Merge pull request #1 from michiyasunaga/main

XikunZhang · web-flow · commit a194c0d7ccb7 · 2021-11-10T23:43:48.000-08:00
add medqa
diff --git a/README.md b/README.md
@@ -53,9 +53,12 @@ You can specify the GPU you want to use in the beginning of the command `CUDA_VI
 
 **TL;DR**. The preprocessing may take long; for your convenience, you can download all the processed data [here](https://drive.google.com/drive/folders/1T6B4nou5P3u-6jr0z6e3IkitO8fNVM6f?usp=sharing) into the top-level directory of this repo and run
 ```
-unzip data_preprocessed.zip 
+unzip data_preprocessed.zip
 ```
 
+**Add MedQA-USMLE**. Besides the commonsense QA datasets (*CommonsenseQA*, *OpenBookQA*) with the ConceptNet knowledge graph, we added a biomedical QA dataset ([*MedQA-USMLE*](https://github.com/jind11/MedQA)) with a biomedical knowledge graph based on Disease Database and DrugBank. You can download all the data for this from [[here]](https://drive.google.com/file/d/1EqbiNt2ACXVrc9gmoXnzTEo9GJTe9Uor/view?usp=sharing). Unzip it and put the `medqa_usmle` and `ddb` folders inside the `data/` directory.
+
+
 The resulting file structure should look like this:
 
 ```plain
@@ -85,11 +88,18 @@ Similarly, to train GreaseLM on OpenbookQA, run
 CUDA_VISIBLE_DEVICES=0 ./run_greaselm.sh obqa --data_dir data/
 ```
 
+To train GreaseLM on MedQA-USMLE, run
+```
+CUDA_VISIBLE_DEVICES=0 ./run_greaselm__medqa_usmle.sh
+```
+
 ### 4. Pretrained model checkpoints
 You can download a pretrained GreaseLM model on CommonsenseQA [here](https://drive.google.com/file/d/1QPwLZFA6AQ-pFfDR6TWLdBAvm3c_HOUr/view?usp=sharing), which achieves an IH-dev acc. of `79.0` and an IH-test acc. of `74.0`.
 
 You can also download a pretrained GreaseLM model on OpenbookQA [here](https://drive.google.com/file/d/1-QqyiQuU9xlN20vwfIaqYQ_uJMP8d7Pv/view?usp=sharing), which achieves an test acc. of `84.8`.
 
+You can also download a pretrained GreaseLM model on MedQA-USMLE [here](https://drive.google.com/file/d/1x5nZEprV0Ht8IWViyz3d07uGLXtNjUN1/view?usp=sharing), which achieves an test acc. of `38.5`.
+
 ### 5. Evaluating a pretrained model checkpoint
 To evaluate a pretrained GreaseLM model checkpoint on CommonsenseQA, run
 ```
@@ -114,4 +124,4 @@ This repo is built upon the following work:
 QA-GNN: Question Answering using Language Models and Knowledge Graphs
 https://github.com/michiyasunaga/qagnn
 ```
-Many thanks to the authors and developers!
+Many thanks to the authors and developers!
diff --git a/greaselm.py b/greaselm.py
@@ -26,6 +26,7 @@
 DECODER_DEFAULT_LR = {
     'csqa': 1e-3,
     'obqa': 3e-4,
+    'medqa_usmle': 1e-3,
 }
 
 import numpy as np
@@ -81,8 +82,11 @@ def construct_model(args, kg):
     ##########################################################
 
     if kg == "cpnet":
-        n_ntype = 4 
+        n_ntype = 4
         n_etype = 38
+    elif kg == "ddb":
+        n_ntype = 4
+        n_etype = 34
     else:
         raise ValueError("Invalid KG.")
     if args.cxt_node_connects_all:
@@ -178,7 +182,7 @@ def calc_eval_accuracy(eval_set, model, loss_type, loss_func, debug, save_test_p
 
 def train(args, resume, has_test_split, devices, kg):
     print("args: {}".format(args))
-    
+
     if resume:
         args.save_dir = os.path.dirname(args.resume_checkpoint)
     if not args.debug:
@@ -211,7 +215,14 @@ def train(args, resume, has_test_split, devices, kg):
 
     # Get the names of the loaded LM parameters
     loading_info = model.lmgnn.loading_info
-    loaded_roberta_keys = [k.replace("roberta.", "lmgnn.mp.") for k in loading_info["all_keys"]]
+    # loaded_roberta_keys = [k.replace("roberta.", "lmgnn.mp.") for k in loading_info["all_keys"]]
+    def _rename_key(key):
+        if key.startswith("roberta."):
+            return key.replace("roberta.", "lmgnn.mp.")
+        else:
+            return "lmgnn.mp." + key
+
+    loaded_roberta_keys = [_rename_key(k) for k in loading_info["all_keys"]]
 
