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History: 46 commits

LoocasGoose's picture

Claude Opus 4.5

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

9895fb8 9 months ago

pfam
savez about 1 year ago
SLURM_JOBS.md
1.6 kB
feat: add verification scripts and multi-model embedding support 9 months ago
compute_fdr_table.py
6.83 kB
fix: FDR computation bug, clean up CLEAN/DALI notebooks 9 months ago
compute_fnr_table.py
6.9 kB
fix: use N=100 for FDR (matches paper), 100 trials, partial thresholds 9 months ago
convert_fasta_to_tsv.py
681 Bytes
bunch of renaming and refactoring about 1 year ago
embed_fasta.sh

2.04 kB
new clean branch 11 months ago
get_probs.py

6.37 kB
new clean branch 11 months ago
merge_fdr_results.py
1.56 kB
refactor: consolidate CLI to single 'cpr search' command 9 months ago
precompute_SVA_probs.py
4.15 kB
fix: use correct calibration dataset (pfam_new_proteins.npy) 9 months ago
precompute_fdr_thresholds.sh

2.96 kB
new clean branch 11 months ago
precompute_fnr_thresholds.sh

3.06 kB
new clean branch 11 months ago
search.py

6.21 kB
new clean branch 11 months ago
search_and_assign_probs.sh

5.09 kB
new clean branch 11 months ago
slurm_build_apptainer.sh
1.82 kB
feat: add FNR threshold computation and partial match support 9 months ago
slurm_compute_fdr_thresholds.sh
1.65 kB
fix: use N=100 for FDR (matches paper), 100 trials, partial thresholds 9 months ago
slurm_compute_fnr_thresholds.sh
1.59 kB
fix: use N=100 for FDR (matches paper), 100 trials, partial thresholds 9 months ago
slurm_embed.sh
1.09 kB
feat: add CLI, fix FDR bug, verify paper result (59/149 = 39.6%) 9 months ago
test_precomputed_probs.py
2.65 kB
feat: add Docker/Apptainer support and FDR investigation tools 9 months ago
translate_fasta.py

1.18 kB
new clean branch 11 months ago
verify_clean.py
4.59 kB
fix: FDR computation bug, clean up CLEAN/DALI notebooks 9 months ago
verify_dali.py
2.61 kB
fix: FDR computation bug, clean up CLEAN/DALI notebooks 9 months ago
verify_fdr_algorithm.py
5.29 kB
feat: add CLI, fix FDR bug, verify paper result (59/149 = 39.6%) 9 months ago
verify_syn30.py
9.76 kB
feat: add CLI, fix FDR bug, verify paper result (59/149 = 39.6%) 9 months ago