--- license: mit base_model: facebook/esm2_t6_8M_UR50D tags: - generated_from_trainer metrics: - precision - recall library_name: peft model-index: - name: esm_ft_Aerin_Yang_et_al_2023 results: [] --- # esm_ft_Aerin_Yang_et_al_2023 This model is a fine-tuned version of [facebook/esm2_t6_8M_UR50D](https://huggingface.co/facebook/esm2_t6_8M_UR50D) on an unknown dataset. It achieves the following results on the evaluation set: - Loss: 39.8878 - Rmse: 21.3236 - Mae: 15.1765 - Spearmanr Corr: 0.8348 - Spearmanr Corr P Value: 0.0000 - Pearsonr Corr: 0.9129 - Pearsonr Corr P Value: 0.0000 - Spearmanr Corr Of Deltas: 0.8678 - Spearmanr Corr Of Deltas P Value: 0.0 - Pearsonr Corr Of Deltas: 0.9127 - Pearsonr Corr Of Deltas P Value: 0.0 - Ranking F1 Score: 0.7761 - Ranking Mcc: 0.6138 - Rmse Enriched: 7.2500 - Mae Enriched: 2.0039 - Spearmanr Corr Enriched: 0.4481 - Spearmanr Corr Enriched P Value: 0.0000 - Pearsonr Corr Enriched: 0.0056 - Pearsonr Corr Enriched P Value: 0.9162 - Spearmanr Corr Of Deltas Enriched: 0.4078 - Spearmanr Corr Of Deltas Enriched P Value: 0.0 - Pearsonr Corr Of Deltas Enriched: 0.0084 - Pearsonr Corr Of Deltas Enriched P Value: 0.0336 - Ranking F1 Score Enriched: 0.6296 - Ranking Mcc Enriched: 0.3165 - Classification Thresh: 0.2 - Mcc: 0.8780 - F1 Score: 0.9418 - Acc: 0.9388 - Auc: 0.9743 - Precision: 0.9381 - Recall: 0.9399 ## Model description More information needed ## Intended uses & limitations More information needed ## Training and evaluation data More information needed ## Training procedure ### Training hyperparameters The following hyperparameters were used during training: - learning_rate: 0.0001 - train_batch_size: 8 - eval_batch_size: 8 - seed: 42 - distributed_type: not_parallel - optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08 - lr_scheduler_type: linear - lr_scheduler_warmup_steps: 200 - num_epochs: 100 - mixed_precision_training: Native AMP ### Training results | Training Loss | Epoch | Step | Validation Loss | Rmse | Mae | Spearmanr Corr | Spearmanr Corr P Value | Pearsonr Corr | Pearsonr Corr P Value | Spearmanr Corr Of Deltas | Spearmanr Corr Of Deltas P Value | Pearsonr Corr Of Deltas | Pearsonr Corr Of Deltas P Value | Ranking F1 Score | Ranking Mcc | Rmse Enriched | Mae Enriched | Spearmanr Corr Enriched | Spearmanr Corr Enriched P Value | Pearsonr Corr Enriched | Pearsonr Corr Enriched P Value | Spearmanr Corr Of Deltas Enriched | Spearmanr Corr Of Deltas Enriched P Value | Pearsonr Corr Of Deltas Enriched | Pearsonr Corr Of Deltas Enriched P Value | Ranking F1 Score Enriched | Ranking Mcc Enriched | Classification Thresh | Mcc | F1 Score | Acc | Auc | Precision | Recall | |:-------------:|:-----:|:-----:|:---------------:|:-------:|:-------:|:--------------:|:----------------------:|:-------------:|:---------------------:|:------------------------:|:--------------------------------:|:-----------------------:|:-------------------------------:|:----------------:|:-----------:|:-------------:|:------------:|:-----------------------:|:-------------------------------:|:----------------------:|:------------------------------:|:---------------------------------:|:-----------------------------------------:|:--------------------------------:|:----------------------------------------:|:-------------------------:|:--------------------:|:---------------------:|:------:|:--------:|:------:|:------:|:---------:|:------:| | 322.4036 | 1.0 | 335 | 170.5273 | 17.7771 | 14.4453 | 0.8087 | 0.0000 | 0.8469 | 0.0000 | 0.8254 | 0.0 | 0.8463 | 0.0 | 0.7495 | 0.5639 | 3.7796 | 2.1388 | 0.4247 | 0.0000 | 0.0251 | 0.6349 | 0.3748 | 0.0 | 0.0269 | 0.0000 | 0.6053 | 0.2814 | 0.1 | 0.8217 | 0.9112 | 0.9090 | 0.9586 | 0.9099 | 0.9118 | | 178.9624 | 2.0 | 670 | 83.5034 | 19.1493 | 14.9378 | 0.8161 | 0.0000 | 0.8602 | 0.0000 | 0.8319 | 0.0 | 0.8596 | 0.0 | 0.7638 | 0.5910 | 5.0134 | 1.7113 | 0.3799 | 0.0000 | 0.0109 | 0.8362 | 0.3223 | 0.0 | 0.0134 | 0.0007 | 0.5917 | 0.2544 | 0.4 | 0.8290 | 0.9207 | 0.9149 | 0.9653 | 0.9148 | 0.9142 | | 58.7267 | 3.0 | 1005 | 49.3526 | 20.8551 | 15.1712 | 0.8377 | 0.0000 | 0.8896 | 0.0000 | 0.8579 | 0.0 | 0.8891 | 0.0 | 0.7757 | 0.6129 | 6.3592 | 1.8552 | 0.4710 | 0.0000 | 0.0074 | 0.8887 | 0.3851 | 0.0 | 0.0101 | 0.0102 | 0.6338 | 0.3245 | 0.1 | 0.8740 | 0.9415 | 0.9373 | 0.9731 | 0.9370 | 0.9370 | | 57.3836 | 4.0 | 1340 | 69.0669 | 21.2627 | 15.0576 | 0.8435 | 0.0000 | 0.8493 | 0.0000 | 0.8530 | 0.0 | 0.8486 | 0.0 | 0.7778 | 0.6168 | 6.3047 | 1.4575 | 0.5105 | 0.0000 | 0.0024 | 0.9645 | 0.4457 | 0.0 | 0.0060 | 0.1309 | 0.6426 | 0.3456 | 0.2 | 0.8333 | 0.9245 | 0.9164 | 0.9723 | 0.9199 | 0.9134 | | 53.7883 | 5.0 | 1675 | 48.1886 | 21.1480 | 15.1387 | 0.8430 | 0.0000 | 0.8926 | 0.0000 | 0.8660 | 0.0 | 0.8921 | 0.0 | 0.7684 | 0.5996 | 7.0220 | 2.0070 | 0.5321 | 0.0000 | 0.0029 | 0.9567 | 0.4401 | 0.0 | 0.0043 | 0.2758 | 0.6507 | 0.3607 | 0.01 | 0.8780 | 0.9418 | 0.9388 | 0.9722 | 0.9381 | 0.9399 | | 52.5999 | 6.0 | 2010 | 44.7967 | 21.3116 | 15.1609 | 0.8499 | 0.0000 | 0.9016 | 0.0000 | 0.8730 | 0.0 | 0.9012 | 0.0 | 0.7816 | 0.6240 | 7.0418 | 1.9243 | 0.5035 | 0.0000 | 0.0034 | 0.9486 | 0.4141 | 0.0 | 0.0058 | 0.1402 | 0.6416 | 0.3463 | 0.2 | 0.8744 | 0.9408 | 0.9373 | 0.9791 | 0.9366 | 0.9378 | | 52.4754 | 7.0 | 2345 | 59.0400 | 21.3311 | 15.1190 | 0.8520 | 0.0000 | 0.8710 | 0.0000 | 0.8642 | 0.0 | 0.8704 | 0.0 | 0.7872 | 0.6342 | 6.4355 | 1.4927 | 0.5187 | 0.0000 | 0.0026 | 0.9606 | 0.4698 | 0.0 | 0.0061 | 0.1250 | 0.6543 | 0.3692 | 0.4 | 0.8624 | 0.9370 | 0.9313 | 0.9726 | 0.9328 | 0.9296 | | 53.8573 | 8.0 | 2680 | 48.6266 | 21.2723 | 15.1655 | 0.7704 | 0.0000 | 0.8929 | 0.0000 | 0.8107 | 0.0 | 0.8925 | 0.0 | 0.7350 | 0.5378 | 7.1861 | 2.1439 | 0.0958 | 0.0699 | 0.0012 | 0.9826 | 0.1100 | 0.0000 | 0.0056 | 0.1558 | 0.4920 | 0.0671 | 0.01 | 0.8831 | 0.9455 | 0.9418 | 0.9676 | 0.9413 | 0.9418 | | 50.3365 | 9.0 | 3015 | 60.9515 | 21.3035 | 15.0752 | 0.8176 | 0.0000 | 0.8665 | 0.0000 | 0.8370 | 0.0 | 0.8659 | 0.0 | 0.7697 | 0.6018 | 6.4208 | 1.4898 | 0.5091 | 0.0000 | 0.0026 | 0.9613 | 0.4736 | 0.0 | 0.0061 | 0.1240 | 0.6481 | 0.3526 | 0.4 | 0.8478 | 0.9306 | 0.9239 | 0.9506 | 0.9263 | 0.9216 | | 56.4606 | 10.0 | 3350 | 47.2109 | 21.1671 | 15.1503 | 0.8581 | 0.0000 | 0.8950 | 0.0000 | 0.8755 | 0.0 | 0.8946 | 0.0 | 0.7921 | 0.6432 | 6.6823 | 2.0974 | 0.5587 | 0.0000 | 0.0040 | 0.9394 | 0.4914 | 0.0 | 0.0084 | 0.0328 | 0.6700 | 0.3979 | 0.2 | 0.8800 | 0.9443 | 0.9403 | 0.9760 | 0.9400 | 0.9400 | | 47.2891 | 11.0 | 3685 | 42.9350 | 21.4256 | 15.2179 | 0.8551 | 0.0000 | 0.9072 | 0.0000 | 0.8768 | 0.0 | 0.9069 | 0.0 | 0.7944 | 0.6473 | 7.5706 | 2.0721 | 0.5064 | 0.0000 | 0.0021 | 0.9681 | 0.4414 | 0.0 | 0.0059 | 0.1345 | 0.6502 | 0.3568 | 0.2 | 0.8837 | 0.9448 | 0.9418 | 0.9788 | 0.9411 | 0.9427 | | 46.1667 | 12.0 | 4020 | 