Publications and Software
Peer Reviewed Publications
- The implications of delayed reopening in controlling the COVID-19 surge in the Southern and West-Central USA
Authors: Dandekar R, Wang E, Barbastathis G, Rackauckas C
Health Data Science - October 2021 - AbstractDifferentiation.jl: Backend-Agnostic Differentiable Programming in Julia
Authors: Frank Schäfer, Mohamed Tarek, Lyndon White, Chris Rackauckas
NeurIPS Differentiable Programming Workshop - December 2021 - A Comparison of Automatic Differentiation and Continuous Sensitivity Analysis for Derivatives of Differential Equation Solutions
Authors: Yingbo Ma, Vaibhav Dixit, Mike Innes, Xingjian Guo, Christopher Rackauckas
IEEE HPEC - September 2021 - Stiff Neural Ordinary Differential Equations(easy access)
Authors: S Kim, W Ji, S Deng, C Rackauckas
Chaos - September 2021 - Composing Modeling and Simulation with Machine Learning in Julia
Authors: C Rackauckas et al
14th International Modelica Conference - September 2021 - High-performance symbolic-numerics via multiple dispatch
Authors: S Gowda, Y Ma, A Cheli, M Gwozdz, V Shah, A Edelman, C Rackauckas
ACM Communications in Computer Algebra - July 2021 - Opening the Blackbox: Accelerating Neural Differential Equations by Regularizing Internal Solver Heuristics
Authors: A Pal, Y Ma, V Shah, C Rackauckas
The Thirty-eighth International Conference on Machine Learning (ICML) - 2021
- Collocation based Training of Neural Ordinary Differential Equations (easy access)
Authors: E Roesch, C Rackauckas, M Stumpf
Statistical Applications in Genetics and Molecular Biology - 2021
- Bayesian Neural Ordinary Differential Equations
Authors: R Dandekar, V Dixit, M Tarek, A Garcia-Valadez, C Rackauckas
POPL-LAFI - 2021
- Accelerating Simulation of Stiff Nonlinear Systems using Continuous-Time Echo State Networks
Authors: Anantharaman R, Ma Y, Gowda S, Laughman C, Shah V, Edelman A, Rackauckas C
AAAI-MLPS - 2021
- Safe Blues: The case for virtual safe virus spread in the long-term fight against epidemics
Authors: R Dandekar, SG Henderson, HM Jansen, J McDonald, S Moka, Y Nazarathy, C Rackauckas, PG Taylor, A Vuorinen
Cell Patterns - March 12, 2021
- Hybrid Mechanistic + Neural Model of Laboratory Helicopter
Authors: C Rackauckas, R Sharma, B Lie
SIMS 2020: 61st International Conference of Scandinavian Simulation Society - March 3, 2021
- A Machine Learning-Aided Global Diagnostic and Comparative Tool to Assess Effect of Quarantine Control in COVID-19 Spread
Authors: Dandekar R, Rackauckas C, Barbastathis G
Cell Patterns - December 11, 2020
- ACED: Accelerated Computational Electrochemical systems Discovery
Authors: Kurchin R et al.
NeurIPS Climate Change Workshop - December 11th, 2020
- Learning non-linear spatio-temporal dynamics with convolutional Neural ODEs
Authors: Shankar V, Portwood G, Mohan A, Mitra P, Rackauckas C, Wilson L, Schmidt D, Viswanathan V
NeurIPS ML4PS Workshop - December 11th, 2020
- Accelerating Simulation of Stiff Nonlinear Systems using Continuous-Time Echo State Networks
Authors: Anantharaman R, Ma Y, Gowda S, Laughman C, Shah V, Edelman A, Rackauckas C
NeurIPS ML4Eng Workshop - December 11th, 2020
- Signal Enhancement for Magnetic Navigation Challenge Problem
Authors: Gnadt A et al.
