MAPPER

Code and analysis snapshot for MAPPER, a multimodal framework for predicting antibiotic mode of action and identifying uncertain or novel mechanistic responses.

This repository accompanies the manuscript Decoding antibiotic modes of action from multimodal cellular responses.

It contains the curated data tables, notebooks, analysis exports, and figure assets used for the current manuscript and Supplementary Information.

Suggested GitHub repository description: MAPPER: multimodal prediction of antibiotic mode of action from cellular response data

Start here

• docs/traceability.md maps manuscript figures to the notebooks and exported assets that generate them.
• docs/paper_fig2_6_code_inventory.md summarizes the code and local runtime artifacts required for Figures 2-6.
• notebooks/figure2 to notebooks/figure6 contain the canonical main-figure workflows.

Repository layout

• notebooks/ – figure, preprocessing, and supplementary notebooks
• scripts/ – reusable generation and preprocessing scripts
• Data/ – curated input matrices and supporting input files used by the notebooks
• Embeddings/ – precomputed text embedding artifacts
• analysis_exports/ – manuscript-facing summary exports and figure-analysis CSVs
• images/ – exported figure assets
• docs/ – code-to-figure mapping and reproducibility notes

Local-only large artifacts

The working project also uses large prediction, model, and result caches under:

• predictions/
• models/
• results/

These are intentionally ignored in the public git history. If they are present in a local workspace, the notebooks and docs may refer to them as canonical runtime artifact roots.

The manuscript build tree under latex/ is also kept local and is not part of the public repository state.

Canonical figure notebooks

Figures 2-6:

• notebooks/figure2/figure2_data_overview.ipynb
• notebooks/figure2/figure2_combined.ipynb
• notebooks/figure3/figure3_llm_parametric_tests.ipynb
• notebooks/figure3/figure3_text_augmentation_effects.ipynb
• notebooks/figure3/figure3_combined.ipynb
• notebooks/figure4/figure4_best_feature_combination.ipynb
• notebooks/figure4/figure4_feature_replot.ipynb
• notebooks/figure4/figure4_shapley_analysis.ipynb
• notebooks/figure4/figure4_structural_novelty_modality_jumps.ipynb
• notebooks/figure4/figure4_combined.ipynb
• notebooks/figure5/figure5_uncertainty_comparison.ipynb
• notebooks/figure5/figure5_combined.ipynb
• notebooks/figure6/figure6_uncertainty_estimator_calibration.ipynb
• notebooks/figure6/figure6_eclipse_instrument.ipynb
• notebooks/figure6/figure6_external_lab.ipynb
• notebooks/figure6/figure6_combined.ipynb

Supplementary utilities:

• notebooks/supplementary/supp_string_analysis_preprocess.ipynb
• notebooks/supplementary/supp_string_tabm_predictions.ipynb
• notebooks/supplementary/supp_table_s7_ci.ipynb
• notebooks/supplementary/regenerate_supplementary_stats.ipynb

Reproducibility notes

• Main manuscript and SI figure numbering/inputs are documented in docs/traceability.md.
• Required code and local artifact roots for Figures 2-6 are summarized in docs/paper_fig2_6_code_inventory.md.
• Small local QA folders such as .figcheck/ and .pagecheck/ are review artifacts and are intentionally ignored.