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Rename and set as a breaking change
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There are a lot of breaking changes in this one, especially the sign change and the mixed adjoint (continuous + discrete) causing changes to the direct version. But the docs are also all fixed so yay!

The reason for the name change is because this package is the core package for all of SciML's integration with AD and sensitivity analysis. For example, the issue with Integrals.jl is that it cannot handle all of the vjps... which are defined here. Optimization.jl needs adjoints, defined here for vjps. Etc. so the name change reflects that, and since we also had a massive breaking API change, it makes sense to pair this together as essentially a new package.
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ChrisRackauckas committed Jun 25, 2022
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2 changes: 1 addition & 1 deletion LICENSE.md
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The DiffEqSensitivity.jl package is licensed under the MIT "Expat" License:
The SciMLSensitivity.jl package is licensed under the MIT "Expat" License:

> Copyright (c) 2016-2020: ChrisRackauckas, Julia Computing.
>
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6 changes: 3 additions & 3 deletions Project.toml
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@@ -1,7 +1,7 @@
name = "DiffEqSensitivity"
uuid = "41bf760c-e81c-5289-8e54-58b1f1f8abe2"
name = "SciMLSensitivity"
uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1"
authors = ["Christopher Rackauckas <[email protected]>", "Yingbo Ma <[email protected]>"]
version = "6.80.0"
version = "7.0.0"

[deps]
Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
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18 changes: 9 additions & 9 deletions README.md
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# DiffEqSensitivity.jl
# SciMLSensitivity.jl


[![Join the chat at https://julialang.zulipchat.com #sciml-bridged](https://img.shields.io/static/v1?label=Zulip&message=chat&color=9558b2&labelColor=389826)](https://julialang.zulipchat.com/#narrow/stream/279055-sciml-bridged)
[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](http:https://sensitivity.sciml.ai/stable/)
[![Global Docs](https://img.shields.io/badge/docs-SciML-blue.svg)](https://docs.sciml.ai/dev/modules/DiffEqSensitivity/)
[![Global Docs](https://img.shields.io/badge/docs-SciML-blue.svg)](https://docs.sciml.ai/dev/modules/SciMLSensitivity/)

[![codecov](https://codecov.io/gh/SciML/DiffEqSensitivity.jl/branch/master/graph/badge.svg?token=FwXaKBNW67)](https://codecov.io/gh/SciML/DiffEqSensitivity.jl)
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[![SciML Code Style](https://img.shields.io/static/v1?label=code%20style&message=SciML&color=9558b2&labelColor=389826)](https://github.com/SciML/SciMLStyle)
[![Package Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/DiffEqSensitivity)](https://pkgs.genieframework.com?packages=DiffEqSensitivity)
[![Package Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/SciMLSensitivity)](https://pkgs.genieframework.com?packages=SciMLSensitivity)

DiffEqSensitivity.jl is a component package in the [SciML Scientific Machine Learning ecosystem](https://sciml.ai/).
SciMLSensitivity.jl is a component package in the [SciML Scientific Machine Learning ecosystem](https://sciml.ai/).
It holds the sensitivity analysis utilities. Users interested in using this
functionality should check out [DifferentialEquations.jl](https://github.com/JuliaDiffEq/DifferentialEquations.jl).

## Tutorials and Documentation

For information on using the package, see the [DiffEqSensitivity](https://docs.sciml.ai/dev/modules/DiffEqSensitivity/) section of the
For information on using the package, see the [SciMLSensitivity](https://docs.sciml.ai/dev/modules/SciMLSensitivity/) section of the
[SciML docs](docs.sciml.ai). For information on specific previous versions of this package, see the
[see the stable DiffEqSensitivity-only documentation](https://sensitivity.sciml.ai/stable/).
[see the stable SciMLSensitivity-only documentation](https://sensitivity.sciml.ai/stable/).
2 changes: 1 addition & 1 deletion docs/Project.toml
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Expand Up @@ -7,7 +7,7 @@ DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
DiffEqFlux = "aae7a2af-3d4f-5e19-a356-7da93b79d9d0"
DiffEqNoiseProcess = "77a26b50-5914-5dd7-bc55-306e6241c503"
DiffEqSensitivity = "41bf760c-e81c-5289-8e54-58b1f1f8abe2"
SciMLSensitivity = "41bf760c-e81c-5289-8e54-58b1f1f8abe2"
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
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8 changes: 4 additions & 4 deletions docs/make.jl
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@@ -1,4 +1,4 @@
using Documenter, DiffEqSensitivity
using Documenter, SciMLSensitivity

