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Adapter allenai/specter2_proximity for allenai/specter2

An adapter for the allenai/specter2 model that was trained on the allenai/scirepeval dataset.

This adapter was created for usage with the adapter-transformers library.


First, install adapter-transformers:

pip install -U adapter-transformers

Note: adapter-transformers is a fork of transformers that acts as a drop-in replacement with adapter support. More

Now, the adapter can be loaded and activated like this:

from transformers import AutoAdapterModel

model = AutoAdapterModel.from_pretrained("allenai/specter2")
adapter_name = model.load_adapter("allenai/specter2_proximity", source="hf", set_active=True)


SPECTER 2.0 is the successor to SPECTER and is capable of generating task specific embeddings for scientific tasks when paired with adapters. Given the combination of title and abstract of a scientific paper or a short texual query, the model can be used to generate effective embeddings to be used in downstream applications.

Model Details

Model Description

SPECTER 2.0 has been trained on over 6M triplets of scientific paper citations, which are available here. Post that it is trained on all the SciRepEval training tasks, with task format specific adapters.

Task Formats trained on:

  • Classification
  • Regression
  • Proximity
  • Adhoc Search

This is a retrieval specific adapter. For tasks where given a paper query, other relevant papers have to be retrieved from a corpus, use this adapter to generate the embeddings.

It builds on the work done in SciRepEval: A Multi-Format Benchmark for Scientific Document Representations and we evaluate the trained model on this benchmark as well.

  • Developed by: Amanpreet Singh, Mike D'Arcy, Arman Cohan, Doug Downey, Sergey Feldman
  • Shared by : Allen AI
  • Model type: bert-base-uncased + adapters
  • License: Apache 2.0
  • Finetuned from model [optional]: allenai/scibert.

Model Sources [optional]


Direct Use

Model Type Name and HF link
Base Transformer allenai/specter2
Classification Adapter allenai/specter2_classification
Regression Adapter allenai/specter2_regression
Retrieval Adapter allenai/specter2_proximity
Adhoc Query Adapter allenai/specter2_adhoc_query
from transformers import AutoTokenizer, AutoModel

# load model and tokenizer
tokenizer = AutoTokenizer.from_pretrained('allenai/specter2')

#load base model
model = AutoModel.from_pretrained('allenai/specter2')

#load the adapter(s) as per the required task, provide an identifier for the adapter in load_as argument and activate it
model.load_adapter("allenai/specter2_proximity", source="hf", load_as="specter2_proximity", set_active=True)

papers = [{'title': 'BERT', 'abstract': 'We introduce a new language representation model called BERT'},
          {'title': 'Attention is all you need', 'abstract': ' The dominant sequence transduction models are based on complex recurrent or convolutional neural networks'}]

# concatenate title and abstract
text_batch = [d['title'] + tokenizer.sep_token + (d.get('abstract') or '') for d in papers]
# preprocess the input
inputs = self.tokenizer(text_batch, padding=True, truncation=True,
                                   return_tensors="pt", return_token_type_ids=False, max_length=512)
output = model(**inputs)
# take the first token in the batch as the embedding
embeddings = output.last_hidden_state[:, 0, :]

Downstream Use [optional]

For evaluation and downstream usage, please refer to https://github.com/allenai/scirepeval/blob/main/evaluation/INFERENCE.md.

Training Details

Training Data

The base model is trained on citation links between papers and the adapters are trained on 8 large scale tasks across the four formats. All the data is a part of SciRepEval benchmark and is available here.

The citation link are triplets in the form

{"query": {"title": ..., "abstract": ...}, "pos": {"title": ..., "abstract": ...}, "neg": {"title": ..., "abstract": ...}}

consisting of a query paper, a positive citation and a negative which can be from the same/different field of study as the query or citation of a citation.

Training Procedure

Please refer to the SPECTER paper.

Training Hyperparameters

The model is trained in two stages using SciRepEval:

  • Base Model: First a base model is trained on the above citation triplets.

batch size = 1024, max input length = 512, learning rate = 2e-5, epochs = 2 warmup steps = 10% fp16

  • Adapters: Thereafter, task format specific adapters are trained on the SciRepEval training tasks, where 600K triplets are sampled from above and added to the training data as well.

batch size = 256, max input length = 512, learning rate = 1e-4, epochs = 6 warmup = 1000 steps fp16


We evaluate the model on SciRepEval, a large scale eval benchmark for scientific embedding tasks which which has [SciDocs] as a subset. We also evaluate and establish a new SoTA on MDCR, a large scale citation recommendation benchmark.

Model SciRepEval In-Train SciRepEval Out-of-Train SciRepEval Avg MDCR(MAP, Recall@5)
BM-25 n/a n/a n/a (33.7, 28.5)
SPECTER 54.7 57.4 68.0 (30.6, 25.5)
SciNCL 55.6 57.8 69.0 (32.6, 27.3)
SciRepEval-Adapters 61.9 59.0 70.9 (35.3, 29.6)
SPECTER 2.0-base 56.3 58.0 69.2 (38.0, 32.4)
SPECTER 2.0-Adapters 62.3 59.2 71.2 (38.4, 33.0)

Please cite the following works if you end up using SPECTER 2.0:

SPECTER paper:

  title={{SPECTER: Document-level Representation Learning using Citation-informed Transformers}},
  author={Arman Cohan and Sergey Feldman and Iz Beltagy and Doug Downey and Daniel S. Weld},

SciRepEval paper

  title={SciRepEval: A Multi-Format Benchmark for Scientific Document Representations},
  author={Amanpreet Singh and Mike D'Arcy and Arman Cohan and Doug Downey and Sergey Feldman},
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Dataset used to train allenai/specter2_proximity