vigipy: Pharmacovigilance & Disproportionality Analysis in Python

The Disproportionality Analysis (DA) Lifecycle

Safety surveillance in spontaneous reporting databases (e.g., FDA FAERS, WHO VigiBase, MAUDE) follows a 4-stage lifecycle. vigipy provides modular, principled tools for each step:

┌────────────────────────────────────────────────────────────────────────┐
│  STAGE 1: DATA INGESTION & PREPARATION                                 │
│  Convert raw tables into typed DataContainers (Sparse, Binary, DDI)    │
│  [ convert()  │  convert_binary()  │  convert_ddi() ]                  │
└───────────────────────────────────┬────────────────────────────────────┘
                                    │
                                    ▼
┌────────────────────────────────────────────────────────────────────────┐
│  STAGE 2: STATISTICAL MODELING & SIGNAL DETECTION                      │
│  Screen for disproportionate drug-event associations via analyze()     │
│  • Frequentist:      PRR, ROR, RFET                                    │
│  • Bayesian:         GPS (Gamma Poisson), BCPNN (Information Component)│
│  • Multivariable:    Relaxed Logistic LASSO (Confounder Adjustment)    │
│  • Syndromic:        SCORE-DA (Indication SVD + Graph Regularization)  │
│  • Multi-Drug/DDI:   SCORE-DDI (Higher-Order Regimen Synergy)          │
└───────────────────────────────────┬────────────────────────────────────┘
                                    │
                  ┌─────────────────┴─────────────────┐
                  ▼                                   ▼
┌───────────────────────────────────┐   ┌────────────────────────────────┐
│  STAGE 3: MULTI-METHOD CONSENSUS  │   │  STAGE 4: TEMPORAL MONITORING  │
│  Triangulate alerts across models │   │  Track signal emergence over   │
│  • Vote tallying & Consensus score│   │  time across quarterly/annual  │
│  • Agreement tiers & Kappa stats  │   │  reporting periods             │
│  • Signal inspection & drill-down │   │  • Cumulative vs. Disjoint     │
│  [ consensus_analysis() ]         │   │  [ LongitudinalModel ]         │
└───────────────────────────────────┘   └────────────────────────────────┘

Installation & Setup

Requirements

• Python 3.9+
• numpy>=1.24, scipy>=1.10, pandas>=2.0, scikit-learn>=1.3, statsmodels>=0.14
• Optional: openpyxl>=3.0 (for Excel .xlsx multi-sheet reports)

# Standard installation
pip install vigipy

# Install with Excel export support
pip install "vigipy[excel]"

Run tests to verify installation:

pytest

Stage 1: Data Preparation & Ingestion

Pharmacovigilance datasets come in different formats: pre-aggregated frequency counts, case-level binary reports, or multi-drug polypharmacy regimens. Choosing the right preprocessor ensures optimal statistical power and memory efficiency.

1. convert(): For Summary Contingency Tables

• When to use: Your data is already aggregated into counts of (Product, Adverse Event, Count).
• Compatible methods: PRR, ROR, RFET, GPS, BCPNN, SCORE-DA.

import pandas as pd
import vigipy as vg

df = pd.read_csv("contingency_counts.csv")
# Columns: 'product_name', 'adverse_event', 'count'

data = vg.convert(
    df,
    product_label="product_name",
    ae_label="adverse_event",
    count_label="count",
    margin_threshold=3,  # Filter out rare events with total counts < 3
)

2. convert_binary(): For Case-Level Reports & Confounder Adjustment

• When to use: You have individual patient report IDs (report_id). Multiple medications and symptoms can appear on the same report.
• Why it matters:
  • Required for LASSO (evaluates all concurrent medications simultaneously).
  • Unlocks SCORE-DA's syndromic graph, ensuring symptom co-occurrence reflects true patient-level clinical syndromes rather than aggregate product correlation.
  • Supports confounder adjustment (e.g. Age, Sex).
  • Uses sparse=True (CSR matrix storage) to handle millions of reports with low memory usage.

