genienlp/README.md

# Genie NLP library

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This library contains the NLP models for the [Genie](https://github.com/stanford-oval/genie-toolkit) toolkit for
virtual assistants. It is derived from the [decaNLP](https://github.com/salesforce/decaNLP) library by Salesforce,
but has diverged significantly.

The library is suitable for all NLP tasks that can be framed as Contextual Question Answering, that is, with 3 inputs:

- text or structured input as _context_
- text input as _question_
- text or structured output as _answer_

As the work by [McCann et al.](https://arxiv.org/abs/1806.08730) shows, many NLP tasks can be framed in this way.
Genie primarily uses the library for semantic parsing, paraphrasing, translation, and dialogue state tracking, and this is
what the models work best for.

## Installation

genienlp is available on PyPi. You can install it with:

```bash
pip3 install genienlp
```

After installation, `genienlp` command becomes available.

## Usage

### Training a semantic parser

The general form is:

```bash
genienlp train --train_tasks almond --train_iterations 50000 --data <datadir> --save <model_dir> <flags>
```

The `<datadir>` should contain a single folder called "almond" (the name of the task). That folder should
contain the files "train.tsv" and "eval.tsv" for train and dev set respectively.

To train a BERT-LSTM (or other MLM-based models) use:

```bash
genienlp train --train_tasks almond --train_iterations 50000 --data <datadir> --save <model_dir> \
  --model TransformerLSTM --pretrained_model bert-base-cased --trainable_decoder_embedding 50
```

To train a BART or other Seq2Seq model, use:

```bash
genienlp train --train_tasks almond --train_iterations 50000 --data <datadir> --save <model_dir> \
  --model TransformerSeq2Seq --pretrained_model facebook/bart-large --gradient_accumulation_steps 20
```

The default batch sizes are tuned for training on a single V100 GPU. Use `--train_batch_tokens` and `--val_batch_size`
to control the batch sizes. See `genienlp train --help` for the full list of options.

**NOTE**: the BERT-LSTM model used by the current version of the library is not comparable with the
one used in our published paper (cited below), because the input preprocessing is different. If you
wish to compare with published results you should use genienlp <= 0.5.0.

### Inference on a semantic parser

In batch mode:

```bash
genienlp predict --tasks almond --data <datadir> --path <model_dir> --eval_dir <output>
```

The `<datadir>` should contain a single folder called "almond" (the name of the task). That folder should
contain the files "train.tsv" and "eval.tsv" for train and dev set respectively. The result of batch prediction
will be saved in `<output>/almond/valid.tsv`, as a TSV file containing ID and prediction.

In interactive mode:

```bash
genienlp server --path <model_dir>
```

Opens a TCP server that listens to requests, formatted as JSON objects containing `id` (the ID of the request),
`task` (the name of the task), `context`, and `question`. The server writes out JSON objects containing `id` and
`answer`. The server listens to port 8401 by default. Use `--port` to specify a different port or `--stdin` to
use standard input/output instead of TCP.

### Calibrating a trained model

Calibrate the confidence scores of a trained model:

1. Calculate and save confidence features of the evaluation set in a pickle file:

   ```bash
   genienlp predict --tasks almond --data <datadir> --path <model_dir> --save_confidence_features --confidence_feature_path <confidence_feature_file>
   ```
2. Train a boosted tree to map confidence features to a score between 0 and 1:

   ```bash
   genienlp calibrate --confidence_path <confidence_feature_file> --save <calibrator_directory> --name_prefix <calibrator_name>
   ````
3. Now if you provide `--calibrator_paths` during prediction, it will output confidence scores for each output:

   ```bash
   genienlp predict --tasks almond --data <datadir> --path <model_dir> --calibrator_paths <calibrator_directory>/<calibrator_name>.calib
   ```

### Paraphrasing

Train a paraphrasing model:

```bash
genienlp train-paraphrase --train_data_file <train_data_file> --eval_data_file <dev_data_file> --output_dir <model_dir> --model_type gpt2 --do_train --do_eval --evaluate_during_training --logging_steps 1000 --save_steps 1000 --max_steps 40000 --save_total_limit 2 --gradient_accumulation_steps 16 --per_gpu_eval_batch_size 4 --per_gpu_train_batch_size 4 --num_train_epochs 1 --model_name_or_path <gpt2/gpt2-medium/gpt2-large/gpt2-xlarge>
```

Generate paraphrases:

```bash
genienlp run-paraphrase --model_name_or_path <model_dir> --temperature 0.3 --repetition_penalty 1.0 --num_samples 4 --batch_size 32 --input_file <input_tsv_file> --input_column 1
```

### Translation

Use the following command for training/ finetuning an NMT model:

```bash
genienlp train --train_tasks almond_translate --data <data_directory> --train_languages <src_lang> --eval_languages <tgt_lang> --no_commit --train_iterations <iterations> --preserve_case --save <save_dir> --exist_ok --skip_cache --model TransformerSeq2Seq --pretrained_model <hf_model_name>
```

We currently support MarianMT, MBART, MT5, and M2M100 models.<br>
To save a pretrained model in genienlp format without any finetuning, set train_iterations to 0. You can then use this model to do inference.

