diff --git a/joss.06611/10.21105.joss.06611.crossref.xml b/joss.06611/10.21105.joss.06611.crossref.xml new file mode 100644 index 0000000000..2cbf795363 --- /dev/null +++ b/joss.06611/10.21105.joss.06611.crossref.xml @@ -0,0 +1,889 @@ + + + + 20240621174942-d2632446a6226ab81fae5176ae14073a4818a1db + 20240621174942 + + JOSS Admin + admin@theoj.org + + The Open Journal + + + + + Journal of Open Source Software + JOSS + 2475-9066 + + 10.21105/joss + https://joss.theoj.org + + + + + 06 + 2024 + + + 9 + + 98 + + + + CBX: Python and Julia Packages for Consensus-Based +Interacting Particle Methods + + + + Rafael + Bailo + https://orcid.org/0000-0001-8018-3799 + + + Alethea + Barbaro + https://orcid.org/0000-0001-9856-2818 + + + Susana N. + Gomes + https://orcid.org/0000-0002-8731-367X + + + Konstantin + Riedl + https://orcid.org/0000-0002-2206-4334 + + + Tim + Roith + https://orcid.org/0000-0001-8440-2928 + + + Claudia + Totzeck + https://orcid.org/0000-0001-6283-7154 + + + Urbain + Vaes + https://orcid.org/0000-0002-7629-7184 + + + + 06 + 21 + 2024 + + + 6611 + + + 10.21105/joss.06611 + + + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + + + + Software archive + 10.5281/zenodo.12207224 + + + GitHub review issue + https://github.com/openjournals/joss-reviews/issues/6611 + + + + 10.21105/joss.06611 + https://joss.theoj.org/papers/10.21105/joss.06611 + + + https://joss.theoj.org/papers/10.21105/joss.06611.pdf + + + + + + Studien über das Gleichgewicht der lebendigen +Kraft zwischen bewegten materiellen Punkten + Boltzmann + Wiener Berichte + 58 + 1868 + Boltzmann, L. 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Journal of Global Optimization. +https://doi.org/10.1007/s10898-024-01369-1 + + + + + + diff --git a/joss.06611/10.21105.joss.06611.pdf b/joss.06611/10.21105.joss.06611.pdf new file mode 100644 index 0000000000..75e93e1c5d Binary files /dev/null and b/joss.06611/10.21105.joss.06611.pdf differ diff --git a/joss.06611/paper.jats/10.21105.joss.06611.jats b/joss.06611/paper.jats/10.21105.joss.06611.jats new file mode 100644 index 0000000000..5feffa3d42 --- /dev/null +++ b/joss.06611/paper.jats/10.21105.joss.06611.jats @@ -0,0 +1,1618 @@ + + +
+ + + + +Journal of Open Source Software +JOSS + +2475-9066 + +Open Journals + + + +6611 +10.21105/joss.06611 + +CBX: Python and Julia Packages for Consensus-Based +Interacting Particle Methods + + + +https://orcid.org/0000-0001-8018-3799 + +Bailo +Rafael + + + + +https://orcid.org/0000-0001-9856-2818 + +Barbaro +Alethea + + + + +https://orcid.org/0000-0002-8731-367X + +Gomes +Susana N. + + + + +https://orcid.org/0000-0002-2206-4334 + +Riedl +Konstantin + + + + + +https://orcid.org/0000-0001-8440-2928 + +Roith +Tim + + + + +https://orcid.org/0000-0001-6283-7154 + +Totzeck +Claudia + + + + +https://orcid.org/0000-0002-7629-7184 + +Vaes +Urbain + + + + + + +Mathematical Institute, University of Oxford, United +Kingdom + + + + +Delft University of Technology, The +Netherlands + + + + +Mathematics Institute, University of Warwick, United +Kingdom + + + + +Technical University of Munich, Germany + + + + +Munich Center for Machine Learning, Germany + + + + +Helmholtz Imaging, Deutsches Elektronen-Synchrotron DESY, +Notkestr. 85, 22607 Hamburg, Germany + + + + +University of Wuppertal, Germany + + + + +MATHERIALS team, Inria Paris, France + + + + +École des Ponts ParisTech, Marne-la-Vallée, +France + + + +9 +98 +6611 + +Authors of papers retain copyright and release the +work under a Creative Commons Attribution 4.0 International License (CC +BY 4.0) +2022 +The article authors + +Authors of papers retain copyright and release the work under +a Creative Commons Attribution 4.0 International License (CC BY +4.0) + + + +Python +Julia +Optimisation +Sampling + + + + + + Summary +

We introduce + CBXPy + and + ConsensusBasedX.jl, + Python and Julia implementations of consensus-based interacting + particle systems (CBX), which generalise consensus-based optimization + methods (CBO) for global, derivative-free optimisation. The + raison d’être of our libraries is twofold: on the one + hand, to offer high-performance implementations of CBX methods that + the community can use directly, while on the other, providing a + general interface that can accommodate and be extended to further + variations of the CBX family. Python and Julia were selected as the + leading high-level languages in terms of usage and performance, as + well as for their popularity among the scientific computing community. + Both libraries have been developed with a common + ethos, ensuring a similar API and core functionality, + while leveraging the strengths of each language and writing idiomatic + code.

