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In this work we present denoiSplit, a method to tackle a new analysis task, i.e. the challenge of joint semantic image splitting and unsupervised denoising. This dual approach has important applications in fluorescence microscopy, where semantic image splitting has important applications but noise does generally hinder the downstream analysis of image content. Image splitting involves dissecting an image into its distinguishable semantic structures. We show that the current state-of-the-art method for this task struggles in the presence of image noise, inadvertently also distributing the noise across the predicted outputs. The method we present here can deal with image noise by integrating an unsupervised denoising sub-task. This integration results in improved semantic image unmixing, even in the presence of notable and realistic levels of imaging noise. A key innovation in denoiSplit is the use of specifically formulated noise models and the suitable adjustment of KL-divergence loss for the high-dimensional hierarchical latent space we are training. We showcase the performance of denoiSplit across 4 tasks on real-world microscopy images. Additionally, we perform qualitative and quantitative evaluations and compare results to existing benchmarks, demonstrating the effectiveness of using denoiSplit: a single Variational Splitting Encoder-Decoder (VSE) Network using two suitable noise models to jointly perform semantic splitting and denoising.

We address the problem of the best uniform approximation of a continuous function on a convex domain. The approximation is by linear combinations of a finite system of functions (not necessarily Chebyshev) under arbitrary linear constraints. By modifying the concept of alternance and of the Remez iterative procedure we present a method, which demonstrates its efficiency in numerical problems. The linear rate of convergence is proved under some favourable assumptions. A special attention is paid to systems of complex exponents, Gaussian functions, lacunar algebraic and trigonometric polynomials. Applications to signal processing, linear ODE, switching dynamical systems, and to Markov-Bernstein type inequalities are considered.

Differential privacy is a mathematical concept that provides an information-theoretic security guarantee. While differential privacy has emerged as a de facto standard for guaranteeing privacy in data sharing, the known mechanisms to achieve it come with some serious limitations. Utility guarantees are usually provided only for a fixed, a priori specified set of queries. Moreover, there are no utility guarantees for more complex - but very common - machine learning tasks such as clustering or classification. In this paper we overcome some of these limitations. Working with metric privacy, a powerful generalization of differential privacy, we develop a polynomial-time algorithm that creates a private measure from a data set. This private measure allows us to efficiently construct private synthetic data that are accurate for a wide range of statistical analysis tools. Moreover, we prove an asymptotically sharp min-max result for private measures and synthetic data for general compact metric spaces. A key ingredient in our construction is a new superregular random walk, whose joint distribution of steps is as regular as that of independent random variables, yet which deviates from the origin logarithmicaly slowly.

Reservoir computing is a machine learning framework that has been shown to be able to replicate the chaotic attractor, including the fractal dimension and the entire Lyapunov spectrum, of the dynamical system on which it is trained. We quantitatively relate the generalized synchronization dynamics of a driven reservoir during the training stage to the performance of the trained reservoir computer at the attractor reconstruction task. We show that, in order to obtain successful attractor reconstruction and Lyapunov spectrum estimation, the largest conditional Lyapunov exponent of the driven reservoir must be significantly more negative than the most negative Lyapunov exponent of the target system. We also find that the maximal conditional Lyapunov exponent of the reservoir depends strongly on the spectral radius of the reservoir adjacency matrix, and therefore, for attractor reconstruction and Lyapunov spectrum estimation, small spectral radius reservoir computers perform better in general. Our arguments are supported by numerical examples on well-known chaotic systems.

PECR is a formal system designed to explore the properties of computability of programs on a real-world computer. As such PECR incorporates the finite resources of the machine upon which a program is to be executed. The main features of the formal system will be presented and its practical applications will be discussed. Of particular interest is the implementation of the formal system to the exploration of the laws of nature that lead to rigorous constructions of computer models of real-world phenomena.

