Add tutorial and README badges #18
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matanninio
reviewed
Nov 13, 2024
| "1. Data Module - A Lightning data module class where we load and process the data for the task.\n", | ||
| "2. `data_preprocessing()` function. Which responsible for formatting the input prompt.\n", | ||
| "3. `process_model_output()` function. Which takes the raw output of the model and translate it into a human-level answers." | ||
| "## The big picture\n", |
There was a problem hiding this comment.
"The Big Picture" is typically with capital B and P
see https://www.merriam-webster.com/dictionary/big%20picture
matanninio
reviewed
Nov 13, 2024
matanninio
reviewed
Nov 13, 2024
| "## The big picture\n", | ||
| "In order to implement a downstream task for the MAMMAL framework, one should implement a `MammalTask` class instance ([source](https://github.com/BiomedSciAI/biomed-multi-alignment/blob/e56a03e0e9f69e42f919a96def739b78e50a47e5/mammal/task.py#L15)). A `MammalTask` class consists of three main components:\n", | ||
| "1. Data Module - A Lightning data module (`LightningDataModule`) where we load and process the data of the task.\n", | ||
| "2. `data_preprocessing()` method. Which responsible for formatting the input prompt to the model's expected format.\n", |
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Should mention that the data processing should include translating known entities to the lexicon/standard the model was trained with.
mosheraboh
reviewed
Nov 21, 2024
| @@ -412,7 +413,12 @@ | |||
| { | |||
| "name": "stdout", | |||
| "output_type": "stream", | |||
| "text": [] | |||
| "text": [ | |||
| "The OrderedVocab you are attempting to save contains holes for indices [314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500], your vocabulary could be corrupted !\n", | |||
mosheraboh
reviewed
Nov 21, 2024
| "name": "stderr", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "\n", |
mosheraboh
reviewed
Nov 21, 2024
| "name": "stderr", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "/dccstor/mm_hcls/usr/sagi/envs/mammal_env/lib/python3.10/site-packages/pytorch_lightning/trainer/connectors/data_connector.py:424: The 'val_dataloader' does not have many workers which may be a bottleneck. Consider increasing the value of the `num_workers` argument` to `num_workers=15` in the `DataLoader` to improve performance.\n", |
mosheraboh
reviewed
Nov 21, 2024
| "evalue": "name 'exit' is not defined", | ||
| "output_type": "error", | ||
| "traceback": [ | ||
| "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", |
mosheraboh
approved these changes
Nov 21, 2024
added 2 commits
November 24, 2024 00:32
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