',\n","  'label': None},\n"," {'fid': '1008', 'idx': 317, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1008', 'idx': 330, 'content': 'A.', 'label': None},\n"," {'fid': '1008',\n","  'idx': 334,\n","  'content': 'Specimen labelled \"Left frontoparietal lesion frozen section\", consists of two soft tissue fragments, 2mm each.',\n","  'label': None},\n"," {'fid': '1008',\n","  'idx': 447,\n","  'content': 'Smearsmade and remainder embedded for frozen section.',\n","  'label': None},\n"," {'fid': '1008',\n","  'idx': 502,\n","  'content': 'FROZEN SECTION REPORT:',\n","  'label': None},\n"," {'fid': '1008', 'idx': 525, 'content': 'Glioblastoma.', 'label': None},\n"," {'fid': '1008',\n","  'idx': 540,\n","  'content': 'Phone results to Dr K Cazzell by Dr K Mcdonagh at 4:15pm on 20.3.14',\n","  'label': None},\n"," {'fid': '1008', 'idx': 608, 'content': 'B.', 'label': None},\n"," {'fid': '1008',\n","  'idx': 612,\n","  'content': 'Specimen labelled \"Left frontoparietal lesion\", consists of two fragments of haemorrhagic soft tan tissue,  14 x 12 x 8mm and 8 x 10 x 5mm.',\n","  'label': None},\n"," {'fid': '1008', 'idx': 753, 'content': 'AE 2 blocks.', 'label': None},\n"," {'fid': '1008',\n","  'idx': 767,\n","  'content': '(TO: KT;KT/vo 23.5.64)',\n","  'label': None},\n"," {'fid': '1008',\n","  'idx': 791,\n","  'content': 'MICROSCOPIC (Reported by Dr K Windschitl):',\n","  'label': None},\n"," {'fid': '1008', 'idx': 834, 'content': 'A & B.', 'label': None},\n"," {'fid': '1008',\n","  'idx': 842,\n","  'content': 'Sections show fragments of glioblastoma multiforme with prominentendothelial proliferation and foci of palisaded necrosis.',\n","  'label': None},\n"," {'fid': '1008',\n","  'idx': 966,\n","  'content': 'There are numerous mitoses and the Ki67 is about 30%.',\n","  'label': None},\n"," {'fid': '1008',\n","  'idx': 1021,\n","  'content': 'The IDH-1 is negative.',\n","  'label': None},\n"," {'fid': '1008',\n","  'idx': 1045,\n","  'content': 'There is also focal venous thrombosis and only a small amount of uninvolved brain is present.',\n","  'label': None},\n"," {'fid': '1008', 'idx': 1139, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1008', 'idx': 1150, 'content': 'A & B.', 'label': None},\n"," {'fid': '1008',\n","  'idx': 1158,\n","  'content': 'Left frontoparietal lesion:  Glioblastoma multiforme, WHO grade 4.',\n","  'label': None},\n"," {'fid': '1009', 'idx': 1, 'content': '673633.LRE', 'label': None},\n"," {'fid': '1009', 'idx': 12, 'content': 'CECCHI, Hilario', 'label': None},\n"," {'fid': '1009', 'idx': 28, 'content': '67K63346', 'label': None},\n"," {'fid': '1009',\n","  'idx': 38,\n","  'content': 'Last edited : 22/5/2064  Page: 2',\n","  'label': None},\n"," {'fid': '1009', 'idx': 71, 'content': 'HISTORY:', 'label': None},\n"," {'fid': '1009', 'idx': 82, 'content': 'Hep B.', 'label': None},\n"," {'fid': '1009', 'idx': 90, 'content': 'Liver lesion.', 'label': None},\n"," {'fid': '1009', 'idx': 105, 'content': 'Segment 7 & 6.', 'label': None},\n"," {'fid': '1009', 'idx': 120, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1009',\n","  'idx': 135,\n","  'content': 'SEGMENT 6/7 LIVER RESECTION.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 167,\n","  'content': 'A portion of liver weighing 102g and measuring 80x60x40mm.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 227,\n","  'content': 'On the capsular surface there is a pale irregular lesion which has been previously incised measuring 35mm in diameter.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 347,\n","  'content': 'On sectioning the lesion is solid with some focal haemorrhage and ?necrosis.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 425,\n","  'content': 'The cross sectional area is up to 28x17mm.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 469,\n","  'content': 'It is located 13mm from the nearest resection margin.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 525,\n","  'content': '(1&2 paired full face tumour; 3 tumour with nearest resection margin; 4&5 paired full face tumour; 6 representative uninvolved liver parenchyma; 7 tumour reserve block).',\n","  'label': None},\n"," {'fid': '1009', 'idx': 696, 'content': 'RS (M-7/FF/ank)', 'label': None},\n"," {'fid': '1009',\n","  'idx': 712,\n","  'content': 'MICROSCOPIC:  (P. Devillez)',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 740,\n","  'content': 'Sections show a 35mm moderately to poorly differentiated hepatocellular carcinoma with trabecular and acinar architecture.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 864,\n","  'content': 'Areas of pleomorphic tumour cells including multinucleated forms are present.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 943,\n","  'content': 'Lymphovascular invasion by the carcinoma is present in adjacent liver parenchyma.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 1026,\n","  'content': 'Focal intracytoplasmic bile production by the carcinoma is present.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 1095,\n","  'content': 'Local excision of the carcinoma appears complete.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 1145,\n","  'content': 'Immunoperoxidase staining of the tumour cells shows positive staining with Cam5.2  and bile canalicular staining pattern with CD10.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 1278,\n","  'content': 'Focal non specific staining with synaptophysin is seen.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 1335,\n","  'content': 'No staining for CK20, AE1/AE3, ubiquitin or chromogranin is present.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 1404,\n","  'content': 'The adjacent liver parenchyma shows a mild chroic hepatitis B.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 1468,\n","  'content': 'There is increased fibrosis including areas of porto-portal bridging fibrosis (F2).',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 1553,\n","  'content': 'There is mild focal piecemeal necrosis within the portal tracts.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 1619,\n","  'content': 'Minimal chronic inflammation is seen in the liver lobules.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 1679,\n","  'content': 'Large cell dysplasia of hepatocytes is present and mild macrovesicular steatosis is also seen.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 1775,\n","  'content': 'Hepatocyte iron and copper content is not increased.',\n","  'label': None},\n"," {'fid': '1009',\n","  'idx': 1829,\n","  'content': 'Immunoperoxidase staining of hepatocytes shows cell membrane and cytoplasmic staining with HBsAg and focal intranuclear staining with HBcAg.',\n","  'label': None},\n"," {'fid': '1009', 'idx': 1973, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1009',\n","  'idx': 1986,\n","  'content': 'SEGMENT 6/7 LIVER RESECTION:',\n","  'label': None},\n"," {'fid': '1009', 'idx': 2015, 'content': '#NAME?', 'label': None},\n"," {'fid': '1009', 'idx': 2131, 'content': '#NAME?', 'label': None},\n"," {'fid': '1009', 'idx': 2166, 'content': '22/5/2064 nh', 'label': None},\n"," {'fid': '1011',\n","  'idx': 1,\n","  'content': 'Episode No:  15G653429Q',\n","  'label': None},\n"," {'fid': '1011', 'idx': 25, 'content': '1526534.GZQ', 'label': None},\n"," {'fid': '1011',\n","  'idx': 38,\n","  'content': \"ROTHSCHILD, Paris, Yvonne'Modesto\",\n","  'label': None},\n"," {'fid': '1011', 'idx': 73, 'content': 'Lab No:  15G65342', 'label': None},\n"," {'fid': '1011', 'idx': 91, 'content': 'Franich', 'label': None},\n"," {'fid': '1011',\n","  'idx': 99,\n","  'content': 'SUNBURY  South Australia  6987',\n","  'label': None},\n"," {'fid': '1011', 'idx': 130, 'content': 'Specimen: Tissue', 'label': None},\n"," {'fid': '1011', 'idx': 147, 'content': 'D.O.B:  20/12/2013', 'label': None},\n"," {'fid': '1011', 'idx': 166, 'content': 'Sex:  F', 'label': None},\n"," {'fid': '1011',\n","  'idx': 174,\n","  'content': 'Collected: 12/03/2014 at 11:14',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 205,\n","  'content': 'Location:  MEDIC/SURGERY WARD-WESTERN DISTRICT HEALTH SERVICE - COLERAINE',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 279,\n","  'content': 'DR Tyler ERIK LUIGI-Fitzsimons',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 310,\n","  'content': 'Distribution:   FILE-COPY,   NSW-CANCER-REGISTRY',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 359,\n","  'content': '***SUPPLEMENTARY REPORT: PR RESULTS (3.5.2064) TD',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 410,\n","  'content': '***SUPPLEMENTARY REPORT: KI-67',\n","  'label': None},\n"," {'fid': '1011', 'idx': 442, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1011',\n","  'idx': 452,\n","  'content': 'Left mastectomy + axillary clearance.