To produce translations for an eval/ test set run the following command:

```bash
genienlp predict --tasks almond_translate --data <data_directory> --pred_languages <src_lang> --pred_tgt_languages <tgt_lang> --path <path_to_saved_model> --eval_dir <eval_dir> --skip_cache --val_batch_size 4000 --evaluate <valid/test>  --overwrite --silent
```

If your dataset is a document or contains long examples, pass `--translate_example_split` to break the examples down into individual sentences before translation for better results. <br>
To use [alignment](https://aclanthology.org/2020.emnlp-main.481.pdf), pass `--do_alignment` which ensures the tokens between quotations marks in the sentence are preserved during translation.

### Named Entity Disambiguation

First run a bootleg model to extract mentions, entity candidates, and contextual embeddings for the mentions.
```bash
genienlp bootleg-dump-features --train_tasks <train_task_names> --save <savedir> --preserve_case --data <dataset_dir> --train_batch_tokens 1200 --val_batch_size 2000 --database_type json --database_dir <database_dir> --min_entity_len 1 --max_entity_len 4 --bootleg_model <bootleg_model>
```
This command generates several output files. In `<dataset_dir>` you should see a `prep` dir which contains preprocessed data (e.g. data converted to memory-mapped format, several arrays to facilitate embedding lookup, etc.) If your dataset doesn't change you can reuse the same files.
It will also generate several files in <results_temp> folder. In `eval_bootleg/[train|eval]/<bootleg_model>/bootleg_lables.jsonl` you can see the examples, mentions, predicted candidates and their probabilities according to bootleg.

Now you can use the extracted features from bootleg in downstream tasks such as semantic parsing to improve named entity understanding and consequently generation:
```bash
genienlp train --train_tasks <train_task_names> --train_iterations <iterations> --preserve_case --save <savedir> --data <dataset_dir> --model TransformerSeq2Seq --pretrained_model facebook/bart-base --train_batch_tokens 1000 --val_batch_size 1000 --do_ned --database_dir <database_dir> --ned_retrieve_method bootleg --entity_attributes type_id type_prob --add_entities_to_text append --bootleg_model <bootleg_model>
```


See `genienlp --help` and `genienlp <command> --help` for more details about each argument.


## Citation

If you use the MultiTask Question Answering model in your work, please cite [*The Natural Language Decathlon: Multitask Learning as Question Answering*](https://arxiv.org/abs/1806.08730).

```bibtex
@article{McCann2018decaNLP,
  title={The Natural Language Decathlon: Multitask Learning as Question Answering},
  author={Bryan McCann and Nitish Shirish Keskar and Caiming Xiong and Richard Socher},
  journal={arXiv preprint arXiv:1806.08730},
  year={2018}
}
```

If you use the BERT-LSTM model (Identity encoder + MQAN decoder), please cite [Schema2QA: High-Quality and Low-Cost Q&A Agents for the Structured Web](https://arxiv.org/abs/2001.05609)

```bibtex
@InProceedings{xu2020schema2qa,
  title={{Schema2QA}: High-Quality and Low-Cost {Q\&A} Agents for the Structured Web},
  author={Silei Xu and Giovanni Campagna and Jian Li and Monica S. Lam},
  booktitle={Proceedings of the 29th ACM International Conference on Information and Knowledge Management},
  year={2020},
  doi={https://doi.org/10.1145/3340531.3411974}
}
```

If you use the paraphrasing model (BART or GPT-2 fine-tuned on a paraphrasing dataset), please cite [AutoQA: From Databases to QA Semantic Parsers with Only Synthetic Training Data](https://arxiv.org/abs/2010.04806)

```bibtex
@inproceedings{xu-etal-2020-autoqa,
    title = "{A}uto{QA}: From Databases to {QA} Semantic Parsers with Only Synthetic Training Data",
    author = "Xu, Silei  and Semnani, Sina  and Campagna, Giovanni  and Lam, Monica",
    booktitle = "Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP)",
    month = nov,
    year = "2020",
    address = "Online",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/2020.emnlp-main.31",
    pages = "422--434",
}
```

If you use multilingual models such as MarianMT, MBART, MT5, or XLMR-LSTM for Seq2Seq tasks, please cite [Localizing Open-Ontology QA Semantic Parsers in a Day Using Machine Translation](https://aclanthology.org/2020.emnlp-main.481/),
[Contextual Semantic Parsing for Multilingual Task-Oriented Dialogues](https://arxiv.org/abs/2111.02574), and the original paper that introduced the model.

```bibtex
@inproceedings{moradshahi-etal-2020-localizing,
    title = "Localizing Open-Ontology {QA} Semantic Parsers in a Day Using Machine Translation",
    author = "Moradshahi, Mehrad and Campagna, Giovanni and Semnani, Sina and Xu, Silei and Lam, Monica",
    booktitle = "Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP)",
    month = November,
    year = "2020",
    address = "Online",
    publisher = "Association for Computational Linguistics",
    url = "https://www.aclweb.org/anthology/2020.emnlp-main.481",
    pages = "5970--5983",
}
```
```bibtex
@article{moradshahi2021contextual,
  title={Contextual Semantic Parsing for Multilingual Task-Oriented Dialogues},
  author={Moradshahi, Mehrad and Tsai, Victoria and Campagna, Giovanni and Lam, Monica S},
  journal={arXiv preprint arXiv:2111.02574},
  year={2021}
}
```