Python Medical-natural-language-processing Resources

ProteinBERT is a universal protein language model pretrained on ~106M proteins from the UniRef90 dataset. Through its Python API, the pretrained model can be fine-tuned on any protein-related task in a matter of minutes. Based on our experiments with a wide range of benchmarks, ProteinBERT usually achieves state-of-the-art performance. ProteinBERT is built on TenforFlow/Keras.

Kaleido-BERT: Vision-Language Pre-training on Fashion Domain Mingchen Zhuge*, Dehong Gao*, Deng-Ping Fan#, Linbo Jin, Ben Chen, Haoming Zhou, Minghui

neurodsp is a collection of approaches for applying digital signal processing to neural time series, including algorithms that have been proposed for the analysis of neural time series. It also includes simulation tools for generating plausible simulations of neural time series.

This codebase supports using language models (LMs) for true few-shot learning: learning to perform a task using a limited number of examples from a single task distribution.

This repository is a proof of principle for performing Molecular Dynamics analysis, in this case with the program VMD, via natural language commands.

Wietse de Vries • Martijn Bartelds • Malvina Nissim • Martijn Wieling Adapting Monolingual Models: Data can be Scarce when Language Similarity is High

Image Crop Analysis This is a repo for the code used for reproducing our Image Crop Analysis paper as shared on our blog post. If you plan to use this

Seeing Out of tHe bOx: End-to-End Pre-training for Vision-Language Representation Learning [CVPR'21, Oral] By Zhicheng Huang*, Zhaoyang Zeng*, Yupan H

MLP GPT - Jax (wip) A GPT, made only of MLPs, in Jax. The specific MLP to be used are gMLPs with the Spatial Gating Units. Working Pytorch implementat

LIBRAS-Image-Classifier This project demonstrates the use of neural networks and computer vision to create a classifier that interprets the Brazilian

Hierarchical Cross-Modal Agent for Robotics Vision-and-Language Navigation This repository is the pytorch implementation of our paper: Hierarchical Cr

Point Cloud Audio Processing Krishna Subramani1, Paris Smaragdis1 1UIUC Paper For the necessary libraries/prerequisites, please use conda/anaconda to

Fork from https://github.com/huggingface/transformers/tree/86d5fb0b360e68de46d40265e7c707fe68c8015b/examples/pytorch/language-modeling at 2021.05.17.

Sign Language Translator Project Description The main purpose of project is translating sign-language to letters. In accordance with this purpose we d

language-models-are-knowledge-graphs-pytorch Language models are open knowledge graphs ( work in progress ) A non official reimplementation of Languag

Given an input image and a hand-drawn trimap (top row), alpha matting estimates the alpha channel of a foreground object which can then be composed onto a different background (bottom row).

pythonnet - Python.NET Python.NET is a package that gives Python programmers nearly seamless integration with the .NET Common Language Runtime (CLR) a

xonsh xonsh is a Python-powered, cross-platform, Unix-gazing shell language and command prompt. The language is a superset of Python 3.6+ with additio

FNet: Mixing Tokens with Fourier Transforms Pytorch implementation of Fnet : Mixing Tokens with Fourier Transforms. Citation: @misc{leethorp2021fnet,

SapBERT: Self-alignment pretraining for BERT This repo holds code for the SapBERT model presented in our NAACL 2021 paper: Self-Alignment Pretraining

PRAnCER (Platform enabling Rapid Annotation for Clinical Entity Recognition) is a web platform that enables the rapid annotation of medical terms within clinical notes. A user can highlight spans of text and quickly map them to concepts in large vocabularies within a single, intuitive platform.

A list of papers about point cloud based place recognition, also known as loop closure detection in SLAM (processing)

A framework for cleaning Chinese dialog data

CVZone This is a Computer vision package that makes its easy to run Image processing and AI functions. At the core it uses OpenCV and Mediapipe librar

FactSumm: Factual Consistency Scorer for Abstractive Summarization FactSumm is a toolkit that scores Factualy Consistency for Abstract Summarization W

ViLT Code for the paper: "ViLT: Vision-and-Language Transformer Without Convolution or Region Supervision" Install pip install -r requirements.txt pip

ViT-V-Net: Vision Transformer for Volumetric Medical Image Registration keywords: vision transformer, convolutional neural networks, image registratio

Photon Documentation in English Lightning fast and portable programming language! What is Photon? Photon is a programming language aimed at filling th

MILES Multilingual Lexical Simplifier Explore the docs » Read LSBert Paper · Report Bug · Request Feature About The Project MILES is a multilingual te

MevonAI - Speech Emotion Recognition

TANL: Structured Prediction as Translation between Augmented Natural Languages Code for the paper "Structured Prediction as Translation between Augmen

A curated list of awesome anomaly detection works in medical imaging, inspired by the other awesome-* initiatives.

