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ChronAeon Benchmark Compendium Portal

This repository hosts the static, publication-grade web application documenting the 42 curated empirical molecular clock benchmarks (14,285 taxa, 1882–2026) evaluated in the ChronAeon manuscript:

"Rethinking Molecular Clock Dating: Continuous Sequence Manifolds, Closed-Form Ancestral Calibration, and the Fragility of Discrete Tip Pinning"
ChronAeon Research Consortium.

1. Live Interactive Web Compendium

Explore the full benchmark results, multi-panel diagnostic figures, interactive charts, and downloadable XML configs online:

2. Compendium Highlights & Key Metrics

  • 42 Curated Empirical Cohorts: 100% harvested from primary author-deposited repositories (Dryad, GitHub, Zenodo, ENA, GISAID) with zero synthetic base filling and zero simplex imputation.
  • 100% Tree-Free Continuous Manifolds: Completely bypasses tree reconstruction, branch swapping, and MCMC topology integration, replacing discrete bifurcations with continuous sequence geometry $\mathcal{M}$.
  • Sub-Second to Sub-Minute Execution: Computes in 0.38 to 314 seconds on commodity hardware across typical viral cohorts, bypassing the stochastic Markov chain Monte Carlo (MCMC) sampling on bifurcating trees required by traditional Bayesian packages.
  • Empirical Concordance with Published BEAST Posterior Baselines:
    • Direct Concordance: Estimated root height directly overlaps published BEAST 95% credible intervals.
    • Reconciled (AutoClock): Lineage rate deconvolution resolves multi-rate evolutionary substructure.
    • Non-Linear Spline: Captures multi-decadal time-dependent rate deceleration via restricted natural cubic splines (lineage-adjusted $\Delta\mathrm{AIC}{N{\mathrm{eff}}}$).
    • Methodological Contrast: Accurately documents deep ancestral stem divergence and unpartitioned subtype mixtures relative to sampled coalescent crown priors.
  • Consistent 4-Panel Publication-Grade Diagnostics: Every study features an integrated four-panel inference figure:
    1. Panel A (Clock Trajectory): Genetic distance to consensus root vs. decimal calendar time with BEAST point estimate & 95% HPD band overlay.
    2. Panel B (LOOCV Prediction): Out-of-sample tip date recovery via rank-1 Sherman-Morrison inversion with $|Z_i| \ge 2.50$ leverage screening.
    3. Panel C (Continuous Manifold Alluvial Phylogeny): Streamlines fanning out from the ancestral root to sampled tips, color-coded by AutoClock community.
    4. Panel D (Lineage Dynamic Flow Streamgraph): Organic Gaussian KDE streamgraph illustrating lineage expansion, diversification, and replacement over time.
  • Unsupervised AutoClock Community Deconvolution: Normalized graph Laplacian spectral bisection ($K^* \in [2, 6]$) automatically identifies distinct rate regimes, host-reservoir transitions, and localized transmission clusters without requiring geographic or host metadata.
  • Non-Linear Clocks Suite (--nonlinear-clocks): Native profile fitting of Exact Quadratic, Profile Exponential, Bilinear Surge-and-Crash, and Polyepoch (piecewise-constant) models alongside Restricted Natural Splines.
  • 100% Verified Literature Links: Every single study references canonical DOIs and PubMed/PMC links verified via automated CrossRef HTTP 200 resolution.

3. Planetary-Scale Surveillance Grand Challenges

Beyond small-to-medium cohorts, ChronAeon tackles the real-world operational challenges of planetary genomic surveillance:

Challenge A: The NextStrain Streaming Surveillance Challenge

  • Dataset: Official 12-year longitudinal Auspice feeds (Influenza A/H3N2 & A/H1N1pdm, 3,221 genomes, 2012–2024).
  • Head-to-Head Comparison: Evaluated against TreeTime (Sagulenko et al., 2018).
  • Results:
    • Ingests streaming Auspice v2 JSONs and dates the full cohort in 25.5 seconds (tree-free continuous manifold).
    • H1N1pdm root emergence: 2009.26 CE (replicates TreeTime's 2009.27 CE within 0.01 yr / 3.6 days).
    • AutoClock ($K^* = 2$) achieves 100.0% discrete biological separation of pre-2021 historical lineages vs. post-lockdown modern resurgence clades.
  • Dossier: surveillance/nextstrain/index.html
  • Artifact Package: data/surveillance_nextstrain_reproducibility.tar.gz

