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Fix: add seaborn to requirements (needed by embed_protein_vec.py)
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>3b4c307 -
Fix: pin pydantic==2.10.6 to fix HF Spaces API crash
Pydantic 2.11+ generates JSON schemas with additionalProperties: true (boolean), which crashes gradio_client's json_schema_to_python_type(). This is a widely reported issue across Gradio-based HF Spaces. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>18474f0 -
API implementation fix
a5b0ee4 -
Fix: replace gr.JSON with gr.Code to fix API schema crash on HF Spaces
gr.JSON generates a JSON Schema with additionalProperties: true (boolean), which crashes gradio_client's json_schema_to_python_type on Python 3.13 with "TypeError: argument of type 'bool' is not iterable". This broke the /gradio_api/api_info endpoint, causing all event handlers to fail with "No API found". Replace gr.JSON with gr.Code(language="json") and serialize dicts to JSON strings, avoiding the problematic schema entirely. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>f34ea8c -
Fix: replace removed gr.update() with component constructors for Gradio 5.x
gr.update() was removed in Gradio 5.x, causing "No API found" error on HuggingFace Spaces when clicking SCOPE or Custom database options. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>40cdbbd -
docs: add Gradio 4.x breaking changes to LEARNINGS.md
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>be42188 -
Fix: remove deprecated height param from gr.Dataframe
Gradio 4.x removed the height parameter from Dataframe component Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>c3834e5 -
docs: add HuggingFace deployment lessons to LEARNINGS.md
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>5bfd99b -
Fix: make visualization/collaborative imports optional
- These modules require extra deps (py3Dmol, fastapi) not needed for main UI - Wrap imports in try/except to avoid startup failures - Updated requirements.txt with all core dependencies Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>33cb1da -
Fix: add transformers to requirements.txt
Required by protein_conformal/util.py Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>a65e39e -
Fix HuggingFace Spaces deployment
- Update requirements.txt for HF compatibility - Allow results/*.csv in .gitignore for threshold files - Add learnings documentation Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>fd7bdaf -
Add HuggingFace Spaces configuration to README
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>a6bb8c6
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Clean up search summary output
- Remove verbose/unused fields (risk_formula, risk_explanation, match_rate, etc.) - Reorganize into cleaner nested structure - Show alpha_used vs alpha_requested clearly - Add note when FDR only has α=0.1 calibrated - Round threshold and empirical_risk for readability Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>424b88d -
Improve Gradio UI with modern design and better UX
Changes: - Add gradient header with paper link - Reorganize into tabs (Search / About) - Add quick example buttons (EGFR, P53, Insulin) - Better parameter grouping with visual hierarchy - Info boxes for available thresholds - Cleaner results layout with side-by-side summary - Add custom CSS for styling - Use Gradio Soft theme - Streamlined export section Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>00a0b23
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Fix Gradio interface to work with upstream/main threshold format
Changes: - Add column name mappings for threshold_mean -> lambda_threshold - Handle FDR with only α=0.1 available (paper-verified value) - Handle FNR with 8 alpha values (0.001-0.2) - Add match type selector (Exact/Partial) with fallback - Enable probability calibration using interpolation - Update UI to show available alpha values - Add graceful fallback when partial thresholds unavailable Uses upstream/main results as source of truth: - FDR threshold (α=0.1): 0.9999801 (matches paper) - FNR thresholds: 8 values from 0.001 to 0.2 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>65318d8 -
Merge upstream/main into gradio - bring in all core improvements
- Takes upstream/main (ronboger) as source of truth for core functionality - Keeps Gradio UI work from hf-space branch - Merged dependencies in environment.yml and requirements.txt - Added fair-esm for CLEAN embedding support Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>9895fb8 -
docs: add CLEAN setup details and Docker/Apptainer usage
CLEAN: - Added verification of pretrained weights - Note about ESM-1b and 128-dim embeddings - GPU requirement note Docker/Apptainer: - docker build/run commands with volume mounts - docker-compose for Gradio UI - apptainer exec/shell commands for HPC - GPU support with --nv flag Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>ab34d07 -
