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NaturalAntibody
/
nanoBERT

Fill-Mask
Transformers
PyTorch
roberta
biology
Inference Endpoints
Model card Files Community
1
tadsatlawa-na commited on
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  1. nanoBERTExample.ipynb +1544 -43
nanoBERTExample.ipynb CHANGED
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  },
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  {
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  },
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- "Requirement already satisfied: transformers in /usr/local/lib/python3.10/dist-packages (4.34.1)\n",
46
- "Requirement already satisfied: filelock in /usr/local/lib/python3.10/dist-packages (from transformers) (3.12.4)\n",
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- "Requirement already satisfied: huggingface-hub<1.0,>=0.16.4 in /usr/local/lib/python3.10/dist-packages (from transformers) (0.17.3)\n",
48
- "Requirement already satisfied: numpy>=1.17 in /usr/local/lib/python3.10/dist-packages (from transformers) (1.23.5)\n",
 
 
 
 
49
  "Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/dist-packages (from transformers) (23.2)\n",
50
  "Requirement already satisfied: pyyaml>=5.1 in /usr/local/lib/python3.10/dist-packages (from transformers) (6.0.1)\n",
51
  "Requirement already satisfied: regex!=2019.12.17 in /usr/local/lib/python3.10/dist-packages (from transformers) (2023.6.3)\n",
52
  "Requirement already satisfied: requests in /usr/local/lib/python3.10/dist-packages (from transformers) (2.31.0)\n",
53
- "Requirement already satisfied: tokenizers<0.15,>=0.14 in /usr/local/lib/python3.10/dist-packages (from transformers) (0.14.1)\n",
54
- "Requirement already satisfied: safetensors>=0.3.1 in /usr/local/lib/python3.10/dist-packages (from transformers) (0.4.0)\n",
55
- "Requirement already satisfied: tqdm>=4.27 in /usr/local/lib/python3.10/dist-packages (from transformers) (4.66.1)\n",
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- "Requirement already satisfied: fsspec in /usr/local/lib/python3.10/dist-packages (from huggingface-hub<1.0,>=0.16.4->transformers) (2023.6.0)\n",
 
 
 
 
57
  "Requirement already satisfied: typing-extensions>=3.7.4.3 in /usr/local/lib/python3.10/dist-packages (from huggingface-hub<1.0,>=0.16.4->transformers) (4.5.0)\n",
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- "Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/dist-packages (from requests->transformers) (3.3.0)\n",
 
 
 
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  "Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests->transformers) (3.4)\n",
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  "Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests->transformers) (2.0.7)\n",
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- "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests->transformers) (2023.7.22)\n"
 