+
+ + Mathematical background +

Consensus-based optimisation (CBO) is an approach to solve, for a + given (continuous) objective function + + + f:d, + the global minimisation problem

+

+ + x*=argminxdf(x),

+

i.e., the task of finding the point + + x* + where + + f + attains its lowest value. Such problems arise in a variety of + disciplines including engineering, where + + + x + might represent a vector of design parameters for a structure and + + + f + a function related to its cost and structural integrity, or machine + learning, where + + x + could comprise the parameters of a neural network and + + + f + the empirical loss, which measures the discrepancy of the neural + network prediction with the observed data.

+

In some cases, so-called gradient-based methods + (those that involve updating a guess of + + x* + by evaluating the gradient + + f) + achieve state-of-the-art performance in the global minimisation + problem. However, in scenarios where + + f + is non-convex (when + + f + could have many local minima), where + + + f + is non-smooth (when + + f + is not well-defined), or where the evaluation of + + + f + is impractical due to cost or complexity, + derivative-free methods are needed. Numerous + techniques exist for derivative-free optimisation, such as + random or pattern search + (Friedman + & Savage, 1947; + Hooke + & Jeeves, 1961; + Rastrigin, + 1963), Bayesian optimisation + (Močkus, + 1975) or simulated annealing + (Henderson + et al., 2003). Here, we focus on particle-based + methods, specifically, consensus-based optimisation (CBO), as + proposed by Pinnau et al. + (2017), + and the consensus-based taxonomy of related techniques, which we term + CBX.

+

CBO uses a finite number + + N + of agents (particles), + + xt=(xt1,,xtN), + dependent on time + + t, + to explore the landscape of + + f + without evaluating any of its derivatives (as do other CBX methods). + The agents evaluate the objective function at their current position, + + + f(xti), + and define a consensus point + + + cα. + This point is an approximation of the global minimiser + + + x*, + and is constructed by weighing each agent’s position against the + Gibbs-like distribution + + + exp(αf) + (Boltzmann, + 1868). More rigorously,

+

+ + cα(xt)=1i=1Nωα(xti)i=1Nxtiωα(xti),whereωα()=exp(αf()),

+

for some + 0]]> + α>0. + The exponential weights in the definition favour those points + + + xti + where + + f(xti) + is lowest, and comparatively ignore the rest, particularly for larger + + + α. + If all the found values of the objective function are approximately + the same, + + cα(xt) + is roughly an arithmetic mean. Instead, if one particle is much better + than the rest, + + cα(xt) + will be very close to its position.

+

Once the consensus point is computed, the particles evolve in time + following the stochastic differential equation + (SDE)

+

+ + dxti=λ(xticα(xt))dtconsensus drift+σxticα(xt)dBtiscaled diffusion,

+

where + + λ + and + + σ + are positive parameters, and where + + Bti + are independent Brownian motions in + + d + dimensions. The consensus drift is a deterministic + term that drives each agent towards the consensus point, with rate + + + λ. + Meanwhile, the scaled diffusion is a stochastic term + that encourages exploration of the landscape. The scaling factor of + the diffusion is proportional to the distance of the particle to the + consensus point. Hence, whenever the position of a particle and the + location of the weighted mean coincide, the particle stops moving. On + the other hand, if the particle is far away from the consensus, its + evolution has a stronger exploratory behaviour. While both the agents’ + positions and the consensus point evolve in time, it has been proven + that all agents eventually reach the same position and that the + consensus point + + cα(xt) + is a good approximation of + + x* + (Carrillo + et al., 2018; + Fornasier, + Klock, et al., 2021). Other variations of the method, such as + CBO with anisotropic noise + (Carrillo + et al., 2021), polarised CBO + (Bungert + et al., 2024), or consensus-based sampling + (CBS) + (Carrillo + et al., 2022) have also been proposed.

