diff --git a/manuscript_code/model/tpu_model copy/0_README.md b/manuscript_code/model/tpu_model copy/0_README.md deleted file mode 100644 index 661a590..0000000 --- a/manuscript_code/model/tpu_model copy/0_README.md +++ /dev/null @@ -1,9 +0,0 @@ -This directory contains the files needed to train and evaluate the transformer(TPU) model. The notebook explains the corresponding code in detail. - -
1_use_tpu_model_to_generate_results.ipynb
.
-
-
-\n", - " | sequence | \n", - "Measured Expression | \n", - "Predicted Expression | \n", - "
---|---|---|---|
0 | \n", - "NNNNNNNNNNTGCATTTTTTTCACAAGAGCACTTGAAGGGCGCCTA... | \n", - "13.708592 | \n", - "13.144622 | \n", - "
1 | \n", - "NNNTGCATTTTTTTCACACATATACTTGGGTGACTTAGATATTTGC... | \n", - "2.553335 | \n", - "4.590216 | \n", - "
2 | \n", - "NTGCATTTTTTTCACACATCTGGATTGTCTGGTGTGCTGGTATCTT... | \n", - "13.369969 | \n", - "13.149384 | \n", - "
3 | \n", - "NTGCATTTTTTTCACACCACCGTGGGGATTCGCAGCTATGTGCATA... | \n", - "3.328683 | \n", - "5.131679 | \n", - "
4 | \n", - "NNTGCATTTTTTTCACACCATGGATTTAAGAATTAATCACCGGACA... | \n", - "10.466688 | \n", - "11.301416 | \n", - "
... | \n", - "... | \n", - "... | \n", - "... | \n", - "
3326 | \n", - "NNTGCATTTTTTTCACTCTTTCACGTGGGGCCTGCGGGGTATCGGT... | \n", - "14.962475 | \n", - "15.238556 | \n", - "
3327 | \n", - "NNNNNNNNNNNNTGCATTTTTTTCACTGATGTGGTGCGCGTAATTT... | \n", - "11.999880 | \n", - "13.480228 | \n", - "
3328 | \n", - "TGCATTTTTTTCACTTCCAGTAATATGCGAAAGGGTGATGTGAACT... | \n", - "4.541188 | \n", - "6.266724 | \n", - "
3329 | \n", - "NNNNNNNNNNNNNNTGCATTTTTTTCACTTCGCACTCCACTTCTCG... | \n", - "7.456650 | \n", - "11.376089 | \n", - "
3330 | \n", - "NNNTGCATTTTTTTCACTTGCCTGGTACGAACACAGGTATCTTTCG... | \n", - "4.870981 | \n", - "5.851082 | \n", - "
3331 rows × 3 columns
\n", - "\n", - " | sequence | \n", - "Measured Expression | \n", - "Predicted Expression | \n", - "
---|---|---|---|
0 | \n", - "TGCATTTTTTTCACATCAAAAAAAAAAAGAAAAACAAAGAAAAAGG... | \n", - "13.168816 | \n", - "14.333738 | \n", - "
1 | \n", - "TGCATTTTTTTCACATCAAAAAAAAAAAGAAAAAGAAACAAAAAGG... | \n", - "13.457919 | \n", - "14.332550 | \n", - "
2 | \n", - "TGCATTTTTTTCACATCAAAAAAAAAAAGAAAAAGAAAGAAAAAGA... | \n", - "13.855758 | \n", - "14.495706 | \n", - "
3 | \n", - "TGCATTTTTTTCACATCAAAAAAAAAAAGAAAAAGAAAGAAAAAGG... | \n", - "12.043120 | \n", - "13.306715 | \n", - "
4 | \n", - "TGCATTTTTTTCACATCAAAAAAAAAAAGAAAAAGAAAGAAAAAGG... | \n", - "13.529583 | \n", - "14.713246 | \n", - "
... | \n", - "... | \n", - "... | \n", - "... | \n", - "
3924 | \n", - "TGCATTTTTTTCACATCTTTTTTGATGCGCTATCATCCATTATTCT... | \n", - "7.344921 | \n", - "7.655699 | \n", - "
3925 | \n", - "TGCATTTTTTTCACATCTTTTTTGATGCGCTATCATCCATTATTCT... | \n", - "6.589246 | \n", - "5.922864 | \n", - "
3926 | \n", - "TGCATTTTTTTCACATCTTTTTTGATGCGCTATCATCCATTATTCT... | \n", - "7.740563 | \n", - "6.864065 | \n", - "
3927 | \n", - "TGCATTTTTTTCACATCTTTTTTGATGCGCTATCATCCCTTATTCT... | \n", - "7.421802 | \n", - "6.316618 | \n", - "
3928 | \n", - "TGCATTTTTTTCACATCTTTTTTGATGCGCTATCATCCGTTATTCT... | \n", - "8.061410 | \n", - "7.728500 | \n", - "
3929 rows × 3 columns
\n", - "\n", - " | sequence | \n", - "Measured Expression | \n", - "Predicted Expression | \n", - "
---|---|---|---|
0 | \n", - "TGCATTTTTTTCACATCCTTTCAATTGGGTGGGGACGCGACGGCGC... | \n", - "11.278011 | \n", - "12.921628 | \n", - "
1 | \n", - "TGCATTTTTTTCACATCCTTTAAATTCGGTGGGGACGCGTCGGCGC... | \n", - "11.725461 | \n", - "13.208659 | \n", - "
2 | \n", - "TGCATTTTTTTCACATCCTTTCAATTGGGTGGGGACGCGACCGCGC... | \n", - "11.725053 | \n", - "13.091141 | \n", - "
