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  1. .config/.last_opt_in_prompt.yaml +1 -0
  2. .config/.last_survey_prompt.yaml +1 -0
  3. .config/.last_update_check.json +1 -0
  4. .config/active_config +1 -0
  5. .config/config_sentinel +0 -0
  6. .config/configurations/config_default +6 -0
  7. .config/default_configs.db +0 -0
  8. .config/gce +1 -0
  9. .config/hidden_gcloud_config_universe_descriptor_data_cache_configs.db +0 -0
  10. .config/logs/2025.09.30/13.38.09.630053.log +765 -0
  11. .config/logs/2025.09.30/13.38.30.649987.log +5 -0
  12. .config/logs/2025.09.30/13.38.39.322666.log +153 -0
  13. .config/logs/2025.09.30/13.38.40.558814.log +5 -0
  14. .config/logs/2025.09.30/13.38.49.447390.log +8 -0
  15. .config/logs/2025.09.30/13.38.50.203542.log +8 -0
  16. .gitattributes +2 -0
  17. .gradio/certificate.pem +31 -0
  18. README.md +12 -12
  19. app.py +229 -0
  20. requirements.txt +7 -0
  21. sample_data/README.md +19 -0
  22. sample_data/anscombe.json +49 -0
  23. sample_data/california_housing_test.csv +0 -0
  24. sample_data/california_housing_train.csv +0 -0
  25. sample_data/mnist_test.csv +3 -0
  26. sample_data/mnist_train_small.csv +3 -0
  27. structure (1).svg +1 -0
  28. structure (2).svg +1 -0
  29. structure (3).svg +939 -0
  30. structure (3.1).svg +939 -0
  31. structure (4).svg +1237 -0
  32. structure (5).svg +1 -0
  33. structure (6).svg +867 -0
  34. structure (6.1).svg +779 -0
  35. structure (7).svg +1 -0
  36. structure (8).svg +0 -0
  37. structure (9).svg +0 -0
  38. structure.svg +1 -0
.config/.last_opt_in_prompt.yaml ADDED
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.config/.last_update_check.json ADDED
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+ {"last_update_check_time": 1759239520.040413, "last_update_check_revision": 20250929142209, "notifications": [], "last_nag_times": {}}
.config/active_config ADDED
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.config/configurations/config_default ADDED
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.config/default_configs.db ADDED
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481
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521
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525
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526
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527
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528
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529
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530
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531
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532
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533
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534
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535
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536
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537
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538
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539
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540
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541
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542
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543
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544
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545
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546
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547
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548
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549
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550
+ 2025-09-30 13:38:23,545 INFO ___FILE_ONLY___ ╝
551
+
552
+ 2025-09-30 13:38:23,553 INFO ___FILE_ONLY___ ╔════════════════════════════════════════════════════════════╗
553
+
554
+ 2025-09-30 13:38:23,553 INFO ___FILE_ONLY___ ╠═ Installing: BigQuery Command Line Tool (Platform Spec... ═╣
555
+
556
+ 2025-09-30 13:38:23,553 INFO ___FILE_ONLY___ ╚
557
+ 2025-09-30 13:38:23,554 INFO ___FILE_ONLY___ ════════════════════════════════════════════════════════════
558
+ 2025-09-30 13:38:23,554 INFO ___FILE_ONLY___ ╝
559
+
560
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561
+
562
+ 2025-09-30 13:38:23,559 INFO ___FILE_ONLY___ ╠═ Installing: Bundled Python 3.12 ═╣
563
+
564
+ 2025-09-30 13:38:23,559 INFO ___FILE_ONLY___ ╚
565
+ 2025-09-30 13:38:23,561 INFO ___FILE_ONLY___ ════════════════════════════════════════════════════════════
566
+ 2025-09-30 13:38:23,561 INFO ___FILE_ONLY___ ╝
567
+
568
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569
+
570
+ 2025-09-30 13:38:23,563 INFO ___FILE_ONLY___ ╠═ Installing: Bundled Python 3.12 (Platform Specific) ═╣
571
+
572
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573
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574
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575
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576
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577
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578
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579
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580
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582
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583
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585
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586
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587
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588
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589
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590
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591
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592
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593
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594
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595
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598
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599
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600
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601
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602
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603
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604
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605
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606
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607
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608
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609
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610
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611
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612
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613
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614
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615
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616
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617
