crherlihy / clinical_nli_artifacts

MedNLI Is Not Immune: Natural Language Inference Artifacts in the Clinical Domain (ACL-IJCNLP '21)

MedNLI Is Not Immune: Natural Language Inference Artifacts in the Clinical Domain

This repository contains the source code required to reproduce the analysis presented in the paper "MedNLI Is Not Immune: Natural Language Inference Artifacts in the Clinical Domain", appearing at ACL-IJCNLP 2021.

Data:

MedNLI can be downloaded from PhysioNet, though credentialed access is required. After you have downloaded the data, put the resulting directory underneath the project root directory. Organization is as follows:

.
├── mednli
│   └── 1.0.0
│       ├── LICENSE.txt
│       ├── README.txt
│       ├── SHA256SUMS.txt
│       ├── index.html
│       ├── mli_dev_v1.jsonl
│       ├── mli_test_v1.jsonl
│       └── mli_train_v1.jsonl

---

Set-up:

Conda environment:

conda env create -f environment.yml

conda activate clinical_nli

scispaCy language model:

General usage is: pip install <Model URL>; en_core_sci_sm and en_core_sci_lg are both used in this pipeline:

• pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_sm-0.4.0.tar.gz
• pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_lg-0.4.0.tar.gz

fastText MIMIC-III embeddings:

Referenced in the original MedNLI paper by Romanov and Shivade (2018); available on the associated repo or via:

• wget https://mednli.blob.core.windows.net/shared/word_embeddings/wiki_en_mimic.fastText.no_clean.300d.pickled

Configuration file:

./example_cfg.ini: Defines paths and task-specific hyper-parameters.

---

Shell and python scripts:

From the project root directory: cd ./scripts && sh parse_embeds_aflite.sh

Note: parse_embeds_aflite.sh has 4 boolean flags:

• fastText: parse MedNLI input files (JSON) and create fastText-formatted .txt files
• ftAllSubsets: create a single fastText-formatted .txt file containing instances from all splits (eg, train, dev test). Useful for AFLite.
• embeddings: recovers embeddings for each instance in the corpus (language model is configurable)
• aflite: runs adversarial filtering algorithm AfLite adapted from Sakaguchi et al. (2019); yields easy and difficult partitions

To replicate reported results, after running sh parse_embeds_aflite.sh with all flags set to True, run:

• sh ft_baseline.sh: computes fastText baseline results; if evalAflite flag is set to True, also computes fastText results for AfLite easy and difficult partitions.
• sh lexical.sh: computes ngram counts, PMI, and mean/median hypothesis length by label.
• sh semantic.sh: uses scispaCy to link named ents to UMLS; conducts statistical hypothesis testing re: heuristics.

From the project root directory, cd ./src/utils and:

• python get_hyp_len.py: Computes hypothesis length for two versions of the corpus (multi-word entities merged and separate).
• python get_partition_ids.py: Creates 2 arrays with instance ids for the easy and difficult AfLite partitions.
  • instance ids will have the format <split><numeric_id>
  • underlying text can be recovered by joining against the ./mednli/fastText/mli_all_w_premise_v1_sep.txt file.

---

If you find this code useful in your research, please consider citing:

@inproceedings{herlihy-rudinger-2021-mednli,
    title = "{M}ed{NLI} Is Not Immune: {N}atural Language Inference Artifacts in the Clinical Domain",
    author = "Herlihy, Christine  and
      Rudinger, Rachel",
    booktitle = "Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 2: Short Papers)",
    month = aug,
    year = "2021",
    address = "Online",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2021.acl-short.129",
    doi = "10.18653/v1/2021.acl-short.129",
    pages = "1020--1027",
}