PySurvival is an open source python package for Survival Analysis modeling

Overview

PySurvival

pysurvival_logo

What is Pysurvival ?

PySurvival is an open source python package for Survival Analysis modeling - the modeling concept used to analyze or predict when an event is likely to happen. It is built upon the most commonly used machine learning packages such NumPy, SciPy and PyTorch.

PySurvival is compatible with Python 2.7-3.7.

Check out the documentation here


Content

PySurvival provides a very easy way to navigate between theoretical knowledge on Survival Analysis and detailed tutorials on how to conduct a full analysis, build and use a model. Indeed, the package contains:


Installation

If you have already installed a working version of gcc, the easiest way to install Pysurvival is using pip

pip install pysurvival

The full description of the installation steps can be found here.


Get Started

Because of its simple API, Pysurvival has been built to provide to best user experience when it comes to modeling. Here's a quick modeling example to get you started:

# Loading the modules
from pysurvival.models.semi_parametric import CoxPHModel
from pysurvival.models.multi_task import LinearMultiTaskModel
from pysurvival.datasets import Dataset
from pysurvival.utils.metrics import concordance_index

# Loading and splitting a simple example into train/test sets
X_train, T_train, E_train, X_test, T_test, E_test = \
	Dataset('simple_example').load_train_test()

# Building a CoxPH model
coxph_model = CoxPHModel()
coxph_model.fit(X=X_train, T=T_train, E=E_train, init_method='he_uniform', 
                l2_reg = 1e-4, lr = .4, tol = 1e-4)

# Building a MTLR model
mtlr = LinearMultiTaskModel()
mtlr.fit(X=X_train, T=T_train, E=E_train, init_method = 'glorot_uniform', 
           optimizer ='adam', lr = 8e-4)

# Checking the model performance
c_index1 = concordance_index(model=coxph_model, X=X_test, T=T_test, E=E_test )
print("CoxPH model c-index = {:.2f}".format(c_index1))

c_index2 = concordance_index(model=mtlr, X=X_test, T=T_test, E=E_test )
print("MTLR model c-index = {:.2f}".format(c_index2))

Citation and License

Citation

If you use Pysurvival in your research and we would greatly appreciate if you could use the following:

@Misc{ pysurvival_cite,
  author =    {Stephane Fotso and others},
  title =     {PySurvival: Open source package for Survival Analysis modeling},
  year =      {2019--},
  url = "https://www.pysurvival.io/"
}

License

Copyright 2019 Square Inc.

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

A Python toolbox to churn out organic alkalinity calculations with minimal brain engagement.

Organic Alkalinity Sausage Machine A Python toolbox to churn out organic alkalinity calculations with minimal brain engagement. Getting started To mak

Charles Turner 1 Feb 01, 2022
A Tools that help Data Scientists and ML engineers train and deploy ML models.

Domino Research This repo contains projects under active development by the Domino R&D team. We build tools that help Data Scientists and ML engineers

Domino Data Lab 73 Oct 17, 2022
This project used bitcoin, S&P500, and gold to construct an investment portfolio that aimed to minimize risk by minimizing variance.

minvar_invest_portfolio This project used bitcoin, S&P500, and gold to construct an investment portfolio that aimed to minimize risk by minimizing var

1 Jan 06, 2022
This repository demonstrates the usage of hover to understand and supervise a machine learning task.

Hover Example Apps (works out-of-the-box on Binder) This repository demonstrates the usage of hover to understand and supervise a machine learning tas

Pavel 43 Dec 03, 2021
Machine Learning approach for quantifying detector distortion fields

DistortionML Machine Learning approach for quantifying detector distortion fields. This project is a feasibility study for training a surrogate model

Joel Bernier 1 Nov 05, 2021
Convoys is a simple library that fits a few statistical model useful for modeling time-lagged conversions.

Convoys is a simple library that fits a few statistical model useful for modeling time-lagged conversions. There is a lot more info if you head over to the documentation. You can also take a look at

Better 240 Dec 26, 2022
Lseng-iseng eksplor Machine Learning dengan menggunakan library Scikit-Learn

Kalo dengar istilah ML, biasanya rada ambigu. Soalnya punya beberapa kepanjangan, seperti Mobile Legend, Makan Lontong, Ma**ng L*v* dan lain-lain. Tapi pada repo ini membahas Machine Learning :)

Alfiyanto Kondolele 1 Apr 06, 2022
[DEPRECATED] Tensorflow wrapper for DataFrames on Apache Spark

TensorFrames (Deprecated) Note: TensorFrames is deprecated. You can use pandas UDF instead. Experimental TensorFlow binding for Scala and Apache Spark

Databricks 757 Dec 31, 2022
A Time Series Library for Apache Spark

Flint: A Time Series Library for Apache Spark The ability to analyze time series data at scale is critical for the success of finance and IoT applicat

Two Sigma 970 Jan 04, 2023
Meerkat provides fast and flexible data structures for working with complex machine learning datasets.

Meerkat makes it easier for ML practitioners to interact with high-dimensional, multi-modal data. It provides simple abstractions for data inspection, model evaluation and model training supported by

Robustness Gym 115 Dec 12, 2022
Mesh TensorFlow: Model Parallelism Made Easier

Mesh TensorFlow - Model Parallelism Made Easier Introduction Mesh TensorFlow (mtf) is a language for distributed deep learning, capable of specifying

1.3k Dec 26, 2022
A python library for Bayesian time series modeling

PyDLM Welcome to pydlm, a flexible time series modeling library for python. This library is based on the Bayesian dynamic linear model (Harrison and W

Sam 438 Dec 17, 2022
Summer: compartmental disease modelling in Python

Summer: compartmental disease modelling in Python Summer is a Python-based framework for the creation and execution of compartmental (or "state-based"

6 May 13, 2022
Probabilistic time series modeling in Python

GluonTS - Probabilistic Time Series Modeling in Python GluonTS is a Python toolkit for probabilistic time series modeling, built around Apache MXNet (

Amazon Web Services - Labs 3.3k Jan 03, 2023
Software Engineer Salary Prediction

Based on 2021 stack overflow data, this machine learning web application helps one predict the salary based on years of experience, level of education and the country they work in.

Jhanvi Mimani 1 Jan 08, 2022
Repositório para o #alurachallengedatascience1

1° Challenge de Dados - Alura A Alura Voz é uma empresa de telecomunicação que nos contratou para atuar como cientistas de dados na equipe de vendas.

Sthe Monica 16 Nov 10, 2022
JMP is a Mixed Precision library for JAX.

Mixed precision training [0] is a technique that mixes the use of full and half precision floating point numbers during training to reduce the memory bandwidth requirements and improve the computatio

DeepMind 108 Dec 31, 2022
Learning --> Numpy January 2022 - winter'22

Numerical-Python Numpy NumPy is a library for the Python programming language, adding support for large, multi-dimensional arrays and matrices, along

Shahzaneer Ahmed 0 Mar 12, 2022
Real-time stream processing for python

Streamz Streamz helps you build pipelines to manage continuous streams of data. It is simple to use in simple cases, but also supports complex pipelin

Python Streamz 1.1k Dec 28, 2022
Course files for "Ocean/Atmosphere Time Series Analysis"

time-series This package contains all necessary files for the course Ocean/Atmosphere Time Series Analysis, an introduction to data and time series an

Jonathan Lilly 107 Nov 29, 2022