Python Systems-biology Resources

KuaiRec: A Fully-observed Dataset for Recommender Systems (Density: Almost 100%) KuaiRec is a real-world dataset collected from the recommendation log

AutoTrader AutoTrader is Python-based platform intended to help in the development, optimisation and deployment of automated trading systems. From sim

Molecular Docking integrated in Jupyter Notebooks Description | Citation | Installation | Examples | Limitations | License Table of content Descriptio

OpenCOOD OpenCOOD is an Open COOperative Detection framework for autonomous driving. It is also the official implementation of the ICRA 2022 paper OPV

Drug Interaction Prediction with Tigerlily Documentation | Example Notebook | Youtube Video | Project Report Tigerlily is a TigerGraph based system de

GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation [OpenReview] [arXiv] [Code] The official implementation of GeoDiff: A Geome

XGI CompleX Group Interactions (XGI) is a Python package for the representation, manipulation, and study of the structure, dynamics, and functions of

Smooth ReLU in PyTorch Unofficial PyTorch reimplementation of the Smooth ReLU (SmeLU) activation function proposed in the paper Real World Large Scale

Molecular Nodes 🧬 🔬 💻 Buy Me a Coffee to Keep Development Going! Join a Community of Blender SciVis People! What is Molecular Nodes? Molecular Node

autolfads-tf2 A TensorFlow 2.0 implementation of LFADS and AutoLFADS. Installati

Diffrax Numerical differential equation solvers in JAX. Autodifferentiable and GPU-capable. Diffrax is a JAX-based library providing numerical differe

The easiest way to the neuroscience world with the shield for RaspberryPi - PIEEG (website). Open-source. Crowdsupply This project is the result of se

Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.

What are the best Systems? New Perspectives on NLP Benchmarking In Machine Learning, a benchmark refers to an ensemble of datasets associated with one

SBINN: Systems-biology informed neural network The source code for the paper M. Daneker, Z. Zhang, G. E. Karniadakis, & L. Lu. Systems biology: Identi

Efficient Deep Learning Systems This repository contains materials for the Efficient Deep Learning Systems course taught at the Faculty of Computer Sc

A mini-scale reproduction code of the AlphaStar program. Note: the original AlphaStar is the AI proposed by DeepMind to play StarCraft II.

Differentiable Simulation of Soft Multi-body Systems Yi-Ling Qiao, Junbang Liang, Vladlen Koltun, Ming C. Lin [Paper] [Code] Updates The C++ backend s

Recommender systems are the systems that are designed to recommend things to the user based on many different factors. The recommender system deals with a large volume of information present by filtering the most important information based on the data provided by a user and other factors that take care of the user’s preference and interest.

A stack-based systems language that supports structures, functions, expressions, and user-defined operator behaviour. Currently compiles to URCL with plans to add additional formats in the future.

Welcome to AirSim AirSim is a simulator for drones, cars and more, built on Unreal Engine (we now also have an experimental Unity release). It is open

A micro-service that can be extended to help in monitoring systems. Be extensible to be incorporated in any of the systems to facilitate timely interventions.

Algorithm and Structured Programming course project for the first semester of the Internet Systems course at IFPB

LabGraph is a a Python-first framework used to build sophisticated research systems with real-time streaming, graph API, and parallelism.

Reverse engineering the dengue virus (under development 🚧 ) What is dengue? Dengue is a viral infection transmitted to humans through the bite of inf

Openspoor The openspoor package is intended to allow easy transformation between different geographical and topological systems commonly used in Dutch

Unicorn can be used for performance analyses of highly configurable systems with causal reasoning. Users or developers can query Unicorn for a performance task.

GAN-based Matrix Factorization for Recommender Systems This repository contains the datasets' splits, the source code of the experiments and their res

On the adaptation of recurrent neural networks for system identification This repository contains the Python code to reproduce the results of the pape

Consumer Fairness in Recommender Systems: Contextualizing Definitions and Mitigations This is the repository for the paper Consumer Fairness in Recomm

Stability Audit This repository contains code used to audit the stability of personality predictions made by two algorithmic hiring systems, Humantic

Rip Raw Rip Raw is a small tool to analyse the memory of compromised Linux systems. It is similar in purpose to Bulk Extractor, but particularly focus

solsim is the Solana complex systems simulator. It simulates behavior of dynamical systems—DeFi protocols, DAO governance, cryptocurrencies, and more—built on the Solana blockchain

pyclimb A library to easily convert climbing route grades between different grading systems. In rock climbing, mountaineering, and other climbing disc

Recommendation-Systems-for-IBM-Watson-Studio-platform Project Overview In this project, I analyze the interactions that users have with articles on th

BioPy is a collection (in-progress) of biologically-inspired algorithms written in Python. Some of the algorithms included are mor

Recommender-Systems Two types of Recommender System : Content-based Recommender System and Colaborating filtering based recommender system So the data

A collection of automation aids to connect various database systems into Lookout for Metrics

GNES is Generic Neural Elastic Search, a cloud-native semantic search system based on deep neural network.

