adapt to super scirep format
Browse files- .gitignore +3 -1
- evaluation/embeddings_generator.py +3 -3
- evaluation/encoders.py +17 -10
- evaluation/eval_datasets.py +33 -44
- evaluation/evaluator.py +6 -6
- full_scirepeval_tasks.jsonl +17 -3
- scirepeval.py +4 -6
- scirepeval_tasks.jsonl +0 -1
- super_scirep.jsonl +16 -0
.gitignore
CHANGED
@@ -157,4 +157,6 @@ huggingface_hub/
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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-
.idea/
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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+
.idea/
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+
results/
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+
data/
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evaluation/embeddings_generator.py
CHANGED
@@ -15,11 +15,11 @@ class EmbeddingsGenerator:
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self.datasets = datasets
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self.models = models
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-
def generate_embeddings(self, save_path: str = None) -> Dict[str, np.ndarray]:
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results = dict()
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try:
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for dataset, model in zip(self.datasets, self.models):
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-
for batch, batch_ids in tqdm(dataset.batches(), total=len(dataset) // dataset.batch_size):
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emb = model(batch, batch_ids)
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for paper_id, embedding in zip(batch_ids, emb.unbind()):
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if type(paper_id) == tuple:
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@@ -50,4 +50,4 @@ class EmbeddingsGenerator:
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line_json = json.loads(line)
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embeddings[line_json['doc_id']] = np.array(line_json['embedding'], dtype=np.float16)
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logger.info(f"Loaded {len(embeddings)} embeddings")
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-
return embeddings
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self.datasets = datasets
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self.models = models
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+
def generate_embeddings(self, save_path: str = None, htrans=False, document=False) -> Dict[str, np.ndarray]:
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results = dict()
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try:
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21 |
for dataset, model in zip(self.datasets, self.models):
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+
for batch, batch_ids in tqdm(dataset.batches(htrans, document), total=len(dataset) // dataset.batch_size):
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emb = model(batch, batch_ids)
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for paper_id, embedding in zip(batch_ids, emb.unbind()):
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25 |
if type(paper_id) == tuple:
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50 |
line_json = json.loads(line)
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embeddings[line_json['doc_id']] = np.array(line_json['embedding'], dtype=np.float16)
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logger.info(f"Loaded {len(embeddings)} embeddings")
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+
return embeddings
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evaluation/encoders.py
CHANGED
@@ -74,7 +74,7 @@ class Model:
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logger.info(f"Task id used: {self._task_id}")
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self.hidden_dim = hidden_dim
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-
self.max_length = max_len
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self.use_fp16 = use_fp16
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@property
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@@ -241,26 +241,33 @@ class HModel:
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[np.concatenate([d[key] for d in sec_inputs]) for key in sec_inputs[0].keys()]))
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if self.config.max_doc_length > 1:
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for sample in batch:
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inputs.append(tokenize_document(self.tokenizer,sample, self.config.max_sent_length, self.config.max_sec_length, self.config.max_doc_length))
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input_ids = dict(zip(inputs[0].keys(), [torch.tensor(np.concatenate([d[key] for d in inputs])) for key in inputs[0].keys()]))
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else:
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for sample in batch:
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-
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tokenized_sample = self.tokenizer(sentences, padding="max_length", truncation=True,
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return_tensors="np", return_token_type_ids=False)
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inputs.append({"input_ids": np.row_stack([tokenized_sample["input_ids"]] + [pad_input_ids] * (self.config.max_sec_length - len(sentences))).reshape((1, self.config.max_sent_length*self.config.max_sec_length)),
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253 |
-
"attention_mask": np.row_stack([tokenized_sample["attention_mask"]] + [pad_attention_mask] * (self.config.max_sec_length - len(sentences))).reshape((1, self.config.max_sent_length*self.config.max_sec_length))
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input_ids = dict(zip(inputs[0].keys(), [torch.tensor(np.concatenate([d[key] for d in inputs])) for key in inputs[0].keys()]))
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input_ids = move_to_device(input_ids, "cuda")
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-
flops = FlopCountAnalysis(self.encoder, input_ids["input_ids"])
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-
def get_parameter_number(model):
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-
total_num = sum(p.numel() for p in model.parameters())
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-
trainable_num = sum(p.numel() for p in model.parameters() if p.requires_grad)
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-
return {'Total': total_num, 'Trainable': trainable_num}