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618
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619
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620
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621
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622
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623
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624
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625
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626
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627
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628
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629
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630
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631
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632
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633
+ 2025-09-30 13:38:28,595 INFO ___FILE_ONLY___ ╝
634
+
635
+ 2025-09-30 13:38:28,651 INFO ___FILE_ONLY___ ╔════════════════════════════════════════════════════════════╗
636
+
637
+ 2025-09-30 13:38:28,651 INFO ___FILE_ONLY___ ╠═ Installing: Cloud Storage Command Line Tool ═╣
638
+
639
+ 2025-09-30 13:38:28,651 INFO ___FILE_ONLY___ ╚
640
+ 2025-09-30 13:38:29,181 INFO ___FILE_ONLY___ ═
641
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642
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645
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646
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647
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648
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650
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657
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658
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659
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660
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661
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662
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663
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664
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665
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666
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667
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668
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669
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670
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672
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673
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674
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675
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676
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677
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678
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679
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680
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681
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682
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683
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684
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685
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686
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687
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688
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689
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690
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691
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692
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693
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694
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695
+ 2025-09-30 13:38:29,957 INFO ___FILE_ONLY___ ═
696
+ 2025-09-30 13:38:29,974 INFO ___FILE_ONLY___ ═
697
+ 2025-09-30 13:38:29,996 INFO ___FILE_ONLY___ ═
698
+ 2025-09-30 13:38:30,014 INFO ___FILE_ONLY___ ═
699
+ 2025-09-30 13:38:30,032 INFO ___FILE_ONLY___ ═
700
+ 2025-09-30 13:38:30,033 INFO ___FILE_ONLY___ ╝
701
+
702
+ 2025-09-30 13:38:30,064 INFO ___FILE_ONLY___ ╔════════════════════════════════════════════════════════════╗
703
+
704
+ 2025-09-30 13:38:30,064 INFO ___FILE_ONLY___ ╠═ Installing: Cloud Storage Command Line Tool (Platform... ═╣
705
+
706
+ 2025-09-30 13:38:30,064 INFO ___FILE_ONLY___ ╚
707
+ 2025-09-30 13:38:30,065 INFO ___FILE_ONLY___ ════════════════════════════════════════════════════════════
708
+ 2025-09-30 13:38:30,065 INFO ___FILE_ONLY___ ╝
709
+
710
+ 2025-09-30 13:38:30,070 INFO ___FILE_ONLY___ ╔════════════════════════════════════════════════════════════╗
711
+
712
+ 2025-09-30 13:38:30,070 INFO ___FILE_ONLY___ ╠═ Installing: Default set of gcloud commands ═╣
713
+
714
+ 2025-09-30 13:38:30,070 INFO ___FILE_ONLY___ ╚
715
+ 2025-09-30 13:38:30,072 INFO ___FILE_ONLY___ ════════════════════════════════════════════════════════════
716
+ 2025-09-30 13:38:30,072 INFO ___FILE_ONLY___ ╝
717
+
718
+ 2025-09-30 13:38:30,074 INFO ___FILE_ONLY___ ╔════════════════════════════════════════════════════════════╗
719
+
720
+ 2025-09-30 13:38:30,074 INFO ___FILE_ONLY___ ╠═ Installing: Google Cloud CLI Core Libraries (Platform... ═╣
721
+
722
+ 2025-09-30 13:38:30,074 INFO ___FILE_ONLY___ ╚
723
+ 2025-09-30 13:38:30,075 INFO ___FILE_ONLY___ ══════════════════════════════
724
+ 2025-09-30 13:38:30,076 INFO ___FILE_ONLY___ ══════════════════════════════
725
+ 2025-09-30 13:38:30,076 INFO ___FILE_ONLY___ ╝
726
+
727
+ 2025-09-30 13:38:30,080 INFO ___FILE_ONLY___ ╔════════════════════════════════════════════════════════════╗
728
+
729
+ 2025-09-30 13:38:30,080 INFO ___FILE_ONLY___ ╠═ Installing: Google Cloud CRC32C Hash Tool ═╣
730
+
731
+ 2025-09-30 13:38:30,080 INFO ___FILE_ONLY___ ╚
732
+ 2025-09-30 13:38:30,082 INFO ___FILE_ONLY___ ════════════════════════════════════════════════════════════
733
+ 2025-09-30 13:38:30,082 INFO ___FILE_ONLY___ ╝
734
+
735
+ 2025-09-30 13:38:30,084 INFO ___FILE_ONLY___ ╔════════════════════════════════════════════════════════════╗
736
+
737
+ 2025-09-30 13:38:30,084 INFO ___FILE_ONLY___ ╠═ Installing: Google Cloud CRC32C Hash Tool (Platform S... ═╣
738
+
739
+ 2025-09-30 13:38:30,084 INFO ___FILE_ONLY___ ╚
740
+ 2025-09-30 13:38:30,121 INFO ___FILE_ONLY___ ══════════════════════════════
741
+ 2025-09-30 13:38:30,122 INFO ___FILE_ONLY___ ══════════════════════════════
742
+ 2025-09-30 13:38:30,122 INFO ___FILE_ONLY___ ╝
743
+
744
+ 2025-09-30 13:38:30,126 INFO ___FILE_ONLY___ ╔════════════════════════════════════════════════════════════╗
745
+
746
+ 2025-09-30 13:38:30,127 INFO ___FILE_ONLY___ ╠═ Installing: gcloud cli dependencies (Platform Specific) ═╣
747
+
748
+ 2025-09-30 13:38:30,127 INFO ___FILE_ONLY___ ╚
749
+ 2025-09-30 13:38:30,127 INFO ___FILE_ONLY___ ════════════════════════════════════════════════════════════
750
+ 2025-09-30 13:38:30,127 INFO ___FILE_ONLY___ ╝
751
+
752
+ 2025-09-30 13:38:30,132 DEBUG root Updating notification cache...