     # Separate the parameters into loaded and not loaded
     loaded_params, not_loaded_params, params_to_freeze, small_lr_params, large_lr_params = sep_params(model, loaded_roberta_keys)
@@ -316,7 +327,7 @@ def train(args, resume, has_test_split, devices, kg):
         model.train()
 
         for qids, labels, *input_data in tqdm(train_dataloader, desc="Batch"):
-            # labels: [bs] 
+            # labels: [bs]
             start_time = time.time()
             optimizer.zero_grad()
             bs = labels.size(0)
@@ -387,11 +398,11 @@ def train(args, resume, has_test_split, devices, kg):
         if not args.debug:
             with open(log_path, 'a') as fout:
                 fout.write('{:3},{:5},{:7.4f},{:7.4f},{:7.4f},{:7.4f},{:3}\n'.format(epoch_id, global_step, dev_acc, test_acc, best_dev_acc, final_test_acc, best_dev_epoch))
-        
+
         wandb.log({"dev_acc": dev_acc, "dev_loss": dev_total_loss, "best_dev_acc": best_dev_acc, "best_dev_epoch": best_dev_epoch}, step=global_step)
         if has_test_split:
             wandb.log({"test_acc": test_acc, "test_loss": test_total_loss, "final_test_acc": final_test_acc}, step=global_step)
-        
+
         # Save the model checkpoint
         if args.save_model:
             model_state_dict = model.state_dict()
@@ -500,10 +511,12 @@ def main(args):
     logging.basicConfig(format='%(asctime)s,%(msecs)d %(levelname)-8s [%(name)s:%(funcName)s():%(lineno)d] %(message)s',
                         datefmt='%m/%d/%Y %H:%M:%S',
                         level=logging.WARNING)
-    
+
     has_test_split = True
     devices = get_devices(args.cuda)
     kg = "cpnet"
+    if args.dataset == "medqa_usmle":
+        kg = "ddb"
 
     if not args.use_wandb:
         wandb_mode = "disabled"
@@ -518,7 +531,7 @@ def main(args):
     args.wandb_id = wandb_id
 
     args.hf_version = transformers.__version__
-                        
+
     with wandb.init(project="KG-LM", config=args, name=args.run_name, resume="allow", id=wandb_id, settings=wandb.Settings(start_method="fork"), mode=wandb_mode):
         print(socket.gethostname())
         print ("pid:", os.getpid())
@@ -537,7 +550,7 @@ def main(args):
 
 if __name__ == '__main__':
     __spec__ = None
-    
+
     parser = parser_utils.get_parser()
     args, _ = parser.parse_known_args()
 
@@ -590,4 +603,4 @@ def main(args):
     parser.add_argument('--init_range', default=0.02, type=float, help='stddev when initializing with normal distribution')
 
     args = parser.parse_args()
-    main(args)
+    main(args)
diff --git a/modeling/modeling_greaselm.py b/modeling/modeling_greaselm.py
@@ -23,6 +23,14 @@
 logger = logging.getLogger(__name__)
 
 
+if os.environ.get('INHERIT_BERT', 0):
+    ModelClass = modeling_bert.BertModel
+else:
+    ModelClass = modeling_roberta.RobertaModel
+    
+print ('ModelClass', ModelClass)
+
+
 class GreaseLM(nn.Module):
 