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-
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-
num_para = get_parameter_number(self.encoder)
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if self.variant == "default":
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output = self.encoder(**input_ids)
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elif type(self._task_id) != dict:
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logger.info(f"Task id used: {self._task_id}")
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self.hidden_dim = hidden_dim
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+
self.max_length = max_len
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self.use_fp16 = use_fp16
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@property
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[np.concatenate([d[key] for d in sec_inputs]) for key in sec_inputs[0].keys()]))
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if self.config.max_doc_length > 1:
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for sample in batch:
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+
if type(sample) == str:
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+
sample = [[sample]]
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246 |
inputs.append(tokenize_document(self.tokenizer,sample, self.config.max_sent_length, self.config.max_sec_length, self.config.max_doc_length))
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input_ids = dict(zip(inputs[0].keys(), [torch.tensor(np.concatenate([d[key] for d in inputs])) for key in inputs[0].keys()]))
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else:
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for sample in batch:
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+
if type(sample) == str:
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+
sample = [sample]
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+
else:
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+
sample = list(chain.from_iterable(sample))
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+
sentences = sample[:self.config.max_sec_length]
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256 |
tokenized_sample = self.tokenizer(sentences, padding="max_length", truncation=True,
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257 |
return_tensors="np", return_token_type_ids=False)
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258 |
inputs.append({"input_ids": np.row_stack([tokenized_sample["input_ids"]] + [pad_input_ids] * (self.config.max_sec_length - len(sentences))).reshape((1, self.config.max_sent_length*self.config.max_sec_length)),
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259 |
+
"attention_mask": np.row_stack([tokenized_sample["attention_mask"]] + [pad_attention_mask] * (self.config.max_sec_length - len(sentences))).reshape((1, self.config.max_sent_length*self.config.max_sec_length)),
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260 |
+
"sec_mask": np.column_stack(
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261 |
+
[np.ones((1, tokenized_sample["input_ids"].shape[0]), dtype=np.int64)] + (
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262 |
+
self.config.max_sec_length - tokenized_sample["input_ids"].shape[0]) * [
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263 |
+
np.zeros((1, 1), dtype=np.int64)]),
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264 |
+
"head_ids": np.array(
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265 |
+
[[self.tokenizer.get_vocab()["<sec>"], self.tokenizer.get_vocab()["<doc>"]]],
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266 |
+
dtype=np.int64)
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267 |
+
})
|
268 |
input_ids = dict(zip(inputs[0].keys(), [torch.tensor(np.concatenate([d[key] for d in inputs])) for key in inputs[0].keys()]))
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input_ids = move_to_device(input_ids, "cuda")
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if self.variant == "default":
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output = self.encoder(**input_ids)
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elif type(self._task_id) != dict:
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evaluation/eval_datasets.py
CHANGED
@@ -10,11 +10,11 @@ logger = logging.getLogger(__name__)
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class SimpleDataset:
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11 |
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12 |
def __init__(self, data_path: Union[str, tuple], sep_token: str, batch_size=32,
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13 |
-
fields: List = None, key: str = None, processing_fn=None
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14 |
self.batch_size = batch_size
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15 |
self.sep_token = sep_token
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16 |
if not fields:
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-
fields = ["title", "abstract"
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self.fields = fields
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19 |
logger.info(f"Loading test metadata from {data_path}")
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if not processing_fn:
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@@ -27,67 +27,56 @@ class SimpleDataset:
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logger.info(f"Loaded {len(self.data)} documents")
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28 |
self.seen_ids = set()
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29 |
self.key = key
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30 |
-
self.document=document
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31 |
-
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32 |
def __len__(self):
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33 |
return len(self.data)
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-
def batches(self):
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-
return self.process_batches(self.data)
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38 |
-
def process_batches(self, data: Union[datasets.Dataset, List]):
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39 |
# create batches
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batch = []
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batch_ids = []
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42 |
batch_size = self.batch_size
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i = 0
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-
if self.