df_reports = pd.read_csv("faers_case_reports.csv")
# Columns: 'report_id', 'drug_name', 'reaction', 'age', 'sex'

binary_data = vg.convert_binary(
    df_reports,
    product_label="drug_name",
    ae_label="reaction",
    report_id_label="report_id",
    covariate_labels=["age", "sex"],  # Standardized continuous, dummy-encoded categorical
    sparse=True,                      # Memory-efficient sparse CSR matrices
)

3. convert_ddi(): For Drug-Drug & Multi-Drug Interactions

• When to use: You want to screen for pairwise drug-drug interactions ($k=2$) or higher-order multi-drug regimens ($k=3, \dots$).
• How it works: Uses sparse matrix intersection ($\mathbf{X}^\top \mathbf{X}$) to automatically find drug combinations meeting min_co_reports, avoiding combinatorial blowup.
• Universal compatibility: Produces a standard DataContainer containing both individual drug baselines and combination entities, allowing any method in vigipy to evaluate combinations.

ddi_container = vg.convert_ddi(
    df_reports,
    product_label="drug_name",
    ae_label="reaction",
    report_id_label="report_id",
    min_co_reports=5,     # Drug combo must appear together on >= 5 reports
    max_order=3,          # Screen pairs (k=2) AND triplets (k=3)
    include_singles=True, # Retain single drugs as reference baselines
    sparse=True,
)

Stage 2: Signal Detection Modeling

vigipy provides a unified interface (analyze()) across all modeling paradigms. Each paradigm addresses specific clinical and statistical questions.

Summary of Signal Detection Methods

The Unified API (analyze)

Configure methods with type-safe dataclasses:

from vigipy import (
    analyze,
    PRRConfig,
    RORConfig,
    GPSConfig,
    LASSOConfig,
    SCOREConfig,
    SCOREDDIConfig,
)

# 1. Classical Frequentist (PRR with False Discovery Rate control)
prr_res = analyze(data, PRRConfig(min_events=3, decision_metric="fdr", fdr_threshold=0.05))

# 2. Empirical Bayes Shrinkage (GPS ranked by EB05)
gps_res = analyze(data, GPSConfig(min_events=5, ranking_statistic="quantile"))

# 3. Multivariable Confounder-Adjusted LASSO
lasso_res = analyze(binary_data, LASSOConfig(min_events=3, relaxed=True, n_jobs=-1))

# 4. Syndromic Low-Rank Discovery (SCORE-DA)
score_res = analyze(data, SCOREConfig(latent_rank=5, syndromic_weight=0.5, fdr_threshold=0.05))

# 5. Multi-Drug Interaction Discovery (SCORE-DDI)
ddi_res = analyze(ddi_container, SCOREDDIConfig(interaction_model="multiplicative", min_events=3))

Method Deep-Dives

Multivariable Relaxed LASSO

When patients take multiple drugs, single-drug methods suffer from confounding by co-prescription (e.g., antiemetics falsely flagged for chemotherapy toxicities).

• vigipy.lasso() fits a high-dimensional regularized logistic regression across all drugs and covariates simultaneously.
• By default (relaxed=True), it runs a two-stage Relaxed LASSO: Stage 1 screens active features; Stage 2 refits an unpenalized model on active features using SVD pseudo-inverse Wald standard errors to return debiased adjusted Reporting Odds Ratios ($\text{aROR}$).

result = vg.lasso(
    binary_data,
    min_events=3,
    relaxed=True,                   # Debiased relaxed refit
    decision_metric="lower_bound",  # Signal if 95% CI lower bound > 1.0
    n_jobs=-1,                      # Parallel across adverse events
)
print(result.signals[["Product", "Adverse Event", "Count", "aROR", "CI Lower", "CI Upper", "p_value"]])

SCORE-DA: Syndromic Cellwise Outlier & Residual Estimation

Traditional disproportionality methods assume independence across symptom columns and suffer from blockbuster masking and indication confounding.

