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Batch effects are pervasive in biomedical studies. One approach to address the batch effects is repeatedly measuring a subset of samples in each batch. These remeasured samples are used to estimate and correct the batch effects. However, rigorous statistical methods for batch effect correction with remeasured samples are severely under-developed. In this study, we developed a framework for batch effect correction using remeasured samples in highly confounded case-control studies. We provided theoretical analyses of the proposed procedure, evaluated its power characteristics, and provided a power calculation tool to aid in the study design. We found that the number of samples that need to be remeasured depends strongly on the between-batch correlation. When the correlation is high, remeasuring a small subset of samples is possible to rescue most of the power.

We collect robust proposals given in the field of regression models with heteroscedastic errors. Our motivation stems from the fact that the practitioner frequently faces the confluence of two phenomena in the context of data analysis: non--linearity and heteroscedasticity. The impact of heteroscedasticity on the precision of the estimators is well--known, however the conjunction of these two phenomena makes handling outliers more difficult. An iterative procedure to estimate the parameters of a heteroscedastic non--linear model is considered. The studied estimators combine weighted $MM-$regression estimators, to control the impact of high leverage points, and a robust method to estimate the parameters of the variance function.

We investigate the link between regularised self-transport problems and maximum likelihood estimation in Gaussian mixture models (GMM). This link suggests that self-transport followed by a clustering technique leads to principled estimators at a reasonable computational cost. Also, robustness, sparsity and stability properties of the optimal transport plan arguably make the regularised self-transport a statistical tool of choice for the GMM.

Quantum computing has recently emerged as a transformative technology. Yet, its promised advantages rely on efficiently translating quantum operations into viable physical realizations. In this work, we use generative machine learning models, specifically denoising diffusion models (DMs), to facilitate this transformation. Leveraging text-conditioning, we steer the model to produce desired quantum operations within gate-based quantum circuits. Notably, DMs allow to sidestep during training the exponential overhead inherent in the classical simulation of quantum dynamics -- a consistent bottleneck in preceding ML techniques. We demonstrate the model's capabilities across two tasks: entanglement generation and unitary compilation. The model excels at generating new circuits and supports typical DM extensions such as masking and editing to, for instance, align the circuit generation to the constraints of the targeted quantum device. Given their flexibility and generalization abilities, we envision DMs as pivotal in quantum circuit synthesis, enhancing both practical applications but also insights into theoretical quantum computation.

Remotely sensed data are dominated by mixed Land Use and Land Cover (LULC) types. Spectral unmixing is a technique to extract information from mixed pixels into their constituent LULC types and corresponding abundance fractions. Traditionally, solving this task has relied on either classical methods that require prior knowledge of endmembers or machine learning methods that avoid explicit endmembers calculation, also known as blind spectral unmixing (BSU). Most BSU studies based on Deep Learning (DL) focus on one time-step hyperspectral or multispectral data. To our knowledge, here we provide the first study on BSU of LULC classes using MODIS multispectral time series, in presence of missing data, with end-to-end DL models. We further boost the performance of a Long-Short Term Memory (LSTM)-based model by incorporating geographic plus topographic (geo-topographic) and climatic ancillary information. Our experiments show that combining spectral-temporal input data together with geo-topographic and climatic information substantially improves the abundance estimation of LULC classes in mixed pixels. To carry out this study, we built a new labeled dataset of the region of Andalusia (Spain) with monthly multispectral time series of pixels for the year 2013 from MODIS at 460m resolution, for two hierarchical levels of LULC classes, named Andalusia MultiSpectral MultiTemporal Unmixing (Andalusia-MSMTU). This dataset provides, at the pixel level, a multispectral time series plus ancillary information annotated with the abundance of each LULC class inside each pixel. The dataset (//zenodo.org/record/7752348##.ZBmkkezMLdo) and code (//github.com/jrodriguezortega/MSMTU) are available to the public.

The term "Normalizing Flows" is related to the task of constructing invertible transport maps between probability measures by means of deep neural networks. In this paper, we consider the problem of recovering the $W_2$-optimal transport map $T$ between absolutely continuous measures $\mu,\nu\in\mathcal{P}(\mathbb{R}^n)$ as the flow of a linear-control neural ODE. We first show that, under suitable assumptions on $\mu,\nu$ and on the controlled vector fields, the optimal transport map is contained in the $C^0_c$-closure of the flows generated by the system. Assuming that discrete approximations $\mu_N,\nu_N$ of the original measures $\mu,\nu$ are available, we use a discrete optimal coupling $\gamma_N$ to define an optimal control problem. With a $\Gamma$-convergence argument, we prove that its solutions correspond to flows that approximate the optimal transport map $T$. Finally, taking advantage of the Pontryagin Maximum Principle, we propose an iterative numerical scheme for the resolution of the optimal control problem, resulting in an algorithm for the practical computation of the approximated optimal transport map.

This paper presents a Bayesian optimization framework for the automatic tuning of shared controllers which are defined as a Model Predictive Control (MPC) problem. The proposed framework includes the design of performance metrics as well as the representation of user inputs for simulation-based optimization. The framework is applied to the optimization of a shared controller for an Image Guided Therapy robot. VR-based user experiments confirm the increase in performance of the automatically tuned MPC shared controller with respect to a hand-tuned baseline version as well as its generalization ability.

This paper proposes two innovative vector transport operators, leveraging the Cayley transform, for the generalized Stiefel manifold embedded with a non-standard inner product. Specifically, it introduces the differentiated retraction and an approximation of the Cayley transform to the differentiated matrix exponential. These vector transports are demonstrated to satisfy the Ring-Wirth non-expansive condition under non-standard metrics while preserving isometry. Building upon the novel vector transport operators, we extend the modified Polak-Ribi$\acute{e}$re-Polyak (PRP) conjugate gradient method to the generalized Stiefel manifold. Under a non-monotone line search condition, we prove our algorithm globally converges to a stationary point. The efficiency of the proposed vector transport operators is empirically validated through numerical experiments involving generalized eigenvalue problems and canonical correlation analysis.

Stochastic filtering is a vibrant area of research in both control theory and statistics, with broad applications in many scientific fields. Despite its extensive historical development, there still lacks an effective method for joint parameter-state estimation in SDEs. The state-of-the-art particle filtering methods suffer from either sample degeneracy or information loss, with both issues stemming from the dynamics of the particles generated to represent system parameters. This paper provides a novel and effective approach for joint parameter-state estimation in SDEs via Rao-Blackwellization and modularization. Our method operates in two layers: the first layer estimates the system states using a bootstrap particle filter, and the second layer marginalizes out system parameters explicitly. This strategy circumvents the need to generate particles representing system parameters, thereby mitigating their associated problems of sample degeneracy and information loss. Moreover, our method employs a modularization approach when integrating out the parameters, which significantly reduces the computational complexity. All these designs ensure the superior performance of our method. Finally, a numerical example is presented to illustrate that our method outperforms existing approaches by a large margin.

Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.