753
+ 2025-09-30 13:38:30,132 INFO ___FILE_ONLY___
754
+
755
+ 2025-09-30 13:38:30,134 INFO ___FILE_ONLY___ Performing post processing steps...
756
+ 2025-09-30 13:38:30,135 DEBUG root Executing command: ['/tools/google-cloud-sdk/bin/gcloud', 'components', 'post-process']
757
+ 2025-09-30 13:38:38,559 DEBUG ___FILE_ONLY___
758
+ 2025-09-30 13:38:38,559 DEBUG ___FILE_ONLY___
759
+ 2025-09-30 13:38:38,675 INFO root descriptor_list: [{'universeDomain': 'googleapis.com', 'universeShortName': '', 'authenticationDomain': 'auth.cloud.google.com', 'projectPrefix': '', 'cloudWebDomain': 'cloud.google.com', 'documentationDomain': 'cloud.google.com', 'version': '1.0.0', 'state': 'primary', 'artifactRegistryDomain': 'pkg.dev'}]
760
+ 2025-09-30 13:38:38,675 INFO ___FILE_ONLY___
761
+ Update done!
762
+
763
+
764
+ 2025-09-30 13:38:38,679 DEBUG root Chosen display Format:none
765
+ 2025-09-30 13:38:38,679 INFO root Display format: "none"
.config/logs/2025.09.30/13.38.30.649987.log ADDED
@@ -0,0 +1,5 @@
 
 
 
 
 
 
1
+ 2025-09-30 13:38:30,650 DEBUG root Loaded Command Group: ['gcloud', 'components']
2
+ 2025-09-30 13:38:30,652 DEBUG root Loaded Command Group: ['gcloud', 'components', 'post_process']
3
+ 2025-09-30 13:38:30,654 DEBUG root Running [gcloud.components.post-process] with arguments: []
4
+ 2025-09-30 13:38:38,452 DEBUG root Chosen display Format:none
5
+ 2025-09-30 13:38:38,452 INFO root Display format: "none"
.config/logs/2025.09.30/13.38.39.322666.log ADDED
@@ -0,0 +1,153 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 2025-09-30 13:38:39,323 DEBUG root Loaded Command Group: ['gcloud', 'components']
2
+ 2025-09-30 13:38:39,354 DEBUG root Loaded Command Group: ['gcloud', 'components', 'update']
3
+ 2025-09-30 13:38:39,357 DEBUG root Running [gcloud.components.update] with arguments: [--quiet: "True", COMPONENT-IDS:8: "['gcloud', 'core', 'bq', 'gsutil', 'compute', 'preview', 'alpha', 'beta']"]
4
+ 2025-09-30 13:38:39,358 INFO ___FILE_ONLY___ Beginning update. This process may take several minutes.
5
+
6
+ 2025-09-30 13:38:39,366 DEBUG urllib3.connectionpool Starting new HTTPS connection (1): dl.google.com:443
7
+ 2025-09-30 13:38:39,384 DEBUG urllib3.connectionpool https://dl.google.com:443 "GET /dl/cloudsdk/channels/rapid/components-2.json HTTP/11" 200 233157
8
+ 2025-09-30 13:38:39,395 WARNING root Component [compute] no longer exists.
