Merge pull request #96 from UCD-BDLab/Analysis-GBMLGG-KIPAN-Datasets

Author: ramosv

.gitignore

@@ -69,8 +69,13 @@ TCGA_BRCA_DATA/
 !bioneuralnet/datasets/brca/
 !bioneuralnet/datasets/brca/**/*.csv
 
-!bioneuralnet/datasets/networks/
-!bioneuralnet/datasets/networks/**/*.csv
+!bioneuralnet/datasets/kipan/
+!bioneuralnet/datasets/kipan/**/*.csv
+
+!bioneuralnet/datasets/gbmlgg/
+!bioneuralnet/datasets/gbmlgg/**/*.csv
+
+
 feature_testing
 
 # Sphinx documentation build
@@ -129,3 +134,5 @@ dpmon_cv_results_SAGE_FINAL
 dpmon_tuning
 GBMLGG
 PAAN
+dpmon_cv_results_GAT_FINAL
+docs_notebooks

CHANGELOG.md

@@ -118,3 +118,32 @@ and this project adheres to [Semantic Versioning](https://semver.org/).
 ## [1.1.3] - 2025-11-01
 
 - **Tag update to Sync Zenodo and PIPY**
+
+## [1.1.4] - 2025-11-08
+
+### **Added**
+- **New Utility Functions and Global Seed**
+
+  - **Imputation**:
+    - `impute_omics`: Imputes missing values (NaNs) using `mean`, `median`, or `zero` strategies.
+
+    - `impute_omics_knn`: Implements **K-Nearest Neighbors (KNN)** imputation for missing values in omics data.
+
+  - **Normalization/Scaling**:
+    - `normalize_omics`: Scales feature data using `Z-score`, `MinMax` scaling, or `Log2` transformation.
+
+  - **Methylation Data Transformation**:
+      - `beta_to_m`: Converts methylation `Beta-values to M-values` (log2 transformation).
+
+  - **Reproducibility Utility**:
+    - `set_seed`: Sets global random seeds across Python, NumPy, and PyTorch, including configuration for deterministic CUDA operations to ensure maximum experimental reproducibility.
+
+- **New TCGA Datasets**
+
+  - **TCGA-KIPAN**: Added the Pan-Kidney cohort (KIRC, KIRP, KICH) to **DatasetLoader**.
+
+  - **TCGA-GBMLGG**: Added the combined Glioblastoma Multiforme and Lower-Grade Glioma cohort to **DatasetLoader**.
+
+### **Changed**
+
+  - **Documentation Update**: Updated the online documentation (Read the Docs/API Reference) to include the new TCGA datasets and their respective classification results using the **DPMON**.

MANIFEST.in

@@ -14,12 +14,8 @@ recursive-include bioneuralnet/utils *.R *.r
 recursive-include bioneuralnet/datasets/monet *.csv
 recursive-include bioneuralnet/datasets/example1 *.csv
 recursive-include bioneuralnet/datasets/brca *.csv
-
-# include bioneuralnet/datasets/brca/clinical.csv
-# include bioneuralnet/datasets/brca/pam50.csv
-# include bioneuralnet/datasets/brca/mirna.csv
-# exclude bioneuralnet/datasets/brca/meth_*.csv
-# exclude bioneuralnet/datasets/brca/rna_*.csv
+recursive-include bioneuralnet/datasets/gbmlgg *.csv
+recursive-include bioneuralnet/datasets/kipan *.csv
 
 # Include documentation source files
 prune docs

README.md

@@ -8,7 +8,7 @@
 [![Documentation](https://img.shields.io/badge/docs-read%20the%20docs-blue.svg)](https://bioneuralnet.readthedocs.io/en/latest/)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17503083.svg)](https://doi.org/10.5281/zenodo.17503083)
 
-## Welcome to BioNeuralNet 1.1.3
+## Welcome to BioNeuralNet 1.1.4
 
 ![BioNeuralNet Logo](assets/LOGO_WB.png)