How foundation-lab-ai/lc_ns_women_chem_graph works
This research toolkit builds mass-difference graphs from untargeted plasma mass-spectrometry data, then evaluates chemical structure and disease-association patterns. The principal workflow is input parsing and feature QC, graph construction, and downstream discovery: testing modules, finding homologous series, proposing identities for unknowns, and diffusing association statistics. Additional scripts evaluate published modules and estimate chance edges. The README documents the study and capabilities; some downstream wiring is inferred only from command-line inputs and is shown only where those inputs are explicit.
Main entry points: discover.py Association discovery · annotate_to_graph.py Feature graph builder · edge_fdr.py Edge FDR · parse_mwtab.py MWTab parser
Components 19
Data preparation
- MWTab parser
scripts/parse_mwtab.py - Feature QC
scripts/prep_results.py - Pair reconstruction
scripts/reconstruct_pairs.py
Chemical graph
- Feature graph builder
scripts/annotate_to_graph.py - Graph data
Graph analysis
- Analysis utilities
scripts/common.py - Association discovery
scripts/discover.py - Edge FDR
scripts/edge_fdr.py - Series detection
scripts/find_series.py - Unknown proposals
scripts/explore_unknowns.py - Graph propagation
scripts/propagate.py
Study validation
- Connectivity test
scripts/module_connectivity.py - ME16 matching
scripts/match_module.py - ME8 evaluation
scripts/run_me8.py
Other components
- Researcher
- MWTab study data
- Results tables
- Published modules
- Compound database
Connections 27
- Researcher → MWTab parser: supplies data
- MWTab study data → MWTab parser: parses
- Results tables → Feature QC: filters features
- MWTab parser → Feature QC: provides metadata
- Feature QC → Feature graph builder: provides features
- Compound database → Feature graph builder: optional annotation
- Feature graph builder → Graph data: writes graph
- Researcher → Feature graph builder: configures build
- Researcher → Pair reconstruction: requests pairing
- Pair reconstruction → MWTab parser: reads metadata
- Researcher → Association discovery: requests analysis
- Association discovery → Graph data: reads graph
- Analysis utilities → Association discovery: provides statistics
- Graph data → Edge FDR: counts edges
- Feature graph builder → Edge FDR: provides transformations
- Graph data → Series detection: enumerates relations
- Edge FDR → Series detection: optional edge filter
- Graph data → Unknown proposals: finds neighbors
- Association discovery → Unknown proposals: supplies feature ranks
- Graph data → Graph propagation: diffuses statistics
- Analysis utilities → Graph propagation: provides statistics
- Edge FDR → Graph propagation: optional edge filter
- Graph data → Connectivity test: tests subgraph
- Published modules → ME16 matching: provides ME16
- Association discovery → ME16 matching: provides feature results
- Published modules → ME8 evaluation: provides ME8
- Association discovery → ME8 evaluation: provides analysis results