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.
Named-entity recognition using neural networks. Easy-to-use and state-of-the-art results.

NeuroNER NeuroNER is a program that performs named-entity recognition (NER). Website: neuroner.com. This page gives step-by-step instructions to insta

Franck Dernoncourt 1.6k Dec 27, 2022
Implementation of TF-IDF algorithm to find documents similarity with cosine similarity

NLP learning Trying to learn NLP to use in my projects! Table of Contents About The Project Built With Getting Started Requirements Run Usage License

Faraz Farangizadeh 3 Aug 25, 2022
In this repository we have tested 3 VQA models on the ImageCLEF-2019 dataset.

Med-VQA In this repository we have tested 3 VQA models on the ImageCLEF-2019 dataset. Two of these are made on top of Facebook AI Reasearch's Multi-Mo

Kshitij Ambilduke 8 Apr 14, 2022
中文空间语义理解评测

中文空间语义理解评测 最新消息 2021-04-10 🚩 排行榜发布: Leaderboard 2021-04-05 基线系统发布: SpaCE2021-Baseline 2021-04-05 开放数据提交: 提交结果 2021-04-01 开放报名: 我要报名 2021-04-01 数据集 pa

40 Jan 04, 2023
Unlimited Call - Text Bombing Tool

FastBomber Unlimited Call - Text Bombing Tool Installation On Termux

Aryan 6 Nov 10, 2022
Performance-Efficiency Trade-offs in Unsupervised Pre-training for Speech Recognition

SEW (Squeezed and Efficient Wav2vec) The repo contains the code of the paper "Performance-Efficiency Trade-offs in Unsupervised Pre-training for Speec

ASAPP Research 67 Dec 01, 2022
Club chatbot

Chatbot Club chatbot Instructions to get the Chatterbot working Step 1. First make sure you are using a version of Python 3 or newer. To check your ve

5 Mar 07, 2022
Chinese NER with albert/electra or other bert descendable model (keras)

Chinese NLP (albert/electra with Keras) Named Entity Recognization Project Structure ./ ├── NER │   ├── __init__.py │   ├── log

2 Nov 20, 2022
Calibre recipe to convert latest issue of Analyse & Kritik into an ebook

Calibre Recipe für "Analyse & Kritik" Dies ist ein "Recipe" für die Konvertierung der aktuellen Ausgabe der Zeitung Analyse & Kritik in ein Ebook. Es

Henning 3 Jan 04, 2022
DeBERTa: Decoding-enhanced BERT with Disentangled Attention

DeBERTa: Decoding-enhanced BERT with Disentangled Attention This repository is the official implementation of DeBERTa: Decoding-enhanced BERT with Dis

Microsoft 1.2k Jan 03, 2023
SimBERT升级版(SimBERTv2)!

RoFormer-Sim RoFormer-Sim,又称SimBERTv2,是我们之前发布的SimBERT模型的升级版。 介绍 https://kexue.fm/archives/8454 训练 tensorflow 1.14 + keras 2.3.1 + bert4keras 0.10.6 下载

317 Dec 23, 2022
Generating new names based on trends in data using GPT2 (Transformer network)

MLOpsNameGenerator Overall Goal The goal of the project is to develop a model that is capable of creating Pokémon names based on its description, usin

Gustav Lang Moesmand 2 Jan 10, 2022
Collection of useful (to me) python scripts for interacting with napari

Napari scripts A collection of napari related tools in various state of disrepair/functionality. Browse_LIF_widget.py This module can be imported, for

5 Aug 15, 2022
🕹 An esoteric language designed so that the program looks like the transcript of a Pokémon battle

PokéBattle is an esoteric language designed so that the program looks like the transcript of a Pokémon battle. Original inspiration and specification

Eduardo Correia 9 Jan 11, 2022
A PyTorch implementation of paper "Learning Shared Semantic Space for Speech-to-Text Translation", ACL (Findings) 2021

Chimera: Learning Shared Semantic Space for Speech-to-Text Translation This is a Pytorch implementation for the "Chimera" paper Learning Shared Semant

Chi Han 43 Dec 28, 2022
[Preprint] Escaping the Big Data Paradigm with Compact Transformers, 2021

Compact Transformers Preprint Link: Escaping the Big Data Paradigm with Compact Transformers By Ali Hassani[1]*, Steven Walton[1]*, Nikhil Shah[1], Ab

SHI Lab 367 Dec 31, 2022
A combination of autoregressors and autoencoders using XLNet for sentiment analysis

A combination of autoregressors and autoencoders using XLNet for sentiment analysis Abstract In this paper sentiment analysis has been performed in or

James Zaridis 2 Nov 20, 2021
A Lightweight NLP Data Loader for All Deep Learning Frameworks in Python

LineFlow: Framework-Agnostic NLP Data Loader in Python LineFlow is a simple text dataset loader for NLP deep learning tasks. LineFlow was designed to

TofuNLP 177 Jan 04, 2023
Official PyTorch code for ClipBERT, an efficient framework for end-to-end learning on image-text and video-text tasks

Official PyTorch code for ClipBERT, an efficient framework for end-to-end learning on image-text and video-text tasks. It takes raw videos/images + text as inputs, and outputs task predictions. ClipB

Jie Lei 雷杰 612 Jan 04, 2023
Image2pcl - Enter the metaverse with 2D image to 3D projections

Image2PCL Enter the metaverse with 2D image to 3D projections! This is an implem

Benjamin Ho 0 Feb 05, 2022