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 491,\n","  'content': 'Metastatic breast cancer multiple rounds of systemic therapy.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 554,\n","  'content': '1. left mastectomy -long lateral, short superior.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 605,\n","  'content': '2. level I axillary LN.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 630,\n","  'content': '3. level II axillary LN.',\n","  'label': None},\n"," {'fid': '1011', 'idx': 655, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1011', 'idx': 668, 'content': 'A.', 'label': None},\n"," {'fid': '1011',\n","  'idx': 672,\n","  'content': 'Specimen labelled \"Left breast short superior long lateral\", consists of a mastectomy specimen without axilla and two sutures as mentioned above.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 819,\n","  'content': 'The entire specimen weighs 754g and measures 250mm from medial to lateral 180mm from superior to inferior 40mm from superficial to deep.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 957,\n","  'content': 'An ellipse of skin measuring 190 x 65 mm, is present with a nipple-areolar complex.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 1042,\n","  'content': 'The nipple measures10mm in diameter and is inverted.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 1096,\n","  'content': 'A verrucous skin lesion measuring 10 x 5 mm, is present 35mm inferolateral to the nipple.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 1187,\n","  'content': 'Remainder of the skin surface is unremarkable.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 1235,\n","  'content': 'The superficial surface is inked blue the deep surface is inked black.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 1307,\n","  'content': 'On the cut surface, an ill-defined pale firm tumour measuring 20 x 10 x 40mm, is presentdeep to the nipple extending laterally.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 1436,\n","  'content': 'It measures 25mm to the closest deep margin.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 1482,\n","  'content': 'The remainder of the breast tissue is fibrofatty.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 1533,\n","  'content': 'No lymph nodes are identified within the lateral aspect of the specimen.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 1608,\n","  'content': 'Blocks: 1 to 4 - full face of tumour with inverted nipple (block 1 with superficial margin, 3 and 4 with deep margin); 5 and 6 - another section of tumour with inverted skin, without surgical margin bisected; 7 - breast tissue medial to tumour; 8 - breast tissue lateral to tumour; 9 - RS upper inner quadrant; 10 - RS lower inner quadrant; 11 - RS upper outer quadrant; 12 - RS lower outer quadrant (blocks 9 to 12 with deep margin); 13 - TS of skin lesion.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 2068,\n","  'content': 'Multiple pieces in 13 blocks.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 2098,\n","  'content': 'FURTHER BLOCKS; 14-16, 17-19, 20-22 Three consecutive slices of UOQ with superficial and deep margins, arranged from lateral to medial (refer to the diagram).',\n","  'label': None},\n"," {'fid': '1011', 'idx': 2258, 'content': 'B.', 'label': None},\n"," {'fid': '1011',\n","  'idx': 2262,\n","  'content': 'Specimen labelled \"Level 1\", consists of a mass of fatty tissue weighing 51g and measuring 70 x 70 x 20mm.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 2370,\n","  'content': 'Twelve possible lymph nodes measuring 1 to 25mm in maximum extent are identified.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 2454,\n","  'content': 'Blocks: 1 - single node; 2 - single node; 3 - single node; 4 - single node; 5 - single node; 6 - single node; 7 - single node; 8 - single node; 9 - three nodes; 10 - two nodes.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 2632,\n","  'content': 'Multiple pieces in 10 blocks.',\n","  'label': None},\n"," {'fid': '1011', 'idx': 2663, 'content': 'C.', 'label': None},\n"," {'fid': '1011',\n","  'idx': 2667,\n","  'content': 'Specimen labelled \"Level 2\", consists of multiple fragments of fatty tissue measuring in aggregate 50 x 50 x 10mm.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 2783,\n","  'content': 'Seven lymph nodes measuring 3 to 15mm in maximum extent are identified.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 2856,\n","  'content': 'Blocks: 1 - single node; 2 - two nodes; 3 - two nodes; 4 - two nodes.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 2927,\n","  'content': 'Multiple pieces in four blocks.',\n","  'label': None},\n"," {'fid': '1011', 'idx': 2960, 'content': '(JS/vo 15.5.64)', 'label': None},\n"," {'fid': '1011',\n","  'idx': 2977,\n","  'content': 'MICROSCOPIC:  (Reported by Dr E Netzel)',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 3017,\n","  'content': 'The left breast tumour is an invasive ductal carcinoma with associated focal DCIS.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 3100,\n","  'content': 'A synoptic for invasive breast carcinoma follows:',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 3151,\n","  'content': 'SYNOPTIC REPORT FOR INVASIVE BREAST CARCINOMA',\n","  'label': None},\n"," {'fid': '1011', 'idx': 3197, 'content': 'Invasive carcinoma:', 'label': None},\n"," {'fid': '1011',\n","  'idx': 3217,\n","  'content': 'Site: Left breast (behind nipple).',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 3253,\n","  'content': 'Type: Invasive ductal carcinoma.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 3287,\n","  'content': 'The carcinoma consists of carcinoma cells arranged in infiltrative glands, trabeculae and linear files.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 3391,\n","  'content': 'The carcinoma is E-Cadherin positive.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 3429,\n","  'content': 'Although the main tumour nodule seen macroscopically is up to 40mm in dimension,focally, tongues of carcinoma extend towards the upper outer quadrant to a maximum dimension of 55mm.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 3611,\n","  'content': 'Invasive tumour size: 55mm (microscopic).',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 3653,\n","  'content': 'Grade (Modified Bloom & Richardson): 2',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 3692,\n","  'content': 'Tubules: 2  Nuclei: 2   Mitoses: 2     Mitotic rate:      10/10hpf.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 3760,\n","  'content': 'Lymphovascular invasion: Foci suspicious for LVSI are present.',\n","  'label': None},\n"," {'fid': '1011', 'idx': 3830, 'content': 'DCIS component:', 'label': None},\n"," {'fid': '1011', 'idx': 3848, 'content': 'DCIS: Present.', 'label': None},\n"," {'fid': '1011',\n","  'idx': 3864,\n","  'content': 'Maximum extent of DCIS: Present in association with invasive carcinoma over an approximate maximum extent of 45mm.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 3979,\n","  'content': 'Nuclear grade: Intermediate.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4009,\n","  'content': 'Architecture: Solid to cribriform.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4045,\n","  'content': 'Necrosis: Not identified.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4072,\n","  'content': 'Calcification: Not identified.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4104,\n","  'content': 'Degree of DCIS in tumour: Minimal.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4140,\n","  'content': 'DCIS in adjacent tissue: Present (focal).',\n","  'label': None},\n"," {'fid': '1011', 'idx': 4182, 'content': 'Excision Margins:', 'label': None},\n"," {'fid': '1011', 'idx': 4202, 'content': 'Invasive component:', 'label': None},\n"," {'fid': '1011',\n","  'idx': 4222,\n","  'content': 'Deep margin: 10mm (A11).',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4247,\n","  'content': 'Remaining margins: Well clear.',\n","  'label': None},\n"," {'fid': '1011', 'idx': 4278, 'content': 'In-situ component:', 'label': None},\n"," {'fid': '1011', 'idx': 4297, 'content': 'Deep margin: >10mm.', 'label': None},\n"," {'fid': '1011',\n","  'idx': 4317,\n","  'content': 'Remaining margins: Well clear.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4349,\n","  'content': 'Receptors: (Block A6)',\n","  'label': None},\n"," {'fid': '1011', 'idx': 4371, 'content': 'ER:   POSITIVE', 'label': None},\n"," {'fid': '1011',\n","  'idx': 4387,\n","  'content': '95% ofnuclei stained',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4409,\n","  'content': 'Predominant intensity of staining: moderate to strong.',\n","  'label': None},\n"," {'fid': '1011', 'idx': 4466, 'content': 'PR:   POSITIVE', 'label': None},\n"," {'fid': '1011', 'idx': 4482, 'content': '% of nuclei stained', 'label': None},\n"," {'fid': '1011',\n","  'idx': 4503,\n","  'content': 'Predominant intensity of staining: (see below)',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4551,\n","  'content': 'HER2 (Novocastra 10A7): Negative.