     def __init__(self, args={}, model_name="roberta-large", k=5, n_ntype=4, n_etype=38,
@@ -31,11 +39,11 @@ def __init__(self, args={}, model_name="roberta-large", k=5, n_ntype=4, n_etype=
                  pretrained_concept_emb=None, freeze_ent_emb=True,
                  init_range=0.02, ie_dim=200, info_exchange=True, ie_layer_num=1, sep_ie_layers=False, layer_id=-1):
         super().__init__()
-        self.lmgnn = LMGNN(args, model_name, k, n_ntype, n_etype, 
+        self.lmgnn = LMGNN(args, model_name, k, n_ntype, n_etype,
                                         n_concept, concept_dim, concept_in_dim, n_attention_head,
                                         fc_dim, n_fc_layer, p_emb, p_gnn, p_fc, pretrained_concept_emb=pretrained_concept_emb, freeze_ent_emb=freeze_ent_emb,
                                         init_range=init_range, ie_dim=ie_dim, info_exchange=info_exchange, ie_layer_num=ie_layer_num,  sep_ie_layers=sep_ie_layers, layer_id=layer_id)
-    
+
     def batch_graph(self, edge_index_init, edge_type_init, n_nodes):
         """
         edge_index_init: list of (n_examples, ). each entry is torch.tensor(2, E)
@@ -59,7 +67,7 @@ def forward(self, *inputs, cache_output=False, detail=False):
                                                          -> (2, total E)
             edge_type:  list of (batch_size, num_choice) -> list of (batch_size * num_choice, ); each entry is torch.tensor(E(variable), )
                                                          -> (total E, )
-        
+
         returns:
         logits: [bs, nc]
         """
@@ -85,7 +93,7 @@ def forward(self, *inputs, cache_output=False, detail=False):
             return logits, attn, concept_ids.view(bs, nc, -1), node_type_ids.view(bs, nc, -1), edge_index_orig, edge_type_orig
             # edge_index_orig: list of (batch_size, num_choice). each entry is torch.tensor(2, E)
             # edge_type_orig: list of (batch_size, num_choice). each entry is torch.tensor(E, )
-            
+
     def get_fake_inputs(self, device="cuda:0"):
         bs = 4
         nc = 5
@@ -129,14 +137,14 @@ def test_GreaseLM(device):
 
 class LMGNN(nn.Module):
 
-    def __init__(self, args={}, model_name="roberta-large", k=5, n_ntype=4, n_etype=38, 
+    def __init__(self, args={}, model_name="roberta-large", k=5, n_ntype=4, n_etype=38,
                  n_concept=799273, concept_dim=200, concept_in_dim=1024, n_attention_head=2,
                  fc_dim=200, n_fc_layer=0, p_emb=0.2, p_gnn=0.2, p_fc=0.2,
                  pretrained_concept_emb=None, freeze_ent_emb=True,
                  init_range=0.02, ie_dim=200, info_exchange=True, ie_layer_num=1, sep_ie_layers=False, layer_id=-1):
         super().__init__()
-        config, _ = modeling_roberta.RobertaModel.config_class.from_pretrained(
-            model_name, 
+        config, _ = ModelClass.config_class.from_pretrained(
+            model_name,
             cache_dir=None, return_unused_kwargs=True,
             force_download=False,
             output_hidden_states=True
@@ -281,11 +289,12 @@ def test_LMGNN(device):
     model.check_outputs(*outputs)
 
 
-class TextKGMessagePassing(modeling_roberta.RobertaModel):
+
+class TextKGMessagePassing(ModelClass):
 
     def __init__(self, config, args={}, k=5, n_ntype=4, n_etype=38, dropout=0.2, concept_dim=200, ie_dim=200, p_fc=0.2, info_exchange=True, ie_layer_num=1, sep_ie_layers=False):
         super().__init__(config=config)
-       
+
         self.n_ntype = n_ntype
         self.n_etype = n_etype
 
@@ -633,7 +642,7 @@ def from_pretrained(cls, pretrained_model_name_or_path, *model_args, **kwargs):
             state_dict = state_dict.copy()
             if metadata is not None:
                 state_dict._metadata = metadata
-            
+
             all_keys = list(state_dict.keys())
 
             # PyTorch's `_load_from_state_dict` does not copy parameters in a module's descendants
@@ -756,7 +765,7 @@ class RoBERTaGAT(modeling_bert.BertEncoder):
 
     def __init__(self, config, k=5, n_ntype=4, n_etype=38, hidden_size=200, dropout=0.2, concept_dim=200, ie_dim=200, p_fc=0.2, info_exchange=True, ie_layer_num=1, sep_ie_layers=False):
         super().__init__(config)
-        
+
         self.k = k
         self.edge_encoder = torch.nn.Sequential(torch.nn.Linear(n_etype + 1 + n_ntype * 2, hidden_size), torch.nn.BatchNorm1d(hidden_size), torch.nn.ReLU(), torch.nn.Linear(hidden_size, hidden_size))
         self.gnn_layers = nn.ModuleList([modeling_gnn.GATConvE(hidden_size, n_ntype, n_etype, self.edge_encoder) for _ in range(k)])
@@ -799,14 +808,14 @@ def forward(self, hidden_states, attention_mask, special_tokens_mask, head_mask,
 
