Persistent homology (PH) encodes global information, such as cycles, and is thus increasingly integrated into graph neural networks (GNNs). PH methods in GNNs typically traverse an increasing sequence of subgraphs. In this work, we first expose limitations of this inclusion procedure. To remedy these shortcomings, we analyze contractions as a principled topological operation, in particular, for graph representation learning. We study the persistence of contraction sequences, which we call Contraction Homology (CH). We establish that forward PH and CH differ in expressivity. We then introduce Hourglass Persistence, a class of topological descriptors that interleave a sequence of inclusions and contractions to boost expressivity, learnability, and stability. We also study related families parametrized by two paradigms. We also discuss how our framework extends to simplicial and cellular networks. We further design efficient algorithms that are pluggable into end-to-end differentiable GNN pipelines, enabling consistent empirical improvements over many PH methods across standard real-world graph datasets. Code is available at \href{https://github.com/Aalto-QuML/Hourglass}{this https URL}.

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.

We study learning to learn for regression problems through the lens of hyperparameter tuning. We propose the Langevin Gradient Descent Algorithm (LGD), which approximates the mean of the posterior distribution defined by the loss function and regularizer of a convex regression task. We prove the existence of an optimal hyperparameter configuration for which the LGD algorithm achieves the Bayes' optimal solution for squared loss. Subsequently, we study generalization guarantees on meta-learning optimal hyperparameters for the LGD algorithm from a given set of tasks in the data-driven setting. For a number of parameters $d$ and hyperparameter dimension $h$, we show a pseudo-dimension bound of $O(dh)$, upto logarithmic terms under mild assumptions on LGD. This matches the dimensional dependence of the bounds obtained in prior work for the elastic net, which only allows for $h=2$ hyperparameters, and extends their bounds to regression on convex loss. Finally, we show empirical evidence of the success of LGD and the meta-learning procedure for few-shot learning on linear regression using a few synthetically created datasets.

Data leakage remains a recurrent source of optimistic bias in biomedical machine learning studies. Standard row-wise cross-validation and globally estimated preprocessing steps are often inappropriate for data with repeated measurements, study-level heterogeneity, batch effects, or temporal dependencies. This paper describes bioLeak, an R package for constructing leakage-aware resampling workflows and for auditing fitted models for common leakage mechanisms. The package provides leakage-aware split construction, train-fold-only preprocessing, cross-validated model fitting, nested hyperparameter tuning, post hoc leakage audits, and HTML reporting. The implementation supports binary classification, multiclass classification, regression, and survival analysis, with task-specific metrics and S4 containers for splits, fits, audits, and inflation summaries. The simulation artifacts show how apparent performance changes under controlled leakage mechanisms, and the case study illustrates how guarded and leaky pipelines can yield materially different conclusions on multi-study transcriptomic data. The emphasis throughout is on software design, reproducible workflows, and interpretation of diagnostic output.

In High Energy Physics, detailed calorimeter simulations and reconstructions are essential for accurate energy measurements and particle identification, but their high granularity makes them computationally expensive. Developing data-driven techniques capable of recovering fine-grained information from coarser readouts, a task known as calorimeter superresolution, offers a promising way to reduce both computational and hardware costs while preserving detector performance. This thesis investigates whether a generative model originally designed for fast simulation can be effectively applied to calorimeter superresolution. Specifically, the model proposed in arXiv:2308.11700 is re-implemented independently and trained on the CaloChallenge 2022 dataset based on the Geant4 Par04 calorimeter geometry. Finally, the model's performance is assessed through a rigorous statistical evaluation framework, following the methodology introduced in arXiv:2409.16336, to quantitatively test its ability to reproduce the reference distributions.

We consider computationally-efficient estimation of population parameters when observations are subject to missing data. In particular, we consider estimation under the realizable contamination model of missing data in which an $ε$ fraction of the observations are subject to an arbitrary (and unknown) missing not at random (MNAR) mechanism. When the true data is Gaussian, we provide evidence towards statistical-computational gaps in several problems. For mean estimation in $\ell_2$ norm, we show that in order to obtain error at most $ρ$, for any constant contamination $ε\in (0, 1)$, (roughly) $n \gtrsim d e^{1/ρ^2}$ samples are necessary and that there is a computationally-inefficient algorithm which achieves this error. On the other hand, we show that any computationally-efficient method within certain popular families of algorithms requires a much larger sample complexity of (roughly) $n \gtrsim d^{1/ρ^2}$ and that there exists a polynomial time algorithm based on sum-of-squares which (nearly) achieves this lower bound. For covariance estimation in relative operator norm, we show that a parallel development holds. Finally, we turn to linear regression with missing observations and show that such a gap does not persist. Indeed, in this setting we show that minimizing a simple, strongly convex empirical risk nearly achieves the information-theoretic lower bound in polynomial time.

Diffusion language models (DLMs) have recently emerged as a promising alternative to autoregressive (AR) approaches, enabling parallel token generation beyond a rigid left-to-right order. Despite growing empirical success, the theoretical understanding of how unmasking schedules -- which specify the order and size of unmasked tokens during sampling -- affect generation quality remains limited. In this work, we introduce a distribution-agnostic unmasking schedule for DLMs that adapts to the (unknown) dependence structure of the target data distribution, without requiring any prior knowledge or hyperparameter tuning. In contrast to prior deterministic procedures that fix unmasking sizes, our method randomizes the number of tokens revealed at each iteration. We show that, for two specific parameter choices, the sampling convergence guarantees -- measured by Kullback-Leibler (KL) divergence -- scale as $\widetilde O(\mathsf{TC}/K)$ and $\widetilde O(\mathsf{DTC}/K)$ respectively. Here, $K$ is the number of iterations, and $\mathsf{TC}$ and $\mathsf{DTC}$ are the total correlation and dual total correlation of the target distribution, capturing the intrinsic dependence structure underlying the data. Importantly, our guarantees hold in the practically relevant parallel-sampling regime $K