NeurIPS ML4Eng Workshop - December 11th, 2020
- A Machine Learning-Aided Global Diagnostic and Comparative Tool to Assess Effect of Quarantine Control in COVID-19 Spread
Authors: Dandekar R, Rackauckas C, Barbastathis G
Cell Patterns - November 17th, 2020
- Beyond Deterministic Models in Drug Development
Authors: Irurzun-Arana I, Rackauckas C, McDonald T, Trocóniz I
Trends in Pharmacological Sciences - October 5th, 2020
- Stability-Optimized High Order Methods and Stiffness Detection for Pathwise Stiff Stochastic Differential Equations (Longer Version)
Authors: Rackauckas C, Nie Q
IEEE HPEC 2020 - September 2020
Awarded IEEE Outstanding Paper Award - StochasticDelayDiffEq.jl - An Integrator Interface for Stochastic Delay Differential
Equations in Julia
Authors: Henrik T Sykora, Christopher V. Rackauckas, David Widmann, and Dániel Bachrathy
ENOC 2020 - July 2020 - Generalized Physics-Informed Learning Through Language-Wide Differentiable
Programming
Authors: Chris Rackauckas, Alan Edelman, Keno Fischer, Mike Innes, Elliot Saba, Viral B. Shah, Will Tebbutt
AAAI Spring Symposium: MLPS 2020 - March 2020 - Sparsity Programming: Automated Sparsity-Aware Optimizations in Differentiable Programming
Authors: Shashi Gowda, Yingbo Ma, Valentin Churavy, Alan Edelman, Christopher Rackauckas
NeurIPS 2019 Workshop Program Transformations - September 2019 - Confederated Modular Differential Equation APIs for Accelerated Algorithm Development and Benchmarking
Authors: Rackauckas C, Nie Q
Advances in Engineering Software - July 2018 - Simulation and Control of Biological Stochasticity
Author: Rackauckas C
PhD Thesis - June 2018
Awarded Kovalevsky Outstanding Ph.D. Thesis Award - Mean-Independent Noise Control of Cell Fates via Intermediate States
Authors: Rackauckas C, Schilling T, Nie Q
iScience - May 2018
Featured as a cover article for iScience - DifferentialEquations.jl – A Performant and Feature-Rich Ecosystem for Solving Differential Equations in Julia
Authors: Rackauckas C, Nie Q
Journal of Open Research Software - May 2017
Awarded DSWeb 2018 Runner-Up by SIAM Dynamical Systems Interest Group - Adaptive Methods for Stochastic Differential Equations via Natural Embeddings and Rejection Sampling with Memory
Authors: Rackauckas C, Nie Q
Discrete and Continuous Dynamical Systems - Series B - December 2016 - Noise modulation in retinoic acid signaling sharpens segmental boundaries of gene expression in the embryonic zebrafish hindbrain
Authors: Sosnik J, Zheng L, Rackauckas C, Digman M, Gratton E, Nie Q, Schilling T
eLife Sciences - April 2016 - On The Budyko-Sellers Energy Balance Climate Model with Ice Line Coupling
Authors: Walsh J, Rackauckas C
Discrete and Continuous Dynamical Systems - Series B - July 2015 - An Application of Robust Regression to Bernanke's Analysis of Nonmonetary Effects in the Great Depression
Authors: Rackauckas C
Journal of Statistical and Econometric Methods - February 7, 2014 - Assessment of Statistical Methods for Water Quality Monitoring in Maryland's Tidal Waterways
Authors: Le R, Rackauckas C, Ross A, Ulloa N.
