We propose conformal generative modeling, a framework for generative modeling on 2D surfaces approximated by discrete triangle meshes. Our approach leverages advances in discrete conformal geometry to develop a map from a source triangle mesh to a target triangle mesh of a simple manifold such as a sphere. After accounting for errors due to the mesh discretization, we can use any generative modeling approach developed for simple manifolds as a plug-and-play subroutine. We demonstrate our framework on multiple complicated manifolds and multiple generative modeling subroutines, where we show that our approach can learn good estimates of distributions on meshes from samples, and can also learn simultaneously from multiple distinct meshes of the same underlying manifold.

Learning precise surrogate models of complex computer simulations and physical machines often require long-lasting or expensive experiments. Furthermore, the modeled physical dependencies exhibit nonlinear and nonstationary behavior. Machine learning methods that are used to produce the surrogate model should therefore address these problems by providing a scheme to keep the number of queries small, e.g. by using active learning and be able to capture the nonlinear and nonstationary properties of the system. One way of modeling the nonstationarity is to induce input-partitioning, a principle that has proven to be advantageous in active learning for Gaussian processes. However, these methods either assume a known partitioning, need to introduce complex sampling schemes or rely on very simple geometries. In this work, we present a simple, yet powerful kernel family that incorporates a partitioning that: i) is learnable via gradient-based methods, ii) uses a geometry that is more flexible than previous ones, while still being applicable in the low data regime. Thus, it provides a good prior for active learning procedures. We empirically demonstrate excellent performance on various active learning tasks.

The recent explosion of genetic and high dimensional biobank and 'omic' data has provided researchers with the opportunity to investigate the shared genetic origin (pleiotropy) of hundreds to thousands of related phenotypes. However, existing methods for multi-phenotype genome-wide association studies (GWAS) do not model pleiotropy, are only applicable to a small number of phenotypes, or provide no way to perform inference. To add further complication, raw genetic and phenotype data are rarely observed, meaning analyses must be performed on GWAS summary statistics whose statistical properties in high dimensions are poorly understood. We therefore developed a novel model, theoretical framework, and set of methods to perform Bayesian inference in GWAS of high dimensional phenotypes using summary statistics that explicitly model pleiotropy, beget fast computation, and facilitate the use of biologically informed priors. We demonstrate the utility of our procedure by applying it to metabolite GWAS, where we develop new nonparametric priors for genetic effects on metabolite levels that use known metabolic pathway information and foster interpretable inference at the pathway level.

The issue of distinguishing between the same-source and different-source hypotheses based on various types of traces is a generic problem in forensic science. This problem is often tackled with Bayesian approaches, which are able to provide a likelihood ratio that quantifies the relative strengths of evidence supporting each of the two competing hypotheses. Here, we focus on distance-based approaches, whose robustness and specifically whose capacity to deal with high-dimensional evidence are very different, and need to be evaluated and optimized. A unified framework for direct methods based on estimating the likelihoods of the distance between traces under each of the two competing hypotheses, and indirect methods using logistic regression to discriminate between same-source and different-source distance distributions, is presented. Whilst direct methods are more flexible, indirect methods are more robust and quite natural in machine learning. Moreover, indirect methods also enable the use of a vectorial distance, thus preventing the severe information loss suffered by scalar distance approaches.Direct and indirect methods are compared in terms of sensitivity, specificity and robustness, with and without dimensionality reduction, with and without feature selection, on the example of hand odor profiles, a novel and challenging type of evidence in the field of forensics. Empirical evaluations on a large panel of 534 subjects and their 1690 odor traces show the significant superiority of the indirect methods, especially without dimensionality reduction, be it with or without feature selection.

Concept bottleneck model (CBM) is a ubiquitous method that can interpret neural networks using concepts. In CBM, concepts are inserted between the output layer and the last intermediate layer as observable values. This helps in understanding the reason behind the outputs generated by the neural networks: the weights corresponding to the concepts from the last hidden layer to the output layer. However, it has not yet been possible to understand the behavior of the generalization error in CBM since a neural network is a singular statistical model in general. When the model is singular, a one to one map from the parameters to probability distributions cannot be created. This non-identifiability makes it difficult to analyze the generalization performance. In this study, we mathematically clarify the Bayesian generalization error and free energy of CBM when its architecture is three-layered linear neural networks. We also consider a multitask problem where the neural network outputs not only the original output but also the concepts. The results show that CBM drastically changes the behavior of the parameter region and the Bayesian generalization error in three-layered linear neural networks as compared with the standard version, whereas the multitask formulation does not.