This is the XLM-T repository, which includes data, code and pre-trained multilingual language models for Twitter. XLM-T - A Multilingual Language Mode

ViLT Code for the paper: "ViLT: Vision-and-Language Transformer Without Convolution or Region Supervision" Install pip install -r requirements.txt pip

Texar-PyTorch is a toolkit aiming to support a broad set of machine learning, especially natural language processing and text generation tasks. Texar

BERT-pytorch Pytorch implementation of Google AI's 2018 BERT, with simple annotation BERT 2018 BERT: Pre-training of Deep Bidirectional Transformers f

MMF is a modular framework for vision and language multimodal research from Facebook AI Research. MMF contains reference implementations of state-of-t

ESPnet: end-to-end speech processing toolkit system/pytorch ver. 1.0.1 1.1.0 1.2.0 1.3.1 1.4.0 1.5.1 1.6.0 1.7.1 1.8.1 ubuntu18/python3.8/pip ubuntu18

⚠️ Checkout develop branch to see what is coming in pyannote.audio 2.0: a much smaller and cleaner codebase Python-first API (the good old pyannote-au

LASER Language-Agnostic SEntence Representations LASER is a library to calculate and use multilingual sentence embeddings. NEWS 2019/11/08 CCMatrix is

** DEPRECATED ** This repo has been deprecated. Please visit Megatron-LM for our up to date Large-scale unsupervised pretraining and finetuning code.

torchaudio: an audio library for PyTorch The aim of torchaudio is to apply PyTorch to the audio domain. By supporting PyTorch, torchaudio follows the

DeepMetaHandles (CVPR2021 Oral) [paper] [animations] DeepMetaHandles is a shape deformation technique. It learns a set of meta-handles for each given

HiFiGAN Denoiser This is a Unofficial Pytorch implementation of the paper HiFi-GAN: High Fidelity Denoising and Dereverberation Based on Speech Deep F

Contextual Action Language Model (CALM) and the ClubFloyd Dataset Code and data for paper Keep CALM and Explore: Language Models for Action Generation

SentiLARE: Sentiment-Aware Language Representation Learning with Linguistic Knowledge Introduction SentiLARE is a sentiment-aware pre-trained language

Meta Language-Specific Layers in Multilingual Language Models This repo contains the source codes for our paper On Negative Interference in Multilingu

Djaq Djaq - pronounced “Jack” - provides an instant remote API to your Django models data with a powerful query language. No server-side code beyond t

NRSC5-DUI is a graphical interface for nrsc5. It makes it easy to play your favorite FM HD radio stations using an RTL-SDR dongle. It will also displa

LightSeq is a high performance inference library for sequence processing and generation implemented in CUDA. It enables highly efficient computation of modern NLP models such as BERT, GPT2, Transformer, etc. It is therefore best useful for Machine Translation, Text Generation, Dialog， Language Modelling, and other related tasks using these models.

One Stop Anomaly Shop (OSAS) Quick start guide Step 1: Get/build the docker image Option 1: Use precompiled image (might not reflect latest changes):

TorchFlare TorchFlare is a simple, beginner-friendly and an easy-to-use PyTorch Framework train your models without much effort. It provides an almost

Graph Evolving Meta-Learning for Low-resource Medical Dialogue Generation Code to be further cleaned... This repo contains the code of the following p

🤗 The largest hub of ready-to-use NLP datasets for ML models with fast, easy-to-use and efficient data manipulation tools

Speech Algorithms Collections

🏆 The 1st Place Submission to AICity Challenge 2021 Natural Language-Based Vehicle Retrieval Track (Alibaba-UTS submission)

AI City 2021: Connecting Language and Vision for Natural Language-Based Vehicle Retrieval 🏆 The 1st Place Submission to AICity Challenge 2021 Natural

CLAP Contrastive Language-Audio Pretraining In due time this repo will be full of lovely things, I hope. Feel free to check out the Issues if you're i

Fine-Grained R2R Code and data of the Fine-Grained R2R Dataset proposed in the EMNLP2020 paper Sub-Instruction Aware Vision-and-Language Navigation. C

PyKale is a PyTorch library for multimodal learning and transfer learning as well as deep learning and dimensionality reduction on graphs, images, texts, and videos. By adopting a unified pipeline-based API design, PyKale enforces standardization and minimalism, via reusing existing resources, reducing repetitions and redundancy, and recycling learning models across areas.

Repository on the collaborative IVADO medical imaging project between the Mila and NeuroPoly labs.

