United States

We propose a similarity measure for sparsely sampled time course data in the form of a log-likelihood ratio of Gaussian processes (GP). The proposed GP similarity is similar to a Bayes factor and provides enhanced robustness to noise in sparse time series, such as those found in various biological settings, e.g., gene transcriptomics. We show that the GP measure is equivalent to the Euclidean distance when the noise variance in the GP is negligible compared to the noise variance of the signal. Our numerical experiments on both synthetic and real data show improved performance of the GP similarity when used in conjunction with two distance-based clustering methods.

UAI 2021

Similarity Measure for Sparse Time Course Data Based on Gaussian Processes

similarity measure

sparse time course

gaussian process

The Conference on Uncertainty in Artificial Intelligence (UAI) is one of the premier international conferences on research related to knowledge representation, learning, and reasoning in the presence of uncertainty. It is supported by the [Association for Uncertainty in Artificial Intelligence (AUAI).](https://www.auai.org/)

The 37th Conference on Uncertainty in Artificial Intelligence (UAI 2021) is held fully online. We have an exciting program consisting of keynote talks by [Susan Murphy](https://www.auai.org/uai2021/program?block=A), [Eric Horvitz](https://www.auai.org/uai2021/program?block=B), [Lenka Zdeborová](https://www.auai.org/uai2021/program?block=C), [Judea Pearl](https://www.auai.org/uai2021/program?block=D) and [Ankur Moitra](https://www.auai.org/uai2021/program?block=E), a town hall meeting, peer-reviewed papers, and three workshops. The main conference is single-track and each paper is show-cased with a live component (either a live discussion and Q&A, or a live lightning talk). All papers are also featured in video presentations and in poster sessions in gather.town. The three parallel workshops on Friday allow for smaller meetings on current topics.

The walkthrough video below shows how you can navigate this site and use the different possibilities for interaction: UAIsland2021 on gather.town for posters and social interactions, the mementor platform for virtual mentoring sessions, and the chat and Q&A systems for discussions about talks and posters.

Have a great UAI 2021! 
<br>
<br>Cassio de Campos and Marloes Maathuis
<br>UAI 2021 Program Chairs
<br>uai2021programchairs@gmail.com

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A ticket is required to access this conference. Please use the provided link to register for the event.

https://auai.org/uai2021/registration

The Conference on Uncertainty in Artificial Intelligence (UAI) is one of the premier international conferences on research related to knowledge representation, learning, and reasoning in the presence of uncertainty. It is supported by the [Association for Uncertainty in Artificial Intelligence (AUAI).](https://www.auai.org/)

lightning talk

This paper describes a new probabilistic generative model for noisy, sparse, and heterogeneous relational data called the hierarchical infinite relational model (HIRM). Given a set of relations defined over a collection of domains, the model first infers multiple non-overlapping clusters of relations using a top-level Chinese restaurant process. Within each cluster of relations, a Dirichlet process mixture is then used to partition the domain entities and model the probability distribution of relation values. The HIRM generalizes the standard infinite relational model and can be used for a variety of data analysis tasks including dependence detection, clustering, and density estimation. We present new algorithms for fully Bayesian posterior inference via Gibbs sampling. We illustrate the efficacy of the method on a density estimation benchmark of twenty object-attribute datasets with up to 18 million cells and use it to discover relational structure in real-world datasets from politics and genomics.

Hierarchical Infinite Relational Model

We present a new non-negative matrix factorization model for $(0,1)$

Doubly Non-Central Beta Matrix Factorization for DNA Methylation Data

Hierarchical clustering is a critical task in numerous domains. Many approaches are based on heuristics and the properties of the resulting clusterings are studied post hoc. However, in several applications, there is a natural cost function that can be used to characterize the quality of the clustering. In those cases, hierarchical clustering can be seen as a combinatorial optimization problem. To that end, we introduce a new approach based on A* search. We overcome the prohibitively large search space by combining A* with a novel trellis data structure. This results in an exact algorithm that scales beyond previous state of the art (from search space with 10^12 trees to 10^15 trees) and an approximate algorithm that improves over baselines, even in enormous search spaces (that contain more than 10^1000 trees). Empirically we demonstrate that our method achieves substantially higher quality results than baselines for a particle physics use case and other clustering benchmarks. We describe how our method provides significantly improved theoretical bounds on the time and space complexity of A* for clustering.

