skip to main content


Title: Embedding Signals on Graphs with Unbalanced Diffusion Earth Mover’s Distance
In modern relational machine learning it is common to encounter large graphs that arise via interactions or similarities between observations in many domains. Further, in many cases the target entities for analysis are actually signals on such graphs. We propose to compare and organize such datasets of graph signals by using an earth mover’s distance (EMD) with a geodesic cost over the underlying graph. Typically, EMD is computed by optimizing over the cost of transporting one probability distribution to another over an underlying metric space. However, this is inefficient when computing the EMD between many signals. Here, we propose an unbalanced graph EMD that efficiently embeds the unbalanced EMD on an underlying graph into an L1 space, whose metric we call unbalanced diffusion earth mover’s distance (UDEMD). Next, we show how this gives distances between graph signals that are robust to noise. Finally, we apply this to organizing patients based on clinical notes, embedding cells modeled as signals on a gene graph, and organizing genes modeled as signals over a large cell graph. In each case, we show that UDEMD-based embeddings find accurate distances that are highly efficient compared to other methods.  more » « less
Award ID(s):
2047856
NSF-PAR ID:
10352695
Author(s) / Creator(s):
; ; ; ; ; ; ;
Date Published:
Journal Name:
EEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)
Page Range / eLocation ID:
5647 to 5651
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Motivation: Intra-sample heterogeneity describes the phenomenon where a genomic sample contains a diverse set of genomic sequences. In practice, the true string sets in a sample are often unknown due to limitations in sequencing technology. In order to compare heterogeneous samples, genome graphs can be used to represent such sets of strings. However, a genome graph is generally able to represent a string set universe that contains multiple sets of strings in addition to the true string set. This difference between genome graphs and string sets is not well characterized. As a result, a distance metric between genome graphs may not match the distance between true string sets. Results: We extend a genome graph distance metric, Graph Traversal Edit Distance (GTED) proposed by Ebrahimpour Boroojeny et al., to FGTED to model the distance between heterogeneous string sets and show that GTED and FGTED always underestimate the Earth Mover’s Edit Distance (EMED) between string sets. We introduce the notion of string set universe diameter of a genome graph. Using the diameter, we are able to upper-bound the deviation of FGTED from EMED and to improve FGTED so that it reduces the average error in empirically estimating the similarity between true string sets. On simulated T-cell receptor sequences and actual Hepatitis B virus genomes, we show that the diameter-corrected FGTED reduces the average deviation of the estimated distance from the true string set distances by more than 250%. Availability and implementation: Data and source code for reproducing the experiments are available at: https:// github.com/Kingsford-Group/gtedemedtest/. 
    more » « less
  2. Understanding generalization and robustness of machine learning models funda- mentally relies on assuming an appropriate metric on the data space. Identifying such a metric is particularly challenging for non-Euclidean data such as graphs. Here, we propose a pseudometric for attributed graphs, the Tree Mover’s Distance (TMD), and study its relation to generalization. Via a hierarchical optimal transport problem, TMD reflects the local distribution of node attributes as well as the distri- bution of local computation trees, which are known to be decisive for the learning behavior of graph neural networks (GNNs). First, we show that TMD captures properties relevant to graph classification: a simple TMD-SVM performs competi- tively with standard GNNs. Second, we relate TMD to generalization of GNNs under distribution shifts, and show that it correlates well with performance drop under such shifts. 
    more » « less
  3. Abstract Motivation

    Intra-sample heterogeneity describes the phenomenon where a genomic sample contains a diverse set of genomic sequences. In practice, the true string sets in a sample are often unknown due to limitations in sequencing technology. In order to compare heterogeneous samples, genome graphs can be used to represent such sets of strings. However, a genome graph is generally able to represent a string set universe that contains multiple sets of strings in addition to the true string set. This difference between genome graphs and string sets is not well characterized. As a result, a distance metric between genome graphs may not match the distance between true string sets.

    Results

    We extend a genome graph distance metric, Graph Traversal Edit Distance (GTED) proposed by Ebrahimpour Boroojeny et al., to FGTED to model the distance between heterogeneous string sets and show that GTED and FGTED always underestimate the Earth Mover’s Edit Distance (EMED) between string sets. We introduce the notion of string set universe diameter of a genome graph. Using the diameter, we are able to upper-bound the deviation of FGTED from EMED and to improve FGTED so that it reduces the average error in empirically estimating the similarity between true string sets. On simulated T-cell receptor sequences and actual Hepatitis B virus genomes, we show that the diameter-corrected FGTED reduces the average deviation of the estimated distance from the true string set distances by more than 250%.

    Availability and implementation

    Data and source code for reproducing the experiments are available at: https://github.com/Kingsford-Group/gtedemedtest/.

    Supplementary information

    Supplementary data are available at Bioinformatics online.

     
    more » « less
  4. Mulzer, Wolfgang ; Phillips, Jeff M (Ed.)
    A Reeb graph is a graphical representation of a scalar function on a topological space that encodes the topology of the level sets. A Reeb space is a generalization of the Reeb graph to a multiparameter function. In this paper, we propose novel constructions of Reeb graphs and Reeb spaces that incorporate the use of a measure. Specifically, we introduce measure-theoretic Reeb graphs and Reeb spaces when the domain or the range is modeled as a metric measure space (i.e., a metric space equipped with a measure). Our main goal is to enhance the robustness of the Reeb graph and Reeb space in representing the topological features of a scalar field while accounting for the distribution of the measure. We first introduce a Reeb graph with local smoothing and prove its stability with respect to the interleaving distance. We then prove the stability of a Reeb graph of a metric measure space with respect to the measure, defined using the distance to a measure or the kernel distance to a measure, respectively. 
    more » « less
  5. Important data mining problems such as nearest-neighbor search and clustering admit theoretical guarantees when restricted to objects embedded in a metric space. Graphs are ubiquitous, and clustering and classification over graphs arise in diverse areas, including, e.g., image processing and social networks. Unfortunately, popular distance scores used in these applications, that scale over large graphs, are not metrics and thus come with no guarantees. Classic graph distances such as, e.g., the chemical and the CKS distance are arguably natural and intuitive, and are indeed also metrics, but they are intractable: as such, their computation does not scale to large graphs. We define a broad family of graph distances, that includes both the chemical and the CKS distance, and prove that these are all metrics. Crucially, we show that our family includes metrics that are tractable. Moreover, we extend these distances by incorporating auxiliary node attributes, which is important in practice, while maintaining both the metric property and tractability. 
    more » « less