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Parameter Estimation Training Dataset

This repository contains scripts to process simulation data for machine learning-based parameter estimation.

Contributors

  • Data Reshaping Scripts: GitHub Copilot created the first version of the data reshaping utilities (reshape_sim_data.py, verify_reshaped_data.py, access_reshaped_data.py)

Overview

The goal is to train a machine learning model to predict decayRate and surfaceTransferFraction parameters based on 56-day time series data from 4 variables:

  • count
  • CDIFF
  • occupancy
  • anyCP

Files

Data Processing

  • generate_training_data.py - Main script to convert sim_data.csv into ML training format
  • test_training_data.py - Validation script to ensure correct dataset format
  • demo_ml_usage.py - Demonstration of how to use the training data for ML
  • predict_observed_data.py - Script to predict parameters for observed data using trained model
  • reshape_sim_data.py - Script to reshape sim_data.csv into grouped time series format (Created by GitHub Copilot)
  • verify_reshaped_data.py - Verification and analysis of reshaped data (Created by GitHub Copilot)
  • access_reshaped_data.py - Example showing how to access reshaped data (Created by GitHub Copilot)

4x56 CNN Implementation

  • cnn_4x56_model.py - Convolutional Neural Network implementation for 4x56 time series arrays
  • test_cnn_4x56.py - Comprehensive test suite for the CNN implementation
  • compare_approaches.py - Side-by-side comparison of flattened vs CNN approaches

Data Files

  • data/sim_data.csv - Raw simulation data (21 runs, 276 time steps each)
  • data/observed_data.csv - Observed data (56 days) used as target length
  • data/training_data.csv - Processed training dataset (generated)

Utilities

  • DataClasses.py - Data class definitions for runs and samples

Usage

Generate Training Dataset

python generate_training_data.py

This creates data/training_data.csv with:

  • 4,641 training samples (221 sequences × 21 runs)
  • Each row represents one 56-day sequence
  • Columns: run, start_day, decayRate, surfaceTransferFraction, plus 224 time series features

Validate Dataset

python test_training_data.py

Run ML Demo (Flattened Approach)

python demo_ml_usage.py

Run CNN Demo (4x56 Arrays)

python cnn_4x56_model.py

Compare Both Approaches

python compare_approaches.py

Test CNN Implementation

python test_cnn_4x56.py

Predict Parameters for Observed Data

python predict_observed_data.py

This script:

  • Trains a neural network model on the simulation data
  • Processes the observed data into the correct input format
  • Predicts decayRate and surfaceTransferFraction for the observed data
  • Displays the predictions with validation information

Dataset Format

The training dataset has the following structure:

Column Description
run Simulation run ID
start_day Starting day of the 56-day sequence
decayRate Target parameter 1
surfaceTransferFraction Target parameter 2
count_0 to count_55 Count time series (56 values)
CDIFF_0 to CDIFF_55 CDIFF time series (56 values)
occupancy_0 to occupancy_55 Occupancy time series (56 values)
anyCP_0 to anyCP_55 AnyCP time series (56 values)

Total: 228 columns (4 metadata + 224 features)

Machine Learning Approaches

This repository now offers two distinct approaches for training models:

Approach 1: Flattened Features (Original)

Uses traditional machine learning with flattened time series:

  • Data format: 224 features per sample (4 variables × 56 days)
  • Model types: Random Forest, SVM, Neural Networks with dense layers
  • Benefits: Simple, interpretable, works with traditional ML algorithms
  • Use case: When temporal structure is less important

Example:

# Each sample is a flat vector: [count_0, count_1, ..., count_55, CDIFF_0, ...]
X_flat = data.reshape(num_samples, 224)

Approach 2: 4x56 CNN Arrays with Sliding Windows (New)

Uses convolutional neural networks with structured arrays and sliding window approach:

  • Data format: 4×56 arrays per sample (variables × time)
  • Sliding windows: Multiple 56-day sequences per run (100-155, 101-156, 102-157, etc.)
  • Training samples: ~4,400 windows from 21 runs (211 windows per run)
  • Model types: Convolutional Neural Networks (CNN)
  • Benefits: Preserves temporal structure, captures spatial relationships, much more training data
  • Use case: When chronological dependencies are important and more training examples are needed