PL-LOW A high-performance deep learning model lightweight pipeline that gradually lightens deep neural networks in order to utilize high-performance d

Private Recommender Systems: How Can Users Build Their Own Fair Recommender Systems without Log Data? (SDM 2022) We consider how a user of a web servi

RPi Example Code Example Python code for building RPi-controlled robotic systems These python files have been compiled / developed by the Neurobionics

Table of contents 1 Introduction 1.1 Major features 1.2 Architecture 2 Code and Installation 2.1 Code 2.2 Installation 3 Repository of DNNs in vision

The project aims to develop a personal-assistant for Windows & Linux-based systems. Samiksha draws its inspiration from virtual assistants like Cortana for Windows, and Siri for iOS. It has been designed to provide a user-friendly interface for carrying out a variety of tasks by employing certain well-defined commands.

SSMLearn Data-driven Reduced Order Models for Nonlinear Dynamical Systems This package perform data-driven identification of reduced order model based

Computational Design and Dynamics of Soft Systems · This is a repository that contains the source code for generating the lecture notes, handouts, exe

Code For the Paper "Understanding Entropy Coding With Asymmetric Numeral Systems (ANS): a Statistician's Perspective" Author: Robert Bamler Date: 22 D

An Evaluation of Generative Adversarial Networks for Collaborative Filtering. This repository was developed by Fernando B. Pérez Maurera. Fernando is

Safe Control for Black-box Dynamical Systems via Neural Barrier Certificates Installation Clone the repository: git clone https://github.com/Zengyi-Qi

Eventify A lightweight python module for building event driven distributed systems. Installation pip install eventify Problem Developers need a easy a

Gordo Building thousands of models with timeseries data to monitor systems. Table of content About Examples Install Uninstall Developer manual How to

DSpaceDL A tool for downloading files from DSpace items. For some reason, DSpace systems have a dogshit UI, and Universities absolutely LOOOVE to use

Operating Systems Lab (ETCS-352) Experiments for Operating Systems Lab (ETCS-352) performed by me in 2021 at uni. All codes are written by me except t

Reproducible research and reusable acyclic workflows in Python. Execute code on HPC systems as if you executed them on your machine! Motivation Would

A Python package that unifies the Google Earth Engine ecosystem. EarthEngine.jl | rgee | rgee+ | eemont GitHub: https://github.com/r-earthengine/ee_ex

PIXEL-LEVEL CRACK DETECTION FROM IMAGES OF LEVEE SYSTEMS : A COMPARATIVE STUDY G

SysIdentPy is a Python module for System Identification using NARMAX models built on top of numpy and is distributed under the 3-Clause BSD license. N

CrossHair An analysis tool for Python that blurs the line between testing and type systems. THE LATEST NEWS: Check out the new crosshair cover command

Detection of Fake Reviews on Online Review Platforms using Deep Learning Architectures Dataset: https://s3.amazonaws.com/fast-ai-nlp/yelp_review_polar

cluster-link-prediction This repository provides some of the code implemented and the data used for the work proposed in "A Cluster-Based Trip Predict

Static Token And Credential Scanner CI Integrations What is it? STACS is a YARA

Awesome Artificial Intelligence, Machine Learning and Deep Learning as we learn it. Study notes and a curated list of awesome resources of such topics.

Conversational AI ChatBot Intelligent ChatBot built with Microsoft's DialoGPT transformer to make conversations with human users! In this project? Thi

Distributed Systems Algorithms ISIS algorithm In an asynchronous system that kee

Tom the AI (version 0.82) WARNING: This software is not yet ready to use, I'm still setting up the GitHub repository. Should be ready in a few days. T

recsys_metrics An efficient PyTorch implementation of the evaluation metrics in recommender systems. Overview • Installation • How to use • Benchmark

Introduction QRec is a Python framework for recommender systems (Supported by Python 3.7.4 and Tensorflow 1.14+) in which a number of influential and

ProjPicker ProjPicker (projection picker) is a Python module that allows the user to select all coordinate reference systems (CRSs) whose extent compl

Before requesting support please consider that this software is not actively developed. I created it in 2014 for managing my Alienware M14X-R1 (where

NeoDTI NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions (Bioinformatics).

