Python Bioinformatics-pipeline Resources

Demo BERT ONNX pipeline written in rust This demo showcase the use of onnxruntime-rs with a GPU on CUDA 11 to run Bert in a data pipeline with Rust. R

Dpex——用户无感知分布式数据预处理组件 一、前言 随着GPU与CPU的算力差距越来越大以及模型训练时的预处理Pipeline变得越来越复杂，CPU部分的数据预处理已经逐渐成为了模型训练的瓶颈所在，这导致单机的GPU配置的提升并不能带来期望的线性加速。预处理性能瓶颈的本质在于每个GPU能够使用的C

simple_diarizer Simplified diarization pipeline using some pretrained models. Made to be a simple as possible to go from an input audio file to diariz

TorchX is a library containing standard DSLs for authoring and running PyTorch related components for an E2E production ML pipeline

Polygonal Building Segmentation by Frame Field Learning We add a frame field output to an image segmentation neural network to improve segmentation qu

Pipeline For NLP with Bloom's Taxonomy Using Improved Question Classification and Question Generation using Deep Learning This repository contains all

BMS-Molecular-Translation Introduction This is a pipeline for Bristol-Myers Squibb – Molecular Translation by Vadim Timakin and Maksim Zhdanov. We got

Journey Towards Tiny Perceptual Super-Resolution Test code for our ECCV2020 paper: https://arxiv.org/abs/2007.04356 Our x4 upscaling pre-trained model

SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization This is the code for our paper ``SumGNN: Multi-typed Drug

Clairvoyance: A Pipeline Toolkit for Medical Time Series Authors: van der Schaar Lab This repository contains implementations of Clairvoyance: A Pipel

upai-gst-dl-plugins Guide & Examples to create deeplearning gstreamer plugins and use them in your pipeline Introduction Thanks to the work done by @j

🍭 KRSH is Alpha version, so many bugs can be reported. If you find a bug, please write an Issue and grow the project together! A declarative Kubeflow

Synthetic Dataset Generator Authors: Stanislava Fedorova Alberto Tono Meher Shashwat Nigam Jiayao Zhang Amirhossein Ahmadnia Cecilia bolognesi Dominik

UnrealPerson: An Adaptive Pipeline for Costless Person Re-identification In our paper (arxiv), we propose a novel pipeline, UnrealPerson, that decreas

AWS Data Engineering Pipeline This is a repository for the Duke University Cloud Computing course project on Serverless Data Engineering Pipeline. For

Collection of useful code related to biological analysis. Much of this is discussed with examples at Blue collar bioinformatics. All code, images and

SARS-CoV-2 processing requests Request execution of Galaxy SARS-CoV-2 variation analysis workflows on input data you provide. Prerequisites This autom

The dataTap Python library is the primary interface for using dataTap's rich data management tools. Create datasets, stream annotations, and analyze model performance all with one library.

ETL Pipeline with Airflow, Spark, s3, MongoDB and Amazon Redshift

Socorro Socorro is a Mozilla-centric ingestion pipeline and analysis tools for crash reports using the Breakpad libraries. Support This is a Mozilla-s

Pseudo-ISP: Learning Pseudo In-camera Signal Processing Pipeline from A Color Image Denoiser Abstract The success of deep denoisers on real-world colo

The mljar-supervised is an Automated Machine Learning Python package that works with tabular data. I

combo: A Python Toolbox for Machine Learning Model Combination Deployment & Documentation & Stats Build Status & Coverage & Maintainability & License

Pytorch-toolbelt A pytorch-toolbelt is a Python library with a set of bells and whistles for PyTorch for fast R&D prototyping and Kaggle farming: What

NVIDIA DALI The NVIDIA Data Loading Library (DALI) is a library for data loading and pre-processing to accelerate deep learning applications. It provi

Deep GNN, Shallow Sampling Hanqing Zeng, Muhan Zhang, Yinglong Xia, Ajitesh Srivastava, Andrey Malevich, Rajgopal Kannan, Viktor Prasanna, Long Jin, R

Overview Nidaba is the central controller for the entire OGL OCR pipeline. It oversees and automates the process of converting raw images into citable