SIAM Undergraduate Research Online - April 18th, 2013
Preprints
- Physics-enhanced deep surrogates for PDEs (PEDS)
Authors: R Pestourie, Y Mroueh, C Rackauckas, P Das, SG Johnson
Arxiv - November 2021 - Validation and parameterization of a novel physics-constrained neural dynamics model applied to turbulent fluid flow
Authors: Varun Shankar, Gavin D. Portwood, Arvind T. Mohan, Peetak P. Mitra, Dilip Krishnamurthy, Christopher Rackauckas, Lucas A. Wilson, David P. Schmidt, Venkatasubramanian Viswanathan
Arxiv - November 2021 - Julia for Biologists
Authors: Elisabeth Roesch, Joe G. Greener, Adam L. MacLean, Huda Nassar, Christopher Rackauckas, Timothy E. Holy, Michael P.H. Stumpf
Arxiv - September 2021 - NeuralPDE: Automating Physics-Informed Neural Networks (PINNs) with Error Approximations
Authors: Kirill Zubov, Zoe McCarthy, Yingbo Ma, Francesco Calisto, Valerio Pagliarino, Simone Azeglio, Luca Bottero, Emmanuel Luján, Valentin Sulzer, Ashutosh Bharambe, Nand Vinchhi, Kaushik Balakrishnan, Devesh Upadhyay, Chris Rackauckas
Arxiv - September 2021 - Stably Accelerating Stiff Quantitative Systems Pharmacology Models: Continuous-Time Echo State Networks as Implicit Machine Learning
Authors: Ranjan Anantharaman, Anas Abdelrehim, Anand Jain, Avik Pal, Danny Sharp, Utkarsh, Chris Rackauckas
Bioarxiv - September 2021 - ModelingToolkit: A Composable Graph Transformation System For Equation-Based Modeling
Authors: Y Ma, S Gowda, R Anantharaman, C Laughman, V Shah, C Rackauckas
Arxiv - March 2021 - Forecasting virus outbreaks with social media data via neural ordinary differential equations
Authors: M Núñez, N Barreiro, R Barrio, C Rackauckas
Medarxiv - January 2021 - Efficient Precision Dosing Under Estimated Uncertainties via Koopman Expectations of Bayesian Posteriors with Pumas
Authors: CV Rackauckas, V Dixit, AR Gerlach, V Ivaturi
Bioarxiv - January 2021 - Accelerated Predictive Healthcare Analytics with Pumas, A High Performance Pharmaceutical Modeling and Simulation Platform
Authors: Rackauckas C et al.
Bioarxiv - December 2020 - Capturing missing physics in climate model parameterizations using neural differential equations
Authors: Ramadhan A, Marshall J, Souza A, Wagner G, Ponnapati M, Rackauckas C
Arxiv - October 2020 - The Koopman Expectation: An Operator Theoretic Method for Efficient Analysis and Optimization of Uncertain Hybrid Dynamical Systems
Authors: Adam R. Gerlach, Andrew Leonard, Jonathan Rogers, Chris Rackauckas
Arxiv - July 2020 - Safe Blues: A Method for Estimation and Control in the Fight Against COVID-19
Authors: Raj Abhijit Dandekar, Shane G. Henderson, Marijn Jansen, Sarat Moka, Yoni Nazarathy, Christopher Rackauckas, Peter G. Taylor, Aapeli Vuorinen
Arxiv - April 2020 - Universal Differential Equations for Scientific Machine Learning
Authors: Christopher Rackauckas, Yingbo Ma, Julius Martensen, Collin Warner, Kirill Zubov, Rohit Supekar, Dominic Skinner, Ali Ramadhan, Alan Edelman
Arxiv - Jan 2020 - dP: A Differentiable Programming System to Bridge
Machine Learning and Scientific Computing
Authors: Mike Innes, Alan Edelman, Keno Fischer, Chris Rackauckas, Elliot Saba, Viral B Shah, Will Tebbutt
Arxiv - July 2019 - DiffEqFlux.jl - A Julia Library for Neural Differential Equations
Authors: Chris Rackauckas, Mike Innes, Yingbo Ma, Jesse Bettencourt, Lyndon White, Vaibhav Dixit
Arxiv - Februrary 2019
Technical Reports
- Doubly Ensemble Movie Prediction with Social Media Data Using TBEEF
Authors: Rackauckas C, Cai W, Jarvis C, Xu C, Ching A
Machine Learning Open Source Software (MLOSS) - August 2012.
