Bioneuralnet

**Added**
- **Simplified requirements**: Requirements.txt was severely simplified. Addtionally removed unnecessary imports from core package
- **New Metrics**: New correlation, evaluations and plot python files
- **Plotting Functions**:
- plot_variance_distribution
- plot_variance_by_feature
- plot_performance
- plot_embeddings
- plot_network
- compare_clusters
- **Correlation Functions**
- omics_correlation
- cluster_correlation
- louvain_to_adjacency
- **Evaluation**
- evaluate_rf
- **New Utilities**: Added files to convert RData (Networks as adjency matrix) files to Pandas Dataframes Adjancy matrix.
- **Variance Functions**:
- remove_variance
- remove_fraction
- network_remove_low_variance
- network_remove_high_zero_fraction
- network_filter
- omics_data_filter

- **Updated Tutorials and Documentation**: New end to end jupiter notebook example.
- **Updated Test**: All test have been updated and new ones have been added.

**Added**
- **Hybrid Louvain Clustering**: New iterative Louvain clustering method with PageRank refinement.
- **DatasetLoader Integration**: Standardized dataset loading for examples & tutorials.
- **GNNEmbedding Improvements**: Enhanced tuning capabilities for better model selection.
- **New Example Workflows**:
- **SmCCNet + GNN Embeddings + Subject Representation**
- **SmCCNet + DPMON for Disease Prediction**
- **Hybrid Louvain Clustering Example**
- **Updated Tutorials**: Expanded documentation with `nbsphinx` support for `.ipynb` notebooks.

**Changed**
- **FAQ Overhaul**: Simplified and updated FAQs based on new features.
- **Improved Documentation**: Rewrote and updated multiple sections for better clarity.
- **Updated README.md**:
- Improved feature descriptions.
- New **quick-start example** for SmCCNet + DPMON.
- Cleaner installation instructions.
- **Refactored Examples**:
- Updated **clustering** and **embedding** workflows to match the latest API changes.

**Fixed**
- **Bug Fixes**:
- Resolved incorrect handling of `tune=True` in Hybrid Louvain.
- Addressed inconsistencies in `GraphEmbedding` parameter parsing.
- Fixed dataset loading issues in example scripts.

**[Unreleased]**
- Multi-Modal Integration