MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.

Plant Disease Epidemiology in R

Indexer is a Python script that generates an .html index of files within a directory

Simulate PK-PD models defined as ODE systems

Read RDS files, in Python

nlmixr2 estimation routines

GPT Meet Zotero.

Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.

A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existing methodologies for data-based modelling

ggPMX R package

An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Set…

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

enables genome-scale simulation of intracellular signaling

PArallel Distributed Deep LEarning: Machine Learning Framework from Industrial Practice （『飞桨』核心框架，深度学习&机器学习高性能单机、分布式训练和跨平台部署）

Neural Laplace: Differentiable Laplace Reconstructions for modelling any time observation with O(1) complexity.

TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics

Neural Graph Differential Equations (Neural GDEs)

Python package for graph neural networks in chemistry and biology

Python package built to ease deep learning on graph, on top of existing DL frameworks.

A powerful and flexible machine learning platform for drug discovery

Graph Neural Network Library for PyTorch

Code to accompany the paper "Discovery of Physics from Data: Universal Laws and Discrepancies"

Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimation

High-Performance Symbolic Regression in Python and Julia

Robust parameter estimation and identifiability analysis with Hybrid Neural Ordinary Differential Equations in Computational Biology

Deep Generative ODE Modelling with Known Unknowns

PyTorch and TensorFlow implementation of NCP, LTC, and CfC wired neural models

Code for "Latent ODEs for Irregularly-Sampled Time Series" paper