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
Code release for NeX: Real-time View Synthesis with Neural Basis Expansion

NeX: Real-time View Synthesis with Neural Basis Expansion Project Page | Video | Paper | COLAB | Shiny Dataset We present NeX, a new approach to novel

537 Jan 05, 2023
Sentence boundary disambiguation tool for Japanese texts (日本語文境界判定器)

Bunkai Bunkai is a sentence boundary (SB) disambiguation tool for Japanese texts. Quick Start $ pip install bunkai $ echo -e '宿を予約しました♪!まだ2ヶ月も先だけど。早すぎ

Megagon Labs 160 Dec 23, 2022
The official implementation of "BERT is to NLP what AlexNet is to CV: Can Pre-Trained Language Models Identify Analogies?, ACL 2021 main conference"

BERT is to NLP what AlexNet is to CV This is the official implementation of BERT is to NLP what AlexNet is to CV: Can Pre-Trained Language Models Iden

Asahi Ushio 20 Nov 03, 2022
An extensive UI tool built using new data scraped from BBC News

BBC-News-Analyzer An extensive UI tool built using new data scraped from BBC New

Antoreep Jana 1 Dec 31, 2021
TensorFlow code and pre-trained models for BERT

BERT ***** New March 11th, 2020: Smaller BERT Models ***** This is a release of 24 smaller BERT models (English only, uncased, trained with WordPiece

Google Research 32.9k Jan 08, 2023
A Python wrapper for simple offline real-time dictation (speech-to-text) and speaker-recognition using Vosk.

Simple-Vosk A Python wrapper for simple offline real-time dictation (speech-to-text) and speaker-recognition using Vosk. Check out the official Vosk G

2 Jun 19, 2022
Fidibo.com comments Sentiment Analyser

Fidibo.com comments Sentiment Analyser Introduction This project first asynchronously grab Fidibo.com books comment data using grabber.py and then sav

Iman Kermani 3 Apr 15, 2022
All the code I wrote for Overwatch-related projects that I still own the rights to.

overwatch_shit.zip This is (eventually) going to contain all the software I wrote during my five-year imprisonment stay playing Overwatch. I'll be add

zkxjzmswkwl 2 Dec 31, 2021
A telegram bot to translate 100+ Languages

🔥 GOOGLE TRANSLATER 🔥 The owner would not be responsible for any kind of bans due to the bot. • ⚡ INSTALLING ⚡ • • 🔰 Deploy To Railway 🔰 • • ✅ OFF

Aɴᴋɪᴛ Kᴜᴍᴀʀ 5 Dec 20, 2021
⚖️ A Statutory Article Retrieval Dataset in French.

A Statutory Article Retrieval Dataset in French This repository contains the Belgian Statutory Article Retrieval Dataset (BSARD), as well as the code

Maastricht Law & Tech Lab 19 Nov 17, 2022
iSTFTNet : Fast and Lightweight Mel-spectrogram Vocoder Incorporating Inverse Short-time Fourier Transform

iSTFTNet : Fast and Lightweight Mel-spectrogram Vocoder Incorporating Inverse Short-time Fourier Transform This repo try to implement iSTFTNet : Fast

Rishikesh (ऋषिकेश) 126 Jan 02, 2023
SimpleChinese2 集成了许多基本的中文NLP功能,使基于 Python 的中文文字处理和信息提取变得简单方便。

SimpleChinese2 SimpleChinese2 集成了许多基本的中文NLP功能,使基于 Python 的中文文字处理和信息提取变得简单方便。 声明 本项目是为方便个人工作所创建的,仅有部分代码原创。

Ming 30 Dec 02, 2022
An easy to use Natural Language Processing library and framework for predicting, training, fine-tuning, and serving up state-of-the-art NLP models.

Welcome to AdaptNLP A high level framework and library for running, training, and deploying state-of-the-art Natural Language Processing (NLP) models

Novetta 407 Jan 03, 2023
Some embedding layer implementation using ivy library

ivy-manual-embeddings Some embedding layer implementation using ivy library. Just for fun. It is based on NYCTaxiFare dataset from kaggle (cut down to

Ishtiaq Hussain 2 Feb 10, 2022
Espresso: A Fast End-to-End Neural Speech Recognition Toolkit

Espresso Espresso is an open-source, modular, extensible end-to-end neural automatic speech recognition (ASR) toolkit based on the deep learning libra

Yiming Wang 919 Jan 03, 2023
A modular Karton Framework service that unpacks common packers like UPX and others using the Qiling Framework.

Unpacker Karton Service A modular Karton Framework service that unpacks common packers like UPX and others using the Qiling Framework. This project is

c3rb3ru5 45 Jan 05, 2023
An assignment on creating a minimalist neural network toolkit for CS11-747

minnn by Graham Neubig, Zhisong Zhang, and Divyansh Kaushik This is an exercise in developing a minimalist neural network toolkit for NLP, part of Car

Graham Neubig 63 Dec 29, 2022
To create a deep learning model which can explain the content of an image in the form of speech through caption generation with attention mechanism on Flickr8K dataset.

To create a deep learning model which can explain the content of an image in the form of speech through caption generation with attention mechanism on Flickr8K dataset.

Ragesh Hajela 0 Feb 08, 2022
PyTorch original implementation of Cross-lingual Language Model Pretraining.

XLM NEW: Added XLM-R model. PyTorch original implementation of Cross-lingual Language Model Pretraining. Includes: Monolingual language model pretrain

Facebook Research 2.7k Dec 27, 2022
Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS)

TOPSIS implementation in Python Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) CHING-LAI Hwang and Yoon introduced TOPSIS

Hamed Baziyad 8 Dec 10, 2022