howey commited on
Commit
33b0cae
1 Parent(s): a63d03e

adapt to super scirep format

Browse files
.gitignore CHANGED
@@ -157,4 +157,6 @@ huggingface_hub/
157
  # be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
158
  # and can be added to the global gitignore or merged into this file. For a more nuclear
159
  # option (not recommended) you can uncomment the following to ignore the entire idea folder.
160
- .idea/
 
 
 
157
  # be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
158
  # and can be added to the global gitignore or merged into this file. For a more nuclear
159
  # option (not recommended) you can uncomment the following to ignore the entire idea folder.
160
+ .idea/
161
+ results/
162
+ data/
evaluation/embeddings_generator.py CHANGED
@@ -15,11 +15,11 @@ class EmbeddingsGenerator:
15
  self.datasets = datasets
16
  self.models = models
17
 
18
- def generate_embeddings(self, save_path: str = None) -> Dict[str, np.ndarray]:
19
  results = dict()
20
  try:
21
  for dataset, model in zip(self.datasets, self.models):
22
- for batch, batch_ids in tqdm(dataset.batches(), total=len(dataset) // dataset.batch_size):
23
  emb = model(batch, batch_ids)
24
  for paper_id, embedding in zip(batch_ids, emb.unbind()):
25
  if type(paper_id) == tuple:
@@ -50,4 +50,4 @@ class EmbeddingsGenerator:
50
  line_json = json.loads(line)
51
  embeddings[line_json['doc_id']] = np.array(line_json['embedding'], dtype=np.float16)
52
  logger.info(f"Loaded {len(embeddings)} embeddings")
53
- return embeddings
 
15
  self.datasets = datasets
16
  self.models = models
17
 
18
+ def generate_embeddings(self, save_path: str = None, htrans=False, document=False) -> Dict[str, np.ndarray]:
19
  results = dict()
20
  try:
21
  for dataset, model in zip(self.datasets, self.models):
22
+ for batch, batch_ids in tqdm(dataset.batches(htrans, document), total=len(dataset) // dataset.batch_size):
23
  emb = model(batch, batch_ids)
24
  for paper_id, embedding in zip(batch_ids, emb.unbind()):
25
  if type(paper_id) == tuple:
 
50
  line_json = json.loads(line)
51
  embeddings[line_json['doc_id']] = np.array(line_json['embedding'], dtype=np.float16)
52
  logger.info(f"Loaded {len(embeddings)} embeddings")
53
+ return embeddings
evaluation/encoders.py CHANGED
@@ -74,7 +74,7 @@ class Model:
74
  logger.info(f"Task id used: {self._task_id}")
75
 
76
  self.hidden_dim = hidden_dim
77
- self.max_length = max_len #self.tokenizer.model_max_length
78
  self.use_fp16 = use_fp16
79
 
80
  @property
@@ -241,26 +241,33 @@ class HModel:
241
  [np.concatenate([d[key] for d in sec_inputs]) for key in sec_inputs[0].keys()]))
242
  if self.config.max_doc_length > 1:
243
  for sample in batch:
 
 
244
  inputs.append(tokenize_document(self.tokenizer,sample, self.config.max_sent_length, self.config.max_sec_length, self.config.max_doc_length))
245
  input_ids = dict(zip(inputs[0].keys(), [torch.tensor(np.concatenate([d[key] for d in inputs])) for key in inputs[0].keys()]))
246
 
247
  else:
248
  for sample in batch:
249
- sentences = sent_tokenize(sample.replace("[SEP]", "."))[:self.config.max_sec_length]
 
 
 
 
250
  tokenized_sample = self.tokenizer(sentences, padding="max_length", truncation=True,
251
  return_tensors="np", return_token_type_ids=False)
252
  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)),
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))})
 
 
 
 
 
 
 
 
254
  input_ids = dict(zip(inputs[0].keys(), [torch.tensor(np.concatenate([d[key] for d in inputs])) for key in inputs[0].keys()]))
255
  input_ids = move_to_device(input_ids, "cuda")
256
- flops = FlopCountAnalysis(self.encoder, input_ids["input_ids"])
257
 
