Methods & Code

Open methods and reproducibility

The Institute's work favors methods that can be inspected, re-run, and challenged: derivations stated explicitly, code deposited publicly, and data released where it can be shared responsibly.

Computational methods

Recurring methodological tools across the programs.

Monte Carlo validation

Large-scale synthetic-cohort validation of clinical decision tools, reported with precision bounds rather than point claims.

Survival & competing risks

Structural-censoring corrections for incidence estimation, including survival-biased effective MDRI and joint bias factors.

Signal processing

Spatial-autocorrelation and correlation-length measures for neurometabolic biomarker discovery.

Algorithmic bias epidemiology

Quantifying synergistic, multiplicative discrimination that is invisible to single-feature fairness checks.

Within-host kinetics

Deriving population-level intervention bounds from mechanistic within-host viral dynamics.

Model reporting integrity

Structured, TRIPOD+AI-aligned assessment of whether prediction models are reported and validated adequately.

Reproducibility practices

  • Persistent IDs Every output carries a DOI; code and analysis are archived on Zenodo.
  • Public code Analysis repositories are released under the Nyx-Dynamics GitHub organization.
  • Open data Datasets are released where they can be shared responsibly, with provenance documented.
  • Explicit derivations Mathematical results are stated from first principles rather than empirical convention.
  • Versioned preprints Preprints are versioned; superseding versions are linked to their predecessors.

Open data

Consolidated dataset

Phase-specific HIV neurometabolic MRS dataset

The first publicly available consolidated dataset of phase-specific HIV neurometabolic magnetic resonance spectroscopy data — 49 observations across 7 independent human cohorts spanning 1985–2021 — released as an independent contribution to the HAND neuroimaging field alongside the Noise Correlation Length preprint.

Associated preprint (bioRxiv)

Code repositories

Public repositories under the Nyx-Dynamics organization.