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-
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-
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-
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-
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-
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-
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-
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-
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-
# text = (f" {self.sep_token} ".join(text)).strip()
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54 |
-
if (i) % batch_size != 0 or i == 0:
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55 |
-
batch_ids.append(bid)
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56 |
-
batch.append(text)
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57 |
-
else:
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58 |
-
yield batch, batch_ids
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59 |
-
batch_ids = [bid]
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60 |
-
batch = [text]
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61 |
-
i += 1
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62 |
-
else:
|
63 |
-
key = "doc_id" if not self.key else self.key
|
64 |
-
for d in data:
|
65 |
-
if key in d and d[key] not in self.seen_ids:
|
66 |
-
bid = d[key]
|
67 |
-
self.seen_ids.add(bid)
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68 |
text = []
|
69 |
for field in self.fields:
|
70 |
if d.get(field):
|
71 |
text.append(str(d[field]))
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72 |
text = (f" {self.sep_token} ".join(text)).strip()
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-
if
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-
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-
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-
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-
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-
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-
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-
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if len(batch) > 0:
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yield batch, batch_ids
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83 |
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84 |
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85 |
class IRDataset(SimpleDataset):
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86 |
-
def __init__(self, data_path, sep_token, batch_size=32, fields=None, key=None, processing_fn=None
|
87 |
-
super().__init__(data_path, sep_token, batch_size, fields, key, processing_fn
|
88 |
self.queries, self.candidates = [], []
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|
89 |
for d in self.data:
|
90 |
if type(d["query"]) == str:
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|
91 |
self.queries.append({"title": d["query"], "doc_id": d["doc_id"]})
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92 |
else:
|
93 |
self.queries.append(d["query"])
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@@ -96,9 +85,9 @@ class IRDataset(SimpleDataset):
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|
96 |
def __len__(self):
|
97 |
return len(self.queries) + len(self.candidates)
|
98 |
|
99 |
-
def batches(self):
|
100 |
-
query_gen = self.process_batches(self.queries)
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101 |
-
cand_gen = self.process_batches(self.candidates)
|
102 |
for q, q_ids in query_gen:
|
103 |
q_ids = [(v, "q") for v in q_ids]
|
104 |
yield q, q_ids
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|
10 |
class SimpleDataset:
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11 |
|
12 |
def __init__(self, data_path: Union[str, tuple], sep_token: str, batch_size=32,
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13 |
+
fields: List = None, key: str = None, processing_fn=None):
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14 |
self.batch_size = batch_size
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15 |
self.sep_token = sep_token
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16 |
if not fields:
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17 |
