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Benchmarks & Interactive Slide Decks

SeroGen maintains reproducible Marimo notebooks in scripts/ covering every stage of the pipeline: single-pass bacterial & prophage ORF prediction, polysaccharide-specific 1D-CNN gene role training and layer sweeping, and de novo capsular polysaccharide (CPS) locus discovery, hybrid MCL clustering, and pan-locus database construction.

Each notebook is configured with a native 16:9 Marimo slide layout (scripts/layouts/*.slides.json) and a cached session snapshot (scripts/__marimo__/session/*.py.json) that exports directly into the interactive slide decks embedded in this section.

  • Single-Pass Bacterial & Prophage ORF Benchmark

    Evaluates OrfPredictor on Escherichia coli K-12 MG1655 (CP014225.1, 4.66 Mb) and its 9 embedded cryptic/lambdoid prophages, demonstrating how 29-state frameshift/overlap decoding and sliding 4-kb GC adaptation recover 95.6% of prophage 3'-stops (+17 rescued ORFs) and 99.1% of host CDSs in a single pass at >60 Mb/s.

    Explore ORF Benchmark

  • Polysaccharide-Specific CNN Gene Role Classifier

    Multi-source reference curation (UniProtKB, UniRef50, NCBI IPG, KEGG), Optuna TPE hyperparameter optimization, Numba-parallel 8-layer representation sweep, and held-out validation (>90% accuracy & Macro F1) across all 29 functional GeneRoles (src/serogen/data/model.npz), beating remote homology in the < 25% identity twilight zone.

    Explore Classifier Deck

  • S. pneumoniae De Novo CPS Locus Discovery & Database

    4-stage validation of de novo CPS locus discovery (LocusPredictor), hybrid CNN-rescued MCL orthogroup clustering (Clusterer), directed pan-locus graph construction (Loci.as_pan_graph), contig-split stitching (100% recovery across intergenic & mid-ORF breaks), and leave-one-out novelty detection (LocusMatcher).

    Explore De Novo CPS Database Deck

Running Notebooks Locally

All notebooks can be launched interactively as reactive web apps, slide presentations, or editable Marimo notebooks via uv:

# Launch any notebook directly in Marimo's fullscreen slide presentation mode
uv run --with marimo --with altair marimo run scripts/benchmark_prophage_orfs.py
uv run --with marimo --with altair marimo run scripts/benchmark_spneumo_db.py
uv run --with marimo --with altair --with optuna marimo run scripts/train_gene_classifier.py

# Open in the reactive Marimo notebook editor
uv run --with marimo --with altair marimo edit scripts/benchmark_prophage_orfs.py

# Re-execute a notebook and update its cached session snapshot in scripts/__marimo__/session/
uv run --with marimo --with altair marimo export session --no-sandbox --force-overwrite scripts/benchmark_prophage_orfs.py

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