 
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  ]
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  ],
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  "metadata": {
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  "id": "vG5ndbr_rYjL"
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  },
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- "execution_count": 10,
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  "outputs": []
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  },
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  {
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  "tokenizer = RobertaTokenizer.from_pretrained(\"NaturalAntibody/nanoBERT\", return_tensors=\"pt\")"
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  ],
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  "metadata": {
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- "id": "1GNqH8HlrzmF"
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  },
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- "execution_count": 11,
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- "outputs": []
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  },
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  {
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  "cell_type": "code",
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  "source": [
96
  "# Initialise model\n",
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- "unmasker = pipeline('fill-mask', model=\"tadsatlawa/nanoBERT\", tokenizer=tokenizer, top_k=20 )"
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  ],
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  "metadata": {
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- "id": "3CYcwIOU3xCY"
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  },
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- "execution_count": 12,
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- "outputs": []
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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  },
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  "cell_type": "code",
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  "base_uri": "https://localhost:8080/"
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- "Amino Acid : S, probability = 0.4827525019645691\n",
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- "Amino Acid : Q, probability = 0.0005539602716453373\n",
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- "Amino Acid : P, probability = 0.00032376404851675034\n"
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  "base_uri": "https://localhost:8080/"
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  "id": "gxL4QKeNqYXI",
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  "outputs": [
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  {
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  "output_type": "stream",
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  "name": "stdout",
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  "text": [
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+ "Collecting transformers\n",
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+ " Downloading transformers-4.34.1-py3-none-any.whl (7.7 MB)\n",
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+ "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m7.7/7.7 MB\u001b[0m \u001b[31m46.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
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+ "Collecting tokenizers<0.15,>=0.14 (from transformers)\n",
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+ "\u001b[?25hCollecting safetensors>=0.3.1 (from transformers)\n",
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+ "Requirement already satisfied: fsspec>=2023.5.0 in /usr/local/lib/python3.10/dist-packages (from huggingface-hub<1.0,>=0.16.4->transformers) (2023.6.0)\n",
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+ "\u001b[?25hRequirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/dist-packages (from requests->transformers) (3.3.0)\n",
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  "Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests->transformers) (3.4)\n",
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  "Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests->transformers) (2.0.7)\n",
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+ "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests->transformers) (2023.7.22)\n",
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+ "Installing collected packages: safetensors, huggingface-hub, tokenizers, transformers\n",
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+ "Successfully installed huggingface-hub-0.17.3 safetensors-0.4.0 tokenizers-0.14.1 transformers-4.34.1\n"
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  "metadata": {
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  "id": "vG5ndbr_rYjL"
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  "outputs": []
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  "tokenizer = RobertaTokenizer.from_pretrained(\"NaturalAntibody/nanoBERT\", return_tensors=\"pt\")"
1471
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1472
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+ "Downloading (…)olve/main/merges.txt: 0.00B [00:00, ?B/s]"
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1562
  "cell_type": "code",
1563
  "source": [
1564
  "# Initialise model\n",
1565
+ "unmasker = pipeline('fill-mask', model=\"NaturalAntibody/nanoBERT\", tokenizer=tokenizer, top_k=20 )"
1566
  ],
1567
  "metadata": {
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  },
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+ "execution_count": 4,
1589
+ "outputs": [
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+ {
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+ "output_type": "display_data",
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+ "data": {
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+ "text/plain": [
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+ ],
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+ }
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  },
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  {
1607
  "cell_type": "code",
 
1621
  "base_uri": "https://localhost:8080/"
1622
  },
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  "id": "6rtUxgbYsygY",
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  },
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+ "execution_count": 5,
1627
  "outputs": [
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  {
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  "output_type": "stream",
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  "name": "stdout",
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  "text": [
1632
+ "Amino Acid : T, probability = 0.28031080961227417\n",
1633
+ "Amino Acid : A, probability = 0.23146940767765045\n",
1634
+ "Amino Acid : K, probability = 0.13046956062316895\n",
1635
+ "Amino Acid : N, probability = 0.12727046012878418\n",
1636
+ "Amino Acid : V, probability = 0.06813304871320724\n",
1637
+ "Amino Acid : S, probability = 0.040362704545259476\n",
1638
+ "Amino Acid : R, probability = 0.02661576308310032\n",
1639
+ "Amino Acid : G, probability = 0.02190057747066021\n",
1640
+ "Amino Acid : I, probability = 0.011736654676496983\n",
1641
+ "Amino Acid : H, probability = 0.011689980514347553\n",
1642
+ "Amino Acid : Y, probability = 0.010142817161977291\n",
1643
+ "Amino Acid : E, probability = 0.007347866427153349\n",
1644
+ "Amino Acid : M, probability = 0.0065687913447618484\n",
1645
+ "Amino Acid : L, probability = 0.00589130399748683\n",
1646
+ "Amino Acid : P, probability = 0.0055612483993172646\n",
1647
+ "Amino Acid : Q, probability = 0.004960155114531517\n",
1648
+ "Amino Acid : D, probability = 0.003958782181143761\n",
1649
+ "Amino Acid : F, probability = 0.0026921925600618124\n",
1650
+ "Amino Acid : C, probability = 0.0016993506578728557\n",
1651
+ "Amino Acid : W, probability = 0.0009979679016396403\n"
1652
  ]
1653
  }
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