9
+ 2025-09-30 13:38:39,396 INFO ___FILE_ONLY___
10
+
11
+ 2025-09-30 13:38:39,397 INFO ___FILE_ONLY___
12
+ Your current Google Cloud CLI version is: 541.0.0
13
+
14
+ 2025-09-30 13:38:39,397 INFO ___FILE_ONLY___ Installing components from version: 541.0.0
15
+
16
+ 2025-09-30 13:38:39,397 INFO ___FILE_ONLY___
17
+
18
+ 2025-09-30 13:38:39,397 DEBUG root Chosen display Format:table[box,title="These components will be removed."](details.display_name:label=Name:align=left,version.version_string:label=Version:align=right,data.size.size(zero="",min=1048576):label=Size:align=right)
19
+ 2025-09-30 13:38:39,397 DEBUG root Chosen display Format:table[box,title="These components will be updated."](details.display_name:label=Name:align=left,version.version_string:label=Version:align=right,data.size.size(zero="",min=1048576):label=Size:align=right)
20
+ 2025-09-30 13:38:39,398 DEBUG root Chosen display Format:table[box,title="These components will be installed."](details.display_name:label=Name:align=left,version.version_string:label=Version:align=right,data.size.size(zero="",min=1048576):label=Size:align=right)
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+ 2025-09-30 13:38:39,414 INFO ___FILE_ONLY___ ┌────────────────────────────────────────────────┐
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+
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+ 2025-09-30 13:38:39,414 INFO ___FILE_ONLY___ │ These components will be installed. │
25
+ 2025-09-30 13:38:39,414 INFO ___FILE_ONLY___
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+
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+ 2025-09-30 13:38:39,414 INFO ___FILE_ONLY___ ├─────────────────────────┬────────────┬─────────┤
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+
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+ 2025-09-30 13:38:39,414 INFO ___FILE_ONLY___ │ Name │ Version │ Size │
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+
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+ 2025-09-30 13:38:39,414 INFO ___FILE_ONLY___ │
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+ 2025-09-30 13:38:39,414 INFO ___FILE_ONLY___ gcloud Alpha Commands
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+ 2025-09-30 13:38:39,414 INFO ___FILE_ONLY___
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+ 2025-09-30 13:38:39,414 INFO ___FILE_ONLY___ │
40
+ 2025-09-30 13:38:39,414 INFO ___FILE_ONLY___ 2025.09.29
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+ 2025-09-30 13:38:39,415 INFO ___FILE_ONLY___ │
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+
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+ 2025-09-30 13:38:39,415 INFO ___FILE_ONLY___ │
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+ 2025-09-30 13:38:39,415 INFO ___FILE_ONLY___ gcloud Beta Commands
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+ 2025-09-30 13:38:39,415 INFO ___FILE_ONLY___ │
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+ 2025-09-30 13:38:39,415 INFO ___FILE_ONLY___ 2025.09.29
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+ 2025-09-30 13:38:39,415 INFO ___FILE_ONLY___ gcloud Preview Commands
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+
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+ 2025-09-30 13:38:39,416 INFO ___FILE_ONLY___
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+
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+ 2025-09-30 13:38:39,416 INFO ___FILE_ONLY___
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+
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+ 2025-09-30 13:38:39,419 DEBUG urllib3.connectionpool Starting new HTTPS connection (1): dl.google.com:443
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+ 2025-09-30 13:38:39,431 DEBUG urllib3.connectionpool https://dl.google.com:443 "GET /dl/cloudsdk/channels/rapid/RELEASE_NOTES HTTP/11" 200 1492432
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+ 2025-09-30 13:38:39,933 INFO ___FILE_ONLY___ For the latest full release notes, please visit:
80
+ https://cloud.google.com/sdk/release_notes
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+
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+
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+ 2025-09-30 13:38:39,933 INFO ___FILE_ONLY___ Performing in place update...
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+
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+ 2025-09-30 13:38:39,936 INFO ___FILE_ONLY___ ╔════════════════════════════════════════════════════════════╗
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+ 2025-09-30 13:38:39,936 INFO ___FILE_ONLY___ ╠═ Downloading: gcloud Alpha Commands ═╣
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+
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+ 2025-09-30 13:38:39,936 INFO ___FILE_ONLY___ ╚
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+ 2025-09-30 13:38:39,938 DEBUG urllib3.connectionpool Starting new HTTPS connection (1): dl.google.com:443
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+ 2025-09-30 13:38:39,948 DEBUG urllib3.connectionpool https://dl.google.com:443 "GET /dl/cloudsdk/channels/rapid/components/google-cloud-sdk-alpha-20250929142209.tar.gz HTTP/11" 200 800
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+ 2025-09-30 13:38:39,951 INFO ___FILE_ONLY___ ╠═ Downloading: gcloud Beta Commands ═╣
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+ 2025-09-30 13:38:39,953 DEBUG urllib3.connectionpool Starting new HTTPS connection (1): dl.google.com:443
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+ 2025-09-30 13:38:39,970 INFO ___FILE_ONLY___ ╠═ Downloading: gcloud Preview Commands ═╣
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+ 2025-09-30 13:38:39,970 INFO ___FILE_ONLY___ ╚
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+ 2025-09-30 13:38:39,972 DEBUG urllib3.connectionpool Starting new HTTPS connection (1): dl.google.com:443
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+ 2025-09-30 13:38:40,020 DEBUG urllib3.connectionpool https://dl.google.com:443 "GET /dl/cloudsdk/channels/rapid/components/google-cloud-sdk-preview-20241115154308.tar.gz HTTP/11" 200 823
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+ 2025-09-30 13:38:40,021 INFO ___FILE_ONLY___ ════════════════════════════════════════════════════════════
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+
118
+ 2025-09-30 13:38:40,023 INFO ___FILE_ONLY___ ╠═ Installing: gcloud Alpha Commands ═╣
119
+
120
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+
126
+ 2025-09-30 13:38:40,029 INFO ___FILE_ONLY___ ╠═ Installing: gcloud Beta Commands ═╣
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+
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+ 2025-09-30 13:38:40,030 INFO ___FILE_ONLY___ ════════════════════════════════════════════════════════════
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134
+ 2025-09-30 13:38:40,034 INFO ___FILE_ONLY___ ╠═ Installing: gcloud Preview Commands ═╣
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142
+
143
+ 2025-09-30 13:38:40,042 INFO ___FILE_ONLY___ Performing post processing steps...