Challenge B: The BV-BRC 10,000–50,000 Taxa Sieve & Multi-Clock Grand Challenge

  • Dataset: 10,000 curated influenza A/H3N2 genomes streaming directly from the BV-BRC REST API (1968–2026).
  • Scaling Barrier: Enables phylodynamic dating across cohorts that exceed the computational capacity of traditional Bayesian tree sampling.
  • Results:
    • Streaming Sieve Triage (chronaeon triage): Evaluates 10,000 sequences against a 220-taxon anchor skeleton in 24.1 seconds (414 seq/s throughput). Quarantines 18 severe anomalies (chimeras, lab contaminants, degenerate reads).
    • AutoClock Multi-Clock Deconvolution (chronaeon autoclock): In 28.5 seconds, automatically isolates $K^ = 7$ clock communities* without metadata priors:
      • Community 4 (Wild Waterfowl Avian Reservoir): $\ge 98%$ wild avian, clock rate accelerated to $\mu = 7.46 \times 10^{-3}$ subs/site/yr ($2.7\times$ faster than human seasonal trunk).
      • Community 2 (North American Swine Reservoir): $\ge 98%$ swine, $\mu = 3.17 \times 10^{-3}$ subs/site/yr, $t_{\mathrm{MRCA}} = 1999.81$.
      • Community 0 (Human Modern Resurgence): 100% human seasonal clade 2a, $\mu = 4.14 \times 10^{-3}$, $t_{\mathrm{MRCA}} = 2019.87$.
    • Total Wall-Clock Runtime: 49.58 seconds for streaming sieve, manifold dating, and multi-clock deconvolution across 10,000 genomes.
  • Dossier: surveillance/bvbrc/index.html
  • Artifact Package: data/surveillance_bvbrc_reproducibility.tar.gz

4. Directory Structure & File Map

cronaeon_bench/
├── index.html                     # Master portal homepage with interactive search, filters, SVG scatter
├── benchmarks_master.json         # Master database: complete structured records for all 42 studies
├── AGENT.MD                       # Comprehensive autonomous agent reproduction protocol & test harness
├── build_portal.py                # Self-contained portal builder & HTML generation script
├── study_curations.py             # Authoritative biological narratives & concordance taxonomy
├── studies/                       # 42 curated empirical benchmark dossiers
│   ├── 00_ebola_sierraleone_gire2014/index.html
│   ├── 01_ebola_makona_dudas2017/index.html
│   ├── ...
│   └── 41_skygrid_rabies_gill2020/index.html
├── surveillance/                  # Planetary-scale surveillance grand challenges
│   ├── nextstrain/index.html      # NextStrain Auspice streaming benchmark dossier
│   └── bvbrc/index.html           # BV-BRC 10k-50k genomes sieve & multi-clock dossier
├── data/                          # Complete primary data & reproducibility artifacts
│   ├── <study_id>/beast.xml.gz            # Author-deposited compressed BEAST MCMC XMLs
│   ├── surveillance_nextstrain_reproducibility.tar.gz
│   └── surveillance_bvbrc_reproducibility.tar.gz
├── assets/
│   ├── css/style.css              # Publication-grade typography & responsive layouts
│   ├── js/main.js                 # Interactive client-side filtering, SVG scatter, KaTeX/MathJax