258
- def get_parameter_number(model):
259
- total_num = sum(p.numel() for p in model.parameters())
260
- trainable_num = sum(p.numel() for p in model.parameters() if p.requires_grad)
261
- return {'Total': total_num, 'Trainable': trainable_num}
262
-
263
- num_para = get_parameter_number(self.encoder)
264
  if self.variant == "default":
265
  output = self.encoder(**input_ids)
266
  elif type(self._task_id) != dict:
 
74
  logger.info(f"Task id used: {self._task_id}")
75
 
76
  self.hidden_dim = hidden_dim
77
+ self.max_length = max_len
78
  self.use_fp16 = use_fp16
79
 
80
  @property
 
241
  [np.concatenate([d[key] for d in sec_inputs]) for key in sec_inputs[0].keys()]))
242
  if self.config.max_doc_length > 1:
243
  for sample in batch:
244
+ if type(sample) == str:
245
+ sample = [[sample]]
246
  inputs.append(tokenize_document(self.tokenizer,sample, self.config.max_sent_length, self.config.max_sec_length, self.config.max_doc_length))
247
  input_ids = dict(zip(inputs[0].keys(), [torch.tensor(np.concatenate([d[key] for d in inputs])) for key in inputs[0].keys()]))
248
 
249
  else:
250
  for sample in batch:
251
+ if type(sample) == str:
252
+ sample = [sample]
253
+ else:
254
+ sample = list(chain.from_iterable(sample))
255
+ sentences = sample[:self.config.max_sec_length]
256
  tokenized_sample = self.tokenizer(sentences, padding="max_length", truncation=True,
257
  return_tensors="np", return_token_type_ids=False)
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)),
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)),
260
+ "sec_mask": np.column_stack(
261
+ [np.ones((1, tokenized_sample["input_ids"].shape[0]), dtype=np.int64)] + (
262
+ self.config.max_sec_length - tokenized_sample["input_ids"].shape[0]) * [
263
+ np.zeros((1, 1), dtype=np.int64)]),
264
+ "head_ids": np.array(
265
+ [[self.tokenizer.get_vocab()["<sec>"], self.tokenizer.get_vocab()["<doc>"]]],
266
+ dtype=np.int64)
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()]))
269
  input_ids = move_to_device(input_ids, "cuda")
 
270
 
 
 
 
 
 
 
271
  if self.variant == "default":
272
  output = self.encoder(**input_ids)
273
  elif type(self._task_id) != dict:
evaluation/eval_datasets.py CHANGED
@@ -10,11 +10,11 @@ logger = logging.getLogger(__name__)
10
  class SimpleDataset:
11
 
12
  def __init__(self, data_path: Union[str, tuple], sep_token: str, batch_size=32,
13
- fields: List = None, key: str = None, processing_fn=None, document=False):
14
  self.batch_size = batch_size
15
  self.sep_token = sep_token
16
  if not fields:
17
- fields = ["title", "abstract", "full_text"]
18
  self.fields = fields
19
  logger.info(f"Loading test metadata from {data_path}")
20
  if not processing_fn:
@@ -27,67 +27,56 @@ class SimpleDataset:
27
  logger.info(f"Loaded {len(self.data)} documents")
28
  self.seen_ids = set()
29
  self.key = key
30
- self.document=document
31
-
32
  def __len__(self):
33
  return len(self.data)
34
 