DeepSceneTextReader This is a c++ project deploying a deep scene text reading pipeline. It reads text from natural scene images. Prerequsites The proj

Real-time-Scene-Text-Detection-and-Recognition-System End-to-end pipeline for real-time scene text detection and recognition. The detection model use

Toy Machine Learning Pipeline Table of Contents About Getting Started ML task description and evaluation procedure Dataset description Repository stru

BatchFlow BatchFlow helps you conveniently work with random or sequential batches of your data and define data processing and machine learning workflo

pdpipe ˨ Easy pipelines for pandas DataFrames (learn how!). Website: https://pdpipe.github.io/pdpipe/ Documentation: https://pdpipe.github.io/pdpipe/d

MLBox is a powerful Automated Machine Learning python library. It provides the following features: Fast reading and distributed data preprocessing/cle

DaCy: A SpaCy NLP Pipeline for Danish DaCy is a Danish preprocessing pipeline trained in SpaCy. At the time of writing it has achieved State-of-the-Ar

The latest information about Galaxy can be found on the Galaxy Community Hub. Community support is available at Galaxy Help. Galaxy Quickstart Galaxy

Text preprocessing, representation and visualization from zero to hero. From zero to hero • Installation • Getting Started • Examples • API • FAQ • Co

This repository contains custom pipes and models related to using spaCy for scientific documents. In particular, there is a custom tokenizer that adds

spacy-transformers: Use pretrained transformers like BERT, XLNet and GPT-2 in spaCy This package provides spaCy components and architectures to use tr

✨ NeuralCoref 4.0: Coreference Resolution in spaCy with Neural Networks. NeuralCoref is a pipeline extension for spaCy 2.1+ which annotates and resolv

Dash Dash is the most downloaded, trusted Python framework for building ML & data science web apps. Built on top of Plotly.js, React and Flask, Dash t

AudioTK Audio ToolKit is a set of audio filters. It helps assembling workflows for specific audio processing workloads. The audio workflow is split in

PipeLayer is a lightweight Python pipeline framework. Define a series of steps, and chain them together to create modular applications

Text preprocessing, representation and visualization from zero to hero. From zero to hero • Installation • Getting Started • Examples • API • FAQ • Co

This repository contains custom pipes and models related to using spaCy for scientific documents. In particular, there is a custom tokenizer that adds

spacy-transformers: Use pretrained transformers like BERT, XLNet and GPT-2 in spaCy This package provides spaCy components and architectures to use tr

✨ NeuralCoref 4.0: Coreference Resolution in spaCy with Neural Networks. NeuralCoref is a pipeline extension for spaCy 2.1+ which annotates and resolv

Haystack is an end-to-end framework for Question Answering & Neural search that enables you to ... ... ask questions in natural language and find gran

Dash Dash is the most downloaded, trusted Python framework for building ML & data science web apps. Built on top of Plotly.js, React and Flask, Dash t

mongo-connector The mongo-connector project originated as a MongoDB mongo-labs project and is now community-maintained under the custody of YouGov, Pl

Pipeline Pipeline is an asset packaging library for Django, providing both CSS and JavaScript concatenation and compression, built-in JavaScript templ

Soda SQL Data testing, monitoring and profiling for SQL accessible data. What does Soda SQL do? Soda SQL allows you to Stop your pipeline when bad dat

Pipeline Pipeline is an asset packaging library for Django, providing both CSS and JavaScript concatenation and compression, built-in JavaScript templ

Collection of useful code related to biological analysis. Much of this is discussed with examples at Blue collar bioinformatics. All code, images and

Dash Dash is the most downloaded, trusted Python framework for building ML & data science web apps. Built on top of Plotly.js, React and Flask, Dash t

MLJAR Automated Machine Learning Documentation: https://supervised.mljar.com/ Source Code: https://github.com/mljar/mljar-supervised Table of Contents

Neuraxle Pipelines Code Machine Learning Pipelines - The Right Way. Neuraxle is a Machine Learning (ML) library for building machine learning pipeline

Steppy What is Steppy? Steppy is a lightweight, open-source, Python 3 library for fast and reproducible experimentation. Steppy lets data scientist fo