1659414049

BesselK.jl: A Fast Differentiable Implementation of Besselk

In this Julia tutorial, we'll learn about BesselK.jl, a package implements one function: the modified second-kind Bessel function Kᵥ(x)

BesselK.jl: An AD-compatible modified second-kind Bessel function

This package implements one function: the modified second-kind Bessel function Kᵥ(x). It is designed specifically to be automatically differentiable with ForwardDiff.jl, including providing derivatives with respect to the order parameter v that are fast and non-allocating in the entire domain for both first and second order.

Derivatives with respect to \nu are significantly faster than any finite differencing method, including the most naive fixed-step minimum-order method, and in almost all of the domain are meaningful more accurate. Particularly near the origin you should expect to gain at least 3-5 digits. Second derivatives are even more dramatic, both in terms of the speedup and accuracy gains, now commonly giving 10+ more digits of accuracy.

As a happy accident/side-effect, if you're willing to give up the last couple digits of accuracy, you could also use ForwardDiff.jl on this code for derivatives with respect to argument for an order-of-magnitude speedup. In some casual testing the argument-derivative errors with this code are never worse than 1e-12, and they turn 1.4 μs with allocations into 140 ns without any allocations.

In order to avoid naming conflicts with SpecialFunctions.besselk, this package exports two functions: adbesselk and adbesselkxv. The first function is Kᵥ(x), and the second function is (xᵛ)*Kᵥ(x). This second function has the nice property of being bounded at the origin when v>0, and comes up in the Matern covariance function, which was the primary motivation for this implementation. The function adbesselk returns SpecialFunctions.besselk if v isa AbstractFloat, since the AMOS besselk is slightly more accurate, and there is a rule in place for the exact argument derivatives. But otherwise, it returns BesselK._besselk(v, x, args...), which is the Julia-native implementation here that provides very accurate derivatives.

Here is a very basic demo:

using ForwardDiff, SpecialFunctions, BesselK

(v, x) = (1.1, 2.1)

# For regular evaluations, you get what you're used to getting:

# But now you also get good (and fast!) derivatves:
@show ForwardDiff.derivative(_v->adbesselk(_v, x), v)   # good to go.
@show ForwardDiff.derivative(_v->adbesselkxv(_v, x), v) # good to go.


A note to people coming here from the paper

You'll see that this repo defines a great deal of specific derivative functions in the files in ./examples and ./paperscripts. This is only because we specifically tested those quantities in the paper. If you're just here to fit a Matern covariance function, then you should not be doing that. Your code, at least in the simplest case, should probably look more like this:


using ForwardDiff, BesselK

function my_covariance_function(loc1, loc2, params)
end

# Create your likelihood and use ForwardDiff for the grad and Hessian:
function nll(params)
K = cholesky!(Symmetric([my_covariance_function(x, y, params)
for x in my_locations, y in my_locations]))
0.5*(logdet(K) + dot(my_data, K\my_data))
end
nllh(params) = ForwardDiff.hessian(nll, params)

my_mle = some_optimizer(init_params, nll, nllg, nllh, ...)


Or something like that. You of course do not have to do it this way, and could manually implement the gradient and Hessian of the likelihood after manually creating derivatives of the covariance function itself (see ./example/matern.jl for a demo of that), and manual implementations, particularly for the Hessian, will be faster if they are thoughtful enough. But what I mean to emphasize here is that in general you should not be doing manual chain rule or derivative computations of your covariance function itself. Let the AD handle that for you and enjoy the power that Julia's composability offers.

Limitations

For the moment there are two primary limitations:

AD compatibility with ForwardDiff.jl only. The issue here is that in one particular case I use a different function branch of one is taking a derivative with respect to v or just evaluating besselk(v, x). The way that is currently checked in the code is with if (v isa AbstractFloat), which may not work properly for other methods.

Only derivatives up to the second are checked and confirmed accurate. The code uses a large number of local polynomial expansions at slightly hairy values of internal intermediate functions, and so at some sufficiently high level of derivative those local polynomials won't give accurate partial information.

Also consider: Bessels.jl

This software package was written with the pretty specific goal of computing derivatives of Kᵥ(x) with respect to the order using ForwardDiff.jl. While it is in general a bit faster than AMOS, we give up a few digits of accuracy here and there in the interest of better and faster derivatives. If you just want the fastest possible Kᵥ(x), then you would probably be better off using Bessels.jl. At the time of writing it only offers Kᵥ(x) for integer orders, but non-integer orders will be available soon enough I'm sure. While differentiability is on the roadmap, they more explicitly target writing the fastest possible base Kᵥ(x), and what they offer is seriously fast.