Software Repository
- The Jormungand Climate Model
Author: Rackauckas C
OhioLink Electronic Theses and Dissertations Center - July 11th, 2013 - Water Quality Monitoring of Maryland's Tidal Waterways, HPCF-2012-12
Authors: Le R, Rackauckas C, Ross A, Ulloa N.
University of Maryland, Baltimore County High Performance Computing Facility - September 2012.
Project Site
Expository Papers and Fun Other Stuff
- An Intuitive Introduction For Understanding and Solving Stochastic Differential Equations
Author: Rackauckas C.
May 2017. - Continuous Dynamics: General Linear Behavior and the Linearization of Nonlinear Systems
Author: Rackauckas C.
Fall 2012. - Automated Geometric Theorem Proving
Author: Rackauckas C.
Fall 2012. - Applications of Group Representation Theory to Quantum Mechanics
Authors: Mark Z, Rackauckas C, Tchernyshyov K
Spring 2012. - The Classical Limit of Bohmian Mechanics Through Coherent States
Author: Rackauckas C.
Winter 2012. - So You Want to Know the Circumference of an Ellipse?
Author: Rackauckas C
Fall 2010. - Adolescent Disclosure and its Relationship to Parental Monitoring and the Legitimacy of Parental Authority
Author: Rackauckas C
Fall 2010.
Accompanying Software
- DifferentialEquations.jl
Author: Rackauckas C
DifferentialEquations.jl is a package for solving numerically solving differential equations in Julia by Chris Rackauckas. The purpose of this package is to supply efficient Julia implementations of solvers for various differential equations. Equations within the realm of this package include ordinary differential equations (ODEs), stochastic ordinary differential equations (SODEs or SDEs), stochastic partial differential equations (SPDEs), partial differential equations (with both finite difference and finite element methods), differential algebraic equations, and differential delay equations. It includes well-optimized implementations classic algorithms and ones from recent research, including algorithms optimized for high-precision and HPC applications. - TBEEF, Triple Bagged Ensemble Ensemble Framework
Authors: Rackauckas C, Cai W, Jarvis C, Xu C, Ching A
Last Updated: August 2013.
In the spring of 2013, Baidu, Inc. hosted a competition for teams to develop new algorithms for movie recommendation systems. The purpose of the competition was to develop better models for rating prediction and suggest methods for incorporating social media data into the prediction models. The goal of our project was to use the information disseminated by the top competitors of the contest to develop new algorithms for recommendation systems. Noting the prevalence of ensemble methods employed on factorization models, our team developed a doubly ensemble framework named TBEEF, a software framework with a plugin interface through which factorization and ensemble models could be easily developed and ran. - Bayesian Robust Multiple Linear Regression
Author: Chris Rackauckas. Adapted from John Kruschke
Last Updated: June 2013.
This program performs a Bayesian Robust Multiple Linear Regression by utilizing a Student's t-distribution for the likelihood. It is written in R and requires the use of the rjags package and the JAGS (Just Another Gibbs Sampler) program for the numerical estimation of the posterior distributions. Included is the dataset used in the paper An Application of Robust Regression to Bernanke's Analysis of Nonmonetary Effects in the Great Depression. Credit goes to John Kruschke for developing the Bayesian Multiple Linear Regression script which was adapted to make this program. - Animated Water Quality Map
Source Code
Authors: Chris Rackauckas and Jeffrey Rackauckas
Last Updated: June 2013.