+
fields = ["title", "abstract"]
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18 |
self.fields = fields
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19 |
logger.info(f"Loading test metadata from {data_path}")
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20 |
if not processing_fn:
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27 |
logger.info(f"Loaded {len(self.data)} documents")
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28 |
self.seen_ids = set()
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29 |
self.key = key
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|
30 |
def __len__(self):
|
31 |
return len(self.data)
|
32 |
|
33 |
+
def batches(self, htrans=False, document=False):
|
34 |
+
return self.process_batches(self.data, htrans=htrans, document=document)
|
35 |
|
36 |
+
def process_batches(self, data: Union[datasets.Dataset, List], htrans=False, document=False):
|
37 |
# create batches
|
38 |
batch = []
|
39 |
batch_ids = []
|
40 |
batch_size = self.batch_size
|
41 |
i = 0
|
42 |
+
key = "doc_id" if not self.key else self.key
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43 |
+
for d in data:
|
44 |
+
if key in d and d[key] not in self.seen_ids:
|
45 |
+
bid = d[key]
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46 |
+
self.seen_ids.add(bid)
|
47 |
+
if htrans:
|
48 |
+
text = [[d["title"]] + sent_tokenize(d["abstract"])]
|
49 |
+
text += [[i["title"]] + i["sentences"] for i in d["full_text"]]
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50 |
+
else:
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51 |
text = []
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52 |
for field in self.fields:
|
53 |
if d.get(field):
|
54 |
text.append(str(d[field]))
|
55 |
text = (f" {self.sep_token} ".join(text)).strip()
|
56 |
+
if document:
|
57 |
+
for sec in d.get("full_text", []):
|
58 |
+
text += (sec["title"] + " ")
|
59 |
+
text += "".join(sec["sentences"])
|
60 |
+
if (i) % batch_size != 0 or i == 0:
|
61 |
+
batch_ids.append(bid)
|
62 |
+
batch.append(text)
|
63 |
+
else:
|
64 |
+
yield batch, batch_ids
|
65 |
+
batch_ids = [bid]
|
66 |
+
batch = [text]
|
67 |
+
i += 1
|
68 |
if len(batch) > 0:
|
69 |
yield batch, batch_ids
|
70 |
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71 |
|
72 |
class IRDataset(SimpleDataset):
|
73 |
+
def __init__(self, data_path, sep_token, batch_size=32, fields=None, key=None, processing_fn=None):
|
74 |
+
super().__init__(data_path, sep_token, batch_size, fields, key, processing_fn)
|
75 |
self.queries, self.candidates = [], []
|
76 |
+
self.search = False
|
77 |
for d in self.data:
|
78 |
if type(d["query"]) == str:
|
79 |
+
self.search = True
|
80 |
self.queries.append({"title": d["query"], "doc_id": d["doc_id"]})
|
81 |
else:
|
82 |
self.queries.append(d["query"])
|
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|
85 |
def __len__(self):
|
86 |
return len(self.queries) + len(self.candidates)
|
87 |
|
88 |
+
def batches(self, htrans=False, document=False):
|
89 |
+
query_gen = self.process_batches(self.queries, htrans=htrans and self.search, document=document and self.search)
|
90 |
+
cand_gen = self.process_batches(self.candidates, htrans=htrans, document=document)
|
91 |
for q, q_ids in query_gen:
|
92 |
q_ids = [(v, "q") for v in q_ids]
|
93 |
yield q, q_ids
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evaluation/evaluator.py
CHANGED
@@ -26,7 +26,7 @@ RANDOM_STATE = 42
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26 |
|
27 |
class Evaluator:
|
28 |
def __init__(self, name: str, meta_dataset: Union[str, tuple], dataset_class, model: Model, batch_size: int,
|
29 |
-
fields: list, key: str = None, process_fn=None
|
30 |
if model:
|
31 |
if type(model) != list:
|
32 |
model = [model]
|
@@ -37,13 +37,13 @@ class Evaluator:
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|
37 |
# m.tokenizer.sep_token = m.tokenizer.eos_token
|
38 |
# m.encoder.resize_token_embeddings(len(m.tokenizer))
|
39 |
datasets = [dataset_class(meta_dataset, m.tokenizer.sep_token, batch_size, fields, key,
|
40 |
-
process_fn
|
41 |
self.embeddings_generator = EmbeddingsGenerator(datasets, model)
|
42 |
self.name = name
|
43 |
|
44 |
-
def generate_embeddings(self, save_path: str = None):
|
45 |