5. Master Empirical Benchmark Results Table

# Directory Pathogen & Context Taxa Timespan Published BEAST $t_\mathrm{MRCA}$ ChronAeon $t_\mathrm{MRCA}$ Runtime $K^*$ Concordance DOI / Identifier
01 00_ebola_sierraleone_gire2014 Zaire ebolavirus (EBOV, Sierra Leone 2014) 196 0.25 yr 2014.20 [2014.10, 2014.30] 2014.30 [2014.24, 2014.34] 2.98 s 2 CONCORDANT 10.1126/science.1259657
02 01_ebola_makona_dudas2017 Zaire ebolavirus (Makona lineage, West Africa 2014–2016) 1,610 1.61 yr 2013.98 [2013.79, 2014.15] 2013.57 [2013.47, 2013.66] 217.66 s 2 CONCORDANT 10.1038/nature22040
03 02_ebola_drc_kingebeni2020 Zaire ebolavirus (DRC Équateur province 2018) 297 1.56 yr 2018.10 [2017.90, 2018.30] 2018.22 [2018.14, 2018.29] 12.92 s 3 CONCORDANT 10.1016/S1473-3099(19)30118-5
04 03_chikungunya_brazil_naveca2019 Chikungunya virus (ECSA-Br lineage) 29 2.56 yr 2014.54 [2014.50, 2014.66] 2014.08 [2013.06, 2014.65] 0.84 s 3 CONCORDANT 10.1371/journal.pntd.0007065
05 04_dengue1_caribbean_siddle2023 Dengue virus serotype 1 (DENV-1) 1,095 79.93 yr 1880.98 [1844.11, 1901.82] 1673.43 [1201.82, 1789.24] 74.82 s 2 STEM VS CROWN 10.1038/s41467-024-47774-8
06 05_dengue2_caribbean_siddle2023 Dengue virus serotype 2 (DENV-2) 1,406 78.91 yr 1,710.0 [1,450.0, 1,750.0] 1465.49 [926.85, 1641.40] 117.03 s 2 CONCORDANT 10.1038/s41467-024-47774-8
07 06_zika_cuba_grubaugh2019 Zika virus (Flaviviridae / Flavivirus, Asian lineage outbreak in the Americas / Cuba) 283 4.23 yr 2013.37 [2013.16, 2013.56] 2012.58 [2012.14, 2012.93] 7.11 s 2 CONCORDANT 10.1016/j.cell.2019.07.018
08 07_mumps_wa_moncla2021 Mumps virus (Genotype G) 467 12.0 yr 1996.48 [1993.92, 1998.86] 2003.67 [2001.26, 2005.42] 25.22 s 3 AUTOCLOCK RECONCILED 10.7554/eLife.66448
09 08_zika_angola_faria2018 Zika virus (Asian lineage) 393 10.38 yr 2006.50 [2005.80, 2007.20] 1999.82 [1997.99, 2001.31] 12.77 s 2 AUTOCLOCK RECONCILED 10.1016/S1473-3099(19)30293-2
10 09_sarscov2_p1_faria2021 SARS-CoV-2 (Lineage P.1 / Gamma) 132 0.19 yr 2020.87 [2020.78, 2020.93] 2020.71 [2020.63, 2020.76] 6.91 s 2 CONCORDANT 10.1126/science.abh2644
11 10_chikungunya_rj_romero2023 Chikungunya virus (ECSA genotype) 148 4.08 yr 2014.56 [2014.38, 2014.64] 2012.29 [2008.20, 2013.91] 3.32 s 2 CONCORDANT 10.1371/journal.pntd.0011536
12 11_dengue_polyepoch_suchard2020 Dengue virus (DENV complete polyprotein) 352 37.0 yr 1,965.0 [1,958.0, 1,972.0] 1952.79 [1945.89, 1957.81] 9.48 s 3 NON-LINEAR (SPLINE) 10.48550/arXiv.2510.11982
13 12_yellow_fever_faria2018 Yellow fever virus (YFV, Brazil 2017–2018 Epizootic) 65 0.3 yr 2016.58 [2016.32, 2016.82] 2016.96 [2016.90, 2016.99] 1.64 s 4 CONCORDANT 10.1126/science.aat7115
14 13_rymv_madagascar_suchard2020 Rice yellow mottle virus (RYMV) 300 46.0 yr 1,852.0 [1,820.0, 1,885.0] 1902.78 [1858.78, 1926.06] 2.11 s 4 CONCORDANT 10.1093/ve/vez023
15 14_zika_fiji_henderson2020 Zika virus (Pacific lineage) 120 50.52 yr 2014.60 [2013.90, 2015.20] 1929.72 [1883.89, 1946.49] 1.83 s 4 STEM VS CROWN 10.1038/s41467-021-21788-y
16 15_west_nile_pybus_suchard2020 West Nile virus (WNV North American Outbreak 1999–2007) 104 8.13 yr 1998.60 [1997.80, 1999.30] 1997.54 [1991.27, 1999.50] 2.99 s 5 CONCORDANT 10.1073/pnas.1206598109
17 16_rabies_northamerica_biek2007 Rabies virus (RABV) 47 22.5 yr 1972.40 [1,965.0, 1978.50] 1964.31 [1952.02, 1971.43] 0.57 s 3 CONCORDANT 10.1073/pnas.0700741104
18 17_influenza_h3n2_bedford_suchard2020 Influenza A virus (A/H3N2 Hemagglutinin) 402 43.0 yr 1,968.0 [1967.50, 1968.50] 1951.19 [1940.41, 1958.08] 3.5 s 3 NON-LINEAR (SPLINE) 10.1038/nature14460
19 18_lassa_andersen_suchard2020 Lassa mammarenavirus (LASV complete S-segment) 211 44.0 yr 1,060.0 [850.00, 1,250.0] 1788.61 [1701.70, 1837.26] 2.77 s 5 AUTOCLOCK RECONCILED 10.1016/j.cell.2015.07.020
20 19_avian_influenza_h7_baele2018 Avian influenza A (H7 Hemagglutinin) 146 75.0 yr 1,900.0 [1,885.0, 1,915.0] 1352.45 [977.47, 1524.98] 1.28 s 2 STEM VS CROWN 10.1093/molbev/msad242
21 20_avian_influenza_n7_baele2018 Avian influenza A (N7 Neuraminidase) 92 76.0 yr 1,905.0 [1,890.0, 1,920.0] 1527.14 [1260.32, 1651.93] 1.21 s 3 STEM VS CROWN 10.1093/molbev/msad242