# Make sure that plots don't throw a bunch of warnings / errors!
ENV["GKSwstype"] = "100"
Expand All @@ -7,11 +7,11 @@ using Plots
include("pages.jl")

makedocs(
sitename = "DiffEqSensitivity.jl",
sitename = "SciMLSensitivity.jl",
authors="Chris Rackauckas et al.",
clean = true,
doctest = false,
modules = [DiffEqSensitivity],
modules = [SciMLSensitivity],

strict = [
:doctest,
Expand All @@ -29,6 +29,6 @@ makedocs(
)

deploydocs(
repo = "github.com/SciML/DiffEqSensitivity.jl.git";
repo = "github.com/SciML/SciMLSensitivity.jl.git";
push_preview = true
)
2 changes: 1 addition & 1 deletion docs/pages.jl
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pages = [
"DiffEqSensitivity.jl: Automatic Differentiation and Adjoints for (Differential) Equation Solvers" => "index.md",
"SciMLSensitivity.jl: Automatic Differentiation and Adjoints for (Differential) Equation Solvers" => "index.md",
"Tutorials" => Any[
"Differentiating Ordinary Differential Equations (ODE) Tutorials" => Any[
"ad_examples/differentiating_ode.md",
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2 changes: 1 addition & 1 deletion docs/src/Benchmark.md
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Expand Up @@ -25,7 +25,7 @@ Quick summary:
- Using `ZygoteVJP` is faster than other vjp choices with FastDense due to the overloads

```julia
using DiffEqFlux, OrdinaryDiffEq, Flux, Optim, Plots, DiffEqSensitivity,
using DiffEqFlux, OrdinaryDiffEq, Flux, Optim, Plots, SciMLSensitivity,
Zygote, BenchmarkTools, Random

u0 = Float32[2.0; 0.0]
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2 changes: 1 addition & 1 deletion docs/src/ad_examples/adjoint_continuous_functional.md
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Expand Up @@ -37,7 +37,7 @@ straightforward since one can simply use the fact that the solution from
`ODEForwardSensitivityProblem` is continuous when `dense=true`. For example,

```@example continuousadjoint
using OrdinaryDiffEq, DiffEqSensitivity
using OrdinaryDiffEq, SciMLSensitivity
function f(du,u,p,t)
du[1] = dx = p[1]*u[1] - p[2]*u[1]*u[2]
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2 changes: 1 addition & 1 deletion docs/src/ad_examples/chaotic_ode.md
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Expand Up @@ -20,7 +20,7 @@ can be seen, for instance, when solving the [Lorenz system](https://en.wikipedia
`1e-14` tolerances with 9th order integrators and a small machine-epsilon perturbation:

```@example chaosode
using OrdinaryDiffEq, DiffEqSensitivity, Zygote
using OrdinaryDiffEq, SciMLSensitivity, Zygote
function lorenz!(du, u, p, t)
du[1] = 10 * (u[2] - u[1])
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2 changes: 1 addition & 1 deletion docs/src/ad_examples/differentiating_ode.md
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Expand Up @@ -78,7 +78,7 @@ to an ODE and computes the gradient of a loss function (the sum of the ODE's out
timepoint with dt=0.1) via the adjoint method:

```@example diffode
using Zygote, DiffEqSensitivity
using Zygote, SciMLSensitivity
function sum_of_solution(u0,p)
_prob = remake(prob,u0=u0,p=p)
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2 changes: 1 addition & 1 deletion docs/src/ad_examples/direct_sensitivity.md
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Expand Up @@ -13,7 +13,7 @@ instead of an ODE type. For example, we generate an ODE with the sensitivity
equations attached for the Lotka-Volterra equations by:

```@example directsense
using OrdinaryDiffEq, DiffEqSensitivity
using OrdinaryDiffEq, SciMLSensitivity
function f(du,u,p,t)
du[1] = dx = p[1]*u[1] - p[2]*u[1]*u[2]
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2 changes: 1 addition & 1 deletion docs/src/dde_fitting/delay_diffeq.md
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Expand Up @@ -5,7 +5,7 @@ supported. For example, we can build a layer with a delay differential equation
like:

