Add protein_aggregator package and example

protein_aggregator/__init__.py

@@ -0,0 +1,38 @@
+"""
+Protein Sequence-Level Prediction with Multiple Token Aggregation Methods.
+
+Extracts residue embeddings from ESM2 (frozen backbone) and performs
+sequence-level prediction (e.g., localization) using 6 aggregation strategies:
+
+1. Mean pooling
+2. Max pooling
+3. CLS token
+4. GLOT (cosine-similarity token graph)
+5. GLOT-Residue (protein residue contact graph via graphein)
+6. Covariance pooling
+
+Reference:
+- GLOT: "Towards Improved Sentence Representations using Token Graphs" (arXiv:2603.03389)
+- Covariance Pooling: https://www.goodfire.ai/research/covariance-pooling
+- Graphein: https://graphein.ai/
+"""
+
+from .model import ProteinSequenceClassifier
+from .aggregators import (
+    MeanPooling,
+    MaxPooling,
+    CLSPooling,
+    GLOTPooling,
+    GLOTResidueGraphPooling,
+    CovariancePooling,
+)
+
+__all__ = [
+    "ProteinSequenceClassifier",
+    "MeanPooling",
+    "MaxPooling",
+    "CLSPooling",
+    "GLOTPooling",
+    "GLOTResidueGraphPooling",
+    "CovariancePooling",
+]