logger.info("Generating embeddings... this might take a while")
|
46 |
-
return self.embeddings_generator.generate_embeddings(save_path)
|
47 |
|
48 |
@abstractmethod
|
49 |
def evaluate(self, embeddings: Union[str, Dict[str, np.ndarray]], **kwargs) -> Dict[str, float]:
|
@@ -172,8 +172,8 @@ class SupervisedEvaluator(Evaluator):
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172 |
|
173 |
class IREvaluator(Evaluator):
|
174 |
def __init__(self, name: str, meta_dataset: Union[str, tuple], test_dataset: Union[str, tuple], model: Model,
|
175 |
-
metrics: tuple, dataset_class=IRDataset, batch_size: int = 16, fields: list = None, key=None
|
176 |
-
super(IREvaluator, self).__init__(name, meta_dataset, dataset_class, model, batch_size, fields, key
|
177 |
self.test_dataset = test_dataset
|
178 |
self.metrics = metrics
|
179 |
|
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|
26 |
|
27 |
class Evaluator:
|
28 |
def __init__(self, name: str, meta_dataset: Union[str, tuple], dataset_class, model: Model, batch_size: int,
|
29 |
+
fields: list, key: str = None, process_fn=None):
|
30 |
if model:
|
31 |
if type(model) != list:
|
32 |
model = [model]
|
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|
37 |
# m.tokenizer.sep_token = m.tokenizer.eos_token
|
38 |
# m.encoder.resize_token_embeddings(len(m.tokenizer))
|
39 |
datasets = [dataset_class(meta_dataset, m.tokenizer.sep_token, batch_size, fields, key,
|
40 |
+
process_fn) for m in model]
|
41 |
self.embeddings_generator = EmbeddingsGenerator(datasets, model)
|
42 |
self.name = name
|
43 |
|
44 |
+
def generate_embeddings(self, save_path: str = None, htrans=False, document=False):
|
45 |
logger.info("Generating embeddings... this might take a while")
|
46 |
+
return self.embeddings_generator.generate_embeddings(save_path, htrans, document)
|
47 |
|
48 |
@abstractmethod
|
49 |
def evaluate(self, embeddings: Union[str, Dict[str, np.ndarray]], **kwargs) -> Dict[str, float]:
|
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|
172 |
|
173 |
class IREvaluator(Evaluator):
|
174 |
def __init__(self, name: str, meta_dataset: Union[str, tuple], test_dataset: Union[str, tuple], model: Model,
|
175 |
+
metrics: tuple, dataset_class=IRDataset, batch_size: int = 16, fields: list = None, key=None):
|
176 |
+
super(IREvaluator, self).__init__(name, meta_dataset, dataset_class, model, batch_size, fields, key)
|
177 |
self.test_dataset = test_dataset
|
178 |
self.metrics = metrics
|
179 |
|
full_scirepeval_tasks.jsonl
CHANGED
@@ -1,3 +1,17 @@
|
|
1 |
-
{"name":"Feeds-1","type":"proximity","data":{"meta":{"name":"
|
2 |
-
{"name":"Feeds-M","type":"proximity","data":{"meta":{"name":"
|
3 |
-
{"name":"Highly Influential Citations","type":"proximity","data":{"meta":{"name":"
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{"name":"Feeds-1","type":"proximity","data":{"meta":{"name":"allenai/scirepeval","config":"feeds_1"},"test":{"name":"allenai/scirepeval_test","config":"feeds_1"}},"metrics":["map"]}
|
2 |
+
{"name":"Feeds-M","type":"proximity","data":{"meta":{"name":"allenai/scirepeval","config":"feeds_m"},"test":{"name":"allenai/scirepeval_test","config":"feeds_m"}},"metrics":["map"]}
|
3 |
+
{"name":"Highly Influential Citations","type":"proximity","data":{"meta":{"name":"allenai/scirepeval","config":"high_influence_cite"},"test":{"name":"allenai/scirepeval_test","config":"high_influence_cite"}},"metrics":["map"]}
|
4 |
+
{"name":"SciDocs Cite","type":"proximity","data":{"simple_format":true, "meta":{"name":"allenai/scirepeval","config":"scidocs_view_cite_read"},"test":{"name":"allenai/scirepeval_test","config":"scidocs_cite"}},"embeddings":{"save":"embeddings/scidocs_view_cite_read.jsonl"},"metrics":["map","ndcg"]}
|
5 |
+
{"name":"SciDocs CoCite","type":"proximity","data":{"simple_format":true, "meta":{"name":"allenai/scirepeval","config":"scidocs_view_cite_read"},"test":{"name":"allenai/scirepeval_test","config":"scidocs_cocite"}},"embeddings":{"load":"embeddings/scidocs_view_cite_read.jsonl"},"metrics":["map","ndcg"]}
|
6 |
+
{"name":"Fields of study","type":"classification","data":{"meta":{"name":"allenai/scirepeval","config":"fos"},"test":{"name":"allenai/scirepeval_test","config":"fos"}},"metrics":["f1_macro"],"few_shot":[{"sample_size":10,"iterations":50},{"sample_size":5,"iterations":100}],"multi_label":true}