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4585,\n","  'content': 'HER SISH:  Performed at Qwest Communications, SOUTH WEST HEALTHCARE - WARRNAMBOOL CAMPUS Hospital, see separate report.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4705,\n","  'content': 'Ki-67 index: Pending.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4727,\n","  'content': 'Nipple: The carcinoma is within breasttissue immediately behind the nipple.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4803,\n","  'content': 'Carcinoma cells abut, but do not appear to involve, the overlying epidermis.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4880,\n","  'content': \"There is no convincing Paget's disease.\",\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4922,\n","  'content': 'LCIS / ALH: Not identified.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 4951,\n","  'content': 'Lymph node(s): See specimens B and C.',\n","  'label': None},\n"," {'fid': '1011', 'idx': 4989, 'content': 'B.', 'label': None},\n"," {'fid': '1011',\n","  'idx': 4993,\n","  'content': 'Sections show metastatic carcinoma in all nine level 1 lymph nodes (9/9).',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 5067,\n","  'content': 'The foci of metastatic carcinoma are up to 9.0mm in maximum dimension.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 5138,\n","  'content': 'Extranodal extension up to 8.0mm is seen.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 5180,\n","  'content': 'There is focal extranodal lymphovascular space invasion.',\n","  'label': None},\n"," {'fid': '1011', 'idx': 5238, 'content': 'C.', 'label': None},\n"," {'fid': '1011',\n","  'idx': 5242,\n","  'content': 'Sections show metastatic carcinoma in all four level 2 lymph nodes (4/4).',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 5316,\n","  'content': 'Extranodal extension up to 3.3mm is seen.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 5358,\n","  'content': 'There is focal nodal lymphovascular space invasion.',\n","  'label': None},\n"," {'fid': '1011', 'idx': 5410, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1011', 'idx': 5421, 'content': 'A.', 'label': None},\n"," {'fid': '1011', 'idx': 5425, 'content': 'Left mastectomy:', 'label': None},\n"," {'fid': '1011',\n","  'idx': 5443,\n","  'content': '55mm grade 2 left breast carcinoma with associated focal intermediate grade DCIS.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 5525,\n","  'content': 'Margins appear clear.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 5548,\n","  'content': 'ER and PR positive; HER-2 negative.',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 5584,\n","  'content': 'Her-2 SISH is being performed and a separate report will be issued.',\n","  'label': None},\n"," {'fid': '1011', 'idx': 5654, 'content': 'B.', 'label': None},\n"," {'fid': '1011',\n","  'idx': 5658,\n","  'content': 'Axillary lymph nodes (level 1): Metastatic carcinoma in nine lymph nodes (9/9).',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 5738,\n","  'content': 'Extranodal extension up to 8.0mm and extranodal lymphovascular space invasion.',\n","  'label': None},\n"," {'fid': '1011', 'idx': 5818, 'content': 'C.', 'label': None},\n"," {'fid': '1011',\n","  'idx': 5822,\n","  'content': 'Axillary lymph nodes (level 2): Metastatic carcinoma in four lymph nodes (4/4).',\n","  'label': None},\n"," {'fid': '1011',\n","  'idx': 5902,\n","  'content': 'Extranodal extension up to 3.3mm is present.',\n","  'label': None},\n"," {'fid': '1012', 'idx': 1, 'content': '7317745.VUY', 'label': None},\n"," {'fid': '1012', 'idx': 13, 'content': 'HICKSON, SHANE-FARAH', 'label': None},\n"," {'fid': '1012', 'idx': 34, 'content': '73C77458,73C77458', 'label': None},\n"," {'fid': '1012',\n","  'idx': 53,\n","  'content': 'Last edited : 5/3/2064  Page: 2',\n","  'label': None},\n"," {'fid': '1012', 'idx': 86, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1012',\n","  'idx': 96,\n","  'content': 'Curettings - grade 1 endometrioid adenoca.',\n","  'label': None},\n"," {'fid': '1012', 'idx': 140, 'content': 'TLH/BSO.', 'label': None},\n"," {'fid': '1012',\n","  'idx': 149,\n","  'content': 'Mismatch repair Immunohistochemistry please.',\n","  'label': None},\n"," {'fid': '1012', 'idx': 195, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1012',\n","  'idx': 208,\n","  'content': 'Specimen labelled \"Bilateral tubes and ovaries, uterus, cervix\", consists of a uterus with attached cervix, bilateral fallopian tubes and ovaries weighing 98g in total.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 378,\n","  'content': 'The uterus measures 80 x 60 x 35mm and has a smooth shiny serosal surface.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 454,\n","  'content': 'The ectocervix measures 36 x 34mm and has an unremarkable surface.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 522,\n","  'content': 'On section, the endometrium is less than 1mm in maximum thickness.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 590,\n","  'content': 'The myometrium is 12mm in maximum thickness.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 636,\n","  'content': 'The myometrium contains two fibroids each 10mm in maximum diameter.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 704,\n","  'content': 'The right fallopian tube measures 50mm in length and 5mm in maximum diameter.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 782,\n","  'content': 'The fimbria is present and appears unremarkable.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 832,\n","  'content': 'The right ovary measures 30 x 15 x 15mm and has an unremarkable cut surface.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 910,\n","  'content': 'The left fallopian tube measures 40mm in length and 5mm in maximum diameter.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 987,\n","  'content': 'The left ovary measures 35 x 15 x 15mm and has an unremarkable cut surface.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 1063,\n","  'content': 'Blocks 1-3 - one full LS of anterior body and cervix; 4-6 - rest of anterior endomyometrium; 7-9 - one full LS of posterior body and cervix; 10-16 - rest of posterior endomyometrium.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 1246,\n","  'content': '(The endometrium has been AE); 17 - right parametrial tissue; 18 - left parametrial tissue; 19 - right fimbria and fallopian tube; 20 - right ovary, representative sections; 21 - left fallopian tube and fimbria; 22 - left ovary.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 1475,\n","  'content': '(TO: FD: LO/ec   30.5.64)',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 1502,\n","  'content': 'MICROSCOPIC: (Reported by Dr S Quintano)',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 1544,\n","  'content': 'The sectionsshow foci of residual endometrioid adenocarcinoma FIGO grade 1 (slide 13 and 14) invading 1 mm in a myometrium 10mm thick.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 1679,\n","  'content': 'No lymphovascular invasion is seen.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 1715,\n","  'content': 'The uninvolved endometrium shows areas of simple hyperplasia without atypia.