The Maryland Department of Natural Resources utilizes monitoring stations throughout the Chesapeake Bay and its surrounding tributaries in order to asses the quality of the water. These monitoring stations collect data on parameters that are important for life to thrive in the waters such as dissolved oxygen, dissolved carbon, etc. The purpose of this map is to show how these parameters change over time. - Jormungand Climate Model MATLAB Scripts
Author: Chris Rackauckas
Last Updated: April 2013
This is a set of MATLAB scripts for generating graphs of the h function for the Budyko-Widiasih model. These are the scripts used in the Jormungand Climate State paper. Included are two programs: one which uses numerical methods to solve for h given any albedo function and another which solves for h using the finite Legendre expansion with geometric singular perturbation theory approximation for an arbitrary smooth alpha_ice. - ARIMA Analysis
Author: Chris Rackauckas. Adapted from Harry Hurd
Last Updated: April 2013
This MATLAB script analyzes time series data, plots graphs of the residuals, autocorrelation fucntions, and partial autocorrelation functions for the best fitting ARIMA models, and presents the user with a printout of the Akaike Information Criterion and the Ljung-Box p-values. This script is an updated version of Harry Hurd's doarima.m. It is known to work with MATLAB R2012a and requires the System Identification Toolbox. - ARIMA Forecaster
Author: Chris Rackauckas.
Last Updated: April 2013
This MATLAB script estimates the specified ARIMA(p,d,q) model and generates a forecast. It can be used to analyze an ARIMA forcast against real data by setting a portion of your data as the validation data. If you wish to only forecast, simply turn the validation step off (VALIDATE=0). One can specify a second ARIMA model estimated using a subset of the dataset by setting TWOARIMA=1 and the program will plot the estimation errors of both models for comparison. It is known to work with MATLAB 2012a and requires the Econometrics Toolbox. - Water Quality Analysis GUI for the Department of Natural Resources
Authors: Authors: Le R, Rackauckas C, Ross A, Ulloa N.
Last Updated: February 2013
This tool was developed by students at the University of Maryland, Baltimore County NSA/NSF funded REU Site. This GUI allows researchers to be able to easily generate graphs and perform the necessary statistical analyses on the water quality readings taken by Maryland's Department of Natural Resources of the Chesapeake Bay.
Presentation Slides
- Did Glaciers Cover the Earth? An Inquiry into Snowball Earth
Presented at the Oberlin College Senior Symposium, 2013.
April 26, 2013 - Did A Jormungand State Exist? An Investigation Using the Budyko-Widiasih Model
Presented at the Mathematics of Climate Research Paleocarbon Webinar.
March 6th and 20th, 2013 - Water Quality Monitoring in Maryland's Tidal Waterways
Presented at the James Madison University SUMS Conference and UMBC's SURF Conference.
September 29th, 2012 and July 8th, 2012
Posters
- Independent Mean/Variance Regulation in the Self-Enhanced Degradation Motif
Presented at the Center for Complex Biological Systems Retreat, 2014.
March 29th, 2014 - Doubly Ensemble Movie Prediction with Social Media Data Using TBEEF
Presented at the Joint Mathematics Meetings, 2014.
January 6th, 2014 - An Approximation of the Budyko-Widiasih Model with the Jormungand Albedo Function
Presented at the Joint Mathematics Meetings, 2013.
January 11th, 2013 - Water Quality Monitoring of Maryland's Tidal Waterways
Presented at the James Madison University SUMS Conference and UMBC's SURF Conference.
September 29th, 2012 and July 8th, 2012
Mathematical Art
- A Finite Representation of an Infinitely Small World
Author: Rackauckas C
Spring 2012. - Analysis of the Monte Carlo Method of Image
Generation
Author: Rackauckas C.
Spring 2012.
Websites
These are the website I have created and/or maintained.
- HPC REU Team 2 Water Quality Monitoring Project Page. Created 2012.
- Oberlin College Residential Education. Migrated to the current CMS 2011. Maintained for four years.
- Ferendo Gomez Herrero's Homepage. Created 2010.
- Acoustik Musik Ltd. and Room with a View Productions. Created 2010-2012.
- My old site. Created 2009 using Flash/Actionscript.