CADLabs Ethereum Economic Model A modular dynamical-systems model of Ethereum's validator economics, based on the open-source Python library radCAD, a

rosny is a lightweight library for building concurrent systems. Installation Tested on: Linux Python = 3.6 From pip: pip install rosny From source: p

DBHTermEcIbP Linux commands Interpreter for Windows and Mac based systems using Python Basic Linux commands supported viewing current working director

Thespian Actor Library This library provides the framework of an Actor model for use by applications implementing Actors. Thespian Site with Documenta

harold A control systems package for Python=3.6. Introduction This package is written with the ambition of providing a full-fledged control systems s

Welcome to Spokestack Python! This library is intended for developing voice interfaces in Python. This can include anything from Raspberry Pi applicat

Unzip JP GUI Unzip Japanese Shift-JIS zip archives on non-Japanese systems. This script unzips the file while converting the file names from Shift-JIS

PwnLnX An advanced multi-threaded, multi-client python reverse shell for hacking linux systems. There's still more work to do so feel free to help out

Prescribed-time Control Prescribed-time control (PTC) blocks in Simulink environment, MATLAB R2020b. For more theoretical details, refer to the papers

DHAP Source code of SIGIR2021 Long Paper: One Chatbot Per Person: Creating Personalized Chatbots based on Implicit User Profiles . Preinstallation Fir

Code Artifacts Code artifacts for the submission "Mind the Gap! A Study on the Transferability of Virtual vs Physical-world Testing of Autonomous Driv

pyscreener A pythonic interface to high-throughput virtual screening software Overview This repository contains the source of pyscreener, both a libra

NetKet NetKet is an open-source project delivering cutting-edge methods for the study of many-body quantum systems with artificial neural networks and

Lens by Credo AI - Responsible AI Assessment Framework Lens is a comprehensive assessment framework for AI systems. Lens standardizes model and data a

De(e)pendable Distributed Control of Port-Hamiltonian Systems (DeepDisCoPH) This repository is associated to the paper [1] and it contains: The full p

Description This script helps the user to update Linux and Mac systems through the terminal. All the user has to install some requirements and then ru

RCD: Relation Map Driven Cognitive Diagnosis for Intelligent Education Systems This is our implementation for the paper: Weibo Gao, Qi Liu*, Zhenya Hu

FREE_7773 Repo containing material for the NYU class (Master of Engineering) I teach on NLP, ML Sys etc. For context on what the class is trying to ac

DPDispatcher DPDispatcher is a python package used to generate HPC(High Performance Computing) scheduler systems (Slurm/PBS/LSF/dpcloudserver) jobs in

Documentation | External Resources | Datasets | Examples ChemicalX is a deep learning library for drug-drug interaction, polypharmacy side effect and

Nebula is an extremely-fast end-to-end interactive big data analytics solution. Nebula is designed as a high-performance columnar data storage and tabular OLAP engine.

qunomon Description A testbed for testing and managing AI system qualities. Demo Sorry. Not deployment public server at alpha version. Requirement Ins

Introduction QRec is a Python framework for recommender systems (Supported by Python 3.7.4 and Tensorflow 1.14+) in which a number of influential and

Fine-grained Post-training for Multi-turn Response Selection Implements the model described in the following paper Fine-grained Post-training for Impr

WideLinears Pytorch parallel Neural Networks A package of pytorch modules for fast paralellization of separate deep neural networks. Ideal for agent-b

Full Spectrum Bioinformatics is a free online text designed to introduce key topics in Bioinformatics using the Python programming language. The text is written in interactive Jupyter Notebooks, which allow you to try out and modify example code and analyses.

Notice: Support for Python 3.6 will be dropped in v.0.2.1, please plan accordingly! Efficient and Scalable Physics-Informed Deep Learning Collocation-

A python package that extends Google Earth Engine GitHub: https://github.com/davemlz/eemont Documentation: https://eemont.readthedocs.io/ PyPI: https:

CAT (Improving Machine Translation Systems via Isotopic Replacement) Machine translation plays an essential role in people’s daily international commu

iDracPowerMonitorMQTT This script publishes iDrac power draw data for iDrac 6 enabled servers to an MQTT broker. This can be used to integrate the pow