• Indication Absorption: Uses Truncated SVD on standardized Pearson residuals to absorb shared drug-class and indication baselines.
• Syndromic Borrowing: Builds a patient-level Graph Laplacian ($\mathbf{L}_{\text{AE}}$) from co-occurring symptoms, allowing related events in a syndrome (e.g. Urticaria + Angioedema + Hypotension) to borrow strength without relying on external ontologies.
• Masking Deflation: Iteratively deflates detected signals to unmask hidden safety signals suppressed by blockbuster drugs.

score_res = vg.score_da(
    data,
    latent_rank=5,           # Number of latent indication/class factors to absorb
    syndromic_weight=0.5,    # Graph Laplacian smoothness coupling
    deflate_iterations=2,    # Iterative deflation passes to eliminate masking
    fdr_threshold=0.05,      # Benjamini-Hochberg FDR cutoff
)
print(score_res.signals[["Product", "Adverse Event", "Count", "SER", "SRR", "fdr", "Syndrome_Cluster"]])

SCORE-DDI: Drug-Drug & Multi-Drug Interaction Discovery

• Unbiased Solo Baselines: When evaluating combinations, score_ddi subtracts co-prescription counts ($C_1 - C_{\text{combo}}$) so the combination's toxicity cannot artificially inflate the single-drug baseline.
• Higher-Order Regimens: Evaluates pairs ($k=2$), triplets ($k=3$), and custom regimens.
• Epidemiological Archetype Classification:
  • EMERGENT: Toxicity appears exclusively upon combination (neither drug active alone).
  • POTENTIATED: One drug has baseline activity; adding the second drug significantly magnifies risk.
  • TWO_HIT / MULTI_HIT: Multiple constituent drugs elevate risk individually; combination triggers compound injury.

ddi_res = vg.score_ddi(
    ddi_container,
    interaction_model="multiplicative",  # or "additive"
    syndromic_weight=0.5,
    min_events=3,
    fdr_threshold=0.05,
)
print(ddi_res.signals[[
    "Components", "Order", "Product", "Adverse Event", "Count",
    "Expected_Null", "SER_Interaction", "DDI_Ratio", "Interaction_Archetype"
]])

Stage 3: Triangulation & Cross-Method Consensus

Different models possess distinct biases: frequentist ratios are noisy on small counts; Bayesian shrinkage can be conservative on rare catastrophic reactions; regression models can be sensitive to collinearity.

consensus_analysis() synthesizes findings across multiple methods in a single unified call:

• Vote Tallying & Consensus Scoring: Normalizes alert votes across methods into composite scores and categorizes signals into agreement tiers (Unanimous, Strong, Moderate, Weak, Isolated).
• Inter-Method Concordance Analytics: Computes pairwise Jaccard similarity, Cohen's Kappa concordance, Spearman rank correlation, and $2 \times 2$ alert overlap matrices.
• Signal Drill-Down: inspect_signal() provides an immediate side-by-side comparison of every method's score, interval, and alert status for any candidate pair.

# Run consensus across default regulatory methods (or pass custom configs)
configs = [
    vg.PRRConfig(min_events=3),
    vg.GPSConfig(min_events=3),
    vg.LASSOConfig(min_events=3),
    vg.SCOREConfig(min_events=3),
]

consensus = vg.consensus_analysis(
    binary_data,
    configs=configs,
    min_consensus=3,  # Retain signals alerted by >= 3 methods
)

# View top consensus signals
print(consensus.signals[[
    "Product", "Adverse Event", "Count", "votes", "consensus_score", "agreement_tier"
]].head())