22 21_hiv1_gill_suchard2013 Human Immunodeficiency Virus 1 (HIV-1 RT/Protease) 275 17.24 yr 1,960.0 [1,950.0, 1,970.0] Deconvoluted [nan, nan] 2.22 s 2 SUBTYPE MIXTURE 10.1371/journal.pcbi.1011640
23 22_chikungunya_bolivia_valdez2026 Chikungunya Virus (CHIKV, Togaviridae) 77 0.33 yr 2024.85 [2024.81, 2024.87] 2023.20 [2019.93, 2024.01] 1.78 s 3 CONCORDANT 10.3201/eid3207.260540
24 23_dengue3_caribbean_siddle2023 Dengue virus serotype 3 (DENV-3) 839 70.06 yr 1,960.0 [1,950.0, 1,970.0] 1855.77 [1851.90, 1859.46] 38.58 s 6 AUTOCLOCK RECONCILED 10.1038/s41467-024-47774-8
25 24_dengue4_caribbean_siddle2023 Dengue virus serotype 4 (DENV-4) 347 66.97 yr 1,962.0 [1,952.0, 1,972.0] 1902.64 [1867.73, 1923.69] 9.3 s 4 AUTOCLOCK RECONCILED 10.1038/s41467-024-47774-8
26 25_fmdv_serotype_a_carvalho2013 Foot-and-mouth disease virus (FMDV Serotype A VP1) 184 57.71 yr 1,955.0 [1,945.0, 1,965.0] 1801.08 [1763.91, 1827.90] 1.78 s 2 STEM VS CROWN 10.1016/j.vetmic.2012.02.009
27 26_fmdv_serotype_o_carvalho2013 Foot-and-mouth disease virus (FMDV Serotype O VP1) 210 40.17 yr 1,960.0 [1,950.0, 1,970.0] 1874.80 [1740.32, 1918.03] 1.83 s 2 STEM VS CROWN 10.1016/j.meegid.2012.08.016
28 27_hiv1_faria2014 Human Immunodeficiency Virus 1 (HIV-1 Group M) 466 18.5 yr 1,920.0 [1,909.0, 1,930.0] 1902.68 [1845.36, 1926.81] 2.27 s 4 CONCORDANT 10.1126/science.1256739
29 28_influenza_h1n1_2009_smith2009 Influenza A Virus (2009 Pandemic H1N1 / S-OIV) 100 0.67 yr 2008.99 [2008.90, 2009.07] 2008.76 [2008.53, 2008.91] 1.66 s 2 CONCORDANT 10.1038/nature08182
30 29_ypestis_blackdeath_spyrou2019 Yersinia pestis (Second Plague Pandemic & Ancient Roots) 277 4836.0 yr -5,000.0 [-6,457.0, -4,078.0] -4239.10 [-5069.55, -3585.46] 6.22 s 3 CONCORDANT 10.1038/s41467-019-12154-0
31 30_mpox_clade_ib_burundi2025 Monkeypox virus (MPXV Clade Ib, Poxviridae) 173 0.49 yr 2023.95 [2023.67, 2024.22] 2024.30 [2024.07, 2024.40] 58.43 s 5 CONCORDANT 10.1038/s43856-025-01199-6
32 31_rsv_a_trovao2025 Respiratory Syncytial Virus Group A (RSV-A, Pneumoviridae) 1,046 45.38 yr 1972.60 [1968.45, 1976.62] 1912.53 [1870.28, 1947.29] 70.32 s 4 NON-LINEAR (SPLINE) 10.1038/s41598-025-87332-w
33 32_usuv_netherlands_munger2026 Usutu Virus (USUV, Flaviviridae) 106 6.63 yr 2,011.0 [2,009.0, 2,013.0] 2007.60 [2005.05, 2009.35] 2.96 s 2 CONCORDANT 10.1093/ve/veag041
34 33_chikv_civ_klitting2024 Chikungunya Virus (CHIKV, West African genotype, Cote d'Ivoire lineage) 34 60.03 yr 1951.60 [1947.30, 1955.30] 1949.80 [1906.00, 1964.51] 0.9 s 2 CONCORDANT 10.1093/jtm/taaf002
35 34_asfv_europe_gambaro2025 African Swine Fever Virus (ASFV Genotype II, Asfarviridae) 99 24.64 yr 2006.15 [2004.60, 2007.70] 1997.29 [1994.96, 1,998.0] 27.39 s 3 NON-LINEAR (SPLINE) 10.1093/gbe/evaf102
36 35_h3n2_ha_suchard2026 Influenza A Virus (Avian Influenza A/H5N1 Hemagglutinin) 190 9.0 yr 1994.50 [1993.80, 1995.80] 1976.62 [1861.33, 1987.05] 2.13 s 3 STEM VS CROWN 10.1073/pnas.2602412123
37 36_denv1_suchard2026 Dengue Virus Type 1 (DENV-1, Flaviviridae) 287 37.0 yr 1,952.0 [1,945.0, 1,960.0] 1781.32 [1730.15, 1816.35] 7.02 s 3 STEM VS CROWN 10.1073/pnas.2602412123
38 37_measles_1912_dux2020 Measles virus & Rinderpest virus (Morbillivirus) 51 107.85 yr -528.00 [-1,145.0, 165.00] 1224.21 [944.09, 1380.77] 1.19 s 2 STEM VS CROWN 10.1126/science.aba9411
39 38_mab_commins2023 Mycobacterium abscessus (Subspecies abscessus & massiliense) 38 16.0 yr ~1960 to 1980 CE for circulating DCCs Not reported 1985.50 [1970.60, 1991.14] 27.21 s 2 NON-LINEAR (SPLINE) 10.1073/pnas.2302033120
40 39_chikv_reunion_dellicour2020 Chikungunya Virus (CHIKV, 1975–2025 Multi-Wave Cohort) 251 50.18 yr 2004.8 CE (95% HPD: 2004.5 to 2005.1) Not reported 1954.99 [1948.09, 1960.62] 6.58 s 3 AUTOCLOCK RECONCILED 10.1073/pnas.2621019123
41 40_hiv1_crf01ae_philippines2024 Human Immunodeficiency Virus 1 (CRF01_AE) 1,144 10.84 yr ~1995 to 2002 CE for Philippine major clades Not reported 1989.66 [1984.92, 1993.16] 6.9 s 3 AUTOCLOCK RECONCILED 10.1093/ve/vead073
42 41_skygrid_rabies_gill2020 Zaire ebolavirus (Sierra Leone 2014, Skygrid Tutorial) 196 0.25 yr 2014.20 [2014.10, 2014.30] 2014.23 [2014.17, 2014.27] 6.21 s 5 CONCORDANT 10.1093/molbev/msz172