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 1793,\n","  'content': 'The uterus also shows intramural leiomyomata with no atypical features and areas of adenomyosis (slide 16).',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 1902,\n","  'content': 'The tumour does not involve the parametria, cervix, fallopian tubes or ovaries.',\n","  'label': None},\n"," {'fid': '1012',\n","  'idx': 1983,\n","  'content': 'No fallopian tube dysplasia is seen.',\n","  'label': None},\n"," {'fid': '1012', 'idx': 2021, 'content': 'CONCLUSION', 'label': None},\n"," {'fid': '1012',\n","  'idx': 2032,\n","  'content': 'Uterus, ovaries and fallopian tubes: Endometrioid adenocarcinoma FIGO grade 1.',\n","  'label': None},\n"," {'fid': '1012', 'idx': 2111, 'content': 'COMMENT', 'label': None},\n"," {'fid': '1012',\n","  'idx': 2119,\n","  'content': 'Immunohistochemistry for mismatch repair proteins has been requested on the previous specimen 73C77458 (endometrial curettings, 5.7.64) and a supplementary report will be added to this report when the stains are available.',\n","  'label': None},\n"," {'fid': '1013', 'idx': 1, 'content': '9473754.JQJ', 'label': None},\n"," {'fid': '1013', 'idx': 13, 'content': 'Bolyard, LAURI DONALD', 'label': None},\n"," {'fid': '1013', 'idx': 35, 'content': '94U37543,94U37543', 'label': None},\n"," {'fid': '1013',\n","  'idx': 54,\n","  'content': 'Last edited : 5/3/2064  Page: 2',\n","  'label': None},\n"," {'fid': '1013', 'idx': 86, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1013', 'idx': 96, 'content': 'Recurrent ovarian Ca.', 'label': None},\n"," {'fid': '1013', 'idx': 120, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1013', 'idx': 133, 'content': 'A.', 'label': None},\n"," {'fid': '1013',\n","  'idx': 137,\n","  'content': 'Specimen labelled \"Transverse colon\" consists of a segment of colon 95mm in length, 75mm in maximum open circumference with attached mesocolon, 70 x 50 x 15mm.',\n","  'label': None},\n"," {'fid': '1013',\n","  'idx': 298,\n","  'content': 'The segment of colon appears unremarkable.',\n","  'label': None},\n"," {'fid': '1013',\n","  'idx': 342,\n","  'content': 'There are multiple nodules present in the mesocolon measuring 35 x 25 x 10mm to 10 x 5 x 5mm.',\n","  'label': None},\n"," {'fid': '1013',\n","  'idx': 437,\n","  'content': 'Two smaller nodules are present on the serosal surface.',\n","  'label': None},\n"," {'fid': '1013',\n","  'idx': 494,\n","  'content': 'The surface of the two smaller nodules is roughened at one aspect and this aspect is inked blue.',\n","  'label': None},\n"," {'fid': '1013',\n","  'idx': 592,\n","  'content': 'There is no involvement of the colon.',\n","  'label': None},\n"," {'fid': '1013',\n","  'idx': 632,\n","  'content': 'Blocks:  1 & 2 -two nodules (one in each); 3 - three lymph nodes; 4 - two lymph nodes; 5 to 9 - largest nodule; 10 & 11 - representative section of the colon.',\n","  'label': None},\n"," {'fid': '1013', 'idx': 791, 'content': 'B.', 'label': None},\n"," {'fid': '1013',\n","  'idx': 795,\n","  'content': 'Specimen labelled \"Small bowel mesentery\" consists of multiple fragments of pale tissue, 15 x 10 x 3mm in total aggregate.',\n","  'label': None},\n"," {'fid': '1013', 'idx': 919, 'content': 'AE 1 block.', 'label': None},\n"," {'fid': '1013', 'idx': 931, 'content': 'C.', 'label': None},\n"," {'fid': '1013',\n","  'idx': 935,\n","  'content': 'Specimen labelled \"Omentum\" consists of a piece of omentum 280 x 150 x 15mm.',\n","  'label': None},\n"," {'fid': '1013',\n","  'idx': 1013,\n","  'content': 'Multiple tumour deposits are noted ranging from 8mm across to 90mm across.',\n","  'label': None},\n"," {'fid': '1013',\n","  'idx': 1090,\n","  'content': 'Blocks:  1 - three nodes; 2 - three nodes; 3 - two nodes; 4 & 5 - representative section from two nodes one in each; 6 - one representative section of the largest node.',\n","  'label': None},\n"," {'fid': '1013', 'idx': 1260, 'content': '(CD/mm 28.5.64)', 'label': None},\n"," {'fid': '1013',\n","  'idx': 1277,\n","  'content': 'MICROSCOPIC (Reported by Dr X Hargreaves):',\n","  'label': None},\n"," {'fid': '1013', 'idx': 1320, 'content': 'A.', 'label': None},\n"," {'fid': '1013',\n","  'idx': 1324,\n","  'content': 'Sections show multiple deposits of metastatic papillary serous adenocarcinoma involving transverse colon mesentery.',\n","  'label': None},\n"," {'fid': '1013',\n","  'idx': 1441,\n","  'content': 'The tumour shows prominent papillary architecture.',\n","  'label': None},\n"," {'fid': '1013',\n","  'idx': 1493,\n","  'content': 'There is widespread psammoma body type calcification.',\n","  'label': None},\n"," {'fid': '1013',\n","  'idx': 1548,\n","  'content': 'The muscle wall and mucosa of transverse colon are unremarkable.',\n","  'label': None},\n"," {'fid': '1013', 'idx': 1613, 'content': 'B & C.', 'label': None},\n"," {'fid': '1013',\n","  'idx': 1621,\n","  'content': 'Sections show multiple deposits of metastatic papillary serous adenocarcinoma involving smallbowel mesentery and omentum.',\n","  'label': None},\n"," {'fid': '1013',\n","  'idx': 1744,\n","  'content': 'The tumour shows similar appearances to those described in the specimen A.',\n","  'label': None},\n"," {'fid': '1013', 'idx': 1819, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1013', 'idx': 1830, 'content': 'A.', 'label': None},\n"," {'fid': '1013',\n","  'idx': 1834,\n","  'content': 'Transverse colon - Metastatic papillary serous adenocarcinoma.',\n","  'label': None},\n"," {'fid': '1013', 'idx': 1897, 'content': 'B.', 'label': None},\n"," {'fid': '1013',\n","  'idx': 1901,\n","  'content': 'Small bowel mesentery - Metastatic papillary serous adenocarcinoma.',\n","  'label': None},\n"," {'fid': '1013', 'idx': 1969, 'content': 'C.', 'label': None},\n"," {'fid': '1013',\n","  'idx': 1973,\n","  'content': 'Omentum - Metastatic papillary serous adenocarcinoma.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 1,\n","  'content': 'Episode No:  42Q306494S',\n","  'label': None},\n"," {'fid': '1014', 'idx': 25, 'content': '4263064.YLS', 'label': None},\n"," {'fid': '1014', 'idx': 38, 'content': 'YALE, Catrice DELINDA', 'label': None},\n"," {'fid': '1014', 'idx': 61, 'content': 'Lab No:  42Q30649', 'label': None},\n"," {'fid': '1014', 'idx': 79, 'content': 'Milbank', 'label': None},\n"," {'fid': '1014', 'idx': 87, 'content': 'MACKAY  QLD  6346', 'label': None},\n"," {'fid': '1014', 'idx': 105, 'content': 'Specimen: Tissue', 'label': None},\n"," {'fid': '1014', 'idx': 122, 'content': 'D.O.B:  20/11/2021', 'label': None},\n"," {'fid': '1014', 'idx': 141, 'content': 'Sex:  F', 'label': None},\n"," {'fid': '1014',\n","  'idx': 149,\n","  'content': 'Collected: 20/03/2014 at 10:30',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 180,\n","  'content': 'Location:  Med Onc-DALBY HOSPITAL HEALTH SERVICE',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 229,\n","  'content': 'PRO BRITT Elvis Ballowe',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 253,\n","  'content': 'Distribution:   FILE-COPY,   NSW-CANCER-REGISTRY',\n","  'label': None},\n"," {'fid': '1014', 'idx': 302, 'content': 'HISTORY:', 'label': None},\n"," {'fid': '1014',\n","  'idx': 313,\n","  'content': 'Intraoperative - peritoneum.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 343,\n","  'content': 'Previous adenocarcinoma.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 369,\n","  'content': 'Tissue from L paracolic, DJ junction, small bowel surface.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 429, 'content': 'Peritonectomy.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 445,\n","  'content': 'Adenocarcinoma - liver surface - diaphragm.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 490, 'content': 'Colorectal cancer.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 510,\n","  'content': 'Frozen section pelvic mass.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 539,\n","  'content': 'Past history CRC and liver mets.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 573,\n","  'content': 'Peritonectomy + liver resection.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 607,\n","  'content': 'Liver segment 3, 5, 7, 8.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 634, 'content': 'Spleen.', 'label': None},\n"," {'fid': '1014', 'idx': 642, 'content': 'Gallbladder.', 'label': None},\n"," {'fid': '1014', 'idx': 655, 'content': 'Colon.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 662,\n","  'content': 'Pelvic peritoneal strip.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 687, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1014', 'idx': 702, 'content': 'A.', 'label': None},\n"," {'fid': '1014', 'idx': 706, 'content': 'JEJUNOSTOMY.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 722,\n","  'content': 'A piece of tissue 3mm in diameter.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 757,\n","  'content': 'F/S : \"Adenocarcinoma and foreign body giant cell reaction\".',\n","  'label': None},\n"," {'fid': '1014', 'idx': 819, 'content': 'AE (1-1)', 'label': None},\n"," {'fid': '1014', 'idx': 828, 'content': 'B.', 'label': None},\n"," {'fid': '1014', 'idx': 832, 'content': 'SMALL BOWEL SURFACE.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 855,\n","  'content': 'A piece of mucoid material 2-3mm in diameter.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 901,\n","  'content': 'F/S : \"? fibroblastic reaction.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 934,\n","  'content': 'Negative for malignancy\".',\n","  'label': None},\n"," {'fid': '1014', 'idx': 961, 'content': 'AE (1-1)', 'label': None},\n"," {'fid': '1014', 'idx': 970, 'content': 'C.', 'label': None},\n"," {'fid': '1014', 'idx': 974, 'content': 'LEFT PARACOLIC.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 993,\n","  'content': 'Multiple fragments of soft pale material 5-6mm in diameter.