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FlowFinal

PyTorch
protein-generation
antimicrobial-peptides
flow-matching
protein-design
esm
amp
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FlowFinal

Commit History

  1. Add comprehensive documentation index

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  2. Add comprehensive documentation: results_analysis_conclusions_latex.tex

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  3. Add comprehensive documentation: cfg_dataset_generation_pipeline_latex.tex

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  4. Add comprehensive documentation: flow_model_training_latex.tex

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  5. Add comprehensive documentation: compressor_decompressor_latex.tex

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  6. Add comprehensive documentation: decoder_process_latex.tex

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  7. Add comprehensive documentation: encoder_process_latex.tex

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  8. Add duplicate sequences file from data2 directory

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  9. Add OLD_MODEL embedding: generated_amps_best_model_very_strong_cfg_20250829_OLD_MODEL.pt

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  10. Add OLD_MODEL embedding: generated_amps_best_model_strong_cfg_20250829_OLD_MODEL.pt

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  11. Add OLD_MODEL embedding: generated_amps_best_model_weak_cfg_20250829_OLD_MODEL.pt

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  12. Add OLD_MODEL embedding: generated_amps_best_model_no_cfg_20250829_OLD_MODEL.pt

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  13. Add OLD_MODEL comparison: decoded_sequences_very_strong_cfg_150_20250829_OLD_MODEL.txt

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  14. Add OLD_MODEL comparison: decoded_sequences_strong_cfg_75_20250829_OLD_MODEL.txt

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  15. Add OLD_MODEL comparison: decoded_sequences_weak_cfg_30_20250829_OLD_MODEL.txt

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  16. Add OLD_MODEL comparison: decoded_sequences_no_cfg_00_20250829_OLD_MODEL.txt

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  17. Add missing file: upload_to_huggingface.py

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  18. Add missing file: generate_paper_figures.py

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  19. Add comprehensive model and results summary

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  20. Add complete dataset sequences

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  21. Add mic_summary_20250829.json

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  22. Add apex_results_all_cfg_comparison_20250829.json

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  23. Add apex_results_very_strong_cfg_150_20250829.json

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  24. Add apex_results_strong_cfg_75_20250829.json

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  25. Add apex_results_weak_cfg_30_20250829.json

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  26. Add apex_results_no_cfg_00_20250829.json

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  27. Add decoded_sequences_very_strong_cfg_150_20250829.txt

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  28. Add decoded_sequences_strong_cfg_75_20250829.txt

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  29. Add decoded_sequences_weak_cfg_30_20250829.txt

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  30. Add decoded_sequences_no_cfg_00_20250829.txt

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  31. Add generated_amps_best_model_very_strong_cfg_20250829.pt

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  32. Add generated_amps_best_model_strong_cfg_20250829.pt

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  33. Add generated_amps_best_model_weak_cfg_20250829.pt

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  34. Add generated_amps_best_model_no_cfg_20250829.pt

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  35. Add summary_statistics.csv

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  36. Add complete_amp_results.csv

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  37. Add hmd_amp_cfg_analysis.csv

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  38. Add hmd_amp_detailed_results.csv

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  39. Add generated_sequences_20250829_144923.fasta

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  40. Add uniprotkb_AND_reviewed_true_AND_model_o_2025_08_29.fasta

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  41. Add cfgdata.fasta

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  42. Add combined_final.fasta

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  43. Add all_peptides_data.json

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  44. Add launch_full_data_training.sh

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  45. Add training_output.log

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  46. Add training_output_h100_max.log

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  47. Add h100_maximized_training.log

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  48. Add fresh_training_aug29.log

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  49. Add latex_tables.tex

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  50. Add supplementary_data.tex

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