Example:

# Each sample is a 4×56 array preserving structure:
# Row 0: count time series [56 consecutive days]
# Row 1: CDIFF time series [56 consecutive days]  
# Row 2: occupancy time series [56 consecutive days]
# Row 3: anyCP time series [56 consecutive days]

# Multiple sliding windows per run:
# Window 1: days 100-155
# Window 2: days 101-156  
# Window 3: days 102-157
# ... and so on
X_4x56 = data.reshape(num_windows, 4, 56, 1)  # Add channel dimension for CNN

CNN Architecture

The 4x56 CNN implementation includes:

  • Sliding Window Data Generation: Creates ~4,400 training examples from 21 runs
  • Conv2D layers to capture spatial patterns between variables
  • MaxPooling along time dimension to reduce dimensionality
  • BatchNormalization for stable training
  • Dropout for regularization
  • Dense layers for final regression to 2 target parameters

Key advantage: The sliding window approach provides much more training data by creating multiple overlapping 56-day sequences from each simulation run, significantly improving model training compared to using only one sequence per run.

model = Sequential([
    Conv2D(32, (2, 3), activation='relu', input_shape=(4, 56, 1)),
    BatchNormalization(),
    MaxPooling2D((1, 2)),  # Pool along time dimension
    # ... additional layers
    Dense(2)  # Output: decayRate, surfaceTransferFraction
])

Machine Learning Usage

The dataset is designed for multi-output regression where:

  • Input (X): Time series data in two formats:
    • Flattened: 224 features (4 variables × 56 days)
    • Structured: 4×56 arrays (variables × time)
  • Output (y): 2 target parameters (decayRate, surfaceTransferFraction)

Example using PyTorch (Flattened approach):

import pandas as pd
import torch
import torch.nn as nn
from torch.utils.data import DataLoader, TensorDataset

# Load data
df = pd.read_csv('data/training_data.csv')

# Prepare features and targets
feature_cols = [col for col in df.columns if any(var in col for var in ['count_', 'CDIFF_', 'occupancy_', 'anyCP_'])]
X = df[feature_cols].values
y = df[['decayRate', 'surfaceTransferFraction']].values

# Convert to PyTorch tensors
X_tensor = torch.FloatTensor(X)
y_tensor = torch.FloatTensor(y)

# Create neural network
model = nn.Sequential(
    nn.Linear(224, 512),
    nn.ReLU(),
    nn.BatchNorm1d(512),
    nn.Dropout(0.2),
    nn.Linear(512, 256),
    nn.ReLU(),
    nn.BatchNorm1d(256),
    nn.Dropout(0.2),
    nn.Linear(256, 128),
    nn.ReLU(),
    nn.BatchNorm1d(128),
    nn.Dropout(0.2),
    nn.Linear(128, 2)
)

# Train model
criterion = nn.MSELoss()
optimizer = torch.optim.Adam(model.parameters(), lr=0.001)

Example using TensorFlow/Keras (4x56 CNN with Sliding Windows):

from cnn_4x56_model import load_and_prepare_4x56_data, create_cnn_model
from sklearn.model_selection import train_test_split
import numpy as np

# Load sliding window data
X, y, run_ids, window_starts, metadata = load_and_prepare_4x56_data()
print(f"Loaded {X.shape[0]} windows from {len(np.unique(run_ids))} runs")

# Split data
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)

# Reshape for CNN (add channel dimension)
X_train_cnn = X_train.reshape(X_train.shape[0], 4, 56, 1)
X_test_cnn = X_test.reshape(X_test.shape[0], 4, 56, 1)

# Create and train CNN model
model = create_cnn_model(input_shape=(4, 56, 1))
model.fit(X_train_cnn, y_train, validation_data=(X_test_cnn, y_test), epochs=100)

Quick Start

Option 1: Use the flattened approach (traditional ML)

python demo_ml_usage.py

Option 2: Use the 4x56 CNN approach with sliding windows

python cnn_4x56_model.py

Option 3: Compare both approaches

python compare_approaches.py

Run tests

python test_cnn_4x56.py