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 1053,\n","  'content': 'F/S : \"Foreign body giant cell reaction\".',\n","  'label': None},\n"," {'fid': '1014', 'idx': 1096, 'content': 'AE (M-1)', 'label': None},\n"," {'fid': '1014', 'idx': 1105, 'content': 'D.', 'label': None},\n"," {'fid': '1014', 'idx': 1109, 'content': 'LIVER SURFACE.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 1126,\n","  'content': 'A piece of pink tissue 4mm in diameter.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 1166,\n","  'content': 'F/S : \"Foreign body giant cell reaction\".',\n","  'label': None},\n"," {'fid': '1014', 'idx': 1209, 'content': 'AE (1-1)', 'label': None},\n"," {'fid': '1014', 'idx': 1218, 'content': 'E.', 'label': None},\n"," {'fid': '1014', 'idx': 1222, 'content': 'DIAPHRAGM.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 1236,\n","  'content': 'A piece of fatty and red tissue 7mm in diameter.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 1287,\n","  'content': 'F/S : \"Foreign body giant cell reaction\".',\n","  'label': None},\n"," {'fid': '1014', 'idx': 1330, 'content': 'AE (1-1)', 'label': None},\n"," {'fid': '1014', 'idx': 1339, 'content': 'F.', 'label': None},\n"," {'fid': '1014', 'idx': 1343, 'content': 'PELVIC MASS.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 1359,\n","  'content': 'A pale piece of tissue 10x5x8mm.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 1394,\n","  'content': 'F/S : \"Fibrosis and F.B. giant cells\".',\n","  'label': None},\n"," {'fid': '1014', 'idx': 1434, 'content': 'AE (2-1)', 'label': None},\n"," {'fid': '1014',\n","  'idx': 1443,\n","  'content': 'F/S : Result for specimens A-C given to anaesthetist by Dr. Dick at 10:10hrs on 20/3/14.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 1533,\n","  'content': 'Result for specimen D&E given by phone to Prof. Lastrape at 1155Hrs.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 1603,\n","  'content': 'Result for specimen F given by phone to Prof. Badeau at 1310Hrs.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 1668, 'content': 'G.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 1672,\n","  'content': 'PERITONEAL DISEASE, GALLBLADDER, SPLEEN, COLON, OMENTUM, PERITONEUM.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 1744,\n","  'content': 'Gallbladder, spleen, a section of colon and multiple pieces of peritoneum and omentum.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 1832,\n","  'content': 'The gallbladder is 80x30mm and has a smooth shiny serosal surface.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 1900, 'content': 'No tumour is seen.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 1919,\n","  'content': 'The wall is 4mm in thickness and the mucosal surface is green and granular.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 1996,\n","  'content': 'No stains are present.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 2020,\n","  'content': 'The spleen is a 110g and is 100x70x20mm.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 2062,\n","  'content': 'The external surface is smooth and shiny, and the cut surface is fleshy red.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 2140, 'content': 'No tumour is seen.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 2160,\n","  'content': 'The colon is 70mm in length and 60mm in circumference.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 2216,\n","  'content': 'There is a small amount of pericolic fat.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 2258,\n","  'content': 'The wall is 60mm in thickness and the mucosa isunremarkable.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 2319,\n","  'content': 'There is no tumour present externally or internally.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 2373,\n","  'content': 'The omentum is approximately 260x140x10-20mm.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 2420,\n","  'content': 'No mucinous deposits or solid lesions are present.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 2472,\n","  'content': 'There are numerous pieces of peritoneum with an aggregate of 100x100x10-30mm.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 2551,\n","  'content': 'No mucinous or solid lesions are present.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 2593,\n","  'content': '(1&2 gallbladder [1 cystic duct, 2 body and fundus]; 3&4 spleen; 5&6 colon [5 resection margins, 6 random sample]; 7-15 omentum; 16-20 peritoneum).',\n","  'label': None},\n"," {'fid': '1014', 'idx': 2742, 'content': 'RS (22-20).', 'label': None},\n"," {'fid': '1014', 'idx': 2754, 'content': 'H.', 'label': None},\n"," {'fid': '1014', 'idx': 2758, 'content': 'LIVER SEGMENT 3.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 2778,\n","  'content': 'A piece of liver 20x20x20mm.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 2808,\n","  'content': 'In the centre there is a white hard lesion 13mm in maximum dimension which comes close to the resection margin.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 2921, 'content': 'AE (7-7)', 'label': None},\n"," {'fid': '1014', 'idx': 2930, 'content': 'J.', 'label': None},\n"," {'fid': '1014', 'idx': 2934, 'content': 'LIVER SEGMENT 5.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 2954,\n","  'content': 'Four irregularly shaped pieces of tissue one of which contains a suture.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 3028,\n","  'content': 'The specimens are from 5x5x3mm to 10x8x5mm in dimension with an aggregate of approximately 10x10x5mm.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 3131, 'content': 'AE (4-2)', 'label': None},\n"," {'fid': '1014', 'idx': 3140, 'content': 'K.', 'label': None},\n"," {'fid': '1014', 'idx': 3144, 'content': 'LIVER SEGMENT 7.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 3164,\n","  'content': 'Piece of liver 20x15x10mm.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 3192,\n","  'content': 'There is a well demarcated white nodule 13mm in diameter within the parenchyma.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 3273, 'content': 'AE (M-5)', 'label': None},\n"," {'fid': '1014', 'idx': 3282, 'content': 'L.', 'label': None},\n"," {'fid': '1014', 'idx': 3286, 'content': 'SEGMENT 8 LIVER.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 3306,\n","  'content': 'A piece of liver 40x30x25mm.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 3336,\n","  'content': 'Within the parenchyma there is a well demarcated white tumour 40mm in maximum dimensions which abuts the resection margin.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 3460, 'content': 'RS (4-4/BI/ank)', 'label': None},\n"," {'fid': '1014',\n","  'idx': 3476,\n","  'content': 'MICROSCOPIC:  (L. Swingle)',\n","  'label': None},\n"," {'fid': '1014', 'idx': 3503, 'content': 'A.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 3507,\n","  'content': 'Sections show fibrofatty tissue with metastatic moderately differentiated adenocarcinoma.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 3597,\n","  'content': 'Adjacent foreign body giant cell reaction is also seen.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 3654, 'content': 'B.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 3658,\n","  'content': 'Sections show an area of fibrosis.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 3693,\n","  'content': 'There is no evidence of malignancy.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 3729, 'content': 'C,D,E&F.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 3738,\n","  'content': 'Sections show fibrous tissue with scattered foreign body giant cells.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 3808,\n","  'content': 'Focal necrotic tissue of uncertain significance is also present in specimen C.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 3888,\n","  'content': 'There is no evidence of malignancy.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 3924, 'content': 'G.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 3928,\n","  'content': 'Sections show small deposits of metastatic adenocarcinoma in keeping with origin from colorectal primary involving omentum and separately submitted peritoneal fragments.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 4099,\n","  'content': 'Sections through the gallbladder show features of chroniccholecystitis including a reactive cystic duct lymph node.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 4216,\n","  'content': 'Sections through the spleen show no significant abnormality.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 4278,\n","  'content': 'Sections throughthe segment of colon show serosal foreign body giant cell reaction and areas of fibrosis and otherwise no significant abnormality with no evidence of tumour.