|
7 |
+
{"name":"Publication Year","type":"regression","data":{"meta":{"name":"allenai/scirepeval","config":"pub_year"},"test":{"name":"allenai/scirepeval_test","config":"pub_year"}},"metrics":["kendalltau"]}
|
8 |
+
{"name":"Search","type":"adhoc_search","data":{"meta":{"name":"allenai/scirepeval","config":"search"},"test":{"name":"allenai/scirepeval_test","config":"search"}},"fields":["title","abstract","venue","year"],"metrics":["ndcg"]}
|
9 |
+
{"name":"Feeds Title","type":"adhoc_search","data":{"meta":{"name":"allenai/scirepeval","config":"feeds_title"},"test":{"name":"allenai/scirepeval_test","config":"feeds_title"}},"metrics":["map"]}
|
10 |
+
{"name":"Paper-Reviewer Matching","type":"proximity","data":{"meta":{"name":"allenai/scirepeval","config":"paper_reviewer_matching"},"test":{"name":"allenai/scirepeval_test","config":"paper_reviewer_matching"},"reviewers":{"name":"allenai/scirepeval_test","config":"reviewers"}},"metrics":["P_5", "P_10"]}
|
11 |
+
{"name":"SciDocs CoView","type":"proximity","data":{"simple_format":true, "meta":{"name":"allenai/scirepeval","config":"scidocs_view_cite_read"},"test":{"name":"allenai/scirepeval_test","config":"scidocs_view"}},"embeddings":{"load":"embeddings/scidocs_view_cite_read.jsonl"},"metrics":["map","ndcg"]}
|
12 |
+
{"name":"SciDocs CoRead","type":"proximity","data":{"simple_format":true, "meta":{"name":"allenai/scirepeval","config":"scidocs_view_cite_read"},"test":{"name":"allenai/scirepeval_test","config":"scidocs_read"}},"embeddings":{"load":"embeddings/scidocs_view_cite_read.jsonl"},"metrics":["map","ndcg"]}
|
13 |
+
{"name":"Peer Review Score","type":"regression","data":{"meta":{"name":"allenai/scirepeval","config":"peer_review_score_hIndex"},"test":{"name":"allenai/scirepeval_test","config":"peer_review_score"}},"embeddings":{"save":"embeddings/peer_review_score_hIndex.jsonl"},"metrics":["kendalltau"]}
|
14 |
+
{"name":"Max hIndex","type":"regression","data":{"meta":{"name":"allenai/scirepeval","config":"peer_review_score_hIndex"},"test":{"name":"allenai/scirepeval_test","config":"hIndex"}},"embeddings":{"load":"embeddings/peer_review_score_hIndex.jsonl"},"metrics":["kendalltau"]}
|
15 |
+
{"name":"Tweet Mentions","type":"regression","data":{"meta":{"name":"allenai/scirepeval","config":"tweet_mentions"},"test":{"name":"allenai/scirepeval_test","config":"tweet_mentions"}},"metrics":["kendalltau"]}
|
16 |
+
{"name":"Citation Count","type":"regression","data":{"meta":{"name":"allenai/scirepeval","config":"cite_count"},"test":{"name":"allenai/scirepeval_test","config":"cite_count"}},"metrics":["kendalltau"]}
|
17 |
+
|
scirepeval.py
CHANGED
@@ -20,7 +20,7 @@ pl.seed_everything(42, workers=True)
|
|
20 |
|
21 |
class SciRepEval:
|
22 |
|
23 |
-
def __init__(self, tasks_config: str = "
|
24 |
task_formats: List[str] = None, batch_size: int = 32, document=False):
|
25 |
tasks_dict = dict()
|
26 |
task_by_formats = dict()
|
@@ -101,8 +101,8 @@ class SciRepEval:
|
|
101 |
evaluator = ReviewerMatchingEvaluator(task_name, model=model, **kwargs)
|
102 |
else:
|
103 |
data_class = SimpleDataset if task_data.get("simple_format") else IRDataset
|
104 |
-
evaluator = IREvaluator(task_name, model=model, dataset_class=data_class,
|
105 |
-
embeddings = evaluator.generate_embeddings(save_path) if not load_path else load_path
|
106 |
results = evaluator.evaluate(embeddings)
|
107 |
if not few_shot_evaluators:
|
108 |
final_results[task_name] = results
|
@@ -121,10 +121,8 @@ class SciRepEval:
|
|
121 |
|
122 |
|
123 |
if __name__ == "__main__":
|
124 |
-
import datasets
|
125 |
-
datasets.load_dataset('howey/super_scirep', "cite_count")
|
126 |
parser = argparse.ArgumentParser()
|
127 |
-
parser.add_argument('--tasks-config', help='path to the task config file', default="
|
128 |
parser.add_argument('--mtype', help='Model variant to be used (default, pals, adapters, fusion)', default="default")
|
129 |
parser.add_argument('--gpt3-model', help='Name of embedding model in case of using openai api', default=None)
|
130 |
parser.add_argument('--model', '-m', help='HuggingFace model to be used')
|
|
|
20 |
|
21 |
class SciRepEval:
|
22 |
|
23 |
+
def __init__(self, tasks_config: str = "super_scirep.jsonl", task_list: List[str] = None,
|
24 |
