This program is designed to provide decision-makers, policymakers and professional working in policy with a foundational understanding of AI technology.
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Although data diffusion embeddings are ubiquitous in unsupervised learning and have proven to be a viable technique for uncovering the under… (see more)lying intrinsic geometry of data, diffusion embeddings are inherently limited due to their discrete nature. To this end, we propose neural FIM, a method for computing the Fisher information metric (FIM) from point cloud data - allowing for a continuous manifold model for the data. Neural FIM creates an extensible metric space from discrete point cloud data such that information from the metric can inform us of manifold characteristics such as volume and geodesics. We demonstrate Neural FIM's utility in selecting parameters for the PHATE visualization method as well as its ability to obtain information pertaining to local volume illuminating branching points and cluster centers embeddings of a toy dataset and two single-cell datasets of IPSC reprogramming and PBMCs (immune cells).
While numerous methods have been proposed for computing distances between probability distributions in Euclidean space, relatively little at… (see more)tention has been given to computing such distances for distributions on graphs. However, there has been a marked increase in data that either lies on graph (such as protein interaction networks) or can be modeled as a graph (single cell data), particularly in the biomedical sciences. Thus, it becomes important to find ways to compare signals defined on such graphs. Here, we propose Graph Fourier MMD (GFMMD), a novel a distance between distributions, or non-negative signals on graphs. GFMMD is defined via an optimal witness function that is both smooth on the graph and maximizes difference in expectation between the pair of distributions on the graph. We find an analytical solution to this optimization problem as well as an embedding of distributions that results from this method. We also prove several properties of this method including scale invariance and applicability to disconnected graphs. We showcase it on graph benchmark datasets as well on single cell RNA-sequencing data analysis. In the latter, we use the GFMMD-based gene embeddings to find meaningful gene clusters. We also propose a novel type of score for gene selection called {\em gene localization score} which helps select genes for cellular state space characterization.
Learning the causal structure of observable variables is a central focus for scientific discovery. Bayesian causal discovery methods tackle… (see more) this problem by learning a posterior over the set of admissible graphs given our priors and observations. Existing methods primarily consider observations from static systems and assume the underlying causal structure takes the form of a directed acyclic graph (DAG). In settings with dynamic feedback mechanisms that regulate the trajectories of individual variables, this acyclicity assumption fails unless we account for time. We focus on learning Bayesian posteriors over cyclic graphs and treat causal discovery as a problem of sparse identification of a dynamical sys-tem. This imposes a natural temporal causal order between variables and captures cyclic feedback loops through time. Under this lens, we propose a new framework for Bayesian causal discovery for dynamical systems and present a novel generative flow network architecture (DynGFN) tailored for this task. Our results indicate that DynGFN learns posteriors that better encapsulate the distributions over admissible cyclic causal structures compared to counterpart state-of-the-art approaches.
Efficient computation of optimal transport distance between distributions is of growing importance in data science. Sinkhorn-based methods a… (see more)re currently the state-of-the-art for such computations, but require O(n2) computations. In addition, Sinkhorn-based methods commonly use an Euclidean ground distance between datapoints. However, with the prevalence of manifold structured scientific data, it is often desirable to consider geodesic ground distance. Here, we tackle both issues by proposing Geodesic Sinkhorn—based on diffusing a heat kernel on a manifold graph. Notably, Geodesic Sinkhorn requires only O(n log n) computation, as we approximate the heat kernel with Chebyshev polynomials based on the sparse graph Laplacian. We apply our method to the computation of barycenters of several distributions of high dimensional single cell data from patient samples undergoing chemotherapy. In particular, we define the barycentric distance as the distance between two such barycenters. Using this definition, we identify an optimal transport distance and path associated with the effect of treatment on cellular data.
2023-01-01
2023 IEEE 33rd International Workshop on Machine Learning for Signal Processing (MLSP) (published)
Anomaly detection is of great interest in fields where abnormalities need to be identified and corrected (e.g., medicine and finance). Deep … (see more)learning methods for this task often rely on autoencoder reconstruction error, sometimes in conjunction with other penalties. We show that this approach exhibits intrinsic biases that lead to undesirable results. Reconstruction-based methods can sometimes show low error on simple-to-reconstruct points that are not part of the training data, for example the all black image. Instead, we introduce a new unsupervised Lipschitz anomaly discriminator (LAD) that does not suffer from these biases. Our anomaly discriminator is trained, similar to the discriminator of a GAN, to detect the difference between the training data and corruptions of the training data. We show that this procedure successfully detects unseen anomalies with guarantees on those that have a certain Wasserstein distance from the data or corrupted training set. These additions allow us to show improved performance on MNIST, CIFAR10, and health record data. Further, LAD does not require decoding back to the original data space, which makes anomaly detection possible in domains where it is difficult to define a decoder, such as in irregular graph structured data. Empirically, we show this framework leads to improved performance on image, health record, and graph data.
In modern relational machine learning it is common to encounter large graphs that arise via interactions or similarities between observation… (see more)s in many domains. Further
In modern relational machine learning it is common to encounter large graphs that arise via interactions or similarities between observation… (see more)s in many domains. Further