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+ 2025-09-30 13:38:48,593 DEBUG ___FILE_ONLY___
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+ 2025-09-30 13:38:48,593 DEBUG ___FILE_ONLY___
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+ 2025-09-30 13:38:48,807 INFO ___FILE_ONLY___
149
+ Update done!
150
+
151
+
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+ 2025-09-30 13:38:48,809 DEBUG root Chosen display Format:none
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+ 2025-09-30 13:38:48,809 INFO root Display format: "none"
.config/logs/2025.09.30/13.38.40.558814.log ADDED
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1
+ 2025-09-30 13:38:40,559 DEBUG root Loaded Command Group: ['gcloud', 'components']
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1
+ 2025-09-30 13:38:49,448 DEBUG root Loaded Command Group: ['gcloud', 'config']
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+ 2025-09-30 13:38:49,546 INFO ___FILE_ONLY___ Updated property [component_manager/disable_update_check].
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+
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+ 2025-09-30 13:38:49,553 DEBUG root SDK update checks are disabled.
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1
+ 2025-09-30 13:38:50,205 DEBUG root Loaded Command Group: ['gcloud', 'config']
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+ 2025-09-30 13:38:50,291 DEBUG root Loaded Command Group: ['gcloud', 'config', 'set']
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+ 2025-09-30 13:38:50,294 DEBUG root Running [gcloud.config.set] with arguments: [SECTION/PROPERTY: "compute/gce_metadata_read_timeout_sec", VALUE: "0"]
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+ 2025-09-30 13:38:50,294 INFO ___FILE_ONLY___ Updated property [compute/gce_metadata_read_timeout_sec].
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+
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+ 2025-09-30 13:38:50,295 DEBUG root Chosen display Format:default
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+ 2025-09-30 13:38:50,296 INFO root Display format: "default"
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+ 2025-09-30 13:38:50,301 DEBUG root SDK update checks are disabled.
.gitattributes CHANGED
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  *tfevents* filter=lfs diff=lfs merge=lfs -text
36
+ sample_data/mnist_test.csv filter=lfs diff=lfs merge=lfs -text
37
+ sample_data/mnist_train_small.csv filter=lfs diff=lfs merge=lfs -text
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README.md CHANGED
@@ -1,12 +1,12 @@
1
- ---
2
- title: Scaffold Strucutre Predictor
3
- emoji: 🐢
4
- colorFrom: pink
5
- colorTo: green
6
- sdk: gradio
7
- sdk_version: 5.48.0
8
- app_file: app.py
9
- pinned: false
10
- ---
11
-
12
- Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
 
1
+
2
+ # Sequence Feature Predictor
3
+
4
+ ## Project Description
5
+ [Briefly describe your project here. What problem does it solve? What does the Gradio app do?]
6
+
7
+ This project provides a Gradio interface to predict structural features of DNA/RNA sequences using a trained Elastic Net regression model.
8
+
9
+ ## How to Run the App
10
+ To run this application, you need to have Python installed along with the necessary libraries.
11
+
12
+ 1. **Clone the repository:** If you are running this locally from a cloned Hugging Face Space, clone the repository.
app.py ADDED
@@ -0,0 +1,229 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+
2
+ import gradio as gr
3
+ import numpy as np
4
+ import pandas as pd
5
+ import scipy.sparse
6
+ import joblib
7
+ from huggingface_hub import hf_hub_download # Import hf_hub_download
8
+
9
+ # Define custom CSS to hide the default image label
10
+ custom_css = """
11
+ .gradio-container label.svelte-10771d6 {
12
+ display: none !important;
13
+ }
14
+ """
15
+
16
+ # Download and load the model using joblib
17
+ repo_id = "aedupuga/multioutput-regression-models"
18
+ filename = "elastic_net_regression.joblib"
19
+ model_path = hf_hub_download(repo_id=repo_id, filename=filename)
20
+ elastic_net_model = joblib.load(model_path)
21
+
22
+ # Assuming one_hot_encode_sequence function is defined elsewhere and available
23
+ # If not, you will need to define it based on your training code.
24
+ def one_hot_encode_sequence(sequence, target_size):
25
+ """
26
+ One-hot encode a DNA/RNA sequence and pad with zeros to a target size.
27
+
28
+ Args:
29
+ sequence: The input DNA/RNA sequence string.
30
+ target_size: The desired length of the one-hot encoded vector.
31
+
32
+ Returns:
33
+ A list representing the one-hot encoded and padded sequence.
