Add VAE downsampling, generation profiles, and timing utilities

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feature/latest-updates into master

Summary

This PR introduces several new features and enhancements to the VAE pipeline:

New Features

  • VAE Downsampling: New script and configuration for data downsampling
  • Generation Profiles: Flexible profile system for model generation
  • Timing Utilities: Performance monitoring and timing utilities

Enhancements

  • Updated model builder with new capabilities
  • Enhanced autoencoder architecture
  • Improved data preprocessing
  • Refactored utility modules for better organization

Documentation

  • Added profile configuration guide
  • Updated README and changelog
  • Enhanced generation guide

Changes

  • 34 files changed (6,812 insertions, 2,833 deletions)
  • Multiple new utility modules added
  • Configuration files updated for new features

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