Multiple Instance Learning (MIL) is a weakly supervised paradigm that has been successfully applied to many different scientific areas and is particularly well suited to medical imaging. Probabilistic MIL methods, and more specifically Gaussian Processes (GPs), have achieved excellent results due to their high expressiveness and uncertainty quantification capabilities. One of the most successful GP-based MIL methods, VGPMIL, resorts to a variational bound to handle the intractability of the logistic function. Here, we formulate VGPMIL using P\'olya-Gamma random variables. This approach yields the same variational posterior approximations as the original VGPMIL, which is a consequence of the two representations that the Hyperbolic Secant distribution admits. This leads us to propose a general GP-based MIL method that takes different forms by simply leveraging distributions other than the Hyperbolic Secant one. Using the Gamma distribution we arrive at a new approach that obtains competitive or superior predictive performance and efficiency. This is validated in a comprehensive experimental study including one synthetic MIL dataset, two well-known MIL benchmarks, and a real-world medical problem. We expect that this work provides useful ideas beyond MIL that can foster further research in the field.

The amount of information in satisfiability problem (SAT) is considered. SAT can be polynomial-time solvable when the solving algorithm holds an exponential amount of information. It is also established that SAT Kolmogorov complexity is constant. It is argued that the amount of information in SAT grows at least exponentially with the size of the input instance. The amount of information in SAT is compared with the amount of information in the fixed code algorithms and generated over runtime.

Explainable AI is crucial in medical imaging. In the challenging field of neuroscience, visual topics present a high level of complexity, particularly within three-dimensional space. The application of neuroscience, which involves identifying brain sulcal features from MRI, faces significant hurdles due to varying annotation protocols among experts and the intricate three-dimension functionality of the brain. Consequently, traditional explainability approaches fall short in effectively validating and evaluating these networks. To address this, we first present a mathematical formulation delineating various categories of explanation needs across diverse computer vision tasks, categorized into self-explanatory, semi-explanatory, non-explanatory, and new-pattern learning applications based on the reliability of the validation protocol. With respect to this mathematical formulation, we propose a 3D explainability framework aimed at validating the outputs of deep learning networks in detecting the paracingulate sulcus an essential brain anatomical feature. The framework integrates local 3D explanations, global explanations through dimensionality reduction, concatenated global explanations, and statistical shape features, unveiling new insights into pattern learning. We trained and tested two advanced 3D deep learning networks on the challenging TOP-OSLO dataset, significantly improving sulcus detection accuracy, particularly on the left hemisphere. During evaluation with diverse annotation protocols for this dataset, we highlighted the crucial role of an unbiased annotation process in achieving precise predictions and effective pattern learning within our proposed 3D framework. The proposed framework not only annotates the variable sulcus but also uncovers hidden AI knowledge, promising to advance our understanding of brain anatomy and function.

Inverse problems, particularly those governed by Partial Differential Equations (PDEs), are prevalent in various scientific and engineering applications, and uncertainty quantification (UQ) of solutions to these problems is essential for informed decision-making. This second part of a two-paper series builds upon the foundation set by the first part, which introduced CUQIpy, a Python software package for computational UQ in inverse problems using a Bayesian framework. In this paper, we extend CUQIpy's capabilities to solve PDE-based Bayesian inverse problems through a general framework that allows the integration of PDEs in CUQIpy, whether expressed natively or using third-party libraries such as FEniCS. CUQIpy offers concise syntax that closely matches mathematical expressions, streamlining the modeling process and enhancing the user experience. The versatility and applicability of CUQIpy to PDE-based Bayesian inverse problems are demonstrated on examples covering parabolic, elliptic and hyperbolic PDEs. This includes problems involving the heat and Poisson equations and application case studies in electrical impedance tomography and photo-acoustic tomography, showcasing the software's efficiency, consistency, and intuitive interface. This comprehensive approach to UQ in PDE-based inverse problems provides accessibility for non-experts and advanced features for experts.

Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.