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README.md

@@ -15,7 +15,7 @@ Pre-trained tabpfn model for transcriptomic data compression.
 - **Mode**: transcriptome-centric compression
 - **Dimensions**: 64
 - **Training data**: TRACERx lung cancer transcriptomics
-- **Created**: 2026-01-09T21:08:36.635126
+- **Created**: 2026-01-10T10:18:42.790457
 
 ## Usage
 
@@ -30,6 +30,7 @@ model = joblib.load(f"{local_dir}/model.joblib")
 # For classical models (PCA/UMAP):
 # model contains: 'pca', 'umap', 'robust_scaler', 'gene_order'
 
-# For TabPFN models:
-# model contains: 'tabpfn_embedding', 'pca_final', 'input_scaler', etc.
+# For TabPFN models (with UMAP reduction):
+# model contains: 'tabpfn_embedding', 'umap_final', 'raw_embeddings', 'input_scaler', etc.
+# Uses UMAP instead of PCA for non-linear dimension reduction of TabPFN embeddings
 ```

metadata.json

@@ -2,12 +2,13 @@
   "model_type": "tabpfn",
   "mode": "transcriptome",
   "dimensions": 64,
-  "created": "2026-01-09T21:08:36.635416",
+  "created": "2026-01-10T10:18:42.790707",
   "keys": [
     "tabpfn_embedding",
     "input_scaler",
     "pca_reduce",
-    "pca_final",
+    "umap_final",
+    "raw_embeddings",
     "kmeans",
     "pseudo_labels",
     "train_indices",
@@ -16,6 +17,7 @@
     "n_components",
     "max_features",
     "data_reduced_shape",
+    "reduction_method",
     "mode",
     "row_ids",
     "feature_ids",

model.joblib

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:5a0fcf9f748c78006a6c46878c9b5f3af94d19a02ec33ae310e4dcd8e7d31882
-size 51311778
+oid sha256:5b90b2f3be85fe5c3ab50456840931dd07c259a37c3cb9b6d3be18e7447f88a0
+size 138129602