34
+ """
35
+ # Example: Simple one-hot encoding (replace with your actual function)
36
+ mapping = {'A': [1, 0, 0, 0], 'T': [0, 1, 0, 0], 'C': [0, 0, 1, 0], 'G': [0, 0, 0, 1], 'N': [0, 0, 0, 0]} # Include N or other characters if present
37
+ encoded_sequence = [mapping.get(base, [0, 0, 0, 0]) for base in sequence] # Removed .upper() here as sequence will be upper in predict_features
38
+ # Flatten the list of lists
39
+ flat_encoded_sequence = [item for sublist in encoded_sequence for item in sublist]
40
+
41
+ # Pad with zeros to the target size
42
+ if len(flat_encoded_sequence) < target_size:
43
+ padding_needed = target_size - len(flat_encoded_sequence)
44
+ flat_encoded_sequence.extend([0] * padding_needed)
45
+ # Truncate if the sequence is longer than the target size (based on training logic)
46
+ elif len(flat_encoded_sequence) > target_size:
47
+ flat_encoded_sequence = flat_encoded_sequence[:target_size]
48
+
49
+ return flat_encoded_sequence
50
+
51
+
52
+ def predict_features(sequence):
53
+ """
54
+ Predicts features based on the input sequence using the loaded Elastic Net model.
55
+
56
+ Args:
57
+ sequence: The input DNA/RNA sequence string.
58
+
59
+ Returns:
60
+ A dictionary containing the predicted features.
61
+ """
62
+ print(f"Received sequence in predict_features: {sequence}") # Added print statement
63
+
64
+ # Convert input sequence to uppercase to handle both capital and small letters
65
+ sequence = sequence.upper()
66
+
67
+ if not sequence:
68
+ # Ensure the number of returned values matches the Gradio outputs
69
+ return (
70
+ 0, # length_bp
71
+ "0 %", # GC_content
72
+ "N/A", # mfe_energy
73
+ "N/A", # num_pairs
74
+ "N/A", # stem_len_mean
75
+ "N/A", # num_stems
76
+ "N/A", # num_hairpins
77
+ "N/A", # num_internal_loops
78
+ )
79
+
80
+
81
+ # 1. Calculate Length and GC Content
82
+ sequence_length = len(sequence)
83
+ gc_content = (sequence.count('G') + sequence.count('C')) / sequence_length if sequence_length > 0 else 0
84
+ at_content = (sequence.count('A') + sequence.count('T')) / sequence_length if sequence_length > 0 else 0
85
+
86
+ # Determine the target size for the one-hot encoded vector
87
+ # Total features expected by model is 109658
88
+ # Assuming 2 numerical features (length, GC content), the one-hot encoded part is 109658 - 2 = 109656
89
+ target_one_hot_size = 109658 - 2 # Adjust if the number of numerical features is different
90
+
91
+
92
+ # 2. One-Hot Encode the Sequence and Pad
93
+ # Use the actual one_hot_encode_sequence function used during training
94
+ encoded_sequence = one_hot_encode_sequence(sequence, target_one_hot_size)
95
+ encoded_sequence_df = pd.DataFrame([encoded_sequence]) # Convert to DataFrame row
96
+
97
+ # 3. Combine Numerical Features with One-Hot Encoded Sequence Features
98
+ # Ensure the order and names of numerical features match the training data
99
+ # Assuming length and GC content were the initial numerical features
100
+ numerical_features_df = pd.DataFrame([[sequence_length, gc_content]], columns=['length', 'gc_content']) # Adjust column names if needed
101
+
102
+ # Combine numerical features with one-hot encoded sequence features
103
+ # The column names for encoded_sequence_df will be numerical (0, 1, 2...)
104
+ # Ensure this matches how your training data features were ordered and named.
105
+ # If you had other numerical features, add them to numerical_features_df
106
+ combined_features_df = pd.concat([numerical_features_df, encoded_sequence_df], axis=1)
107
+
108
+ # Convert to a format suitable for the model (e.g., NumPy array or sparse matrix)
109
+ # If your model was trained on a sparse matrix, convert to sparse
110
+ # If trained on a dense NumPy array, convert to numpy
111
+ # This example assumes a dense NumPy array input is acceptable for joblib loaded scikit-learn models
112
+ numerical_features = combined_features_df.values # Convert to NumPy array
113
+
114
+
115
+ # Use the loaded Elastic Net model to predict the features
116
+ # The model is expected to be a multi-output regression model
117
+ try:
118
+ predicted_values = elastic_net_model.predict(numerical_features)[0] # Get the predictions for the single input
119
+ # Ensure predicted_values has at least 6 elements, pad with None if not
120
+ while len(predicted_values) < 6:
121
+ predicted_values = np.append(predicted_values, None)
122
+
123
+ mfe_energy = round(predicted_values[0], 1) if isinstance(predicted_values[0], (int, float, np.number)) else "N/A"
124
+ num_pairs = round(predicted_values[1], 1) if isinstance(predicted_values[1], (int, float, np.number)) else "N/A"
