Behavioral Testing of Clinical NLP Models

Overview

Behavioral Testing of Clinical NLP Models

This repository contains code for testing the behavior of clinical prediction models based on patient letters. For a detailed description of the testing framework see our paper What Do You See in this Patient? Behavioral Testing of Clinical NLP Models.

From an existing test set we create test groups by altering specific tokens in the clinical note. We then analyse the change in predictions which reveals the impact of the mention on the clinical NLP model.

Usage

Install requirements: pip install -r requirements.txt

Run main.py, e.g. for diagnosis prediction test on gender, age and ethnicity:

python main.py 
    --test_set_path ./path_to_test_set
    --model_path bvanaken/CORe-clinical-diagnosis-prediction
    --task diagnosis
    --shift_keys gender,age,ethnicity
    --save_dir ./results
    --gpu False
Parameter Description
test_set_path Path to original test set file
model_path Path to model or Huggingface model hub checkpoint
task Current options: diagnosis, mortality
shift_keys Which patient characteristics to test. Current options: age, gender, ethnicity, weight, intersectional (gender + ethnicity)
save_dir Directory to save results, default: "./results"
gpu Whether to use a gpu during inference or not, default: False

Using Non-Transformer models

The framework currently focuses on testing Transformer-based models. However, it is easy to extend it to any other prediction model. To do so, simply create a new class implementing the Predictor interface and add it to the TASK_MAP in main.py.

Cite

@inproceedings{vanAken2021,
  author    = {Betty van Aken and
               Sebastian Herrmann and
               Alexander Löser},
  title     = {What Do You See in this Patient? Behavioral Testing of Clinical NLP Models},
  booktitle = {Bridging the Gap: From Machine Learning Research to Clinical Practice, 
               Research2Clinics Workshop @ NeurIPS 2021},
  year      = {2021}
}
Owner
Betty van Aken
PhD student at Beuth University of Applied Sciences in Berlin doing research in Clinical NLP & Explainability
Betty van Aken
Faster, modernized fork of the language identification tool langid.py

py3langid py3langid is a fork of the standalone language identification tool langid.py by Marco Lui. Original license: BSD-2-Clause. Fork license: BSD

Adrien Barbaresi 12 Nov 05, 2022
State of the Art Natural Language Processing

Spark NLP: State of the Art Natural Language Processing Spark NLP is a Natural Language Processing library built on top of Apache Spark ML. It provide

John Snow Labs 3k Jan 05, 2023
chaii - hindi & tamil question answering

chaii - hindi & tamil question answering This is the solution for rank 5th in Kaggle competition: chaii - Hindi and Tamil Question Answering. The comp

abhishek thakur 33 Dec 18, 2022
This program do translate english words to portuguese

Python-Dictionary This program is used to translate english words to portuguese. Web-Scraping This program use BeautifulSoap to make web scraping, so

João Assalim 1 Oct 10, 2022
nlpcommon is a python Open Source Toolkit for text classification.

nlpcommon nlpcommon, Python Text Tool. Guide Feature Install Usage Dataset Contact Cite Reference Feature nlpcommon is a python Open Source

xuming 3 May 29, 2022
Snips Python library to extract meaning from text

Snips NLU Snips NLU (Natural Language Understanding) is a Python library that allows to extract structured information from sentences written in natur

Snips 3.7k Dec 30, 2022
ALBERT: A Lite BERT for Self-supervised Learning of Language Representations

ALBERT ***************New March 28, 2020 *************** Add a colab tutorial to run fine-tuning for GLUE datasets. ***************New January 7, 2020

Google Research 3k Dec 26, 2022
The Sudachi synonym dictionary in Solar format.

solr-sudachi-synonyms The Sudachi synonym dictionary in Solar format. Summary Run a script that checks for updates to the Sudachi dictionary every hou

Karibash 3 Aug 19, 2022
p-tuning for few-shot NLU task

p-tuning_NLU Overview 这个小项目是受乐于分享的苏剑林大佬这篇p-tuning 文章启发,也实现了个使用P-tuning进行NLU分类的任务, 思路是一样的,prompt实现方式有不同,这里是将[unused*]的embeddings参数抽取出用于初始化prompt_embed后

3 Dec 29, 2022
Code for CodeT5: a new code-aware pre-trained encoder-decoder model.

CodeT5: Identifier-aware Unified Pre-trained Encoder-Decoder Models for Code Understanding and Generation This is the official PyTorch implementation

Salesforce 564 Jan 08, 2023
This Project is based on NLTK It generates a RANDOM WORD from a predefined list of words, From that random word it read out the word, its meaning with parts of speech , its antonyms, its synonyms

This Project is based on NLTK(Natural Language Toolkit) It generates a RANDOM WORD from a predefined list of words, From that random word it read out the word, its meaning with parts of speech , its

SaiVenkatDhulipudi 2 Nov 17, 2021
Semi-automated vocabulary generation from semantic vector models

vec2word Semi-automated vocabulary generation from semantic vector models This script generates a list of potential conlang word forms along with asso

9 Nov 25, 2022
What are the best Systems? New Perspectives on NLP Benchmarking

What are the best Systems? New Perspectives on NLP Benchmarking In Machine Learning, a benchmark refers to an ensemble of datasets associated with one

Pierre Colombo 12 Nov 03, 2022
1 Jun 28, 2022
Simple Annotated implementation of GPT-NeoX in PyTorch

Simple Annotated implementation of GPT-NeoX in PyTorch This is a simpler implementation of GPT-NeoX in PyTorch. We have taken out several optimization

labml.ai 101 Dec 03, 2022
Code for CodeT5: a new code-aware pre-trained encoder-decoder model.

CodeT5: Identifier-aware Unified Pre-trained Encoder-Decoder Models for Code Understanding and Generation This is the official PyTorch implementation

Salesforce 564 Jan 08, 2023
Stanford CoreNLP provides a set of natural language analysis tools written in Java

Stanford CoreNLP Stanford CoreNLP provides a set of natural language analysis tools written in Java. It can take raw human language text input and giv

Stanford NLP 8.8k Jan 07, 2023
Natural language Understanding Toolkit

Natural language Understanding Toolkit TOC Requirements Installation Documentation CLSCL NER References Requirements To install nut you need: Python 2

Peter Prettenhofer 119 Oct 08, 2022
Blender addon - Scrub timeline from viewport with a shortcut

Viewport scrub timeline Move in the timeline directly in viewport and snap to nearest keyframe Note : This standalone feature will be added in the nat

Samuel Bernou 40 Nov 07, 2022
The source code of HeCo

HeCo This repo is for source code of KDD 2021 paper "Self-supervised Heterogeneous Graph Neural Network with Co-contrastive Learning". Paper Link: htt

Nian Liu 106 Dec 27, 2022