```@example dde
using DifferentialEquations, Optimization, DiffEqSensitivity,
using DifferentialEquations, Optimization, SciMLSensitivity,
OptimizationPolyalgorithms
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2 changes: 1 addition & 1 deletion docs/src/hybrid_jump_fitting/bouncing_ball.md
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Expand Up @@ -8,7 +8,7 @@ data. Assume we have data for the ball's height after 15 seconds. Let's
first start by implementing the ODE:

```@example bouncing_ball
using Optimization, OptimizationPolyalgorithms, DiffEqSensitivity, DifferentialEquations
using Optimization, OptimizationPolyalgorithms, SciMLSensitivity, DifferentialEquations
function f(du,u,p,t)
du[1] = u[2]
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14 changes: 7 additions & 7 deletions docs/src/index.md
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@@ -1,6 +1,6 @@
# DiffEqSensitivity: Automatic Differentiation and Adjoints for (Differential) Equation Solvers
# SciMLSensitivity: Automatic Differentiation and Adjoints for (Differential) Equation Solvers

DiffEqSensitivity.jl is the automatic differentiation and adjoints system for the SciML
SciMLSensitivity.jl is the automatic differentiation and adjoints system for the SciML
ecosystem. Also known as local sensitivity analysis, these methods allow for calculation
of fast derivatives of SciML problem types which are commonly used to analyze model
sensitivities, callibrate models to data, train neural ODEs, perform automated model
Expand All @@ -9,7 +9,7 @@ a high level interface that pulls together all of the tools with heuristics
and helper functions to make solving inverse problems and inferring models
as easy as possible without losing efficiency.

Thus, what DiffEqSensitivity.jl provides is:
Thus, what SciMLSensitivity.jl provides is:

- Automatic differentiation overloads for improving the performance and flexibility
of AD calls over `solve`.
Expand Down Expand Up @@ -163,8 +163,8 @@ With this package, you can explore various ways to integrate the two methodologi

## Note on Modularity and Composability with Solvers

Note that DiffEqSensitivity.jl purely built on composable and modular infrastructure.
DiffEqSensitivity provides high level helper functions and documentation for the user, but the
Note that SciMLSensitivity.jl purely built on composable and modular infrastructure.
SciMLSensitivity provides high level helper functions and documentation for the user, but the
code generation stack is modular and composes in many different ways. For example, one can
use and swap out the ODE solver between any common interface compatible library, like:

Expand All @@ -176,7 +176,7 @@ use and swap out the ODE solver between any common interface compatible library,
- [... etc. many other choices!](https://diffeq.sciml.ai/stable/solvers/ode_solve/)

In addition, due to the composability of the system, none of the components are directly
tied to the Flux.jl machine learning framework. For example, you can [use DiffEqSensitivity.jl
tied to the Flux.jl machine learning framework. For example, you can [use SciMLSensitivity.jl
to generate TensorFlow graphs and train the neural network with TensorFlow.jl](https://youtu.be/n2MwJ1guGVQ?t=284),
[use PyTorch arrays via Torch.jl](https://github.com/FluxML/Torch.jl), and more all with
single line code changes by utilizing the underlying code generation. The tutorials shown here
Expand All @@ -192,7 +192,7 @@ Julia packages.

## Citation

If you use DiffEqSensitivity.jl or are influenced by its ideas, please cite:
If you use SciMLSensitivity.jl or are influenced by its ideas, please cite:

```
@article{rackauckas2020universal,
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6 changes: 3 additions & 3 deletions docs/src/manual/differential_equation_sensitivities.md
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# [Sensitivity Algorithms for Differential Equations with Automatic Differentiation (AD)](@id sensitivity_diffeq)

