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We develop a new, unsupervised symmetry learning method that starts with raw data, and gives the minimal (discrete) generator of an underlying Lie group of symmetries, together with a symmetry equivariant representation of the data. The method is able to learn the pixel translation operator from a dataset with only an approximate translation symmetry, and can learn quite different types of symmetries which are not apparent to the naked eye, equally well. The method is based on the formulation of an information-theoretic loss function that measures both the degree to which the dataset is symmetric under a given candidate symmetry, and also, the degree of locality of the samples in the dataset with respect to this symmetry. We demonstrate that this coupling between symmetry and locality, together with a special optimization technique developed for entropy estimation, results in a highly stable system that gives reproducible results. The symmetry actions we consider are group representations, however, we believe the approach has the potential to be generalized to more general, nonlinear actions of non-commutative Lie groups.

With the increase in computational power for the available hardware, the demand for high-resolution data in computer graphics applications increases. Consequently, classical geometry processing techniques based on linear algebra solutions are starting to become obsolete. In this setting, we propose a novel approach for tackling mesh deformation tasks on high-resolution meshes. By reducing the input size with a fast remeshing technique and preserving a consistent representation of the original mesh with local reference frames, we provide a solution that is both scalable and robust in multiple applications, such as as-rigid-as-possible deformations, non-rigid isometric transformations, and pose transfer tasks. We extensively test our technique and compare it against state-of-the-art methods, proving that our approach can handle meshes with hundreds of thousands of vertices in tens of seconds while still achieving results comparable with the other solutions.

Extended multi-adjoint logic programming arises as an extension of multi-adjoint normal logic programming where constraints and a special type of aggregator operator have been included. The use of this general aggregator operator permits to consider, for example, different negation operators in the body of the rules of a logic program. We have introduced the syntax and the semantics of this new paradigm, as well as an interesting mechanism for obtaining a multi-adjoint normal logic program from an extended multi-adjoint logic program. This mechanism will allow us to establish technical properties relating the different stable models of both logic programming frameworks. Moreover, it makes possible that the already developed and future theory associated with stable models of multi-adjoint normal logic programs can be applied to extended multi-adjoint logic programs.

A Gaussian process is proposed as a model for the posterior distribution of the local predictive ability of a model or expert, conditional on a vector of covariates, from historical predictions in the form of log predictive scores. Assuming Gaussian expert predictions and a Gaussian data generating process, a linear transformation of the predictive score follows a noncentral chi-squared distribution with one degree of freedom. Motivated by this we develop a noncentral chi-squared Gaussian process regression to flexibly model local predictive ability, with the posterior distribution of the latent GP function and kernel hyperparameters sampled by Hamiltonian Monte Carlo. We show that a cube-root transformation of the log scores is approximately Gaussian with homoscedastic variance, making it possible to estimate the model much faster by marginalizing the latent GP function analytically. A multi-output Gaussian process regression is also introduced to model the dependence in predictive ability between experts, both for inference and prediction purposes. Linear pools based on learned local predictive ability are applied to predict daily bike usage in Washington DC.

Structural global parameter identifiability indicates whether one can determine a parameter's value in an ODE model from given inputs and outputs. If a given model has parameters for which there is exactly one value, such parameters are called globally identifiable. Given an ODE model involving not globally identifiable parameters, first we transform the system into one with locally identifiable parameters. As a main contribution of this paper, then we present a procedure for replacing, if possible, the ODE model with an equivalent one that has globally identifiable parameters. We first derive this as an algorithm for one-dimensional ODE models and then reuse this approach for higher-dimensional models.

Sampling from generative models has become a crucial tool for applications like data synthesis and augmentation. Diffusion, Flow Matching and Continuous Normalizing Flows have shown effectiveness across various modalities, and rely on Gaussian latent variables for generation. For search-based or creative applications that require additional control over the generation process, it has become common to manipulate the latent variable directly. However, existing approaches for performing such manipulations (e.g. interpolation or forming low-dimensional representations) only work well in special cases or are network or data-modality specific. We propose Combination of Gaussian variables (COG) as a general purpose interpolation method that is easy to implement yet outperforms recent sophisticated methods. Moreover, COG naturally addresses the broader task of forming general linear combinations of latent variables, allowing the construction of subspaces of the latent space, dramatically simplifying the creation of expressive low-dimensional spaces of high-dimensional objects.

