Merge pull request #299 from mims-harvard/geneformer_deploy

Geneformer deploy

requirements.txt

@@ -10,7 +10,6 @@ numpy>=1.26.4,<2.0.0
 openpyxl>=3.0.10,<4.0.0
 pandas>=2.1.4,<3.0.0
 requests>=2.31.0,<3.0.0
-# scikit-learn>=1.2.2,<2.0.0
 scikit-learn==1.2.2
 seaborn>=0.12.2,<1.0.0
 tqdm>=4.65.0,<5.0.0

tdc/tdc_hf.py

@@ -14,6 +14,8 @@
     'CYP3A4_Veith-AttentiveFP',
 ]
 
+model_hub = ["Geneformer"]
+
 
 class tdc_hf_interface:
     '''
@@ -29,7 +31,10 @@ class tdc_hf_interface:
 
     def __init__(self, repo_name):
         self.repo_id = "tdc/" + repo_name
-        self.model_name = repo_name.split('-')[1]
+        try:
+            self.model_name = repo_name.split('-')[1]
+        except:
+            self.model_name = repo_name
 
     def upload(self, folder_path):
         create_repo(repo_id=self.repo_id)
@@ -47,6 +52,21 @@ def file_download(self, save_path, filename):
     def repo_download(self, save_path):
         snapshot_download(repo_id=self.repo_id, cache_dir=save_path)
 
+    def load(self):
+        if self.model_name not in model_hub:
+            raise Exception("this model is not in the TDC model hub GH repo.")
+        elif self.model_name == "Geneformer":
+            # Load model directly
+            from transformers import AutoTokenizer, AutoModelForMaskedLM, pipeline
+            # tokenizer = AutoTokenizer.from_pretrained("ctheodoris/Geneformer")
+            model = AutoModelForMaskedLM.from_pretrained(
+                "ctheodoris/Geneformer")
+            # pipe = pipeline("fill-mask", model=model, tokenizer=tokenizer)
+            # pipe = pipeline("fill-mask", model="ctheodoris/Geneformer")
+            # return pipe
+            return model
+        raise Exception("Not implemented yet!")
+
     def load_deeppurpose(self, save_path):
         if self.repo_id[4:] in deeppurpose_repo:
             save_path = save_path + '/' + self.repo_id[4:]

tdc/test/test_hf.py

@@ -0,0 +1,66 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import division
+from __future__ import print_function
+
+import os
+import sys
+
+import unittest
+import shutil
+import pytest
+
+# temporary solution for relative imports in case TDC is not installed
+# if TDC is installed, no need to use the following line
+sys.path.append(
+    os.path.abspath(os.path.join(os.path.dirname(__file__), "../..")))
+# TODO: add verification for the generation other than simple integration
+
+
+class TestHF(unittest.TestCase):
+
+    def setUp(self):
+        print(os.getcwd())
+        pass
+
+    @pytest.mark.skip(
+        reason="This test is skipped due to deeppurpose installation dependency"
+    )
+    @unittest.skip(reason="DeepPurpose")
+    def test_hf_load_predict(self):
+        from tdc.single_pred import Tox
+        data = Tox(name='herg_karim')
+
+        from tdc import tdc_hf_interface
+        tdc_hf = tdc_hf_interface("hERG_Karim-CNN")
+        # load deeppurpose model from this repo
+        dp_model = tdc_hf.load_deeppurpose('./data')
+        tdc_hf.predict_deeppurpose(dp_model, ['CC(=O)NC1=CC=C(O)C=C1'])
+
+    def test_hf_transformer(self):
+        from tdc import tdc_hf_interface
+        # from transformers import Pipeline
+        from transformers import BertForMaskedLM as BertModel
+        geneformer = tdc_hf_interface("Geneformer")
+        model = geneformer.load()
+        # assert isinstance(pipeline, Pipeline)
+        assert isinstance(model, BertModel), type(model)
+
+    # def test_hf_load_new_pytorch_standard(self):
+    #     from tdc import tdc_hf_interface
+    #     # from tdc.resource.dataloader import DataLoader
+    #     # data = DataLoader(name="pinnacle_dti")
+    #     tdc_hf = tdc_hf_interface("mli-PINNACLE")
+    #     dp_model = tdc_hf.load()
+    #     assert dp_model is not None
+
+    def tearDown(self):
+        try:
+            print(os.getcwd())
+            shutil.rmtree(os.path.join(os.getcwd(), "data"))
+        except:
+            pass
+
+
+if __name__ == "__main__":
+    unittest.main()