There is and will be some cross-pollination between the two software projects, and at some point I expect to switch adbesselk to use Bessels.besselk where possible instead of SpecialFunctions.besselk. And at some point if the order derivatives become available there might not be much reason to use this package instead of that one, although I think for the moment if you want to fit a Matern covariance function you probably need to be here.

On the topic, the following methods are lifted directly from Bessels.jl so that we can go fast in the meantime:

• Integer order \nu when \nu isa AbstractFloat.

Implementation details

See the reference for an entire paper discussing the implementation. But in a word, this code uses several routines to evaluate Kᵥ accurately on different parts of the domain, and has to use some non-standard to maintain AD compatibility and correctness. When v is an integer or half-integer, for example, a lot of additional work is required.

The code is also pretty well-optimized, and you can benchmark for yourself or look at the paper to see that in several cases the ForwardDiff.jl-generated derivatives are faster than a single call to SpecialFunctions.besselk. To achieve this performance, particularly for second derivatives, some work was required to make sure that all of the function calls are non-allocating, which means switching from raw Tuples to Polynomial types in places where the polynomials are large enough and things like that. Again this arguably makes the code look a bit disorganized or inconsistent, but to my knowledge it is all necessary. If somebody looking at the source finds a simplification, I would love to see it, either in terms of an issue or a PR or an email or a patch file or anything.

A to-do item (written 2022/07/27), I think, is to re-organize the code a bit so that there is a function _besselk_vdual that only gets called when v isa ForwardDiff.Dual and a function _besselk_abstractfloat when v isa AbstractFloat. For the initial release, adbesselk always defaulted to SpecialFunctions.besselk where possible to give people what they expected and every digit possible. But as Bessels.jl matures, I think lifting at least a few of those routines in the interim is appealing but means that there is awkwardly a lot of control flow in BesselK._besselk as well as BesselK.adbesselk now. Probably better to compartmentalize those two domain partitionings. Defaulting to Bessels.besselk when v isa AbstractFloat is probably a good intermediate goal once it's ready for all arguments.

Citation

If you use this package in your research that gets compiled into some kind of report/article/poster/etc, please cite this paper:

@misc{GMSS_2022,
title={Fitting Mat\'ern Smoothness Parameters Using Automatic Differentiation},
author={Christopher J. Geoga and Oana Marin and Michel Schanen and Michael L. Stein},
year={2022},
eprint={2201.00090},
archivePrefix={arXiv},
primaryClass={stat.CO}
}


While this package ostensibly only covers a single function, putting all of this together and making it this fast and accurate was really a lot of work. I would really appreciate you citing this paper if this package was useful in your research. Like, for example, if you used this package to fit a Matern smoothness parameter with second order optimization methods.

Also, if you're reading this a few months into 2022 or later, we would also really appreciate it if you check back here or even open an issue/email to ask if there is an official journal reference by that point. Thanks in advance!

Author: cgeoga
Source Code: https://github.com/cgeoga/BesselK.jl
#julia

1659414049

BesselK.jl: A Fast Differentiable Implementation of Besselk

In this Julia tutorial, we'll learn about BesselK.jl, a package implements one function: the modified second-kind Bessel function Kᵥ(x)

BesselK.jl: An AD-compatible modified second-kind Bessel function

This package implements one function: the modified second-kind Bessel function Kᵥ(x). It is designed specifically to be automatically differentiable with ForwardDiff.jl, including providing derivatives with respect to the order parameter v that are fast and non-allocating in the entire domain for both first and second order.

Derivatives with respect to \nu are significantly faster than any finite differencing method, including the most naive fixed-step minimum-order method, and in almost all of the domain are meaningful more accurate. Particularly near the origin you should expect to gain at least 3-5 digits. Second derivatives are even more dramatic, both in terms of the speedup and accuracy gains, now commonly giving 10+ more digits of accuracy.

As a happy accident/side-effect, if you're willing to give up the last couple digits of accuracy, you could also use ForwardDiff.jl on this code for derivatives with respect to argument for an order-of-magnitude speedup. In some casual testing the argument-derivative errors with this code are never worse than 1e-12, and they turn 1.4 μs with allocations into 140 ns without any allocations.

