named_entity_recognition_modelcard.md

---
license: mit
---

# Model Card for named_entity_recognition.pt

This is a fine-tuned model checkpoint for the named entity recognition (NER) task used in the biodata resource inventory performed by the
[Global Biodata Coalition](https://globalbiodata.org/) in collaboration with [Chan Zuckerberg Initiative](https://chanzuckerberg.com/).

# Model Details

## Model Description

This model has been fine-tuned to detect resource names in scientific articles (title and abstract). This is done using a token classification which assigns predicted
token labels following the [BIO scheme](https://en.wikipedia.org/wiki/Inside%E2%80%93outside%E2%80%93beginning_(tagging)). These are post-processed to determine the
predicted "common names" (often an acronym) and "full names" of a resource present in an article.



- **Developed by:** Ana-Maria Istrate and Kenneth E. Schackart III
- **Shared by:** Kenneth E. Schackart III
- **Model type:** RoBERTa (BERT; Transformer)
- **Language(s) (NLP):** Python
- **License:** MIT
- **Finetuned from model:** https://huggingface.co/allenai/dsp_roberta_base_dapt_biomed_tapt_rct_500

## Model Sources

- **Repository:** https://github.com/globalbiodata/inventory_2022/tree/inventory_2022_dev
- **Paper [optional]:** TBA
- **Demo [optional]:** TBA

# Uses

This model can be used find predicted biodata resource names in an article's title and abstract

## Direct Use

Direct use of the model has not been assessed or designed.

## Out-of-Scope Use

Model should not be used for anything other than the use described in [uses](named_entity_recognition_modelcard.md#uses).

# Bias, Risks, and Limitations

Biases may have been introduced at several stages of the development and training of this model. First, the model was trained on biomedical corpora
as described in [Gururangan S., *et al.,* 2020](http://arxiv.org/abs/2004.10964). Second, The model was fine-tuned on scientific articles that were
manually annotated by 2 curators. Biases in the manual annotation may have affected model fine-tuning. Additionally, manually annotated data were
procured using a specific search query to Europe PMC, so generalizability may be limited when applying to articles from other sources.

## Recommendations

The model should only be used for identifying resource names in articles from Europe PMC using the
[query](https://github.com/globalbiodata/inventory_2022/blob/inventory_2022_dev/config/query.txt) present in the GitHub repository.
Additionally, only article predicted or known to describe a biodata resource should be used.

## How to Get Started with the Model

Follow the direction in the [GitHub repository](https://github.com/globalbiodata/inventory_2022/tree/inventory_2022_dev).

# Training Details

## Training Data

The model was trained on the training split from the [labeled training data](https://github.com/globalbiodata/inventory_2022/blob/inventory_2022_dev/data/manual_ner_extraction.csv).

*Note*: The data can be split into consistent training, validation, testing splits using the procedures detailed in the GitHub repository.

## Training Procedure

The model was trained for 10 epochs, and *F*1-score, precision, recall, and loss were computed after each epoch. The model checkpoint with the highest *F*1-score on the validation
set was saved (regardless of epoch number).

### Preprocessing

To generate the input to the model, the article title and abstracts were concatenated, separating with one white space character, into a contiguous string. All
XML tags were removed using a regular expression.

### Speeds, Sizes, Times

The model checkpoint is 496 MB. Speed has not been benchmarked.

# Evaluation

<!-- This section describes the evaluation protocols and provides the results. -->

## Testing Data, Factors & Metrics

### Testing Data

<!-- This should link to a Data Card if possible. -->

The model was evaluated using the test split of the [labeled data](https://github.com/globalbiodata/inventory_2022/blob/inventory_2022_dev/data/manual_ner_extraction.csv).

### Metrics

<!-- These are the evaluation metrics being used, ideally with a description of why. -->

The model was evaluated using *F*1-score, precision, and recall. Precision was prioritized during fine-tuning and model selection.

## Results

- *F*1-score: 0.717
- Precision: 0.689
- Recall: 0.748

### Summary



# Model Examination

The model works satisfactorily for identifying resource names from articles describing biodata resources in the literature.

## Model Architecture and Objective

The base model architecture is as described in [Gururangan S., *et al.,* 2020](http://arxiv.org/abs/2004.10964). Token classification is performed using
a linear sequence classification layer initialized using [transformers.AutoModelForTokenClassification()](https://huggingface.co/docs/transformers/model_doc/auto).

## Compute Infrastructure

Model was fine-tuned on Google Colaboratory.

### Hardware

Model was fine-tuned using GPU acceleration provided by Google Colaboratory.

### Software

Training software was written in Python.

# Citation

<!-- If there is a paper or blog post introducing the model, the APA and Bibtex information for that should go in this section. -->

TBA

**BibTeX:**

TBA

**APA:**

TBA

# Model Card Authors

This model card was written by Kenneth E. Schackart III.

# Model Card Contact

Ken Schackart: <schackartk1@gmail.com>