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History: 46 commits

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Merge upstream/main into gradio - bring in all core improvements

9895fb8 3 months ago

pfam
savez 9 months ago
SLURM_JOBS.md

1.6 kB
feat: add verification scripts and multi-model embedding support 3 months ago
compute_fdr_table.py

6.83 kB
fix: FDR computation bug, clean up CLEAN/DALI notebooks 3 months ago
compute_fnr_table.py

6.9 kB
fix: use N=100 for FDR (matches paper), 100 trials, partial thresholds 3 months ago
convert_fasta_to_tsv.py

681 Bytes
bunch of renaming and refactoring 9 months ago
embed_fasta.sh

2.04 kB
new clean branch 5 months ago
get_probs.py

6.37 kB
new clean branch 5 months ago
merge_fdr_results.py

1.56 kB
refactor: consolidate CLI to single 'cpr search' command 3 months ago
precompute_SVA_probs.py

4.15 kB
fix: use correct calibration dataset (pfam_new_proteins.npy) 3 months ago
precompute_fdr_thresholds.sh

2.96 kB
new clean branch 5 months ago
precompute_fnr_thresholds.sh

3.06 kB
new clean branch 5 months ago
search.py

6.21 kB
new clean branch 5 months ago
search_and_assign_probs.sh

5.09 kB
new clean branch 5 months ago
slurm_build_apptainer.sh

1.82 kB
feat: add FNR threshold computation and partial match support 3 months ago
slurm_compute_fdr_thresholds.sh

1.65 kB
fix: use N=100 for FDR (matches paper), 100 trials, partial thresholds 3 months ago
slurm_compute_fnr_thresholds.sh

1.59 kB
fix: use N=100 for FDR (matches paper), 100 trials, partial thresholds 3 months ago
slurm_embed.sh

1.09 kB
feat: add CLI, fix FDR bug, verify paper result (59/149 = 39.6%) 3 months ago
test_precomputed_probs.py

2.65 kB
feat: add Docker/Apptainer support and FDR investigation tools 3 months ago
translate_fasta.py

1.18 kB
new clean branch 5 months ago
verify_clean.py

4.59 kB
fix: FDR computation bug, clean up CLEAN/DALI notebooks 3 months ago
verify_dali.py

2.61 kB
fix: FDR computation bug, clean up CLEAN/DALI notebooks 3 months ago
verify_fdr_algorithm.py

5.29 kB
feat: add CLI, fix FDR bug, verify paper result (59/149 = 39.6%) 3 months ago
verify_syn30.py

9.76 kB
feat: add CLI, fix FDR bug, verify paper result (59/149 = 39.6%) 3 months ago