In order to avoid naming conflicts with SpecialFunctions.besselk, this package exports two functions: adbesselk and adbesselkxv. The first function is Kᵥ(x), and the second function is (xᵛ)*Kᵥ(x). This second function has the nice property of being bounded at the origin when v>0, and comes up in the Matern covariance function, which was the primary motivation for this implementation. The function adbesselk returns SpecialFunctions.besselk if v isa AbstractFloat, since the AMOS besselk is slightly more accurate, and there is a rule in place for the exact argument derivatives. But otherwise, it returns BesselK._besselk(v, x, args...), which is the Julia-native implementation here that provides very accurate derivatives.

Here is a very basic demo:

using ForwardDiff, SpecialFunctions, BesselK

(v, x) = (1.1, 2.1)

# For regular evaluations, you get what you're used to getting:

# But now you also get good (and fast!) derivatves:
@show ForwardDiff.derivative(_v->adbesselk(_v, x), v)   # good to go.
@show ForwardDiff.derivative(_v->adbesselkxv(_v, x), v) # good to go.


A note to people coming here from the paper

You'll see that this repo defines a great deal of specific derivative functions in the files in ./examples and ./paperscripts. This is only because we specifically tested those quantities in the paper. If you're just here to fit a Matern covariance function, then you should not be doing that. Your code, at least in the simplest case, should probably look more like this:


using ForwardDiff, BesselK

function my_covariance_function(loc1, loc2, params)
end

# Create your likelihood and use ForwardDiff for the grad and Hessian:
function nll(params)
K = cholesky!(Symmetric([my_covariance_function(x, y, params)
for x in my_locations, y in my_locations]))
0.5*(logdet(K) + dot(my_data, K\my_data))
end
nllh(params) = ForwardDiff.hessian(nll, params)

my_mle = some_optimizer(init_params, nll, nllg, nllh, ...)


Or something like that. You of course do not have to do it this way, and could manually implement the gradient and Hessian of the likelihood after manually creating derivatives of the covariance function itself (see ./example/matern.jl for a demo of that), and manual implementations, particularly for the Hessian, will be faster if they are thoughtful enough. But what I mean to emphasize here is that in general you should not be doing manual chain rule or derivative computations of your covariance function itself. Let the AD handle that for you and enjoy the power that Julia's composability offers.

Limitations

For the moment there are two primary limitations:

AD compatibility with ForwardDiff.jl only. The issue here is that in one particular case I use a different function branch of one is taking a derivative with respect to v or just evaluating besselk(v, x). The way that is currently checked in the code is with if (v isa AbstractFloat), which may not work properly for other methods.

Only derivatives up to the second are checked and confirmed accurate. The code uses a large number of local polynomial expansions at slightly hairy values of internal intermediate functions, and so at some sufficiently high level of derivative those local polynomials won't give accurate partial information.

Also consider: Bessels.jl

This software package was written with the pretty specific goal of computing derivatives of Kᵥ(x) with respect to the order using ForwardDiff.jl. While it is in general a bit faster than AMOS, we give up a few digits of accuracy here and there in the interest of better and faster derivatives. If you just want the fastest possible Kᵥ(x), then you would probably be better off using Bessels.jl. At the time of writing it only offers Kᵥ(x) for integer orders, but non-integer orders will be available soon enough I'm sure. While differentiability is on the roadmap, they more explicitly target writing the fastest possible base Kᵥ(x), and what they offer is seriously fast.

There is and will be some cross-pollination between the two software projects, and at some point I expect to switch adbesselk to use Bessels.besselk where possible instead of SpecialFunctions.besselk. And at some point if the order derivatives become available there might not be much reason to use this package instead of that one, although I think for the moment if you want to fit a Matern covariance function you probably need to be here.

On the topic, the following methods are lifted directly from Bessels.jl so that we can go fast in the meantime:

• Integer order \nu when \nu isa AbstractFloat.

Implementation details

See the reference for an entire paper discussing the implementation. But in a word, this code uses several routines to evaluate Kᵥ accurately on different parts of the domain, and has to use some non-standard to maintain AD compatibility and correctness. When v is an integer or half-integer, for example, a lot of additional work is required.