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 4453, 'content': 'H,J,K&L.', 'label': None},\n"," {'fid': '1014',\n","  'idx': 4463,\n","  'content': 'Sections show liver with metastatic moderately differentiated adenocarcinoma including extensive areas of necrosis in keeping with origin from a colorectal primary.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 4628,\n","  'content': 'The carcinoma appears to extend to surgical margins of resection.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 4694,\n","  'content': 'Adjacent liver parenchyma shows no intrinsic abnormality.',\n","  'label': None},\n"," {'fid': '1014', 'idx': 4753, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1014',\n","  'idx': 4766,\n","  'content': 'JEJUNOSTOMY:  METASTATIC ADENOCARCINOMA.',\n","  'label': None},\n"," {'fid': '1014',\n","  'idx': 4808,\n","  'content': 'SMALL BOWEL SURFACE,  LEFT PARACOLIC, LIVER SURFACE,DIAPHRAGM AND PELVIC MASS:',\n","  'label': None},\n"," {'fid': '1014', 'idx': 4888, 'content': '#NAME?', 'label': None},\n"," {'fid': '1014',\n","  'idx': 4930,\n","  'content': 'PERITONEAL DISEASE, GALLBLADDER, SPLEEN, OMENTAL AND PERITONEUM:',\n","  'label': None},\n"," {'fid': '1014', 'idx': 4996, 'content': '#NAME?', 'label': None},\n"," {'fid': '1014',\n","  'idx': 5069,\n","  'content': 'LIVER SEGMENT 3, 5, 7 AND 8:',\n","  'label': None},\n"," {'fid': '1014', 'idx': 5102, 'content': '#NAME?', 'label': None},\n"," {'fid': '1014', 'idx': 5143, 'content': '26/5/64 ht', 'label': None},\n"," {'fid': '1015', 'idx': 1, 'content': '004326.ONG', 'label': None},\n"," {'fid': '1015', 'idx': 12, 'content': 'Rotch, Forrest LESTER', 'label': None},\n"," {'fid': '1015', 'idx': 34, 'content': '00M32655', 'label': None},\n"," {'fid': '1015',\n","  'idx': 44,\n","  'content': 'Last edited : 29/5/2064  Page: 2',\n","  'label': None},\n"," {'fid': '1015', 'idx': 77, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1015',\n","  'idx': 87,\n","  'content': 'Sentinel node A and B identified with gamma probe excised from left axilla.',\n","  'label': None},\n"," {'fid': '1015', 'idx': 163, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1015', 'idx': 176, 'content': 'A.', 'label': None},\n"," {'fid': '1015',\n","  'idx': 180,\n","  'content': 'Specimen labelled \"Sentinel node A left breast\", consists of a lymph node measuring 12 x 10 x 5mm.',\n","  'label': None},\n"," {'fid': '1015',\n","  'idx': 280,\n","  'content': 'Specimen transversely sectioned AE 1 block.',\n","  'label': None},\n"," {'fid': '1015', 'idx': 325, 'content': 'B.', 'label': None},\n"," {'fid': '1015',\n","  'idx': 329,\n","  'content': 'Specimen labelled \"Sentinel node B left breast\",consists of a lymph node measuring 6 x 3 x 3mm.',\n","  'label': None},\n"," {'fid': '1015',\n","  'idx': 426,\n","  'content': 'Specimen transversely sectioned AE 1 block.',\n","  'label': None},\n"," {'fid': '1015', 'idx': 471, 'content': '(CI/vo 27.5.64)', 'label': None},\n"," {'fid': '1015',\n","  'idx': 488,\n","  'content': 'MICROSCOPIC (Reported by Dr A Schoeninger):',\n","  'label': None},\n"," {'fid': '1015', 'idx': 532, 'content': 'A & B.', 'label': None},\n"," {'fid': '1015',\n","  'idx': 540,\n","  'content': 'Two (2) lymph nodes are identified in total.',\n","  'label': None},\n"," {'fid': '1015',\n","  'idx': 586,\n","  'content': 'The lymph nodes are unremarkable.',\n","  'label': None},\n"," {'fid': '1015',\n","  'idx': 621,\n","  'content': 'Both histological and immunohistochemical examinations show no evidence of tumour metastasis.',\n","  'label': None},\n"," {'fid': '1015', 'idx': 715, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1015', 'idx': 726, 'content': 'A & B.', 'label': None},\n"," {'fid': '1015',\n","  'idx': 734,\n","  'content': 'Left breast sentinel lymph nodes - No significant abnormality (0/2).',\n","  'label': None},\n"," {'fid': '1019', 'idx': 1, 'content': '0562081.PYA', 'label': None},\n"," {'fid': '1019',\n","  'idx': 13,\n","  'content': 'Aschan, Verdell Tristan',\n","  'label': None},\n"," {'fid': '1019', 'idx': 37, 'content': '05Q20816,05Q20816', 'label': None},\n"," {'fid': '1019',\n","  'idx': 56,\n","  'content': 'Last edited :3/6/2064  Page: 2',\n","  'label': None},\n"," {'fid': '1019', 'idx': 87, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1019', 'idx': 97, 'content': 'Recurrent ovarian Ca.', 'label': None},\n"," {'fid': '1019', 'idx': 121, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1019', 'idx': 134, 'content': 'A.', 'label': None},\n"," {'fid': '1019',\n","  'idx': 138,\n","  'content': 'Specimen labelled \"Transverse colon\" consists of a segment of colon 95mm in length, 75mm in maximum open circumference with attached mesocolon, 70 x 50 x 15mm.',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 299,\n","  'content': 'The segment of colon appears unremarkable.',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 343,\n","  'content': 'There are multiple nodules present in the mesocolon measuring 35 x 25 x 10mm to 10 x 5 x 5mm.',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 438,\n","  'content': 'Two smaller nodules are present on the serosal surface.',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 495,\n","  'content': 'The surface of the two smaller nodules is roughened at one aspect and this aspect is inked blue.',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 593,\n","  'content': 'There is no involvement of the colon.',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 633,\n","  'content': 'Blocks:  1 & 2 - two nodules (one in each); 3 - three lymph nodes; 4 - two lymph nodes; 5 to 9 - largest nodule; 10 & 11 - representative section of the colon.',\n","  'label': None},\n"," {'fid': '1019', 'idx': 793, 'content': 'B.', 'label': None},\n"," {'fid': '1019',\n","  'idx': 797,\n","  'content': 'Specimen labelled \"Small bowel mesentery\" consistsof multiple fragments of pale tissue, 15 x 10 x 3mm in total aggregate.',\n","  'label': None},\n"," {'fid': '1019', 'idx': 920, 'content': 'AE 1 block.', 'label': None},\n"," {'fid': '1019', 'idx': 932, 'content': 'C.', 'label': None},\n"," {'fid': '1019',\n","  'idx': 936,\n","  'content': 'Specimen labelled \"Omentum\" consists of a piece of omentum 280 x 150 x 15mm.',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 1014,\n","  'content': 'Multiple tumour deposits are noted ranging from 8mm across to 90mm across.',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 1091,\n","  'content': 'Blocks:  1 - three nodes; 2 - three nodes; 3 - two nodes; 4 & 5 - representative section from two nodes one in each; 6 - one representative section of the largest node.',\n","  'label': None},\n"," {'fid': '1019', 'idx': 1261, 'content': '(ZA/mm 28.5.64)', 'label': None},\n"," {'fid': '1019',\n","  'idx': 1278,\n","  'content': 'MICROSCOPIC (Reported by Dr B Cusic):',\n","  'label': None},\n"," {'fid': '1019', 'idx': 1316, 'content': 'A.', 'label': None},\n"," {'fid': '1019',\n","  'idx': 1320,\n","  'content': 'Sections show multiple deposits of metastatic papillary serous adenocarcinoma involving transverse colon mesentery.',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 1437,\n","  'content': 'The tumour shows prominent papillary architecture.',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 1489,\n","  'content': 'There is widespread psammoma body type calcification.The muscle wall and mucosa of transverse colon are unremarkable.',\n","  'label': None},\n"," {'fid': '1019', 'idx': 1607, 'content': 'B & C.', 'label': None},\n"," {'fid': '1019',\n","  'idx': 1615,\n","  'content': 'Sections show multiple deposits of metastatic papillary serous adenocarcinoma involving small bowel mesentery and omentum.',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 1739,\n","  'content': 'The tumour shows similar appearances to those described in the specimen A.',\n","  'label': None},\n"," {'fid': '1019', 'idx': 1814, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1019', 'idx': 1825, 'content': 'A.', 'label': None},\n"," {'fid': '1019',\n","  'idx': 1829,\n","  'content': 'Transverse colon - Metastaticpapillary serous adenocarcinoma.',\n","  'label': None},\n"," {'fid': '1019', 'idx': 1891, 'content': 'B.', 'label': None},\n"," {'fid': '1019',\n","  'idx': 1895,\n","  'content': 'Small bowel mesentery - Metastatic papillary serous adenocarcinoma.',\n","  'label': None},\n"," {'fid': '1019', 'idx': 1963, 'content': 'C.', 'label': None},\n"," {'fid': '1019',\n","  'idx': 1967,\n","  'content': 'Omentum - Metastatic papillary serous adenocarcinoma.',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 2021,\n","  'content': 'SUPPLEMENTARY REPORT (3/6/2064):',\n","  'label': None},\n"," {'fid': '1019',\n","  'idx': 2054,\n","  'content': 'In the specimen A to C. the metastatic papillary serous adenocarcinoma is high grade.