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Medstats module

Collection of scripts and modules for biostatistics and data science simple automation for research process.

Medstats is a child project of YASP! by Aleksandr Suvorov, senior statistician of Center of analysis of Complex Systems.

Module contents

Describe

Desribe is a module providing various basic statistical functions, plotting, comparative criterial approaches typically used in clinical trials.

Module uses rpy2-module and basic R libraries.

Module is under heavy readjustment.

ModPerf

ModPerf is a module that assesses typical metrics known in medical trials for machine learning algorithms.

Metric functions:

  • ModPerf_AUC - computes AUC and AUC 95%CI using bootstrap for binary classifier, probabilities for binary classifier, some quantitative variable;
  • ModPerf_Binary - computes confusion matrix and Se, Sp, NPV, PPV and 95%CI using bootstrap for binary classifier output (not probabilities);
  • ModPerf_Multiclass - computes confusion matrix and Se, Sp, NPV, PPV and 95%CI using bootstrap for vulticlass classifier output (not probabilities);
  • ModPerf_thresholds - computes thresholds for probabilities for binary classifier, some quantitative variable with confusion matrix, Se, Sp, NPV, PPV and 95%CI using bootstrap;

Plotting functions

  • ROCPlotter_Binary - plots AUC curve for binary classifier, probabilities for binary classifier, some quantitative variable;
  • ROCPlotter_Multiclass - plots AUC curve for multiclass classifier, probabilities for multiclass classifier;

Parenclitic

Parenclitic module involve various functions for network approaches from works of M. Zanin, A. Gorban, A. Zaikin, H. Whitwell, M. Krivonisov, T. Nazarenko.

Various approaches for network analysis:

  • parenclitic graphs with a threshold;
  • weighted parenclitic graphs;
  • synolitic graphs;
  • correlation graphs for time series

Common classes

  • DataFrameLoader - common class for loading data (for all types of approaches);
  • Prct - common class for parenclytic approach;
  • Snltc - common class for synolytic approach;
  • Corr - common class for correlation approach;

Common functions

  • graph_plotter - plots single weighted graph;
  • chars -computes various characteristics of a single graph;

PhisioPatterns

  • test module for time series and longitudinal data (ECG, EEG). Under heavy development;

Test platform

  • MLSelectionFlow_devel - programm for automatic feature selection (SHAP) and model selection (optuna module);