Fixed style merge conflicts.

VectorInstitute · May 1, 2024 · bd28037 · bd28037
2 parents 4dab179 + 08af4fb
commit bd28037
Showing 1 changed file with 11 additions and 27 deletions.
diff --git a/odyssey/models/cehr_mamba/mamba-dev.ipynb b/odyssey/models/cehr_mamba/mamba-dev.ipynb
@@ -59,7 +59,7 @@
     "    get_run_id,\n",
     "    load_config,\n",
     "    load_pretrain_data,\n",
-    "    load_finetune_data\n",
+    "    load_finetune_data,\n",
     ")\n",
     "from odyssey.utils.utils import seed_everything\n",
     "\n",
@@ -108,16 +108,12 @@
     "\n",
     "\n",
     "_, fine_test = load_finetune_data(\n",
-    "        args.data_dir,\n",
-    "        args.sequence_file,\n",
-    "        args.id_file,\n",
-    "        'few_shot',\n",
-    "        'all'\n",
+    "    args.data_dir, args.sequence_file, args.id_file, \"few_shot\", \"all\"\n",
     ")\n",
     "test_dataset = PretrainDatasetDecoder(\n",
-    "        data=fine_test,\n",
-    "        tokenizer=tokenizer,\n",
-    "        max_len=args.max_len,\n",
+    "    data=fine_test,\n",
+    "    tokenizer=tokenizer,\n",
+    "    max_len=args.max_len,\n",
     ")"
    ]
   },
@@ -216,9 +212,9 @@
    ],
    "source": [
     "# Load pretrained model\n",
-    "checkpoint = torch.load('checkpoints/mamba_pretrain/best.ckpt', map_location=device)\n",
-    "state_dict = checkpoint['state_dict']\n",
-    "state_dict = {k.replace('model.', ''): v for k, v in state_dict.items()}\n",
+    "checkpoint = torch.load(\"checkpoints/mamba_pretrain/best.ckpt\", map_location=device)\n",
+    "state_dict = checkpoint[\"state_dict\"]\n",
+    "state_dict = {k.replace(\"model.\", \"\"): v for k, v in state_dict.items()}\n",
     "model.load_state_dict(state_dict)\n",
     "model"
    ]
@@ -273,8 +269,8 @@
     }
    ],
    "source": [
-    "input_ids = sample['concept_ids'].squeeze().tolist()\n",
-    "input_ids = input_ids[:input_ids.index(0)]\n",
+    "input_ids = sample[\"concept_ids\"].squeeze().tolist()\n",
+    "input_ids = input_ids[: input_ids.index(0)]\n",
     "print(tokenizer.decode(input_ids))"
    ]
   },
@@ -317,7 +313,7 @@
    "source": [
     "output = model.generate(\n",
     "    torch.tensor(input_ids[:-10], dtype=torch.int32).unsqueeze(0).to(device),\n",
-    "    max_new_tokens=10\n",
+    "    max_new_tokens=10,\n",
     ")\n",
     "\n",
     "tokenizer.decode(output.squeeze().tolist()[-10:])"
@@ -1075,18 +1071,6 @@
    "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.9"
   }
  },
  "nbformat": 4,