# Inspect a specific signal across all methods
detail = consensus.inspect_signal("DRUG_A", "ACUTE_KIDNEY_INJURY")
print(detail)
# Displays Method, Alert, Metric, Score, CI Lower, CI Upper, p-value, FDR, Count

# Inter-method agreement metrics
print("Cohen's Kappa Concordance Matrix:")
print(consensus.method_agreement["kappa"].round(3))

# Export multi-sheet consensus report to Excel
consensus.export("consensus_report.xlsx")

Stage 4: Temporal & Longitudinal Surveillance

Post-market safety surveillance requires monitoring how disproportionality metrics evolve over time. The LongitudinalModel applies any signal detection algorithm across resampled time slices.

• Cumulative Mode (run): Progressively incorporates historical data up to each time boundary, tracking accumulating evidence and detecting the exact calendar date an emerging signal crosses threshold.
• Disjoint Mode (run_disjoint): Evaluates each time window independently (e.g. quarterly or annually) without historical accumulation. Ideal for detecting transient reporting anomalies, batch contaminations, or media-driven notoriety effects.

from vigipy import LongitudinalModel, gps

df_time = pd.read_csv("longitudinal_safety_data.csv")
# Requires: 'date', 'name', 'AE', 'count'

# Initialize with annual ('YE'), quarterly ('QE'), or monthly ('ME') slices
lm = LongitudinalModel(df_time, time_unit="QE", count_col="count")

# Run GPS cumulatively with hyperprior warm-starting across time slices
lm.run(gps, warm_start=True, store_all_signals=False)

# Or evaluate disjoint quarterly intervals in parallel across CPU cores
lm.run_disjoint(gps, n_jobs=-1)

# Inspect chronological signal evolution
for timestamp, result in lm.results:
    if result is not None:
        print(f"Quarter ending {timestamp.date()}: {result.num_signals} active signals")
        print(result.signals[["Product", "Adverse Event", "Count", "quantile"]].head(2))

Decision Guide: Which Tool Should I Use?

Result Exporting, Serialization & Logging

Structured Result Container (AnalysisResult & ConsensusResult)

All analysis methods return structured AnalysisResult (or ConsensusResult) objects with built-in export utilities supporting Excel, Parquet, and CSV:

from pathlib import Path
import vigipy as vg

result = vg.analyze(data, vg.GPSConfig(min_events=3))

# Access primary attributes
signals_df = result.signals       # Filtered signals meeting decision criteria
all_df = result.all_signals       # Full candidate dataset with all computed metrics (includes EBGM, LowerBound, UpperBound)
num_alerts = result.num_signals   # Number of detected signals
model_meta = result.params        # Audit trail of parameters used

# Export to Excel (.xlsx), Parquet (.parquet), or CSV (.csv)
# Accepts str or pathlib.Path
result.export("safety_audit.xlsx")                   # Multi-tab workbook ('Signals' and 'all_data')
result.export(Path("signals.parquet"))               # Fast, columnar Parquet export (default: which="signals")
result.export("audit.parquet", which="both")          # Generates audit_signals.parquet & audit_all.parquet
result.export("signals_only.csv")                    # Comma-separated signals export

Logging & Diagnostics

vigipy provides structured diagnostic logging via Python's standard logging library under the "vigipy" namespace:

import logging

# Configure vigipy to display solver iterations, SVD factorizations, and GLM diagnostics
logging.basicConfig(level=logging.INFO, format="%(asctime)s [%(levelname)s] %(name)s: %(message)s")
logging.getLogger("vigipy").setLevel(logging.DEBUG)

Authors & Citation

• David Beery (@Shakesbeery)

Citation

If you use vigipy in your research or regulatory surveillance pipelines, please cite:

@software{beery2026vigipy,
  author = {David Beery},
  title = {vigipy: Disproportionality Analysis and Pharmacovigilance Toolkit in Python},
  year = {2026},
  url = {https://github.com/Shakesbeery/vigipy}
}

License

vigipy is distributed under the MIT License.