+

In practice, the solution to the SDE above cannot be found exactly. + Instead, an Euler–Maruyama scheme + (Kloeden + & Platen, 1992) is used to update the position of the + agents. The update is given by

+

+ + xixiλΔt(xicα(x))+σΔtxicα(x)ξi,

+

where + 0]]> + Δt>0 + is the step size and + + ξi𝒩(0,Id) + are independent, identically distributed, standard normal random + vectors.

+

As a particle-based family of methods, CBX is conceptually related + to other optimisation approaches which take inspiration from biology, + like particle-swarm optimisation (PSO) + (Kennedy + & Eberhart, 1995), from physics, like simulated + annealing (SA) + (Henderson + et al., 2003), or from other heuristics + (Bayraktar + et al., 2013; + Chandra + Mohan & Baskaran, 2012; + Karaboga + et al., 2012; + Yang, + 2009). However, unlike many such methods, CBX has been designed + to be compatible with rigorous convergence analysis at the mean-field + level (the infinite-particle limit, see + Huang + & Qiu, 2022). Many convergence results have been shown, + whether in the original formulation + (Carrillo + et al., 2018; + Fornasier, + Klock, et al., 2021), for CBO with anisotropic noise + (Carrillo + et al., 2021; + Fornasier + et al., 2022), with memory effects + (Riedl, + 2023), with truncated noise + (Fornasier + et al., 2024), for polarised CBO + (Bungert + et al., 2024), and PSO + (Huang + et al., 2023). The relation between CBO and stochastic + gradient descent has been recently established by Riedl et + al. + (2023), + which suggests a previously unknown yet fundamental connection between + derivative-free and gradient-based approaches.

+ +

Typical evolution of a CBO method minimising the Ackley + function + (Ackley, + 1987).

+ +
+

CBX methods have been successfully applied and extended to several + different settings, such as constrained optimisation problems + (Borghi + et al., 2023b; + Fornasier, + Huang, et al., 2021), multi-objective optimisation + (Borghi + et al., 2023a; + Klamroth + et al., 2024), saddle-point problems + (Huang + et al., 2024), federated learning tasks + (Carrillo + et al., 2023), uncertainty quantification + (Althaus + et al., 2023), or sampling + (Carrillo + et al., 2022).

+
+ + Statement of need +

In general, very few implementations of CBO already exist, and none + have been designed with the generality of other CBX methods in mind. + Here, we summarise the related software:

+

Regarding Python, we refer to PyPop7 + (Duan + et al., 2022) and scikit-opt + (Guo, + 2021) for a collection of various derivative-free optimisation + strategies. For packages connected to Bayesian optimisation, we refer + to BayesO + (Kim + & Choi, 2023), bayesian-optimization + (Nogueira, + 2014–), GPyOpt + (The + GPyOpt authors, 2016), GPflowOpt + (Knudde + et al., 2017), pyGPGO + (Jiménez + & Ginebra, 2017), PyBADS + (Singh + & Acerbi, 2024) and BoTorch + (Balandat + et al., 2020). Furthermore, CMA-ES + (Hansen + & Ostermeier, 1996) was implemented in + pycma + (Hansen + et al., 2019). To the best of our knowledge the connection + between consensus-based methods and evolution strategies is not fully + understood, and is therefore an interesting future direction. PSO and + SA implementations are already available in + PySwarms + (Miranda, + 2018), scikit-opt + (Guo, + 2021), DEAP + (Fortin + et al., 2012) and pagmo + (Biscani + et al., 2017). They are widely used by the community and + provide a rich framework for the respective methods. However, + adjusting these implementations to CBO is not straightforward. The + first publicly available Python packages implementing CBX algorithms + were given by some of the authors together with collaborators. Tukh + & Riedl + (2022) + implement standard CBO + (Pinnau + et al., 2017), and the package PolarCBO + (Roith + et al., 2023) provides an implementation of polarised CBO + (Bungert + et al., 2024). + CBXPy + is a significant extension of the latter, which was tailored to the + polarised variant. The code architecture was generalised, which + allowed the implementation of the whole CBX family within a common + framework.

+

Regarding Julia, PSO and SA methods are, among others, implemented + in Optim.jl + (Mogensen + & Riseth, 2018), Metaheuristics.jl + (Mejı́a-de-Dios + & Mezura-Montes, 2022), and + Manopt.jl + (Bergmann, + 2022). PSO and SA are also included in the meta-library + Optimization.jl + (Dixit + & Rackauckas, 2023), as well as Nelder–Mead, which is a + direct search method. The latter is also implemented in + Manopt.jl + (Bergmann, + 2022), which further provides a manifold variant of CMA-ES + (Colutto + et al., 2009). One of the authors gave the first specific Julia + implementation of standard CBO Consensus.jl + (Bailo, + 2023). That package has now been deprecated in favour of + ConsensusBasedX.jl, + which improves the performance of the CBO implementation with a + type-stable and allocation-free implementation. The package also adds + a CBS implementation, and overall presents a more general interface + that accomodates the wider CBX class of methods.