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 0,\n","  'content': 'Episode No:  79Z048569U',\n","  'label': None},\n"," {'fid': '1021', 'idx': 24, 'content': '7990485.RXU', 'label': None},\n"," {'fid': '1021',\n","  'idx': 37,\n","  'content': 'Gerberich, Virgilio-Martha',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 65,\n","  'content': 'Lab No:  79Z04856,79Z04856',\n","  'label': None},\n"," {'fid': '1021', 'idx': 92, 'content': 'Fulready', 'label': None},\n"," {'fid': '1021',\n","  'idx': 101,\n","  'content': 'CABOOLTURE  QLD  1160',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 123,\n","  'content': 'Specimen: Washings,Tissue',\n","  'label': None},\n"," {'fid': '1021', 'idx': 149, 'content': 'D.O.B:  21/12/2007', 'label': None},\n"," {'fid': '1021', 'idx': 168, 'content': 'Sex:  F', 'label': None},\n"," {'fid': '1021',\n","  'idx': 176,\n","  'content': 'Collected: 29/5/2064 at :',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 202,\n","  'content': 'Location:  Douglas Hanly Moir - WEST WIMMERA HEALTH SERVICE - KANIVA',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 271,\n","  'content': 'DR Kelley Rodney FORBESS',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 296,\n","  'content': 'Distribution:   FILE-COPY',\n","  'label': None},\n"," {'fid': '1021', 'idx': 323, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1021',\n","  'idx': 333,\n","  'content': 'Curettings - grade 1 endometrioid adenoca.',\n","  'label': None},\n"," {'fid': '1021', 'idx': 377, 'content': 'TLH/BSO.', 'label': None},\n"," {'fid': '1021',\n","  'idx': 386,\n","  'content': 'Mismatch repair Immunohistochemistry please.',\n","  'label': None},\n"," {'fid': '1021', 'idx': 432, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1021',\n","  'idx': 445,\n","  'content': 'Specimen labelled \"Bilateral tubesand ovaries, uterus, cervix\", consists of a uterus with attached cervix, bilateral fallopian tubes and ovaries weighing 98g in total.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 614,\n","  'content': 'The uterus measures 80 x 60 x 35mm and has a smooth shiny serosal surface.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 690,\n","  'content': 'The ectocervix measures 36 x 34mm and has an unremarkable surface.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 758,\n","  'content': 'On section, the endometrium is less than 1mm in maximum thickness.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 826,\n","  'content': 'The myometrium is 12mm in maximum thickness.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 872,\n","  'content': 'The myometrium contains two fibroids each 10mm in maximum diameter.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 940,\n","  'content': 'The right fallopian tube measures 50mm in length and 5mm in maximum diameter.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 1018,\n","  'content': 'The fimbria is present and appears unremarkable.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 1068,\n","  'content': 'The right ovary measures 30x 15 x 15mm and has an unremarkable cut surface.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 1145,\n","  'content': 'The left fallopian tube measures 40mm in length and 5mm in maximum diameter.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 1222,\n","  'content': 'The left ovary measures 35 x 15 x 15mm and has an unremarkable cut surface.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 1298,\n","  'content': 'Blocks 1-3 - one full LS of anterior body and cervix; 4-6 - rest of anterior endomyometrium; 7-9 - one full LS of posterior body and cervix; 10-16 - rest of posterior endomyometrium.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 1481,\n","  'content': '(The endometrium has been AE); 17 - right parametrial tissue; 18 -left parametrial tissue; 19 - right fimbria and fallopian tube; 20 - right ovary, representative sections; 21 - left fallopian tube and fimbria; 22 - left ovary.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 1709,\n","  'content': '(TO: HC: MM/ec   30.5.64)',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 1736,\n","  'content': 'MICROSCOPIC: (Reported by Dr T Devotie)',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 1777,\n","  'content': 'The sections show foci of residual endometrioid adenocarcinoma FIGO grade 1 (slide 13 and 14) invading 1 mm in a myometrium 10mm thick.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 1913,\n","  'content': 'No lymphovascular invasion is seen.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 1949,\n","  'content': 'The uninvolved endometrium shows areas of simple hyperplasia without atypia.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 2027,\n","  'content': 'The uterus also shows intramural leiomyomata with no atypical features and areas of adenomyosis (slide 16).',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 2136,\n","  'content': 'The tumour does not involve the parametria, cervix, fallopian tubes or ovaries.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 2217,\n","  'content': 'No fallopian tube dysplasia is seen.',\n","  'label': None},\n"," {'fid': '1021', 'idx': 2255, 'content': 'CONCLUSION', 'label': None},\n"," {'fid': '1021',\n","  'idx': 2266,\n","  'content': 'Uterus, ovaries and fallopian tubes: Endometrioid adenocarcinoma FIGO grade 1.',\n","  'label': None},\n"," {'fid': '1021', 'idx': 2345, 'content': 'COMMENT', 'label': None},\n"," {'fid': '1021',\n","  'idx': 2353,\n","  'content': 'Immunohistochemistry for mismatch repair proteins has been requested on the previous specimen 79Z04856 (endometrial curettings, 5.7.64) and a supplementary report will be added to this report when the stains are available.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 2577,\n","  'content': 'SUPPLEMENTARY REPORT (6.3.64)',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 2608,\n","  'content': 'Immunoperoxidase stains were done on block 1, 79Z04856.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 2664,\n","  'content': 'Mismatch Repair Deficiency (MMRD) Status',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 2706,\n","  'content': 'MLH1  Loss of nuclear staining in tumour cells',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 2753,\n","  'content': 'PMS2  Loss of nuclear staining in tumour cells',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 2800,\n","  'content': 'MSH2  Preserved nuclear staining in tumour cells',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 2849,\n","  'content': 'MSH6  Preserved nuclear staining in tumour cells',\n","  'label': None},\n"," {'fid': '1021', 'idx': 2898, 'content': 'Comment:', 'label': None},\n"," {'fid': '1021',\n","  'idx': 2907,\n","  'content': 'Absence (loss) of nuclear staining for any of the mismatch repair enzymes MLH1, PMS2, MSH2 or MSH6 is associated with microsatellite instability phenotype (MSI), and may reflect the presence of a germline mutation or somatic inactivation of that mismatch repair gene.',\n","  'label': None},\n"," {'fid': '1021',\n","  'idx': 3175,\n","  'content': 'Preserved nuclear staining of a carcinoma for MLH1, PMS2, MSH2 and MSH6 indicates a low likelihood of microsatellite instability phenotype.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 0,\n","  'content': 'Episode No:  37W069527D',\n","  'label': None},\n"," {'fid': '1022', 'idx': 24, 'content': '3780695.GSD', 'label': None},\n"," {'fid': '1022',\n","  'idx': 37,\n","  'content': 'Lorenzana, MEG Lyndsay',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 61,\n","  'content': 'Lab No:  37W06952,37W06952',\n","  'label': None},\n"," {'fid': '1022', 'idx': 88, 'content': 'Alta Verde', 'label': None},\n"," {'fid': '1022',\n","  'idx': 99,\n","  'content': 'MOSS VALE  Northern Territory  2803',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 135,\n","  'content': 'Specimen: Washings,Tissue',\n","  'label': None},\n"," {'fid': '1022', 'idx': 161, 'content': 'D.O.B:  8/3/2004', 'label': None},\n"," {'fid': '1022', 'idx': 178, 'content': 'Sex:  F', 'label': None},\n"," {'fid': '1022',\n","  'idx': 186,\n","  'content': 'Collected: 9/10/2063 at :',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 212,\n","  'content': 'Location:  UROLOGY OPD - COLLIE DISTRICT HOSPITAL',\n","  'label': None},\n"," {'fid': '1022', 'idx': 262, 'content': 'DR Jett Omer Syed', 'label': None},\n"," {'fid': '1022',\n","  'idx': 280,\n","  'content': 'Distribution:   FILE-COPY,   NSW-CANCER-REGISTRY',\n","  'label': None},\n"," {'fid': '1022', 'idx': 329, 'content': 'CLINICAL:', 'label': None},\n"," {'fid': '1022',\n","  'idx': 339,\n","  'content': '64 yr old woman presumed endometrioid cancer through curettings.',\n","  'label': None},\n"," {'fid': '1022', 'idx': 405, 'content': 'ER PR negative.', 'label': None},\n"," {'fid': '1022',\n","  'idx': 422,\n","  'content': 'Intraop frozen section of left common iliac lymph node sent to assist surgical decision making.