             if output_attentions:
                 all_attentions = all_attentions + (layer_outputs[1],)
-            
+
             if i >= self.num_hidden_layers - self.k:
                 # GNN
                 gnn_layer_index = i - self.num_hidden_layers + self.k
                 _X = self.gnn_layers[gnn_layer_index](_X, edge_index, edge_type, _node_type, _node_feature_extra)
                 _X = self.activation(_X)
                 _X = F.dropout(_X, self.dropout_rate, training = self.training)
-            
+
                 # Exchange info between LM and GNN hidden states (Modality interaction)
                 if self.info_exchange == True or (self.info_exchange == "every-other-layer" and (i - self.num_hidden_layers + self.k) % 2 == 0):
                     X = _X.view(bs, -1, _X.size(1)) # [bs, max_num_nodes, node_dim]
@@ -861,7 +870,7 @@ def check_outputs(self, outputs, _X):
 
 def test_RoBERTaGAT(device):
     config, _ = modeling_roberta.RobertaModel.config_class.from_pretrained(
-        "roberta-large", 
+        "roberta-large",
         cache_dir=None, return_unused_kwargs=True,
         force_download=False,
         output_hidden_states=True
@@ -880,11 +889,11 @@ def test_RoBERTaGAT(device):
     utils.print_cuda_info()
     free_gpus = utils.select_free_gpus()
     device = torch.device("cuda:{}".format(free_gpus[0]))
-    
+
     # test_RoBERTaGAT(device)
 
     # test_TextKGMessagePassing(device)
 
     # test_LMGNN(device)
 
-    test_GreaseLM(device)
+    test_GreaseLM(device)
diff --git a/run_greaselm__medqa_usmle.sh b/run_greaselm__medqa_usmle.sh
@@ -0,0 +1,69 @@
+#!/bin/bash
+export INHERIT_BERT=1
+export CUDA_VISIBLE_DEVICES=0
+export TOKENIZERS_PARALLELISM=true
+dt=`date '+%Y%m%d_%H%M%S'`
+
+
+dataset="medqa_usmle"
+shift
+encoder='cambridgeltl/SapBERT-from-PubMedBERT-fulltext'
+args=$@
+
+
+elr="5e-5"
+dlr="1e-3"
+bs=128
+mbs=2
+unfreeze_epoch=0
+k=3 #num of gnn layers
+gnndim=200
+
+# Existing arguments but changed for GreaseLM
+encoder_layer=-1
+max_node_num=200
+seed=5
+lr_schedule=fixed
+
+n_epochs=20
+max_epochs_before_stop=10
+ie_dim=400
+
+max_seq_len=512
+ent_emb=ddb
+inhouse=false
+
+# Added for GreaseLM
+info_exchange=true
+ie_layer_num=1
+resume_checkpoint=None
+resume_id=None
+sep_ie_layers=false
+random_ent_emb=false
+
+echo "***** hyperparameters *****"
+echo "dataset: $dataset"
+echo "enc_name: $encoder"
+echo "batch_size: $bs mini_batch_size: $mbs"
+echo "learning_rate: elr $elr dlr $dlr"
+echo "gnn: dim $gnndim layer $k"
+echo "ie_dim: ${ie_dim}, info_exchange: ${info_exchange}"
+echo "******************************"
+
+save_dir_pref='runs'
+mkdir -p $save_dir_pref
+
+run_name=greaselm__ds_${dataset}__ih_${inhouse}__enc_sapbert__k${k}__sd${seed}__iedim${ie_dim}__unfrz${unfreeze_epoch}__${dt}
+log=logs/train_${dataset}__${run_name}.log.txt
+
+###### Training ######
+python3 -u greaselm.py \
+    --dataset $dataset \
+    --encoder $encoder -k $k --gnn_dim $gnndim -elr $elr -dlr $dlr -bs $bs --seed $seed -mbs ${mbs} --unfreeze_epoch ${unfreeze_epoch} --encoder_layer=${encoder_layer} -sl ${max_seq_len} --max_node_num ${max_node_num} \
+    --n_epochs $n_epochs --max_epochs_before_stop ${max_epochs_before_stop} \
+    --save_dir ${save_dir_pref}/${dataset}/${run_name} \
+    --run_name ${run_name} \
+    --ie_dim ${ie_dim} --info_exchange ${info_exchange} --ie_layer_num ${ie_layer_num} --resume_checkpoint ${resume_checkpoint} --resume_id ${resume_id} --sep_ie_layers ${sep_ie_layers} --random_ent_emb ${random_ent_emb} --ent_emb ${ent_emb//,/ } --lr_schedule ${lr_schedule} -ih ${inhouse} \
+    --data_dir data \
+> ${log}
+# echo log: ${log}
diff --git a/utils_biomed/preprocess_medqa_usmle.ipynb b/utils_biomed/preprocess_medqa_usmle.ipynb