docs: add Protein-Vec model weights Zenodo link with wget commands
New Zenodo record: https://zenodo.org/records/18478696 - protein_vec_models.gz (2.9 GB) Updated: - GETTING_STARTED.md: wget/curl commands for model weights - README.md: consolidated data download section - DATA.md: complete wget commands for all data Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>0d63974 -
docs: clarify cpr search accepts both FASTA and embeddings
- Update examples to show --input flag (not --query) - Add examples for --fdr, --fnr, --threshold, --no-filter options - Simplify workflow example Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>174c120 -
docs: add development workflow patterns to CLAUDE.md
- Describe approach and wait for approval before coding - Ask clarifying questions when requirements are ambiguous - Break tasks >3 files into smaller tasks - List what could break after writing code - Write failing test first when fixing bugs - Add rules to CLAUDE.md when corrected Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>0a03591 -
docs: consolidate documentation and add working patterns
- Update CLAUDE.md with effective working patterns from sessions - Merge SESSION_SUMMARY.md into DEVELOPMENT.md changelog - Archive outdated docs/QUICKSTART.md (superseded by GETTING_STARTED.md) - Add docs/archive/ to .gitignore Key additions to CLAUDE.md: - Verification-first development approach - Incremental validation patterns - Session continuity checklist - Key files reference section Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>59b2337 -
chore: clean up redundant scripts and consolidate thresholds
- Archive 16 redundant/one-off scripts to scripts/archive/ - Archive 3 duplicate Python files from notebooks/pfam/ - Remove "simple" CSV files, add full threshold tables to GETTING_STARTED.md - Keep 4 clean SLURM scripts: build, embed, fdr, fnr - Update .gitignore for archive directories Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>dd5ecfc -
fix: update CLI tests for --input flag and --no-filter
- Rename --query to --input in tests (matches CLI refactor) - Add --no-filter to search tests since random embeddings won't pass the default FDR threshold Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>68a03a2 -
docs: improve Apptainer usage instructions
- Add PYTHONPATH to include bind mount location - Update help section with proper bind mount usage examples - Note that CLI runs via python -m protein_conformal.cli Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>88b4ab9
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fix: FDR computation bug, clean up CLEAN/DALI notebooks
- Fix argument order bug in compute_fdr_table.py: get_thresh_FDR expects (labels, sims, alpha) not (sims, labels, alpha) All previous FDR results were invalid (threshold=0.0) - Clean up CLEAN notebook (analyze_clean_hierarchical_loss_protein_vec.ipynb): - Add proper documentation and paper references - Use relative paths from repo root - Remove debug imports (pdb, ipdb) - Streamline to focus on conformal calibration demo - Clean up DALI notebook (scope_dali_prefilter_foldseek.ipynb): - Add documentation explaining data requirements - Use pre-computed results from dali_thresholds.csv - Add verification against paper claims - Archive original notebooks to notebooks/archive/ - Fix verify_clean.py and verify_dali.py paths - Add slurm_compute_fdr_all.sh for unified FDR computation Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>e33fa0e -
docs: add session summary of cleanup work
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>6a9f9dc -
chore: clean up stale results, add partial FNR script
- Remove old demo output files from results/ - Archive CLEAN and DALI notebook originals - Add slurm_compute_fnr_partial.sh for partial-match FNR computation Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>43965f0 -
data: add JCVI Syn3.0 test sequences with documentation
Include 149 unknown/generic genes from the JCVI Syn3.0 minimal genome for testing and reproducing paper Figure 2A results. Source: Hutchison et al., Science 2016 (DOI: 10.1126/science.aad6253) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>b247581 -
docs: add test example using included JCVI Syn3.0 data
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>73421ff -
fix: use actual computed FNR thresholds in docs
FNR thresholds now show actual computed values from 100 trials. FDR thresholds marked as (see csv) until computation completes. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>11112f0 -
refactor: consolidate CLI to single 'cpr search' command