3 | \n", - "TGCATTTTTTTCACATCTTTTCCGTGCAACGGCCTAGAGGACAGTC... | \n", - "9.008385 | \n", - "10.215848 | \n", - "
4 | \n", - "TGCATTTTTTTCACATCTTTTCCGTGCAACGGCCTAGACGACAGTC... | \n", - "10.695459 | \n", - "11.634071 | \n", - "
... | \n", - "... | \n", - "... | \n", - "... | \n", - "
2978 | \n", - "TGCATTTTTTTCACATCTCGCTAGCCGCAGGTATGAATATCGTAAC... | \n", - "12.134682 | \n", - "13.292812 | \n", - "
2979 | \n", - "TGCATTTTTTTCACATCTCGCTAGCCGCAGGTACGAGTATCGTAAC... | \n", - "13.562228 | \n", - "14.617356 | \n", - "
2980 | \n", - "TGCATTTTTTTCACATCGGAACGTTAACATCAATCCGGTCACCACG... | \n", - "10.788450 | \n", - "11.057049 | \n", - "
2981 | \n", - "TGCATTTTTTTCACATCGGAACGTTAATATCCATCCGGTCACCACG... | \n", - "12.423164 | \n", - "13.211720 | \n", - "
2982 | \n", - "TGCATTTTTTTCACATCGGAACGTTAATATCCATCCGGTCACCTCG... | \n", - "12.081855 | \n", - "13.192696 | \n", - "
2983 rows × 3 columns
\n", - "\n", - " | sequence | \n", - "Measured Expression | \n", - "Predicted Expression | \n", - "
---|---|---|---|
0 | \n", - "TGCATTTTTTTCACATCAAAAAAAAAAAAAAAAAAAAAAACTAGCA... | \n", - "11.000000 | \n", - "11.353749 | \n", - "
1 | \n", - "TGCATTTTTTTCACATCAAAAAAAAAAAAAAAAAAAAAAACTAGCA... | \n", - "11.000000 | \n", - "11.353749 | \n", - "
2 | \n", - "TGCATTTTTTTCACATCAAAAAAAAAAAAAAAGAATTCGCGCATTT... | \n", - "14.000000 | \n", - "15.208617 | \n", - "
3 | \n", - "TGCATTTTTTTCACATCAAAAAAAAAAAAAAAGAATTCGCGCATTT... | \n", - "15.000000 | \n", - "15.420066 | \n", - "
4 | \n", - "TGCATTTTTTTCACATCAAAAAAAAAAAAAAAGAATTCGCGCATTT... | \n", - "15.783623 | \n", - "15.327061 | \n", - "
... | \n", - "... | \n", - "... | \n", - "... | \n", - "
10317 | \n", - "TGCATTTTTTTCACATCTTTTTTTTCTTCGTACATAGTGACGGGAC... | \n", - "15.644227 | \n", - "15.528503 | \n", - "
10318 | \n", - "TGCATTTTTTTCACATCTTTTTTTTCTTCGTACATAGTGACGGGAC... | \n", - "14.604007 | \n", - "15.545308 | \n", - "
10319 | \n", - "TGCATTTTTTTCACATCTTTTTTTTCTTCGTACATAGTGACGGGAC... | \n", - "14.581721 | \n", - "15.556981 | \n", - "
10320 | \n", - "TGCATTTTTTTCACATCTTTTTTTTCTTCGTACATAGTGACGGGAC... | \n", - "13.727267 | \n", - "15.543314 | \n", - "
10321 | \n", - "TGCATTTTTTTCACATCTTTTTTTTCTTCGTACATAGTGACGGGAC... | \n", - "15.000000 | \n", - "15.557623 | \n", - "
10322 rows × 3 columns
\n", - "\n", - " | sequence | \n", - "Measured Expression | \n", - "Predicted Expression | \n", - "
---|---|---|---|
0 | \n", - "TGCATTTTTTTCACATCAAAAGGCTATTTGATATGTTAAAAGAAGG... | \n", - "1.244706 | \n", - "4.143212 | \n", - "
1 | \n", - "TGCATTTTTTTCACATCAAACAATCTCTTGATGTGTCAGAAATAAG... | \n", - "0.980188 | \n", - "4.331097 | \n", - "
2 | \n", - "TGCATTTTTTTCACATCAAACAATGGGTTGTCATCTTCTAAGATAG... | \n", - "2.764484 | \n", - "4.326525 | \n", - "
3 | \n", - "TGCATTTTTTTCACATCAAACTATTGTTAGATGTCAAATGAACTAC... | \n", - "1.414264 | \n", - "4.208059 | \n", - "
4 | \n", - "TGCATTTTTTTCACATCAAACTCTATCATTTCTGCAGAGGTTGCAA... | \n", - "2.241734 | \n", - "4.199040 | \n", - "
... | \n", - "... | \n", - "... | \n", - "... | \n", - "
977 | \n", - "TGCATTTTTTTCACATCTTTTGATATAACCTGGTCGAATATACTAT... | \n", - "3.232783 | \n", - "4.162705 | \n", - "
978 | \n", - "TGCATTTTTTTCACATCTTTTGCAACTATTTCACCAAATGGTATCC... | \n", - "3.432195 | \n", - "4.147635 | \n", - "
979 | \n", - "TGCATTTTTTTCACATCTTTTGTAATAGTAGATGTCAATGGGATAG... | \n", - "3.305018 | \n", - "4.145849 | \n", - "
980 | \n", - "TGCATTTTTTTCACATCTTTTTCCGGGTGACGGCGCGACTTTGTGC... | \n", - "15.260873 | \n", - "15.632592 | \n", - "
981 | \n", - "TGCATTTTTTTCACATCTTTTTTTGTCGCCGCGTGGGTTTTTGACT... | \n", - "15.430414 | \n", - "15.770001 | \n", - "
982 rows × 3 columns
\n", - "