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 519,\n","  'content': 'Modified radical hysterectomy, bilateral salpingo-oophorectomy, left common iliac nodes.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 609,\n","  'content': 'Pyometra noted at opening uterus intraop.',\n","  'label': None},\n"," {'fid': '1022', 'idx': 653, 'content': 'MACROSCOPIC:', 'label': None},\n"," {'fid': '1022', 'idx': 666, 'content': 'A.', 'label': None},\n"," {'fid': '1022',\n","  'idx': 670,\n","  'content': 'Specimen labelled \"Left common iliac lymph node\" consists of ?three lymph nodes.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 752,\n","  'content': 'Blocks:  1 & 2 - frozen section; 3- remainder of tissue AE.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 814,\n","  'content': 'FROZEN SECTION REPORT:',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 837,\n","  'content': 'Large node contains capsular aggregates of metastaticcarcinoma.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 902,\n","  'content': 'One other smaller node has one or two tiny clusters of suspicious cells.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 977,\n","  'content': 'Phone result to Dr Ference by Dr I Grantier/I Menes at 9.50am on 07.08.13.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 1052,\n","  'content': '.  Specimen labelled \"Uterus, cervix, bilateral tubes and ovaries\" consists of a uterus with attached cervix, bilateral fallopian tubes and ovaries weighing 115g.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 1216,\n","  'content': 'The uterus measures 85 x 50 x 25mm and has a smooth shiny serosal surface.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 1292,\n","  'content': 'The cervix measures 30 x 30mm and appears unremarkable.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 1349,\n","  'content': 'A slightly roughened cream polypoid area is identified in both the anterior and posterior uterus measuring 25 x 22mm (anteriorly) and 45 x 30mm (posteriorly).',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 1509,\n","  'content': 'Posteriorly there are larger amounts of roughened loose material received in the canal.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 1598,\n","  'content': 'Anteriorly this tumour appears to invade to a maximum depth of 20mm over a total wall thickness 25mm.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 1701,\n","  'content': 'Posteriorly the tumour appears to invade to a maximum depth of 18mm over a wall thickness of 24mm.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 1801,\n","  'content': 'The tumour extensively involves the lower segment and canal.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 1863,\n","  'content': 'The right fallopian tube measures 65mm in length with a maximum external diameter of 7mm.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 1954,\n","  'content': 'The right ovary measures 30 x 14 x 8mm and has an unremarkable cut surface.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 2031,\n","  'content': 'The left tube measures 55mm in length with a maximum external diameter of 6mm.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 2111,\n","  'content': 'The left ovary measures 25 x 14 x 8mm and has an unremarkable cut surface.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 2186,\n","  'content': 'Blocks:  1 to 4 - full longitudinal section of anterior body andcervix; 5 to 8 - full longitudinal section of posterior body and cervix; 9 & 10 - further anterior uterus and cervix at deepest point of invasion; 11 to 13 - further posterior uterus and cervix at deepest point of invasion; 14 - right tube; 15 - right ovary; 16 - left tube; 17 - left ovary; 18 - reserve block.',\n","  'label': None},\n"," {'fid': '1022', 'idx': 2562, 'content': 'C.', 'label': None},\n"," {'fid': '1022',\n","  'idx': 2566,\n","  'content': 'Specimen labelled \"Right common iliac lymph node\" consists of a piece of partly tan and fatty tissue 25mm.',\n","  'label': None},\n"," {'fid': '1022', 'idx': 2674, 'content': 'AE 1 block.', 'label': None},\n"," {'fid': '1022',\n","  'idx': 2687,\n","  'content': '(TO:  RH: WM/mm 10.10.63)',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 2714,\n","  'content': 'MICROSCOPIC:  (Reported by Dr I Ruhmann)',\n","  'label': None},\n"," {'fid': '1022', 'idx': 2756, 'content': 'A.', 'label': None},\n"," {'fid': '1022',\n","  'idx': 2760,\n","  'content': 'One of three lymph nodes shows tiny subcapsular and sinus deposits of metastatic adenocarcinoma.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 2858,\n","  'content': '(These are best seen on the frozen section slide).',\n","  'label': None},\n"," {'fid': '1022', 'idx': 2909, 'content': 'B.', 'label': None},\n"," {'fid': '1022',\n","  'idx': 2913,\n","  'content': 'Sections show a moderately differentiated adenocarcinoma of the endocervix, with a maximum depth of invasion of 20mm through a wall 21mm thick, and a length of 56mm.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 3080,\n","  'content': 'Focal lymphvascular invasion is present.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 3122,\n","  'content': 'There is no associated AIS or CIN.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 3158,\n","  'content': 'Tumour is well clear (>10mm) of the vaginal cuff margin.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 3215,\n","  'content': 'The tumour is strongly and diffusely positive for p16, focally positive for CEA, negative for Vimentin and PR, and focally weakly positive for ER.',\n","  'label': None},\n"," {'fid': '1022', 'idx': 3364, 'content': 'C.', 'label': None},\n"," {'fid': '1022',\n","  'idx': 3368,\n","  'content': 'Two lymph nodes show no evidence of malignancy.',\n","  'label': None},\n"," {'fid': '1022', 'idx': 3416, 'content': 'DIAGNOSIS:', 'label': None},\n"," {'fid': '1022',\n","  'idx': 3427,\n","  'content': 'Moderately differentiated adenocarcinoma of the endocervix, depth 20mm through a wall 21mm thick, length 56mm.',\n","  'label': None},\n"," {'fid': '1022',\n","  'idx': 3539,\n","  'content': 'One of five (1 of 5) lymph nodes shows metastatic adenocarcinoma.',\n","  'label': None},\n"," {'fid': '1023',\n","  'idx': 1,\n","  'content': 'Episode No:  32A841134C',\n","  'label': None},\n"," {'fid': '1023', 'idx': 25, 'content': '3208411.IKC', 'label': None},\n"," {'fid': '1023', 'idx': 38, 'content': 'Garthwaite, CRISTA', 'label': None},\n"," {'fid': '1023',\n","  'idx': 58,\n","  'content': 'Lab No:  32A84113,32A84113',\n","  'label': None},\n"," {'fid': '1023', 'idx': 85, 'content': 'Parkhall', 'label': None},\n"," {'fid': '1023',\n","  'idx': 94,\n","  'content': 'BLI BLI  South Australia  4627',\n","  'label': None},\n"," {'fid': '1023',\n","  'idx': 125,\n","  'content': 'Specimen: Washings,Tissue',\n","  'label': None},\n"," {'fid': '1023', 'idx': 151, 'content': 'D.O.B:  6/3/2008', 'label': None},\n"," {'fid': '1023', 'idx': 168, 'content': 'Sex:  F', 'label': None},\n"," {'fid': '1023',\n","  'idx': 176,\n","  'content': 'Collected: 29/05/2013 at 10:37',\n","  'label': None},\n"," ...]"]},"metadata":{},"execution_count":20}],"source":["from datasets import load_dataset, Features, Value\n","valid_data = load_dataset(\"csv\", data_files=\"/content/drive/MyDrive/aicup/PublicDataset_phase3/opendid_valid.tsv\", delimiter='\\t',\n","                          features = Features({\n","                              'fid': Value('string'), 'idx': Value('int64'),\n","                              'content': Value('string'), 'label': Value('string')}),\n","                              column_names=['fid', 'idx', 'content', 'label'])\n","valid_list= list(valid_data['train'])\n","valid_list"]},{"cell_type":"code","execution_count":21,"metadata":{"colab":{"base_uri":"https://localhost:8080/","height":49,"referenced_widgets":["3d450ea6eb8d49b59a0d5b2c1b025e25","fabe34ce64ed490aab74a9534ebfe31c","e37af785ab634191b95be459d7fcfc57","7e6f8142981040ac83bcc255ae477c99","7428016c330146aa9d46a69bb8444a21","371e4dd4aeee4b0fbf1c3d003def28d2","e2518507acc24b3a8c185c465ceb1026","7232cdf9c6434b7ba2b9bf43c2db46ac","182c407ffd964adf9d3a8721a5f23cb6","06551747ee1b43e0836573d3ba87dad5","7981a0b9a00d40baac289978d8eddc20"]},"id":"uujx76DJ34qi","outputId":"f8c7f50a-cc3c-441b-917e-1b47338505f9","executionInfo":{"status":"ok","timestamp":1698892862604,"user_tz":-480,"elapsed":703166,"user":{"displayName":"Ovien Lee","userId":"03762575040929066529"}}},"outputs":[{"output_type":"display_data","data":{"text/plain":["  0%|          | 0/1387 [00:00<?, 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