task_formats: List[str] = None, batch_size: int = 32, document=False):
|
25 |
tasks_dict = dict()
|
26 |
task_by_formats = dict()
|
|
|
101 |
evaluator = ReviewerMatchingEvaluator(task_name, model=model, **kwargs)
|
102 |
else:
|
103 |
data_class = SimpleDataset if task_data.get("simple_format") else IRDataset
|
104 |
+
evaluator = IREvaluator(task_name, model=model, dataset_class=data_class, **kwargs)
|
105 |
+
embeddings = evaluator.generate_embeddings(save_path, htrans=args.htrans, document=args.document) if not load_path else load_path
|
106 |
results = evaluator.evaluate(embeddings)
|
107 |
if not few_shot_evaluators:
|
108 |
final_results[task_name] = results
|
|
|
121 |
|
122 |
|
123 |
if __name__ == "__main__":
|
|
|
|
|
124 |
parser = argparse.ArgumentParser()
|
125 |
+
parser.add_argument('--tasks-config', help='path to the task config file', default="super_scirep.jsonl")
|
126 |
parser.add_argument('--mtype', help='Model variant to be used (default, pals, adapters, fusion)', default="default")
|
127 |
parser.add_argument('--gpt3-model', help='Name of embedding model in case of using openai api', default=None)
|
128 |
parser.add_argument('--model', '-m', help='HuggingFace model to be used')
|
scirepeval_tasks.jsonl
CHANGED
@@ -4,7 +4,6 @@
|
|
4 |
{"name":"Feeds-M","type":"proximity","data":{"meta":{"name":"allenai/scirepeval","config":"feeds_m"},"test":{"name":"allenai/scirepeval_test","config":"feeds_m"}},"metrics":["map"]}
|
5 |
{"name":"Feeds Title","type":"adhoc_search","data":{"meta":{"name":"allenai/scirepeval","config":"feeds_title"},"test":{"name":"allenai/scirepeval_test","config":"feeds_title"}},"metrics":["map"]}
|
6 |
{"name":"TREC-CoVID","type":"adhoc_search","data":{"meta":{"name":"allenai/scirepeval","config":"trec_covid"},"test":{"name":"allenai/scirepeval_test","config":"trec_covid"}},"metrics":["ndcg"]}
|
7 |
-
{"name":"Paper-Reviewer Matching","type":"proximity","data":{"meta":{"name":"allenai/scirepeval","config":"paper_reviewer_matching"},"test":{"name":"allenai/scirepeval_test","config":"paper_reviewer_matching"},"reviewers":{"name":"allenai/scirepeval_test","config":"reviewers"}},"metrics":["P_5", "P_10"]}
|
8 |
{"name":"Peer Review Score","type":"regression","data":{"meta":{"name":"allenai/scirepeval","config":"peer_review_score_hIndex"},"test":{"name":"allenai/scirepeval_test","config":"peer_review_score"}},"embeddings":{"save":"embeddings/peer_review_score_hIndex.jsonl"},"metrics":["kendalltau"]}
|
9 |
{"name":"Max hIndex","type":"regression","data":{"meta":{"name":"allenai/scirepeval","config":"peer_review_score_hIndex"},"test":{"name":"allenai/scirepeval_test","config":"hIndex"}},"embeddings":{"load":"embeddings/peer_review_score_hIndex.jsonl"},"metrics":["kendalltau"]}
|
10 |
{"name":"Tweet Mentions","type":"regression","data":{"meta":{"name":"allenai/scirepeval","config":"tweet_mentions"},"test":{"name":"allenai/scirepeval_test","config":"tweet_mentions"}},"metrics":["kendalltau"]}
|
|
|
4 |
{"name":"Feeds-M","type":"proximity","data":{"meta":{"name":"allenai/scirepeval","config":"feeds_m"},"test":{"name":"allenai/scirepeval_test","config":"feeds_m"}},"metrics":["map"]}
|
5 |
{"name":"Feeds Title","type":"adhoc_search","data":{"meta":{"name":"allenai/scirepeval","config":"feeds_title"},"test":{"name":"allenai/scirepeval_test","config":"feeds_title"}},"metrics":["map"]}
|
6 |
{"name":"TREC-CoVID","type":"adhoc_search","data":{"meta":{"name":"allenai/scirepeval","config":"trec_covid"},"test":{"name":"allenai/scirepeval_test","config":"trec_covid"}},"metrics":["ndcg"]}
|
|
|
7 |
{"name":"Peer Review Score","type":"regression","data":{"meta":{"name":"allenai/scirepeval","config":"peer_review_score_hIndex"},"test":{"name":"allenai/scirepeval_test","config":"peer_review_score"}},"embeddings":{"save":"embeddings/peer_review_score_hIndex.jsonl"},"metrics":["kendalltau"]}
|
8 |
{"name":"Max hIndex","type":"regression","data":{"meta":{"name":"allenai/scirepeval","config":"peer_review_score_hIndex"},"test":{"name":"allenai/scirepeval_test","config":"hIndex"}},"embeddings":{"load":"embeddings/peer_review_score_hIndex.jsonl"},"metrics":["kendalltau"]}
|
9 |
{"name":"Tweet Mentions","type":"regression","data":{"meta":{"name":"allenai/scirepeval","config":"tweet_mentions"},"test":{"name":"allenai/scirepeval_test","config":"tweet_mentions"}},"metrics":["kendalltau"]}
