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mlr-org

mlr3tuning:Hyperparameter Optimization for 'mlr3'

Hyperparameter optimization package of the 'mlr3' ecosystem. It features highly configurable search spaces via the 'paradox' package and finds optimal hyperparameter configurations for any 'mlr3' learner. 'mlr3tuning' works with several optimization algorithms e.g. Random Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband (in 'mlr3hyperband'). Moreover, it can automatically optimize learners and estimate the performance of optimized models with nested resampling.

Maintained by Marc Becker. Last updated 3 months ago.

bbotkhyperparameter-optimizationhyperparameter-tuningmachine-learningmlr3optimizationtunetuning

55 stars 11.53 score 384 scripts 11 dependents

doubleml

DoubleML:Double Machine Learning in R

Implementation of the double/debiased machine learning framework of Chernozhukov et al. (2018) <doi:10.1111/ectj.12097> for partially linear regression models, partially linear instrumental variable regression models, interactive regression models and interactive instrumental variable regression models. 'DoubleML' allows estimation of the nuisance parts in these models by machine learning methods and computation of the Neyman orthogonal score functions. 'DoubleML' is built on top of 'mlr3' and the 'mlr3' ecosystem. The object-oriented implementation of 'DoubleML' based on the 'R6' package is very flexible. More information available in the publication in the Journal of Statistical Software: <doi:10.18637/jss.v108.i03>.

Maintained by Philipp Bach. Last updated 4 months ago.

causal-inferencedata-sciencedouble-machine-learningeconometricsmachine-learningmlr3statistics

139 stars 9.16 score 267 scripts 1 dependents

mlr-org

mlr3mbo:Flexible Bayesian Optimization

A modern and flexible approach to Bayesian Optimization / Model Based Optimization building on the 'bbotk' package. 'mlr3mbo' is a toolbox providing both ready-to-use optimization algorithms as well as their fundamental building blocks allowing for straightforward implementation of custom algorithms. Single- and multi-objective optimization is supported as well as mixed continuous, categorical and conditional search spaces. Moreover, using 'mlr3mbo' for hyperparameter optimization of machine learning models within the 'mlr3' ecosystem is straightforward via 'mlr3tuning'. Examples of ready-to-use optimization algorithms include Efficient Global Optimization by Jones et al. (1998) <doi:10.1023/A:1008306431147>, ParEGO by Knowles (2006) <doi:10.1109/TEVC.2005.851274> and SMS-EGO by Ponweiser et al. (2008) <doi:10.1007/978-3-540-87700-4_78>.

Maintained by Lennart Schneider. Last updated 26 days ago.

automlbayesian-optimizationbbotkblack-box-optimizationgaussian-processhpohyperparameterhyperparameter-optimizationhyperparameter-tuningmachine-learningmlr3model-based-optimizationoptimizationoptimizerrandom-foresttuning

25 stars 8.57 score 120 scripts 3 dependents

mlr-org

mlr3verse:Easily Install and Load the 'mlr3' Package Family

The 'mlr3' package family is a set of packages for machine-learning purposes built in a modular fashion. This wrapper package is aimed to simplify the installation and loading of the core 'mlr3' packages. Get more information about the 'mlr3' project at <https://mlr3book.mlr-org.com/>.

Maintained by Marc Becker. Last updated 3 months ago.

machine-learningmetamlr3

55 stars 8.32 score 720 scripts 1 dependents

mlr-org

mlr3fselect:Feature Selection for 'mlr3'

Feature selection package of the 'mlr3' ecosystem. It selects the optimal feature set for any 'mlr3' learner. The package works with several optimization algorithms e.g. Random Search, Recursive Feature Elimination, and Genetic Search. Moreover, it can automatically optimize learners and estimate the performance of optimized feature sets with nested resampling.

Maintained by Marc Becker. Last updated 2 months ago.

evolutionary-algorithmsexhaustive-searchfeature-selectionmachine-learningmlr3optimizationrandom-searchrecursive-feature-eliminationsequential-feature-selection

23 stars 8.12 score 70 scripts 2 dependents

mlr-org

mlr3hyperband:Hyperband for 'mlr3'

Successive Halving (Jamieson and Talwalkar (2016) <doi:10.48550/arXiv.1502.07943>) and Hyperband (Li et al. 2018 <doi:10.48550/arXiv.1603.06560>) optimization algorithm for the mlr3 ecosystem. The implementation in mlr3hyperband features improved scheduling and parallelizes the evaluation of configurations. The package includes tuners for hyperparameter optimization in mlr3tuning and optimizers for black-box optimization in bbotk.

Maintained by Marc Becker. Last updated 9 months ago.

automlbbotkhyperbandhyperparameter-tuningmachine-learningmlr3optimizationtunetuning

18 stars 7.36 score 44 scripts 3 dependents

dandls

counterfactuals:Counterfactual Explanations

Modular and unified R6-based interface for counterfactual explanation methods. The following methods are currently implemented: Burghmans et al. (2022) <doi:10.48550/arXiv.2104.07411>, Dandl et al. (2020) <doi:10.1007/978-3-030-58112-1_31> and Wexler et al. (2019) <doi:10.1109/TVCG.2019.2934619>. Optional extensions allow these methods to be applied to a variety of models and use cases. Once generated, the counterfactuals can be analyzed and visualized by provided functionalities.