35
- def batches(self):
36
- return self.process_batches(self.data)
37
 
38
- def process_batches(self, data: Union[datasets.Dataset, List]):
39
  # create batches
40
  batch = []
41
  batch_ids = []
42
  batch_size = self.batch_size
43
  i = 0
44
- if self.document:
45
- key = "corpus_id" if not self.key else self.key
46
- for d in data:
47
- if key in d and str(d[key]) not in self.seen_ids:
48
- bid = str(d[key])
49
- self.seen_ids.add(bid)
50
- if "full_text" in d and d["full_text"] != []:
51
- text = [[d["title"]] + sent_tokenize(d["abstract"])]
52
- text += [[i["title"]] + i["sentences"] for i in d["full_text"]]
53
- # text = (f" {self.sep_token} ".join(text)).strip()
54
- if (i) % batch_size != 0 or i == 0:
55
- batch_ids.append(bid)
56
- batch.append(text)
57
- else:
58
- yield batch, batch_ids
59
- batch_ids = [bid]
60
- batch = [text]
61
- i += 1
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)
68
  text = []
69
  for field in self.fields:
70
  if d.get(field):
71
  text.append(str(d[field]))
72
  text = (f" {self.sep_token} ".join(text)).strip()
73
- if (i) % batch_size != 0 or i == 0:
74
- batch_ids.append(bid)
75
- batch.append(text)
76
- else:
77
- yield batch, batch_ids
78
- batch_ids = [bid]
79
- batch = [text]
80
- i += 1
 
 
 
 
81
  if len(batch) > 0:
82
  yield batch, batch_ids
83
 
84
 
85
  class IRDataset(SimpleDataset):
86
- def __init__(self, data_path, sep_token, batch_size=32, fields=None, key=None, processing_fn=None, document=False):
87
- super().__init__(data_path, sep_token, batch_size, fields, key, processing_fn, document)
88
  self.queries, self.candidates = [], []
 
89
  for d in self.data:
90
  if type(d["query"]) == str:
 
91
  self.queries.append({"title": d["query"], "doc_id": d["doc_id"]})
92
  else:
93
  self.queries.append(d["query"])
@@ -96,9 +85,9 @@ class IRDataset(SimpleDataset):
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)
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
 
10
  class SimpleDataset:
11
 
12
  def __init__(self, data_path: Union[str, tuple], sep_token: str, batch_size=32,
13
+ fields: List = None, key: str = None, processing_fn=None):
14
  self.batch_size = batch_size
15
  self.sep_token = sep_token
16
  if not fields:
17
+ fields = ["title", "abstract"]
18
  self.fields = fields
19
  logger.info(f"Loading test metadata from {data_path}")
20
  if not processing_fn:
 
27
  logger.info(f"Loaded {len(self.data)} documents")
28
  self.seen_ids = set()
29
  self.key = key
 
 
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
43
+ for d in data:
44
+ if key in d and d[key] not in self.seen_ids:
45
+ bid = d[key]
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"]]
50
+ else:
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
51
  text = []
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
 
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"])
 
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
evaluation/evaluator.py CHANGED
@@ -26,7 +26,7 @@ RANDOM_STATE = 42
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, document=False):
30
  if model:
31
  if type(model) != list:
32
  model = [model]
@@ -37,13 +37,13 @@ class Evaluator:
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, document=document) 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):
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):
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, document=False):
176
- super(IREvaluator, self).__init__(name, meta_dataset, dataset_class, model, batch_size, fields, key, document=document)
177
  self.test_dataset = test_dataset
178
  self.metrics = metrics
179
 
 
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
  # 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]:
 
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":"howey/fullscirep_feeds_1", "config":""},"test":{"name":"howey/fullscirep_test_feeds_1","config":""}},"metrics":["map"]}
2
- {"name":"Feeds-M","type":"proximity","data":{"meta":{"name":"howey/fullscirep_feeds_m","config":""},"test":{"name":"howey/fullscirep_test_feeds_m","config":""}},"metrics":["map"]}
3
- {"name":"Highly Influential Citations","type":"proximity","data":{"meta":{"name":"howey/fullscirep_high_influence_cite","config":""},"test":{"name":"howey/fullscirep_test_high_influence_cite","config":""}},"metrics":["map"]}
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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 = "scirepeval_tasks.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()
@@ -101,8 +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, document=self.document, **kwargs)
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="scirepeval_tasks.jsonl")
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"]}