125
+ stem_len_mean = round(predicted_values[2], 1) if isinstance(predicted_values[2], (int, float, np.number)) else "N/A"
126
+ num_stems = round(predicted_values[3], 1) if isinstance(predicted_values[3], (int, float, np.number)) else "N/A"
127
+ num_hairpins = round(predicted_values[4], 1) if isinstance(predicted_values[4], (int, float, np.number)) else "N/A"
128
+ num_internal_loops = round(predicted_values[5], 1) if isinstance(predicted_values[5], (int, float, np.number)) else "N/A"
129
+
130
+ except Exception as e:
131
+ print(f"Error during model prediction: {e}")
132
+ print(f"Input shape to model: {numerical_features.shape}")
133
+ # Return placeholder values if prediction fails - Ensure correct number of outputs
134
+ return (
135
+ sequence_length, # length_bp
136
+ f"{gc_content * 100:.1f} %", # GC_content
137
+ "Prediction Error", # mfe_energy
138
+ "Prediction Error", # num_pairs
139
+ "Prediction Error", # stem_len_mean
140
+ "Prediction Error", # num_stems
141
+ "Prediction Error", # num_hairpins
142
+ "Prediction Error", # num_internal_loops
143
+ )
144
+
145
+
146
+ # Return a tuple of predicted values in the order expected by the Gradio interface outputs
147
+ # The order should match the outputs list in cell 24df2117
148
+ return (
149
+ sequence_length, # Maps to length_output
150
+ f"{gc_content * 100:.1f} %", # Maps to gc_content_output
151
+ mfe_energy, # Maps to mfe_energy_output
152
+ num_pairs, # Maps to num_pairs_output
153
+ stem_len_mean, # Maps to stem_len_mean_output
154
+ num_stems, # Maps to num_stems_output
155
+ num_hairpins, # Maps to num_hairpins_output
156
+ num_internal_loops, # Maps to num_internal_loops_output
157
+ # Ensure the number and order match the outputs list in cell 24df2117
158
+ )
159
+
160
+ # Create the Gradio interface
161
+ iface = gr.Blocks(theme="soft", css=custom_css) # Added css parameter
162
+ with iface:
163
+ gr.Markdown("## Sequence Feature Predictor")
164
+ gr.Markdown("Enter a DNA/RNA sequence to predict its features.")
165
+
166
+ with gr.Row():
167
+ sequence_input = gr.Textbox(label="Enter DNA/RNA Sequence", lines=5, placeholder="Paste DNA sequence here...")
168
+
169
+ gr.Markdown("### Sequence Features:")
170
+
171
+ with gr.Column():
172
+ with gr.Row(): # Grouping label and explanation
173
+ length_output = gr.Textbox(label="Sequence Length (base pairs)", scale=2) # Adjusted scale
174
+ gr.Markdown("*(e.g., A T G C G A T C G A -> 10 bases)*") # Removed scale
175
+ with gr.Row(): # Groupdicteding label and explanation
176
+ gc_content_output = gr.Textbox(label="GC Content (%)", scale=2) # Adjusted scale
177
+ gr.Markdown("*(e.g., A T **G C G** A T **C G** A -> 50% GC content)*") # Removed scale
178
+
179
+
180
+ gr.Markdown("#### Predicted Structural Features:")
181
+
182
+ with gr.Row(): # Grouping label and explanation
183
+ mfe_energy_output = gr.Textbox(label="Minimum Free Energy (kcal/mol)", lines=3, scale=2) # Adjusted scale
184
+ gr.Markdown("*(More negative MFE, more stable the structure)*") # Removed scale
185
+
186
+ with gr.Row(): # First row for structural features (3 items)
187
+
188
+ with gr.Column(scale=1, min_width=75): # Column for Number of Base Pairs, adjusted min_width
189
+ num_pairs_output = gr.Textbox(label="Number of Base Pairs") # Updated label
190
+ gr.Markdown("_Example: Image below shows 6 Base Pairs_") # Moved markdown above image and updated text
191
+ gr.Image(value="/content/structure (6).svg", scale=0.5, width=50, height=100, show_label=False, image_mode="1") # Reduced scale and added explicit dimensions, removed label, added image_mode
192
+ with gr.Column(scale=1, min_width=75): # Column for Mean Stem Length, adjusted min_width
193
+ stem_len_mean_output = gr.Textbox(label="Mean Stem Length") # Updated label
194
+ gr.Markdown("_Example: Image below shows Mean Stem Length 3.5 base pairs (bp)_") # Moved markdown above image and updated text
195
+ gr.Image(value="/content/structure (3).svg", scale=0.5, width=50, height=100, show_label=False) # Reduced scale and added explicit dimensions, removed label
196
+ with gr.Column(scale=1, min_width=75): # Column for Number of Stems, adjusted min_width
197
+ num_stems_output = gr.Textbox(label="Number of Stems") # Updated label
198
+ gr.Markdown("_Example: Image below shows 3 Stems_") # Moved markdown above image and updated text
199
+ gr.Image(value="/content/structure (3.1).svg", scale=0.5, width=50, height=100,show_label=False) # Reduced scale and added explicit dimensions, removed label
200
+
201