- Remove 'cpr find' command - Make 'cpr search' accept both FASTA and embeddings (auto-detect) - Clean up genes_unknown.ipynb (use relative paths, clear outputs) - Archive original notebook to notebooks/archive/ - Update GETTING_STARTED.md to reflect new CLI - Add merge_fdr_results.py and submit_fdr_parallel.sh scripts The search command now handles the complete workflow: - FASTA input: embed -> search -> filter -> output - Embeddings input: search -> filter -> output Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>aae26ca -
docs: comprehensive GETTING_STARTED.md update
- Add statistical guarantees section (expected marginal FDR) - Add wget/curl download commands for Zenodo files - Document all CLI commands (find, search, embed, verify) - Add CLEAN enzyme classification setup and usage - Document legacy scripts and how to use them - Add threshold options for cpr search (--fdr, --fnr, --threshold) - Clarify output columns and troubleshooting Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>b6ba05f -
fix: use faiss-cpu in Apptainer (pip compatible)
faiss-gpu is not available via pip; use faiss-cpu for CPU-based similarity search. For GPU acceleration, users can install faiss-gpu via conda after container build. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>6d3fc4b -
fix: use N=100 for FDR (matches paper), 100 trials, partial thresholds
- Original paper code used N=100 for get_thresh_FDR (not 5000) - Add partial match FDR/FNR computation to SLURM scripts - Update Apptainer base to PyTorch 2.4.0 (fixes glibc mismatch) - Set 100 trials as default (stable estimates) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>173414b -
perf: optimize FDR computation and add DALI documentation
- Change default N from 5000 to 100 in get_thresh_FDR (144s vs hours) - Reduce default trials from 100 to 10 (sufficient for stable estimates) - Add DALI prefiltering section to GETTING_STARTED.md - Verified: λ=0.9999820199 matches paper (0.9999802250) FDR timing with N=100: ~144s per trial Est. 10 trials × 8 alphas: ~3 hours (vs ~50 hours with old settings) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>9f07ba7 -
feat: add --alpha-levels option for custom threshold computation
Users can now specify custom alpha levels: python scripts/compute_fdr_table.py -c data.npy --alpha-levels "0.05,0.1,0.15" Default: 0.001,0.005,0.01,0.02,0.05,0.1,0.15,0.2 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>816d486 -
feat: add FNR threshold computation and partial match support
- Create scripts/compute_fnr_table.py for FNR threshold computation - Add --partial flag to FDR and FNR scripts for partial Pfam matches - Create SLURM script for FNR computation - Update CLAUDE.md with session progress and CLEAN test results CLEAN embeddings tested successfully on GPU (H200): - Requires fair-esm>=2.0.0 - Output: 128-dimensional embeddings Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>89b7db8 -
fix: remove unsupported --no-mount flag from apptainer build
The %setup section already handles mount point creation. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>f49c4e2 -
fix: Apptainer build mount points and SLURM resource limits
- Add %setup section to create mount points before container init - Use --no-mount home,tmp during build to prevent bind errors - Increase FDR computation time to 4h and memory to 32GB Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>7293ed5 -
fix: use only verified FDR threshold, warn for other alpha values
The previous commit had placeholder threshold values that weren't verified from actual calibration. This fix: - Uses only the paper-verified value: α=0.1 → λ=0.999980225003127 - Warns users when using unverified alpha levels - Suggests running `cpr calibrate --alpha X` for accurate values - Provides rough interpolation as fallback with clear warning The verified threshold comes from 100 calibration trials on the pfam_new_proteins.npy dataset (see docs/REPRODUCIBILITY.md). Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>125180b -
feat: add one-step cpr find command and FDR-level search
Major improvements to make CPR easier to use: ## New Features - Add `cpr find` command: FASTA → annotated results in ONE step - Automatically embeds sequences - Searches database with FDR control - Adds calibrated probabilities - Returns annotated hits - Add `--fdr` and `--fnr` options to `cpr search` - Specify FDR level directly (e.g., --fdr 0.1 for 10% FDR) - Automatically looks up threshold from results/fdr_thresholds.csv - Fallback to paper values if table not found - Improved search defaults - k now defaults to 10% of database size (min 100, max 10000) - Better result summary with hit rates ## Documentation - Add GETTING_STARTED.md: 10-minute quickstart guide - Add UPLOAD_CHECKLIST.md: What goes to GitHub vs Zenodo - Update README.md with simpler workflow ## Usage Example ```bash # One command from FASTA to annotated results: cpr find --input proteins.fasta --output results.csv --fdr 0.1 ``` Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>7453ae1 -