Improving Vision-and-Language Navigation with Image-Text Pairs from the Web Arjun Majumdar, Ayush Shrivastava, Stefan Lee, Peter Anderson, Devi Parikh

Human Attention for Text Classification Re-implementation of the paper Human Attention Maps for Text Classification: Do Humans and Neural Networks Foc

Skeleton Aware Multi-modal Sign Language Recognition By Songyao Jiang, Bin Sun, Lichen Wang, Yue Bai, Kunpeng Li and Yun Fu. Smile Lab @ Northeastern

Learning the Best Pooling Strategy for Visual Semantic Embedding Official PyTorch implementation of the paper Learning the Best Pooling Strategy for V

OCTIS : Optimizing and Comparing Topic Models is Simple! OCTIS (Optimizing and Comparing Topic models Is Simple) aims at training, analyzing and compa

Labelled data remains a scarce resource in many practical NLP scenarios. This is especially the case when working with resource-poor languages (or text domains), or when using task-specific labels without pre-existing datasets. The only available option is often to collect and annotate texts by hand, which is expensive and time-consuming.

Datasets from Instructions (DINO 🦕 ) This repository contains the code for Generating Datasets with Pretrained Language Models. The paper introduces

Generating Persona Consistent Dialogues by Exploiting Natural Language Inference Source code for RCDG model in AAAI20 Generating Persona Consistent Di

Trove Trove is a research framework for building weakly supervised (bio)medical named entity recognition (NER) and other entity attribute classifiers

FedNLP is a research-oriented benchmarking framework for advancing federated learning (FL) in natural language processing (NLP). It uses FedML repository as the git submodule. In other words, FedNLP only focuses on adavanced models and dataset, while FedML supports various federated optimizers (e.g., FedAvg) and platforms (Distributed Computing, IoT/Mobile, Standalone).

GrammarTagger — A Neural Multilingual Grammar Profiler for Language Learning GrammarTagger is an open-source toolkit for grammatical profiling for lan

GLM GLM is a General Language Model pretrained with an autoregressive blank-filling objective and can be finetuned on various natural language underst

Text detection and recognition This repository contains tool which allow to detect region with text and translate it one by one. Description Two pretr

Kornia is a differentiable computer vision library for PyTorch. It consists of a set of routines and differentiable modules to solve generic computer

Welcome to MedicalTorch MedicalTorch is an open-source framework for PyTorch, implementing an extensive set of loaders, pre-processors and datasets fo

Awesome-NLP-Research (ANLP)

We will first introduce the how to run the IPython notebook demo by downloading our pretrained models. Then, we will introduce how to run our training and evaluation code.

QA-GNN: Question Answering using Language Models and Knowledge Graphs This repo provides the source code & data of our paper: QA-GNN: Reasoning with L

I-BERT: Integer-only BERT Quantization HuggingFace Implementation I-BERT is also available in the master branch of HuggingFace! Visit the following li

Keyword: Speech Translation, Spoken Language Processing, Natural Language Processing

PClean: A Domain-Specific Probabilistic Programming Language for Bayesian Data Cleaning Warning: This is a rapidly evolving research prototype.

FasySeq FasySeq is a shorthand as a Fast and easy sequential modeling toolkit. It aims to provide a seq2seq model to researchers and developers, which

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Welcome to the lidar package lidar is Python package for delineating the nested hierarchy of surface depressions in digital elevation models (DEMs). I

eo-box eobox is a Python package with a small collection of tools for working with Remote Sensing / Earth Observation data. Package Overview So far, t

pyroSAR A Python Framework for Large-Scale SAR Satellite Data Processing The pyroSAR package aims at providing a complete solution for the scalable or

GIPPY Gippy is a Python library for image processing of geospatial raster data. The core of the library is implemented as a C++ library, libgip, with

rio-tiler User friendly Rasterio plugin to read raster datasets. Documentation: https://cogeotiff.github.io/rio-tiler/ Source Code: https://github.com

Documentation | Documentation (dev version) | Contact | Part of the Fatiando a Terra project About Verde is a Python library for processing spatial da

mahotas-imread: Read Image Files IO with images and numpy arrays. Mahotas-imread is a simple module with a small number of functions: imread Reads an

Tool for visualizing attention in the Transformer model (BERT, GPT-2, Albert, XLNet, RoBERTa, CTRL, etc.)

CLASP - Contrastive Language-Aminoacid Sequence Pretraining Repository for creating models pretrained on language and aminoacid sequences similar to C

A Python Library for Document Layout Understanding

wav2vec-toolkit A collection of scripts to preprocess ASR datasets and finetune language-specific Wav2Vec2 XLSR models This repository accompanies the

Invertible Image Signal Processing This repository includes official codes for "Invertible Image Signal Processing (CVPR2021)". Figure: Our framework

⚡ Automatically decrypt encryptions without knowing the key or cipher, decode encodings, and crack hashes ⚡

Cutoff: A Simple Data Augmentation Approach for Natural Language This repository contains source code necessary to reproduce the results presented in

CheXbert: Combining Automatic Labelers and Expert Annotations for Accurate Radiology Report Labeling Using BERT CheXbert is an accurate, automated dee

InversePrompting Paper: Controllable Generation from Pre-trained Language Models via Inverse Prompting Code: The code is provided in the "chinese_ip"