+
202
+ with gr.Row(): # Second row for structural features (2 items)
203
+ with gr.Column(scale=1, min_width=75): # Column for Number of Hairpins, adjusted min_width
204
+ num_hairpins_output = gr.Textbox(label="Number of Hairpins") # Updated label
205
+ gr.Markdown("_Example: Image below shows 3 Hairpins_") # Moved markdown above image and updated text
206
+ gr.Image(value="/content/structure (4).svg", scale=0.1, width=50, height=100,show_label=False) # Reduced scale and added explicit dimensions, removed label
207
+ with gr.Column(scale=1, min_width=75): # Column for Number of Internal Loops, adjusted min_width
208
+ num_internal_loops_output = gr.Textbox(label="Number of Internal Loops") # Updated label
209
+ gr.Markdown("_Example: Image below shows 1 Internal Loop_") # Moved markdown above image and updated text
210
+ gr.Image(value="/content/structure (6.1).svg", scale=0.1, width=50, height=100, show_label=False) # Reduced scale and added explicit dimensions, removed label
211
+
212
+
213
+ sequence_input.change(
214
+ fn=predict_features,
215
+ inputs=sequence_input,
216
+ outputs=[
217
+ length_output,
218
+ gc_content_output,
219
+ mfe_energy_output,
220
+ num_pairs_output,
221
+ stem_len_mean_output,
222
+ num_stems_output,
223
+ num_hairpins_output,
224
+ num_internal_loops_output,
225
+ ]
226
+ )
227
+
228
+ # Launch the interface
229
+ iface.launch(debug=True)
requirements.txt ADDED
@@ -0,0 +1,7 @@
 
 
 
 
 
 
 
 
1
+
2
+ gradio
3
+ joblib
4
+ huggingface_hub
5
+ numpy
6
+ pandas
7
+ scipy
sample_data/README.md ADDED
@@ -0,0 +1,19 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ This directory includes a few sample datasets to get you started.
2
+
3
+ * `california_housing_data*.csv` is California housing data from the 1990 US
4
+ Census; more information is available at:
5
+ https://docs.google.com/document/d/e/2PACX-1vRhYtsvc5eOR2FWNCwaBiKL6suIOrxJig8LcSBbmCbyYsayia_DvPOOBlXZ4CAlQ5nlDD8kTaIDRwrN/pub
6
+
7
+ * `mnist_*.csv` is a small sample of the
8
+ [MNIST database](https://en.wikipedia.org/wiki/MNIST_database), which is
9
+ described at: http://yann.lecun.com/exdb/mnist/
10
+
11
+ * `anscombe.json` contains a copy of
12
+ [Anscombe's quartet](https://en.wikipedia.org/wiki/Anscombe%27s_quartet); it
13
+ was originally described in
14
+
15
+ Anscombe, F. J. (1973). 'Graphs in Statistical Analysis'. American
16
+ Statistician. 27 (1): 17-21. JSTOR 2682899.
17
+
18
+ and our copy was prepared by the
19
+ [vega_datasets library](https://github.com/altair-viz/vega_datasets/blob/4f67bdaad10f45e3549984e17e1b3088c731503d/vega_datasets/_data/anscombe.json).
sample_data/anscombe.json ADDED
@@ -0,0 +1,49 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
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+ {"Series":"I", "X":4.0, "Y":4.26},
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+
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+ {"Series":"II", "X":6.0, "Y":6.13},
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23
+ {"Series":"II", "X":7.0, "Y":7.26},
24
+ {"Series":"II", "X":5.0, "Y":4.74},
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+
26
+ {"Series":"III", "X":10.0, "Y":7.46},
27
+ {"Series":"III", "X":8.0, "Y":6.77},
28
+ {"Series":"III", "X":13.0, "Y":12.74},
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+ {"Series":"III", "X":9.0, "Y":7.11},
30
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31
+ {"Series":"III", "X":14.0, "Y":8.84},
32
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33
+ {"Series":"III", "X":4.0, "Y":5.39},
34
+ {"Series":"III", "X":12.0, "Y":8.15},
35
+ {"Series":"III", "X":7.0, "Y":6.42},
36
+ {"Series":"III", "X":5.0, "Y":5.73},
37
+
38
+ {"Series":"IV", "X":8.0, "Y":6.58},
39
+ {"Series":"IV", "X":8.0, "Y":5.76},
40
+ {"Series":"IV", "X":8.0, "Y":7.71},
41
+ {"Series":"IV", "X":8.0, "Y":8.84},
42
+ {"Series":"IV", "X":8.0, "Y":8.47},
43
+ {"Series":"IV", "X":8.0, "Y":7.04},
44
+ {"Series":"IV", "X":8.0, "Y":5.25},
45
+ {"Series":"IV", "X":19.0, "Y":12.50},
46
+ {"Series":"IV", "X":8.0, "Y":5.56},
47
+ {"Series":"IV", "X":8.0, "Y":7.91},
48
+ {"Series":"IV", "X":8.0, "Y":6.89}
49
+ ]
sample_data/california_housing_test.csv ADDED
The diff for this file is too large to render. See raw diff
 
sample_data/california_housing_train.csv ADDED
The diff for this file is too large to render. See raw diff
 
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structure (1).svg ADDED
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structure (9).svg ADDED
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