DiffEqSensitivity.jl's high level interface allows for specifying a
SciMLSensitivity.jl's high level interface allows for specifying a
sensitivity algorithm (`sensealg`) to control the method by which
`solve` is differentiated in an automatic differentiation (AD)
context by a compatible AD library. The underlying algorithms then
Expand All @@ -19,7 +19,7 @@ system are:
Take for example this simple differential equation solve on Lotka-Volterra:

```julia
using DiffEqSensitivity, OrdinaryDiffEq, Zygote
using SciMLSensitivity, OrdinaryDiffEq, Zygote

function fiip(du,u,p,t)
du[1] = dx = p[1]*u[1] - p[2]*u[1]*u[2]
Expand All @@ -39,7 +39,7 @@ and `dp` is the derivative of the loss function with respect to the parameters.

Because the gradient is calculated by `Zygote.gradient` and Zygote.jl is one of
the compatible AD libraries, this derivative calculation will be captured
by the `sensealg` system, and one of DiffEqSensitivity.jl's adjoint overloads
by the `sensealg` system, and one of SciMLSensitivity.jl's adjoint overloads
will be used to compute the derivative. By default, if the `sensealg` keyword
argument is not defined, then a smart polyalgorithm is used to automatically
determine the most appropriate method for a given equation.
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4 changes: 2 additions & 2 deletions docs/src/neural_ode/neural_gde.md
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Expand Up @@ -12,7 +12,7 @@ using GraphNeuralNetworks.GNNGraphs: normalized_adjacency
using Lux, NNlib, Optimisers, Zygote, Random, ComponentArrays
using Lux: AbstractExplicitLayer, glorot_normal, zeros32
import Lux: initialparameters, initialstates
using DiffEqSensitivity
using SciMLSensitivity
using Statistics: mean
using MLDatasets: Cora
using CUDA
Expand Down Expand Up @@ -152,7 +152,7 @@ using GraphNeuralNetworks.GNNGraphs: normalized_adjacency
using Lux, NNlib, Optimisers, Zygote, Random, ComponentArrays
using Lux: AbstractExplicitLayer, glorot_normal, zeros32
import Lux: initialparameters, initialstates
using DiffEqSensitivity
using SciMLSensitivity
using Statistics: mean
using MLDatasets: Cora
using CUDA
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6 changes: 3 additions & 3 deletions docs/src/neural_ode/neural_ode_flux.md
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@@ -1,6 +1,6 @@
# Neural Ordinary Differential Equations with Flux

All of the tools of DiffEqSensitivity.jl can be used with Flux.jl. A lot of the examples
All of the tools of SciMLSensitivity.jl can be used with Flux.jl. A lot of the examples
have been written to use `FastChain` and `sciml_train`, but in all cases this
can be changed to the `Chain` and `Flux.train!` workflow.

Expand All @@ -10,7 +10,7 @@ This should work almost automatically by using `solve`. Here is an
example of optimizing `u0` and `p`.

```@example neuralode1
using OrdinaryDiffEq, DiffEqSensitivity, Flux, Plots
using OrdinaryDiffEq, SciMLSensitivity, Flux, Plots
u0 = Float32[2.; 0.]
datasize = 30
Expand Down Expand Up @@ -83,7 +83,7 @@ Notice that Optimization.jl works on a vector input, so we have to concatenate `
and `p` and then in the loss function split to the pieces.

```@example neuralode2
using Flux, OrdinaryDiffEq, DiffEqSensitivity, Optimization, OptimizationOptimisers, OptimizationOptimJL, Plots
using Flux, OrdinaryDiffEq, SciMLSensitivity, Optimization, OptimizationOptimisers, OptimizationOptimJL, Plots
u0 = Float32[2.; 0.]
datasize = 30
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4 changes: 2 additions & 2 deletions docs/src/ode_fitting/optimization_ode.md
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Expand Up @@ -7,7 +7,7 @@ follow.

```@example optode_cp
using DifferentialEquations, Optimization, OptimizationPolyalgorithms, OptimizationOptimJL,
DiffEqSensitivity, Zygote, Plots
SciMLSensitivity, Zygote, Plots
function lotka_volterra!(du, u, p, t)
x, y = u
Expand Down Expand Up @@ -73,7 +73,7 @@ more details, [see the DifferentialEquations.jl documentation](http:https://docs.julia

```@example optode
using DifferentialEquations, Optimization, OptimizationPolyalgorithms, OptimizationOptimJL,
DiffEqSensitivity, Zygote, Plots
SciMLSensitivity, Zygote, Plots
function lotka_volterra!(du, u, p, t)
x, y = u
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2 changes: 1 addition & 1 deletion docs/src/ode_fitting/second_order_adjoints.md
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@@ -1,7 +1,7 @@
# Newton and Hessian-Free Newton-Krylov with Second Order Adjoint Sensitivity Analysis

In many cases it may be more optimal or more stable to fit using second order
Newton-based optimization techniques. Since DiffEqSensitivity.jl provides
Newton-based optimization techniques. Since SciMLSensitivity.jl provides
second order sensitivity analysis for fast Hessians and Hessian-vector
products (via forward-over-reverse), we can utilize these in our neural/universal
differential equation training processes.
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6 changes: 3 additions & 3 deletions docs/src/optimal_control/SDE_control.md
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Expand Up @@ -20,7 +20,7 @@ follow a full explanation of the definition and training process:
```julia
# load packages
using DiffEqFlux
using DiffEqSensitivity
using SciMLSensitivity
using Optimization
using StochasticDiffEq, DiffEqCallbacks, DiffEqNoiseProcess
using Statistics, LinearAlgebra, Random
Expand Down Expand Up @@ -304,7 +304,7 @@ visualization_callback(res.u, loss(res.u); doplot=true)
### Load packages
```julia
using DiffEqFlux
using DiffEqSensitivity
using SciMLSensitivity
using Optimization
using StochasticDiffEq, DiffEqCallbacks, DiffEqNoiseProcess
using Statistics, LinearAlgebra, Random
Expand Down Expand Up @@ -626,7 +626,7 @@ of the neural network.
`sensealg` allows one to switch between the different [sensitivity modes](https://diffeqflux.sciml.ai/dev/ControllingAdjoints/).
`InterpolatingAdjoint` and `BacksolveAdjoint` are the two possible continuous adjoint
sensitivity methods. The necessary correction between Ito and Stratonovich integrals
is computed under the hood in the DiffEqSensitivity package.
is computed under the hood in the SciMLSensitivity package.