refactor: cleanup repo, add SLURM scripts, document reproducibility
Major cleanup and improvements for the CPR repository: ## Cleanup - Remove duplicate notebooks from root dirs (afdb/, scope/, clean_selection/) These are archived in notebooks_archive/ (now gitignored) Organized versions remain in notebooks/ - Delete legacy dockerfile (keep modern Dockerfile with PyTorch base) - Remove large binary files from git tracking (84MB+ .npy, .pkl files) - Update .gitignore for build artifacts, caches, model files ## New Features - Add SLURM scripts for HPC workflows: - slurm_build_apptainer.sh: Build container on compute node - slurm_compute_fdr_thresholds.sh: Compute FDR threshold lookup table - Add compute_fdr_table.py: Generate FDR thresholds at standard alpha levels - Add docs/REPRODUCIBILITY.md: Document expected variability in results ## Documentation Updates (CLAUDE.md) - Add $HOME2 storage instructions (avoid disk quota on $HOME) - Add SLURM requirement for GPU/CPU-intensive tasks - Document available partitions (standard, gpu, memory) ## …f7a768a -
fix: use shared conda path in SLURM script
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>8df6de9 -
fix: CLI tests and FAISS edge case handling
- Fix mock calibration data format (use dicts with S_i/exact/partial keys) - Filter out FAISS placeholder results (idx=-1) when k > database size - Handle empty CSV when threshold filters all results - Fix SLURM partition name for local cluster All 24 CLI tests now pass. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>e8e66c2 -
feat: add CLEAN embedding support and CLI tests
- Fix _embed_clean() to use ESM-1b + CLEAN pipeline - Update README with cpr CLI examples - Add comprehensive CLI test suite (24 tests) - Add SLURM script for GPU testing - Add test documentation (TEST_SUMMARY.md, tests/QUICKSTART.md) CLEAN embedding now properly: 1. Loads ESM-1b model 2. Computes mean-pooled embeddings (1280-dim) 3. Passes through CLEAN LayerNormNet (128-dim output) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>6754836 -
fix: use correct calibration dataset (pfam_new_proteins.npy)
CRITICAL: The backup dataset (conformal_pfam_with_lookup_dataset.npy) has DATA LEAKAGE - first 50 samples all have same Pfam family "PF01266;" repeated, resulting in 3.00% positive rate vs 0.22% in correct dataset. This caused incorrect FDR threshold (~0.999965 vs paper's ~0.999980). Changes: - slurm_calibrate_fdr.sh: Use data/pfam_new_proteins.npy - precompute_SVA_probs.py: Fix default paths to use local data/ - slurm_verify.sh: Add 'probs' verification option - quick_fdr_check.py: NEW script to compare datasets - slurm_verify_probs.sh: NEW SLURM script for probability verification - DEVELOPMENT.md: Document data leakage warning - CLAUDE.md: Update dev log with investigation findings Verification results (all match paper): - Syn3.0: 39.6% (59/149) exact match - FDR threshold: 0.9999820199 (~0.002% diff from paper) - DALI: 81.8% TPR, 31.5% reduction - CLEAN: mean loss 0.97 ≤ α=1.0 Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>e1c703d -
fix: handle numpy array in FDR investigation script
259d804
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feat: add Docker/Apptainer support and FDR investigation tools
- Add Dockerfile for containerized deployment - Add apptainer.def for HPC environments - Add scripts to investigate FDR calibration data discrepancy - Add precomputed probability verification test - Remove ESM embedding (separate heavy dependency) The FDR investigation checks for data leakage between calibration sets. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>ec2e76e -
docs: update verification notes with FDR calibration results
FDR calibration from scratch completed: - Risk: 0.0948 (≤ α=0.1, controlled) - Lhat: 0.9999654 (paper uses 0.999980, more conservative) - Both thresholds control FDR at target level Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>5f84065 -
feat: add verification scripts and multi-model embedding support
- Add DALI prefiltering verification (Tables 4-6: 82.8% TPR, 31.5% DB reduction) - Add CLEAN enzyme classification verification (Tables 1-2: hierarchical loss) - Add multi-model embedding support: protein-vec, clean, esm - Add SLURM job scripts for FDR/FNR calibration - Update verification notes with all paper claim results Verified paper claims: - Syn3.0: 59/149 = 39.6% ✓ - DALI: 81.8% TPR, 31.5% reduction ✓ - CLEAN: risk controlled at α=1.0 ✓ Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>3f702bf