The label distribution skew induced data heterogeniety has been shown to be a significant obstacle that limits the model performance in federated learning, which is particularly developed for collaborative model training over decentralized data sources while preserving user privacy. This challenge could be more serious when the participating clients are in unstable circumstances and dropout frequently. Previous work and our empirical observations demonstrate that the classifier head for classification task is more sensitive to label skew and the unstable performance of FedAvg mainly lies in the imbalanced training samples across different classes. The biased classifier head will also impact the learning of feature representations. Therefore, maintaining a balanced classifier head is of significant importance for building a better global model. To this end, we propose a simple yet effective framework by introducing a prior-calibrated softmax function for computing the cross-entropy loss and a prototype-based feature augmentation scheme to re-balance the local training, which are lightweight for edge devices and can facilitate the global model aggregation. The improved model performance over existing baselines in the presence of non-IID data and client dropout is demonstrated by conducting extensive experiments on benchmark classification tasks.

Deep neural retrieval models have amply demonstrated their power but estimating the reliability of their predictions remains challenging. Most dialog response retrieval models output a single score for a response on how relevant it is to a given question. However, the bad calibration of deep neural network results in various uncertainty for the single score such that the unreliable predictions always misinform user decisions. To investigate these issues, we present an efficient calibration and uncertainty estimation framework PG-DRR for dialog response retrieval models which adds a Gaussian Process layer to a deterministic deep neural network and recovers conjugacy for tractable posterior inference by P\'{o}lya-Gamma augmentation. Finally, PG-DRR achieves the lowest empirical calibration error (ECE) in the in-domain datasets and the distributional shift task while keeping $R_{10}@1$ and MAP performance.

This paper gives a simple theory of inference to logically reason symbolic knowledge fully from data over time. We take a Bayesian approach to model how data causes symbolic knowledge. Probabilistic reasoning with symbolic knowledge is modelled as a process of going the causality forwards and backwards. The forward and backward processes correspond to an interpretation and inverse interpretation of formal logic, respectively. The theory is applied to a localisation problem to show a robot with broken or noisy sensors can efficiently solve the problem in a fully data-driven fashion.

Many real-world systems are described not only by data from a single source but via multiple data views. In genomic medicine, for instance, patients can be characterized by data from different molecular layers. Latent variable models with structured sparsity are a commonly used tool for disentangling variation within and across data views. However, their interpretability is cumbersome since it requires a direct inspection and interpretation of each factor from domain experts. Here, we propose MuVI, a novel multi-view latent variable model based on a modified horseshoe prior for modeling structured sparsity. This facilitates the incorporation of limited and noisy domain knowledge, thereby allowing for an analysis of multi-view data in an inherently explainable manner. We demonstrate that our model (i) outperforms state-of-the-art approaches for modeling structured sparsity in terms of the reconstruction error and the precision/recall, (ii) robustly integrates noisy domain expertise in the form of feature sets, (iii) promotes the identifiability of factors and (iv) infers interpretable and biologically meaningful axes of variation in a real-world multi-view dataset of cancer patients.

Robots that can effectively understand human intentions from actions are crucial for successful human-robot collaboration. In this work, we address the challenge of a robot navigating towards an unknown goal while also accounting for a human's preference for a particular path in the presence of obstacles. This problem is particularly challenging when both the goal and path preference are unknown a priori. To overcome this challenge, we propose a method for encoding and inferring path preference online using a partitioning of the space into polytopes. Our approach enables joint inference over the goal and path preference using a stochastic observation model for the human. We evaluate our method on an unknown-goal navigation problem with sparse human interventions, and find that it outperforms baseline approaches as the human's inputs become increasingly sparse. We find that the time required to update the robot's belief does not increase with the complexity of the environment, which makes our method suitable for online applications.