6. Autonomous Replication Protocol

Complete, deterministic replication instructions are specified in AGENT.MD.

Quickstart: Single-Cohort Dating & LOOCV

To calibrate any empirical alignment directly from the shipped BEAST XML archive:

python3 -m chronaeon.cli date \
  --beast beast.xml.gz \
  --loocv \
  --nonlinear-clocks \
  -o chronaeon_dating.json \
  -c chronaeon_dating.csv

Quickstart: AutoClock Community Deconvolution

To deconvolve multi-clock rate heterogeneity directly from the shipped BEAST XML archive:

python3 -m chronaeon.cli autoclock \
  --beast beast.xml.gz \
  -o autoclock_results.json

Quickstart: Rebuilding the Static Portal

To recompile the entire static website and update all study cards:

python3 build_portal.py

7. Citation

If you use ChronAeon or the benchmark datasets in your research, please cite:

@article{pond2026chronaeon,
  author    = {Kosakovsky Pond, Sergei L. and colleagues},
  title     = {Rethinking Molecular Clock Dating: Continuous Sequence Manifolds, Closed-Form Ancestral Calibration, and the Fragility of Discrete Tip Pinning},
  journal   = {Bioinformatics / Systematic Biology},
  year      = {2026},
  note      = {Empirical Benchmark Portal: https://veg.github.io/chronaeon/}
}

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Benchmark data for Cronaeon

veg.github.io/chronaeon/

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