64.4558 | 21.2132 | 15.0403 | 0.7896 | 0.0000 | 0.8587 | 0.0000 | 0.8116 | 0.0 | 0.8581 | 0.0 | 0.7476 | 0.5604 | 5.7742 | 1.3566 | 0.3547 | 0.0000 | -0.0005 | 0.9932 | 0.3391 | 0.0 | 0.0026 | 0.5119 | 0.5858 | 0.2399 | 0.1 | 0.8486 | 0.9314 | 0.9239 | 0.9542 | 0.9278 | 0.9208 | | 52.2836 | 13.0 | 4355 | 43.7076 | 21.3301 | 15.1676 | 0.8437 | 0.0000 | 0.9041 | 0.0000 | 0.8679 | 0.0 | 0.9038 | 0.0 | 0.7821 | 0.6248 | 7.0591 | 1.8864 | 0.4418 | 0.0000 | 0.0042 | 0.9367 | 0.3915 | 0.0 | 0.0085 | 0.0315 | 0.6212 | 0.3086 | 0.2 | 0.8775 | 0.9422 | 0.9388 | 0.9792 | 0.9381 | 0.9395 | | 49.2196 | 14.0 | 4690 | 44.0100 | 21.3915 | 15.1924 | 0.8669 | 0.0000 | 0.9039 | 0.0000 | 0.8834 | 0.0 | 0.9035 | 0.0 | 0.7951 | 0.6492 | 7.0582 | 1.8005 | 0.5986 | 0.0000 | 0.0035 | 0.9480 | 0.5072 | 0.0 | 0.0087 | 0.0283 | 0.6849 | 0.4232 | 0.2 | 0.8891 | 0.9483 | 0.9448 | 0.9800 | 0.9443 | 0.9448 | | 44.0102 | 15.0 | 5025 | 39.9849 | 21.3490 | 15.1845 | 0.8337 | 0.0000 | 0.9132 | 0.0000 | 0.8677 | 0.0 | 0.9130 | 0.0 | 0.7865 | 0.6328 | 7.2932 | 2.0215 | 0.5070 | 0.0000 | 0.0061 | 0.9079 | 0.4234 | 0.0 | 0.0099 | 0.0121 | 0.6487 | 0.3579 | 0.2 | 0.8814 | 0.9430 | 0.9403 | 0.9633 | 0.9397 | 0.9417 | | 49.9841 | 16.0 | 5360 | 59.4978 | 21.3604 | 15.1175 | 0.8496 | 0.0000 | 0.8705 | 0.0000 | 0.8638 | 0.0 | 0.8700 | 0.0 | 0.7807 | 0.6224 | 6.2476 | 1.4632 | 0.5222 | 0.0000 | 0.0023 | 0.9653 | 0.4646 | 0.0 | 0.0064 | 0.1052 | 0.6518 | 0.3623 | 0.2 | 0.8503 | 0.9317 | 0.9254 | 0.9774 | 0.9268 | 0.9235 | | 48.9333 | 17.0 | 5695 | 46.9142 | 21.2059 | 15.2101 | 0.8260 | 0.0000 | 0.8980 | 0.0000 | 0.8585 | 0.0 | 0.8977 | 0.0 | 0.7676 | 0.5979 | 8.1980 | 2.7610 | 0.3826 | 0.0000 | 0.0047 | 0.9289 | 0.3499 | 0.0 | 0.0078 | 0.0487 | 0.5998 | 0.2721 | 0.2 | 0.8594 | 0.9306 | 0.9284 | 0.9756 | 0.9286 | 0.9308 | | 44.6202 | 18.0 | 6030 | 50.6476 | 21.3743 | 15.1230 | 0.8300 | 0.0000 | 0.8897 | 0.0000 | 0.8506 | 0.0 | 0.8892 | 0.0 | 0.7703 | 0.6029 | 5.9865 | 1.3225 | 0.4918 | 0.0000 | 0.0005 | 0.9918 | 0.4423 | 0.0 | 0.0045 | 0.2561 | 0.6426 | 0.3432 | 0.2 | 0.8744 | 0.9426 | 0.9373 | 0.9672 | 0.9389 | 0.9355 | | 45.736 | 19.0 | 6365 | 42.7219 | 21.3199 | 15.1342 | 0.8487 | 0.0000 | 0.9061 | 0.0000 | 0.8702 | 0.0 | 0.9057 | 0.0 | 0.7740 | 0.6101 | 6.4299 | 1.5214 | 