```julia
# optimize the parameters for a few epochs with ADAM on time span
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2 changes: 1 addition & 1 deletion docs/src/optimal_control/feedback_control.md
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Expand Up @@ -11,7 +11,7 @@ equation to stay close to 1.

```@example udeneuralcontrol
using Flux, Optimization, OptimizationPolyalgorithms, OptimizationOptimJL,
DiffEqSensitivity, Zygote, DifferentialEquations, Plots, Random
SciMLSensitivity, Zygote, DifferentialEquations, Plots, Random
rng = Random.default_rng()
u0 = 1.1f0
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2 changes: 1 addition & 1 deletion docs/src/optimal_control/optimal_control.md
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Expand Up @@ -37,7 +37,7 @@ of a local minimum. This looks like:

```@example neuraloptimalcontrol
using Flux, DifferentialEquations, Optimization, OptimizationOptimJL, OptimizationFlux,
DiffEqSensitivity, Zygote, Plots, Statistics, Random
SciMLSensitivity, Zygote, Plots, Statistics, Random
rng = Random.default_rng()
tspan = (0.0f0,8.0f0)
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4 changes: 2 additions & 2 deletions docs/src/sde_fitting/optimization_sde.md
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@@ -1,7 +1,7 @@
# Optimization of Stochastic Differential Equations

Here we demonstrate `sensealg = ForwardDiffSensitivity()` (provided by
DiffEqSensitivity.jl) for forward-mode automatic differentiation of a small
SciMLSensitivity.jl) for forward-mode automatic differentiation of a small
stochastic differential equation. For large parameter equations, like neural
stochastic differential equations, you should use reverse-mode automatic
differentiation. However, forward-mode can be more efficient for low numbers
Expand All @@ -15,7 +15,7 @@ is a stochastic process. Each time we solve this equation we get a different
solution, so we need a sensible data source.

```@example sde
using DifferentialEquations, DiffEqSensitivity, Plots
using DifferentialEquations, SciMLSensitivity, Plots
function lotka_volterra!(du,u,p,t)
x,y = u
Expand Down
2 changes: 1 addition & 1 deletion docs/src/training_tips/divergence.md
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Expand Up @@ -28,7 +28,7 @@ end
A full example making use of this trick is:

```@example divergence
using DifferentialEquations, DiffEqSensitivity, Optimization, OptimizationFlux, OptimizationOptimJL, Plots
using DifferentialEquations, SciMLSensitivity, Optimization, OptimizationFlux, OptimizationOptimJL, Plots
function lotka_volterra!(du,u,p,t)
rab, wol = u
Expand Down
2 changes: 1 addition & 1 deletion docs/src/training_tips/local_minima.md
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Expand Up @@ -159,7 +159,7 @@ one could use a mix of (4) and (5), or breaking up the trajectory into chunks an

```@example resetic
using Flux, Plots, DifferentialEquations, DiffEqSensitivity
using Flux, Plots, DifferentialEquations, SciMLSensitivity
#Starting example with tspan (0, 5)
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2 changes: 1 addition & 1 deletion src/DiffEqSensitivity.jl
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@@ -1,4 +1,4 @@
module DiffEqSensitivity
module SciMLSensitivity

using DiffEqBase, ForwardDiff, Tracker, FiniteDiff, Statistics
using DiffEqCallbacks, QuadGK, RecursiveArrayTools, LinearAlgebra
Expand Down
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