Maintained by Susanne Dandl. Last updated 5 months ago.

interpretable-machine-learninglocal-explanationsmodel-agnostic-explanations

21 stars 7.14 score 22 scripts

bioc

SIAMCAT:Statistical Inference of Associations between Microbial Communities And host phenoTypes

Pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes (SIAMCAT). A primary goal of analyzing microbiome data is to determine changes in community composition that are associated with environmental factors. In particular, linking human microbiome composition to host phenotypes such as diseases has become an area of intense research. For this, robust statistical modeling and biomarker extraction toolkits are crucially needed. SIAMCAT provides a full pipeline supporting data preprocessing, statistical association testing, statistical modeling (LASSO logistic regression) including tools for evaluation and interpretation of these models (such as cross validation, parameter selection, ROC analysis and diagnostic model plots).

Maintained by Jakob Wirbel. Last updated 5 months ago.

immunooncologymetagenomicsclassificationmicrobiomesequencingpreprocessingclusteringfeatureextractiongeneticvariabilitymultiplecomparisonregression

6.72 score 147 scripts

r-forge

tramnet:Penalized Transformation Models

Partially penalized versions of specific transformation models implemented in package 'mlt'. Available models include a fully parametric version of the Cox model, other parametric survival models (Weibull, etc.), models for binary and ordered categorical variables, normal and transformed-normal (Box-Cox type) linear models, and continuous outcome logistic regression. Hyperparameter tuning is facilitated through model-based optimization functionalities from package 'mlr3MBO'. The methodology is described in Kook et al. (2021) <doi:10.32614/RJ-2021-054>. Transformation models and model-based optimization are described in Hothorn et al. (2019) <doi:10.1111/sjos.12291> and Bischl et al. (2016) <arxiv:1703.03373>, respectively.

Maintained by Lucas Kook. Last updated 10 days ago.

4.13 score 2 scripts

mb706

mlrintermbo:Model-Based Optimization for 'mlr3' Through 'mlrMBO'

The 'mlrMBO' package can ordinarily not be used for optimization within 'mlr3', because of incompatibilities of their respective class systems. 'mlrintermbo' offers a compatibility interface that provides 'mlrMBO' as an 'mlr3tuning' 'Tuner' object, for tuning of machine learning algorithms within 'mlr3', as well as a 'bbotk' 'Optimizer' object for optimization of general objective functions using the 'bbotk' black box optimization framework. The control parameters of 'mlrMBO' are faithfully reproduced as a 'paradox' 'ParamSet'.

Maintained by Martin Binder. Last updated 5 months ago.

4 stars 4.08 score 12 scripts

molaison

MantaID:A Machine-Learning Based Tool to Automate the Identification of Biological Database IDs

The number of biological databases is growing rapidly, but different databases use different IDs to refer to the same biological entity. The inconsistency in IDs impedes the integration of various types of biological data. To resolve the problem, we developed 'MantaID', a data-driven, machine-learning based approach that automates identifying IDs on a large scale. The 'MantaID' model's prediction accuracy was proven to be 99%, and it correctly and effectively predicted 100,000 ID entries within two minutes. 'MantaID' supports the discovery and exploitation of ID patterns from large quantities of databases. (e.g., up to 542 biological databases). An easy-to-use freely available open-source software R package, a user-friendly web application, and API were also developed for 'MantaID' to improve applicability. To our knowledge, 'MantaID' is the first tool that enables an automatic, quick, accurate, and comprehensive identification of large quantities of IDs, and can therefore be used as a starting point to facilitate the complex assimilation and aggregation of biological data across diverse databases.

Maintained by Zhengpeng Zeng. Last updated 6 months ago.

3.78 score 2 scripts

erhard-lab

HetSeq:Identifying Modulators of Cellular Responses Leveraging Intercellular Heterogeneity

Cellular responses to perturbations are highly heterogeneous and depend largely on the initial state of cells. Connecting post-perturbation cells via cellular trajectories to untreated cells (e.g. by leveraging metabolic labeling information) enables exploitation of intercellular heterogeneity as a combined knock-down and overexpression screen to identify pathway modulators, termed Heterogeneity-seq (see 'Berg et al' <doi:10.1101/2024.10.28.620481>). This package contains functions to generate cellular trajectories based on scSLAM-seq (single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing) time courses, functions to identify pathway modulators and to visualize the results.

Maintained by Kevin Berg. Last updated 2 months ago.

3.54 score

cran

BioM2:Biologically Explainable Machine Learning Framework

Biologically Explainable Machine Learning Framework for Phenotype Prediction using omics data described in Chen and Schwarz (2017) <doi:10.48550/arXiv.1712.00336>.Identifying reproducible and interpretable biological patterns from high-dimensional omics data is a critical factor in understanding the risk mechanism of complex disease. As such, explainable machine learning can offer biological insight in addition to personalized risk scoring.In this process, a feature space of biological pathways will be generated, and the feature space can also be subsequently analyzed using WGCNA (Described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559> ) methods.

Maintained by Shunjie Zhang. Last updated 1 months ago.

2.54 score

pigian

sense:Automatic Stacked Ensemble for Regression Tasks

Stacked ensemble for regression tasks based on 'mlr3' framework with a pipeline for preprocessing numeric and factor features and hyper-parameter tuning using grid or random search.

Maintained by Giancarlo Vercellino. Last updated 9 months ago.

1.78 score

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