The code is also pretty well-optimized, and you can benchmark for yourself or look at the paper to see that in several cases the ForwardDiff.jl-generated derivatives are faster than a single call to SpecialFunctions.besselk. To achieve this performance, particularly for second derivatives, some work was required to make sure that all of the function calls are non-allocating, which means switching from raw Tuples to Polynomial types in places where the polynomials are large enough and things like that. Again this arguably makes the code look a bit disorganized or inconsistent, but to my knowledge it is all necessary. If somebody looking at the source finds a simplification, I would love to see it, either in terms of an issue or a PR or an email or a patch file or anything.

A to-do item (written 2022/07/27), I think, is to re-organize the code a bit so that there is a function _besselk_vdual that only gets called when v isa ForwardDiff.Dual and a function _besselk_abstractfloat when v isa AbstractFloat. For the initial release, adbesselk always defaulted to SpecialFunctions.besselk where possible to give people what they expected and every digit possible. But as Bessels.jl matures, I think lifting at least a few of those routines in the interim is appealing but means that there is awkwardly a lot of control flow in BesselK._besselk as well as BesselK.adbesselk now. Probably better to compartmentalize those two domain partitionings. Defaulting to Bessels.besselk when v isa AbstractFloat is probably a good intermediate goal once it's ready for all arguments.

Citation

If you use this package in your research that gets compiled into some kind of report/article/poster/etc, please cite this paper:

@misc{GMSS_2022,
title={Fitting Mat\'ern Smoothness Parameters Using Automatic Differentiation},
author={Christopher J. Geoga and Oana Marin and Michel Schanen and Michael L. Stein},
year={2022},
eprint={2201.00090},
archivePrefix={arXiv},
primaryClass={stat.CO}
}


While this package ostensibly only covers a single function, putting all of this together and making it this fast and accurate was really a lot of work. I would really appreciate you citing this paper if this package was useful in your research. Like, for example, if you used this package to fit a Matern smoothness parameter with second order optimization methods.

Also, if you're reading this a few months into 2022 or later, we would also really appreciate it if you check back here or even open an issue/email to ask if there is an official journal reference by that point. Thanks in advance!

Author: cgeoga
Source Code: https://github.com/cgeoga/BesselK.jl
#julia

1612595276

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1660370580

ranger: A Fast Implementation of Random Forests

Marvin N. Wright

Introduction

ranger is a fast implementation of random forests (Breiman 2001) or recursive partitioning, particularly suited for high dimensional data. Classification, regression, and survival forests are supported. Classification and regression forests are implemented as in the original Random Forest (Breiman 2001), survival forests as in Random Survival Forests (Ishwaran et al. 2008). Includes implementations of extremely randomized trees (Geurts et al. 2006) and quantile regression forests (Meinshausen 2006).

ranger is written in C++, but a version for R is available, too. We recommend to use the R version. It is easy to install and use and the results are readily available for further analysis. The R version is as fast as the standalone C++ version.

Installation

R version

To install the ranger R package from CRAN, just run

install.packages("ranger")


R version >= 3.1 is required. With recent R versions, multithreading on Windows platforms should just work. If you compile yourself, the new RTools toolchain is required.

To install the development version from GitHub using devtools, run

devtools::install_github("imbs-hl/ranger")


Standalone C++ version

To install the C++ version of ranger in Linux or Mac OS X you will need a compiler supporting C++11 (i.e. gcc >= 4.7 or Clang >= 3.0) and Cmake. To build start a terminal from the ranger main directory and run the following commands

cd cpp_version
mkdir build
cd build
cmake ..
make


After compilation there should be an executable called "ranger" in the build directory.

To run the C++ version in Microsoft Windows please cross compile or ask for a binary.

Usage

R version

For usage of the R version see ?ranger in R. Most importantly, see the Examples section. As a first example you could try

ranger(Species ~ ., data = iris)


Standalone C++ version

In the C++ version type

./ranger --help


for a list of commands. First you need a training dataset in a file. This file should contain one header line with variable names and one line with variable values per sample (numeric only). Variable names must not contain any whitespace, comma or semicolon. Values can be seperated by whitespace, comma or semicolon but can not be mixed in one file. A typical call of ranger would be for example

./ranger --verbose --file data.dat --depvarname Species --treetype 1 --ntree 1000 --nthreads 4


If you find any bugs, or if you experience any crashes, please report to us. If you have any questions just ask, we won't bite.

Please cite our paper if you use ranger.