library
mlr3torch: A Deep Learning Framework in R based on mlr3 and torch
Fischer, Sebastian, Burk, Lukas, Zhang, Carson, Bischl, Bernd, Binder, Martin
Deep learning (DL) has become a cornerstone of modern machine learning (ML) praxis. We introduce the R package mlr3torch, which is an extensible DL framework for the mlr3 ecosystem. It is built upon the torch package, and simplifies the definition, training, and evaluation of neural networks for both tabular data and generic tensors (e.g., images) for classification and regression. The package implements predefined architectures, and torch models can easily be converted to mlr3 learners. It also allows users to define neural networks as graphs. This representation is based on the graph language defined in mlr3pipelines and allows users to define the entire modeling workflow, including preprocessing, data augmentation, and network architecture, in a single graph. Through its integration into the mlr3 ecosystem, the package allows for convenient resampling, benchmarking, preprocessing, and more. We explain the package's design and features and show how to customize and extend it to new problems. Furthermore, we demonstrate the package's capabilities using three use cases, namely hyperparameter tuning, fine-tuning, and defining architectures for multimodal data. Finally, we present some runtime benchmarks.
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fastml: Guarded Resampling Workflows for Safer Automated Machine Learning in R
Korkmaz, Selcuk, Goksuluk, Dincer, Karaismailoglu, Eda
Preprocessing leakage arises when scaling, imputation, or other data-dependent transformations are estimated before resampling, inflating apparent performance while remaining hard to detect. We present fastml, an R package that provides a single-call interface for leakage-aware machine learning through guarded resampling, where preprocessing is re-estimated inside each resample and applied to the corresponding assessment data. The package supports grouped and time-ordered resampling, blocks high-risk configurations, audits recipes for external dependencies, and includes sandboxed execution and integrated model explanation. We evaluate fastml with a Monte Carlo simulation contrasting global and fold-local normalization, a usability comparison with tidymodels under matched specifications, and survival benchmarks across datasets of different sizes. The simulation demonstrates that global preprocessing substantially inflates apparent performance relative to guarded resampling. fastml matched held-out performance obtained with tidymodels while reducing workflow orchestration, and it supported consistent benchmarking of multiple survival model classes through a unified interface.
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A Robust SINDy Autoencoder for Noisy Dynamical System Identification
Sparse identification of nonlinear dynamics (SINDy) has been widely used to discover the governing equations of a dynamical system from data. It uses sparse regression techniques to identify parsimonious models of unknown systems from a library of candidate functions. Therefore, it relies on the assumption that the dynamics are sparsely represented in the coordinate system used. To address this limitation, one seeks a coordinate transformation that provides reduced coordinates capable of reconstructing the original system. Recently, SINDy autoencoders have extended this idea by combining sparse model discovery with autoencoder architectures to learn simplified latent coordinates together with parsimonious governing equations. A central challenge in this framework is robustness to measurement error. Inspired by noise-separating neural network structures, we incorporate a noise-separation module into the SINDy autoencoder architecture, thereby improving robustness and enabling more reliable identification of noisy dynamical systems. Numerical experiments on the Lorenz system show that the proposed method recovers interpretable latent dynamics and accurately estimates the measurement noise from noisy observations.
Sparse Weak-Form Discovery of Stochastic Generators
A, Eshwar R, Honnavar, Gajanan V.
The proposed algorithm seeks to provide a novel data-driven framework for the discovery of stochastic differential equations (SDEs) by application of the Weak-formulation to stochastic SINDy. This Weak formulation of the algorithm provides a noise-robust methodology that avoids traditional noisy derivative computation using finite differences. An additional novelty is the adoption of spatial Gaussian test functions in place of temporal test functions, wherein the use of the kernel weight $K_j(X_{t_n})$ guarantees unbiasedness in expectation and prevents the structural regression bias that is otherwise pertinent with temporal test functions. The proposed framework converts the SDE identification problem into two SINDy based linear sparse identification problems. We validate the algorithm on three SDEs, for which we recover all active non-linear terms with coefficient errors below 4%, stationary-density total-variation distances below 0.01, and autocorrelation functions that reproduce true relaxation timescales across all three benchmarks faithfully.
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Learning Libraries of Subroutines for Neurally–Guided Bayesian Program Induction
Successful approaches to program induction require a hand-engineered domain-specific language (DSL), constraining the space of allowed programs and imparting prior knowledge of the domain. We contribute a program induction algorithm that learns a DSL while jointly training a neural network to efficiently search for programs in the learned DSL. We use our model to synthesize functions on lists, edit text, and solve symbolic regression problems, showing how the model learns a domain-specific library of program components for expressing solutions to problems in the domain.
Provably Correct Automatic Sub-Differentiation for Qualified Programs
The \emph{Cheap Gradient Principle}~\citep{Griewank:2008:EDP:1455489} --- the computational cost of computing a $d$-dimensional vector of partial derivatives of a scalar function is nearly the same (often within a factor of $5$) as that of simply computing the scalar function itself --- is of central importance in optimization; it allows us to quickly obtain (high-dimensional) gradients of scalar loss functions which are subsequently used in black box gradient-based optimization procedures. The current state of affairs is markedly different with regards to computing sub-derivatives: widely used ML libraries, including TensorFlow and PyTorch, do \emph{not} correctly compute (generalized) sub-derivatives even on simple differentiable examples. This work considers the question: is there a \emph{Cheap Sub-gradient Principle}? Our main result shows that, under certain restrictions on our library of non-smooth functions (standard in non-linear programming), provably correct generalized sub-derivatives can be computed at a computational cost that is within a (dimension-free) factor of $6$ of the cost of computing the scalar function itself.
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