0.5348 | 0.0000 | 0.0030 | 0.9544 | 0.4618 | 0.0 | 0.0075 | 0.0583 | 0.6632 | 0.3820 | 0.2 | 0.8920 | 0.95 | 0.9463 | 0.9753 | 0.9462 | 0.9458 | | 42.4466 | 20.0 | 6700 | 49.4293 | 21.3812 | 15.1290 | 0.8166 | 0.0000 | 0.8920 | 0.0000 | 0.8477 | 0.0 | 0.8917 | 0.0 | 0.7661 | 0.5951 | 6.3871 | 1.4594 | 0.3867 | 0.0000 | 0.0022 | 0.9664 | 0.3756 | 0.0 | 0.0074 | 0.0593 | 0.6053 | 0.2738 | 0.2 | 0.8800 | 0.9449 | 0.9403 | 0.9673 | 0.9409 | 0.9391 | | 44.6269 | 21.0 | 7035 | 51.7803 | 21.3407 | 15.1073 | 0.8373 | 0.0000 | 0.8865 | 0.0000 | 0.8591 | 0.0 | 0.8861 | 0.0 | 0.7778 | 0.6169 | 6.4531 | 1.5002 | 0.5360 | 0.0000 | 0.0028 | 0.9572 | 0.4885 | 0.0 | 0.0075 | 0.0586 | 0.6621 | 0.3817 | 0.2 | 0.8740 | 0.9421 | 0.9373 | 0.9658 | 0.9379 | 0.9361 | | 43.6578 | 22.0 | 7370 | 47.6016 | 21.3924 | 15.2455 | 0.8066 | 0.0000 | 0.8992 | 0.0000 | 0.8468 | 0.0 | 0.8988 | 0.0 | 0.7646 | 0.5927 | 8.7133 | 2.8206 | 0.3334 | 0.0000 | 0.0017 | 0.9750 | 0.3019 | 0.0 | 0.0030 | 0.4492 | 0.5840 | 0.2392 | 0.2 | 0.8636 | 0.9316 | 0.9299 | 0.9650 | 0.9308 | 0.9328 | | 46.4904 | 23.0 | 7705 | 42.1610 | 21.2646 | 15.1456 | 0.8504 | 0.0000 | 0.9070 | 0.0000 | 0.8789 | 0.0 | 0.9067 | 0.0 | 0.7924 | 0.6437 | 6.5963 | 1.8549 | 0.5553 | 0.0000 | 0.0041 | 0.9385 | 0.4936 | 0.0 | 0.0082 | 0.0376 | 0.6659 | 0.3893 | 0.2 | 0.8889 | 0.9487 | 0.9448 | 0.9734 | 0.9448 | 0.9442 | | 39.9749 | 24.0 | 8040 | 39.7221 | 21.3645 | 15.1815 | 0.8412 | 0.0000 | 0.9132 | 0.0000 | 0.8692 | 0.0 | 0.9130 | 0.0 | 0.7797 | 0.6203 | 6.6229 | 1.6823 | 0.5055 | 0.0000 | 0.0031 | 0.9527 | 0.4472 | 0.0 | 0.0072 | 0.0664 | 0.6514 | 0.3619 | 0.2 | 0.8950 | 0.9512 | 0.9478 | 0.9721 | 0.9474 | 0.9476 | | 38.3662 | 25.0 | 8375 | 40.5885 | 21.3899 | 15.1735 | 0.8552 | 0.0000 | 0.9116 | 0.0000 | 0.8772 | 0.0 | 0.9115 | 0.0 | 0.7865 | 0.6331 | 6.9604 | 1.7973 | 0.5424 | 0.0000 | 0.0045 | 0.9326 | 0.4661 | 0.0 | 0.0083 | 0.0355 | 0.6613 | 0.3809 | 0.2 | 0.8834 | 0.9451 | 0.9418 | 0.9780 | 0.9411 | 0.9422 | | 44.2025 | 26.0 | 8710 | 43.1233 | 21.1791 | 15.1035 | 0.8464 | 0.0000 | 0.9042 | 0.0000 | 0.8657 | 0.0 | 0.9039 | 0.0 | 0.7773 | 0.6162 | 6.0269 | 1.4761 | 0.4770 | 0.0000 | 0.0052 | 0.9215 | 0.4639 | 0.0 | 0.0088 | 0.0251 | 0.6389 | 0.3318 | 0.2 | 0.8890 | 0.9485 | 0.9448 | 0.9811 | 0.9446 | 0.9444 | | 39.2364 | 27.0 | 9045 | 41.0239 | 21.3000 | 15.1537 | 0.8521 | 0.0000 | 0.9099 | 0.0000 | 0.8789 | 0.0 | 0.9096 | 0.0 | 0.7881 | 0.6358 | 6.7786 | 1.8539 | 0.5215 | 0.0000 | 0.0047 | 0.9297 | 0.4590 | 0.0 | 0.0081 | 0.0407 | 0.6539 | 0.3687 | 0.2 | 0.8891 | 0.9483 | 0.9448 | 0.9780 | 0.9443 | 0.9448 | | 34.0631 | 28.0 | 9380 | 37.2483 | 21.4183 | 15.1928 | 0.8369 | 0.0000 | 0.9193 | 0.0000 | 0.8707 | 0.0 | 0.9191 | 0.0 | 0.7806 | 0.6220 | 7.0196 | 1.7789 | 0.5115 | 0.0000 | 0.0057 | 0.9140 | 0.4615 | 0.0 | 0.0085 | 0.0321 | 0.6569 | 0.3714 | 0.1 | 0.9013 | 0.9536 | 0.9507 | 0.9666 | 0.9501 | 0.9512 | | 40.0891 | 29.0 | 9715 | 46.0297 | 21.2290 | 15.1126 | 0.8209 | 0.0000 | 0.8981 | 0.0000 | 0.8494 | 0.0 | 0.8977 | 0.0 | 0.7661 | 0.5950 | 6.3359 | 1.5989 | 0.4640 | 0.0000 | 0.0025 | 0.9621 | 0.4145 | 0.0 | 0.0052 | 0.1908 | 0.6328 | 0.3269 | 0.2 | 0.8769 | 0.9433 | 0.9388 | 0.9634 | 0.9390 | 0.9380 | | 32.5745 | 30.0 | 10050 | 60.5604 | 21.1329 | 15.0569 | 0.8462 | 0.0000 | 0.8658 | 0.0000 | 0.8583 | 0.0 | 0.8653 | 0.0 | 0.7811 | 0.6232 | 5.9604 | 1.5502 | 0.5403 | 0.0000 | 0.0008 | 0.9887 | 0.4635 | 0.0 | 0.0048 | 0.2207 | 0.6632 | 0.3848 | 0.2 | 0.8536 | 0.9333 | 0.9269 | 0.9734 | 0.9289 | 0.9247 | | 30.2815 | 31.0 | 10385 | 35.5872 | 21.5131 | 15.2808 | 0.8172 | 0.0000 | 0.9235 | 0.0000 | 0.8543 | 0.0 | 0.9232 | 0.0 | 0.7633 | 0.5901 | 6.9169 | 1.8155 | 0.3620 | 0.0000 | 0.0051 | 0.9238 | 0.3457 | 0.0 | 0.0076 | 0.0534 | 0.5901 | 0.2497 | 0.2 | 0.9013 | 0.9536 | 0.9507 | 0.9703 | 0.9501 | 0.9512 | | 36.0448 | 32.0 | 10720 | 42.6942 | 21.3322 | 15.1173 | 0.8447 | 0.0000 | 0.9063 | 0.0000 | 0.8705 | 0.0 | 0.9059 | 0.0 | 0.7788 | 0.6189 | 5.9659 | 1.3238 | 0.5151 | 0.0000 | 0.0006 | 0.9911 | 0.4581 | 0.0 | 0.0016 | 0.6793 | 0.6536 | 0.3628 | 0.2 | 0.8980 | 0.9530 | 0.9493 | 0.9732 | 0.9497 | 0.9483 | | 34.7347 | 33.0 | 11055 | 39.8878 | 21.3236 | 15.1765 | 0.8348 | 0.0000 | 0.9129 | 0.0000 | 0.8678 | 0.0 | 0.9127 | 0.0 | 0.7761 | 0.6138 | 7.2500 | 2.0039 | 0.4481 | 0.0000 | 0.0056 | 0.9162 | 0.4078 | 0.0 | 0.0084 | 0.0336 | 0.6296 | 0.3165 | 0.2 | 0.8780 | 0.9418 | 0.9388 | 0.9743 | 0.9381 | 0.9399 | ### Framework versions - PEFT 0.13.2 - Transformers 4.41.2 - Pytorch 2.5.1+cu118 - Datasets 3.1.0 - Tokenizers 0.19.1