|
super_scirep.jsonl
ADDED
@@ -0,0 +1,16 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
{"name":"Feeds-1","type":"proximity","data":{"meta":{"name":"howey/super_scirep","config":"feeds_1"},"test":{"name":"howey/super_scirep_test","config":"feeds_1"}},"metrics":["map"]}
|
2 |
+
{"name":"Feeds-M","type":"proximity","data":{"meta":{"name":"howey/super_scirep","config":"feeds_m"},"test":{"name":"howey/super_scirep_test","config":"feeds_m"}},"metrics":["map"]}
|
3 |
+
{"name":"Highly Influential Citations","type":"proximity","data":{"meta":{"name":"howey/super_scirep","config":"high_influence_cite"},"test":{"name":"howey/super_scirep_test","config":"high_influence_cite"}},"metrics":["map"]}
|
4 |
+
{"name":"SciDocs Cite","type":"proximity","data":{"simple_format":true, "meta":{"name":"howey/super_scirep","config":"scidocs_view_cite_read"},"test":{"name":"howey/super_scirep_test","config":"scidocs_cite"}},"embeddings":{"save":"embeddings/scidocs_view_cite_read.jsonl"},"metrics":["map","ndcg"]}
|
5 |
+
{"name":"SciDocs CoCite","type":"proximity","data":{"simple_format":true, "meta":{"name":"howey/super_scirep","config":"scidocs_view_cite_read"},"test":{"name":"howey/super_scirep_test","config":"scidocs_cocite"}},"embeddings":{"load":"embeddings/scidocs_view_cite_read.jsonl"},"metrics":["map","ndcg"]}
|
6 |
+
{"name":"Fields of study","type":"classification","data":{"meta":{"name":"howey/super_scirep","config":"fos"},"test":{"name":"howey/super_scirep_test","config":"fos"}},"metrics":["f1_macro"],"few_shot":[{"sample_size":10,"iterations":50},{"sample_size":5,"iterations":100}],"multi_label":true}
|
7 |
+
{"name":"Publication Year","type":"regression","data":{"meta":{"name":"howey/super_scirep","config":"pub_year"},"test":{"name":"howey/super_scirep_test","config":"pub_year"}},"metrics":["kendalltau"]}
|
8 |
+
{"name":"Search","type":"adhoc_search","data":{"meta":{"name":"howey/super_scirep","config":"search"},"test":{"name":"howey/super_scirep_test","config":"search"}},"fields":["title","abstract","venue","year"],"metrics":["ndcg"]}
|
9 |
+
{"name":"Feeds Title","type":"adhoc_search","data":{"meta":{"name":"howey/super_scirep","config":"feeds_title"},"test":{"name":"howey/super_scirep_test","config":"feeds_title"}},"metrics":["map"]}
|
10 |
+
{"name":"Paper-Reviewer Matching","type":"proximity","data":{"meta":{"name":"howey/super_scirep","config":"paper_reviewer_matching"},"test":{"name":"howey/super_scirep_test","config":"paper_reviewer_matching"},"reviewers":{"name":"howey/super_scirep_test","config":"reviewers"}},"metrics":["P_5", "P_10"]}
|
11 |
+
{"name":"SciDocs CoView","type":"proximity","data":{"simple_format":true, "meta":{"name":"howey/super_scirep","config":"scidocs_view_cite_read"},"test":{"name":"howey/super_scirep_test","config":"scidocs_view"}},"embeddings":{"load":"embeddings/scidocs_view_cite_read.jsonl"},"metrics":["map","ndcg"]}
|
12 |
+
{"name":"SciDocs CoRead","type":"proximity","data":{"simple_format":true, "meta":{"name":"howey/super_scirep","config":"scidocs_view_cite_read"},"test":{"name":"howey/super_scirep_test","config":"scidocs_read"}},"embeddings":{"load":"embeddings/scidocs_view_cite_read.jsonl"},"metrics":["map","ndcg"]}
|
13 |
+
{"name":"Peer Review Score","type":"regression","data":{"meta":{"name":"howey/super_scirep","config":"peer_review_score_hIndex"},"test":{"name":"howey/super_scirep_test","config":"peer_review_score"}},"embeddings":{"save":"embeddings/peer_review_score_hIndex.jsonl"},"metrics":["kendalltau"]}
|
14 |
+
{"name":"Max hIndex","type":"regression","data":{"meta":{"name":"howey/super_scirep","config":"peer_review_score_hIndex"},"test":{"name":"howey/super_scirep_test","config":"hIndex"}},"embeddings":{"load":"embeddings/peer_review_score_hIndex.jsonl"},"metrics":["kendalltau"]}
|
15 |
+
{"name":"Tweet Mentions","type":"regression","data":{"meta":{"name":"howey/super_scirep","config":"tweet_mentions"},"test":{"name":"howey/super_scirep_test","config":"tweet_mentions"}},"metrics":["kendalltau"]}
|
16 |
+
{"name":"Citation Count","type":"regression","data":{"meta":{"name":"howey/super_scirep","config":"cite_count"},"test":{"name":"howey/super_scirep_test","config":"cite_count"}},"metrics":["kendalltau"]}
|