+
+ + Features +

CBXPy + and + ConsensusBasedX.jl + provide a lightweight and high-level interface. An existing function + can be optimised with just one call. Method selection, parameters, + different approaches to particle initialisation, and termination + criteria can be specified directly through this interface, offering a + flexible point of entry for the casual user. Some of the methods + provided are standard CBO + (Pinnau + et al., 2017), CBO with mini-batching + (Carrillo + et al., 2021), polarised CBO + (Bungert + et al., 2024), CBO with memory effects + (Grassi + & Pareschi, 2021; + Riedl, + 2023), and consensus-based sampling (CBS) + (Carrillo + et al., 2022). Parallelisation tools are available.

+

A more proficient user will benefit from the fully documented + interface, which allows the specification of advanced options (e.g., + debug output, the noise model, or the numerical approach to the matrix + square root of the weighted ensemble covariance matrix). Both + libraries offer performance evaluation methods as well as + visualisation tools.

+

Ultimately, a low-level interface (including documentation and + full-code examples) is provided. Both libraries have been designed to + express common abstractions in the CBX family while allowing + customisation. Users can easily implement new CBX methods or modify + the behaviour of the existing implementation by strategically + overriding certain hooks. The stepping of the methods can also be + controlled manually.

+ + CBXPy + +

CBXPy logo.

+ +
+

Most of the + CBXPy + implementation uses basic Python functionality, and the agents are + handled as an array-like structure. For certain specific features, + like broadcasting-behaviour, array copying, and index selection, we + fall back to the numpy implementation + (Harris + et al., 2020). However, it should be noted that an adaptation + to other array or tensor libraries like PyTorch + (Paszke + et al., 2019) is straightforward. Compatibility with the + latter enables gradient-free deep learning directly on the GPU, as + demonstrated in the documentation. +

+

The library is available on + GitHub + and can be installed via pip. It is licensed + under the MIT license. Below, we provide a short example on how to + optimise a function with CBXPy.

+ from cbx.dynamics import CBO # import the CBO class +f = lambda x: x[0]**2 + x[1]**2 # define the function to minimise +x = CBO(f, d=2).optimize() # run the optimisation +

More examples and details on the implementation are available in + the + documentation.

+
+ + ConsensusBasedX.jl + +

ConsensusBasedX.jl logo.

+ +
+

ConsensusBasedX.jl + has been almost entirely written in native Julia (with the exception + of a single call to LAPACK). The code has been developed with + performance in mind, thus the critical routines are fully + type-stable and allocation-free. A specific tool is provided to + benchmark a typical method iteration, which can be used to detect + allocations. Through this tool, unit tests are in place to ensure + zero allocations in all the provided methods. The benchmarking tool + is also available to users, who can use it to test their + implementations of + + f, + as well as any new CBX methods.

+

Basic function minimisation can be performed by running:

+ using ConsensusBasedX # load the ConsensusBasedX package +f(x) = x[1]^2 + x[2]^2 # define the function to minimise +x = minimise(f, D = 2) # run the minimisation +

The library is available on + GitHub. + It has been registered in the + general + Julia registry, and therefore it can be installed by + running ]add ConsensusBasedX. It is licensed + under the MIT license. More examples and full instructions are + available in the + documentation.

+
+
+ + Acknowledgements +

We thank the Lorentz Center in Leiden for their kind hospitality + during the workshop “Purpose-driven particle systems” in Spring 2023, + where this work was initiated. RB was supported by the Advanced Grant + Nonlocal-CPD (Nonlocal PDEs for Complex Particle Dynamics: Phase + Transitions, Patterns and Synchronisation) of the European Research + Council Executive Agency (ERC) under the European Union’s Horizon 2020 + research and innovation programme (grant agreement No. 883363) and by + the EPSRC grant EP/T022132/1 “Spectral element methods for fractional + differential equations, with applications in applied analysis and + medical imaging”. KR acknowledges support from the German Federal + Ministry of Education and Research and the Bavarian State Ministry for + Science and the Arts. TR acknowledges support from DESY (Hamburg, + Germany), a member of the Helmholtz Association HGF. This research was + supported in part through the Maxwell computational resources operated + at Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany. UV + acknowledges support from the Agence Nationale de la Recherche under + grant ANR-23-CE40-0027 (IPSO).

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