Toward Model Interpretability in Medical NLP

Overview

Toward Model Interpretability in Medical NLP

LING380: Topics in Computational Linguistics Final Project James Cross ([email protected]) and Daniel Kim ([email protected]), December 2021

Code Organization

  • data: contains medical report data [LINK TO THAT REPO] used in model fine-tuning and analysis, clinical stop words, and saved accuracy and entropy metrics during evaluation
  • models: checkpoints of the best performing BERT and BioBERT models after hyperparameter optimization
  • notebooks:
  • model_training.ipynb: code to train and fine-tune BERT and BioBERT
  • model_evaluation.ipynb: code to run various model evaluations, visualize word importances, perform post-training clinical stopword masking, and other analyses
  • scripts: same functionality as in the notebooks, in executable python scripts / functions

Dependencies

All packages needed to run the code are available in the default Google Colab environment (see documentation for full list), with the exception of huggingface (transformers), used for loading transformer models, and captum.ai (captum), which provides access for a variety of model interpretation tools.

How to run code

Two options available to run the code; on Google colab and/or locally on your machine.

Option 1) Google Colab

Model training notebook: [https://colab.research.google.com/drive/1uPIi-OVchs_8A-SNcQtLfwelr0ccsz19?usp=sharing] Model evaluation/analysis notebook: [https://colab.research.google.com/drive/1Hfy58JvyPbx55lKKhQAzzrhJIbN_Io0j?usp=sharing]

Option 2) Local Machine

Notebooks: You can run the model_training.ipynb or model_evaluation.ipynb notebooks as is, changing directory paths when needed.

Owner
Junior @ Yale. Research Assistant in Turk-Browne Lab.
Translation to python of Chris Sims' optimization function

pycsminwel This is a locol minimization algorithm. Uses a quasi-Newton method with BFGS update of the estimated inverse hessian. It is robust against

Gustavo Amarante 1 Mar 21, 2022
Harvis is designed to automate your C2 Infrastructure.

Harvis Harvis is designed to automate your C2 Infrastructure, currently using Mythic C2. 📌 What is it? Harvis is a python tool to help you create mul

Thiago Mayllart 99 Oct 06, 2022
hashily is a Python module that provides a variety of text decoding and encoding operations.

hashily is a python module that performs a variety of text decoding and encoding functions. It also various functions for encrypting and decrypting text using various ciphers.

DevMysT 5 Jul 17, 2022
Model parallel transformers in JAX and Haiku

Table of contents Mesh Transformer JAX Updates Pretrained Models GPT-J-6B Links Acknowledgments License Model Details Zero-Shot Evaluations Architectu

Ben Wang 4.9k Jan 04, 2023
OpenChat: Opensource chatting framework for generative models

OpenChat is opensource chatting framework for generative models.

Hyunwoong Ko 427 Jan 06, 2023
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
customer care chatbot made with Rasa Open Source.

Customer Care Bot Customer care bot for ecomm company which can solve faq and chitchat with users, can contact directly to team. 🛠 Features Basic E-c

Dishant Gandhi 23 Oct 27, 2022
Tools and data for measuring the popularity & growth of various programming languages.

growth-data Tools and data for measuring the popularity & growth of various programming languages. Install the dependencies $ pip install -r requireme

3 Jan 06, 2022
Phrase-BERT: Improved Phrase Embeddings from BERT with an Application to Corpus Exploration

Phrase-BERT: Improved Phrase Embeddings from BERT with an Application to Corpus Exploration This is the official repository for the EMNLP 2021 long pa

70 Dec 11, 2022
Code for the paper "BERT Loses Patience: Fast and Robust Inference with Early Exit".

Patience-based Early Exit Code for the paper "BERT Loses Patience: Fast and Robust Inference with Early Exit". NEWS: We now have a better and tidier i

Kevin Canwen Xu 54 Jan 04, 2023
Bidirectional LSTM-CRF and ELMo for Named-Entity Recognition, Part-of-Speech Tagging and so on.

anaGo anaGo is a Python library for sequence labeling(NER, PoS Tagging,...), implemented in Keras. anaGo can solve sequence labeling tasks such as nam

Hiroki Nakayama 1.5k Dec 05, 2022
PocketSphinx is a lightweight speech recognition engine, specifically tuned for handheld and mobile devices, though it works equally well on the desktop

molten A minimal, extensible, fast and productive API framework for Python 3. Changelog: https://moltenframework.com/changelog.html Community: https:/

3.2k Dec 28, 2022
MASS: Masked Sequence to Sequence Pre-training for Language Generation

MASS: Masked Sequence to Sequence Pre-training for Language Generation

Microsoft 1.1k Dec 17, 2022
Tool to add main subject to items on Wikidata using a WMFs CirrusSearch for named entity recognition or a manually supplied list of QIDs

ItemSubjector Tool made to add main subject statements to items based on the title using a home-brewed CirrusSearch-based Named Entity Recognition alg

Dennis Priskorn 9 Nov 17, 2022
Language Models as Zero-Shot Planners: Extracting Actionable Knowledge for Embodied Agents

Language Models as Zero-Shot Planners: Extracting Actionable Knowledge for Embodied Agents [Project Page] [Paper] [Video] Wenlong Huang1, Pieter Abbee

Wenlong Huang 114 Dec 29, 2022
HuggingTweets - Train a model to generate tweets

HuggingTweets - Train a model to generate tweets Create in 5 minutes a tweet generator based on your favorite Tweeter Make my own model with the demo

Boris Dayma 318 Jan 04, 2023
pkuseg多领域中文分词工具; The pkuseg toolkit for multi-domain Chinese word segmentation

pkuseg:一个多领域中文分词工具包 (English Version) pkuseg 是基于论文[Luo et. al, 2019]的工具包。其简单易用,支持细分领域分词,有效提升了分词准确度。 目录 主要亮点 编译和安装 各类分词工具包的性能对比 使用方式 论文引用 作者 常见问题及解答 主要

LancoPKU 6k Dec 29, 2022
An End-to-End Trainable Neural Network for Image-based Sequence Recognition and Its Application to Scene Text Recognition

CRNN paper:An End-to-End Trainable Neural Network for Image-based Sequence Recognition and Its Application to Scene Text Recognition 1. create your ow

Tsukinousag1 3 Apr 02, 2022
Quick insights from Zoom meeting transcripts using Graph + NLP

Transcript Analysis - Graph + NLP This program extracts insights from Zoom Meeting Transcripts (.vtt) using TigerGraph and NLTK. In order to run this

Advit Deepak 7 Sep 17, 2022
Official PyTorch Implementation of paper "NeLF: Neural Light-transport Field for Single Portrait View Synthesis and Relighting", EGSR 2021.

NeLF: Neural Light-transport Field for Single Portrait View Synthesis and Relighting Official PyTorch Implementation of paper "NeLF: Neural Light-tran

Ken Lin 38 Dec 26, 2022