Exact and Approximate Hierarchical Clustering Using A*

Parametric path problems arise independently in diverse domains, ranging from transportation to finance, where they are studied under various assumptions. We formulate a general path problem with relaxed assumptions, and describe how this formulation is applicable in these domains.

Generalized Parametric Path Problems

Machine-learning models contain information about the data they were trained

Measuring Data Leakage in Machine-Learning Models with Fisher Information

In this paper, we study the differentially private Principal Component Analysis (PCA) problem in stochastic optimization settings. We first propose

Principal Component Analysis in the Stochastic Differential Privacy Model

Auxiliary particle filters (APFs) are a class of sequential Monte Carlo (SMC) methods for Bayesian inference in state-space models. In their original derivation, APFs operate in an extended state space using an auxiliary variable to improve inference. In this work, we propose optimized auxiliary particle filters, a framework where the traditional APF auxiliary variables are interpreted as weights in a importance sampling mixture proposal. Under this interpretation, we devise a mechanism for proposing the mixture weights that is inspired by recent advances in multiple and adaptive importance sampling. In particular, we propose to select the mixture weights by formulating a convex optimization problem, with the aim of approximating the filtering posterior at each timestep. Further, we propose a weighting scheme that generalizes previous results on the APF (Pitt et al. 2012), proving unbiasedness and consistency of our estimators. Our framework demonstrates significantly improved estimates on a range of metrics compared to state-of-the-art particle filters at similar computational complexity in challenging and widely used dynamical models.

Optimized Auxiliary Particle Filters

Conventional methods in causal effect inferencetypically rely on specifying a valid set of control variables. When this set is unknown or misspecified, inferences will be erroneous. We propose a method for inferring average causal effects when all potential confounders are observed, but thecontrol variables are unknown. When the data-generating process belongs to the class of acyclical linear structural causal models, we prove that themethod yields asymptotically valid confidence intervals. Our results build upon a smooth characterization of linear directed acyclic graphs. We verify the capability of the method to produce valid confidence intervals for average causal effects using synthetic data, even when the appropriate specification of control variables is unknown.

Inference of Causal Effects when Control Variables are Unknown

Dimension reduction plays a pivotal role in analysing high-dimensional data. However, observations with missing values present serious difficulties in directly applying standard dimension reduction techniques. As a large number of dimension reduction approaches are based on the Gram matrix, we first investigate the effects of missingness on dimension reduction by studying the statistical properties of the Gram matrix with or without missing data, and then we present a bias-corrected Gram matrix with nice statistical properties under heterogeneous missingness. Extensive empirical results, on both simulated and publicly available real datasets, show that the proposed unbiased Gram matrix can significantly improve a broad spectrum of representative dimension reduction approaches.

Dimension reduction for data with heterogeneous missingness

Estimation of probability density function from samples is one of the central problems in statistics and machine learning. Modern neural network-based models can learn high dimensional distributions but have problems with hyperparameter selection and are often prone to instabilities during training and inference. We propose a new efficient tensor train-based model for density estimation (TTDE). Such density parametrization allows exact sampling, calculation of cumulative and marginal density functions, and partition function. It also has very intuitive hyperparameters. We develop an efficient non-adversarial training procedure for TTDE based on the Riemannian optimization. Experimental results demonstrate the competitive performance of the proposed method in density estimation and sampling tasks, while TTDE significantly outperforms competitors in training speed.

Similarity Measure for Sparse Time Course Data Based on Gaussian Processes

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