{
  "topic": {
    "id": 406168,
    "title": "ESM2 final-layer embeddings",
    "authorName": "andreylalaley",
    "commentCount": 5,
    "votes": 47,
    "postDate": "2023-05-01T07:22:19.583000"
  },
  "comments": [
    {
      "id": 2246037,
      "authorName": "Viktor Fairuschin",
      "votes": 4,
      "postDate": "2023-05-04T19:12:30.773000",
      "content": "<p>Great job! I have created a similar <a href=\"https://www.kaggle.com/code/viktorfairuschin/extracting-esm-2-embeddings-from-fasta-files\" target=\"_blank\">notebook</a> that runs on Kaggle. </p>"
    },
    {
      "id": 2351169,
      "authorName": "Lt. Cmdr. Data",
      "votes": 2,
      "postDate": "2023-07-19T21:47:56.127000",
      "content": "<p>Nice! thanks for sharing! these embeddings can take considerable time / compute to create.</p>"
    },
    {
      "id": 2296265,
      "authorName": "Julien Tetar",
      "votes": 2,
      "postDate": "2023-06-11T17:19:49.813000",
      "content": "<p>Thank you for the dataset ! We are still struggling to run our own embedding and this is gold.</p>"
    },
    {
      "id": 2271422,
      "authorName": "Andrés Cardoso Cordero",
      "votes": 2,
      "postDate": "2023-05-23T22:03:57.950000",
      "content": "<p>Hello! First of all, thank you very much for sharing this dataset, it is very helpful for those of us who do not have much computing power.</p>\n<p>I've tried using your embedding <strong><em>esm2_t36_3B</em></strong>, but got a shape error:</p>\n<p><code>test_ids.py</code> has a size of <code>(141865,)</code> while <code>test_embeddings</code>is <code>(142246, 2560)</code>.</p>\n<p>I understand that they should share the number of rows. Any tips to fix this problem?</p>\n<p>All the best!</p>"
    },
    {
      "id": 2276780,
      "authorName": "andreylalaley",
      "votes": 2,
      "postDate": "2023-05-27T07:49:01.317000",
      "content": "<p>Hello! Thank you for your comment, it is my fault during embedings creation. In embeding creation script i initially create zero matrix with needed shape and then redefine rows in loop. I created zero matrix for test with the same shape as the matrix of train. So rows from 141865 to 142246 are all zero and you can freely cut them. I will also make and update with these changes, shortly</p>"
    }
  ],
  "index": {
    "id": "406168",
    "title": "ESM2 final-layer embeddings",
    "authorName": "",
    "commentCount": "5",
    "votes": "47",
    "postDate": "2023-05-01 07:22:19.583000"
  },
  "competition": "cafa-5-protein-function-prediction"
}