We develop confidence sets which provide spatial uncertainty guarantees for the output of a black-box machine learning model designed for image segmentation. To do so we adapt conformal inference to the imaging setting, obtaining thresholds on a calibration dataset based on the distribution of the maximum of the transformed logit scores within and outside of the ground truth masks. We prove that these confidence sets, when applied to new predictions of the model, are guaranteed to contain the true unknown segmented mask with desired probability. We show that learning appropriate score transformations on a learning dataset before performing calibration is crucial for optimizing performance. We illustrate and validate our approach on a polpys tumor dataset. To do so we obtain the logit scores from a deep neural network trained for polpys segmentation and show that using distance transformed scores to obtain outer confidence sets and the original scores for inner confidence sets enables tight bounds on tumor location whilst controlling the false coverage rate.

Rationally identifying variables responsible for changes to a biological system can enable myriad applications in disease understanding and cell engineering. From a causality perspective, we are given two datasets generated by the same causal model, one observational (control) and one interventional (perturbed). The goal is to isolate the subset of measured variables (e.g. genes) that were the targets of the intervention, i.e. those whose conditional independencies have changed. Knowing the causal graph would limit the search space, allowing us to efficiently pinpoint these variables. However, current algorithms that infer causal graphs in the presence of unknown intervention targets scale poorly to the hundreds or thousands of variables in biological data, as they must jointly search the combinatorial spaces of graphs and consistent intervention targets. In this work, we propose a causality-inspired approach for predicting perturbation targets that decouples the two search steps. First, we use an amortized causal discovery model to separately infer causal graphs from the observational and interventional datasets. Then, we learn to map these paired graphs to the sets of variables that were intervened upon, in a supervised learning framework. This approach consistently outperforms baselines for perturbation modeling on seven single-cell transcriptomics datasets, each with thousands of measured variables. We also demonstrate significant improvements over six causal discovery algorithms in predicting intervention targets across a variety of tractable, synthetic datasets.

Functional principal component analysis has been shown to be invaluable for revealing variation modes of longitudinal outcomes, which serves as important building blocks for forecasting and model building. Decades of research have advanced methods for functional principal component analysis often assuming independence between the observation times and longitudinal outcomes. Yet such assumptions are fragile in real-world settings where observation times may be driven by outcome-related reasons. Rather than ignoring the informative observation time process, we explicitly model the observational times by a counting process dependent on time-varying prognostic factors. Identification of the mean, covariance function, and functional principal components ensues via inverse intensity weighting. We propose using weighted penalized splines for estimation and establish consistency and convergence rates for the weighted estimators. Simulation studies demonstrate that the proposed estimators are substantially more accurate than the existing ones in the presence of a correlation between the observation time process and the longitudinal outcome process. We further examine the finite-sample performance of the proposed method using the Acute Infection and Early Disease Research Program study.

Graph-centric artificial intelligence (graph AI) has achieved remarkable success in modeling interacting systems prevalent in nature, from dynamical systems in biology to particle physics. The increasing heterogeneity of data calls for graph neural architectures that can combine multiple inductive biases. However, combining data from various sources is challenging because appropriate inductive bias may vary by data modality. Multimodal learning methods fuse multiple data modalities while leveraging cross-modal dependencies to address this challenge. Here, we survey 140 studies in graph-centric AI and realize that diverse data types are increasingly brought together using graphs and fed into sophisticated multimodal models. These models stratify into image-, language-, and knowledge-grounded multimodal learning. We put forward an algorithmic blueprint for multimodal graph learning based on this categorization. The blueprint serves as a way to group state-of-the-art architectures that treat multimodal data by choosing appropriately four different components. This effort can pave the way for standardizing the design of sophisticated multimodal architectures for highly complex real-world problems.