Lucy L. Gao

Lucy L. Gao, Jane J. Ye, Haian Yin et al.

Bilevel programming has emerged as a valuable tool for hyperparameter selection, a central concern in machine learning. In a recent study by Ye et al. (2023), a value function-based difference of convex algorithm was introduced to address bilevel programs. This approach proves particularly powerful when dealing with scenarios where the lower-level problem exhibits convexity in both the upper-level and lower-level variables. Examples of such scenarios include support vector machines and $\ell_1$ and $\ell_2$ regularized regression. In this paper, we significantly expand the range of applications, now requiring convexity only in the lower-level variables of the lower-level program. We present an innovative single-level difference of weakly convex reformulation based on the Moreau envelope of the lower-level problem. We further develop a sequentially convergent Inexact Proximal Difference of Weakly Convex Algorithm (iP-DwCA). To evaluate the effectiveness of the proposed iP-DwCA, we conduct numerical experiments focused on tuning hyperparameters for kernel support vector machines on simulated data.

Anna C. Neufeld, Lucy L. Gao, Daniela M. Witten

We consider conducting inference on the output of the Classification and Regression Tree (CART) [Breiman et al., 1984] algorithm. A naive approach to inference that does not account for the fact that the tree was estimated from the data will not achieve standard guarantees, such as Type 1 error rate control and nominal coverage. Thus, we propose a selective inference framework for conducting inference on a fitted CART tree. In a nutshell, we condition on the fact that the tree was estimated from the data. We propose a test for the difference in the mean response between a pair of terminal nodes that controls the selective Type 1 error rate, and a confidence interval for the mean response within a single terminal node that attains the nominal selective coverage. Efficient algorithms for computing the necessary conditioning sets are provided. We apply these methods in simulation and to a dataset involving the association between portion control interventions and caloric intake.

Lucy L. Gao, Jacob Bien, Daniela Witten

Classical tests for a difference in means control the type I error rate when the groups are defined a priori. However, when the groups are instead defined via clustering, then applying a classical test yields an extremely inflated type I error rate. Notably, this problem persists even if two separate and independent data sets are used to define the groups and to test for a difference in their means. To address this problem, in this paper, we propose a selective inference approach to test for a difference in means between two clusters. Our procedure controls the selective type I error rate by accounting for the fact that the choice of null hypothesis was made based on the data. We describe how to efficiently compute exact p-values for clusters obtained using agglomerative hierarchical clustering with many commonly-used linkages. We apply our method to simulated data and to single-cell RNA-sequencing data.

Lucy L. Gao, Daniela Witten, Jacob Bien

In this paper, we consider data consisting of multiple networks, each comprised of a different edge set on a common set of nodes. Many models have been proposed for the analysis of such multi-view network data under the assumption that the data views are closely related. In this paper, we provide tools for evaluating this assumption. In particular, we ask: given two networks that each follow a stochastic block model, is there an association between the latent community memberships of the nodes in the two networks? To answer this question, we extend the stochastic block model for a single network view to the two-view setting, and develop a new hypothesis test for the null hypothesis that the latent community memberships in the two data views are independent. We apply our test to protein-protein interaction data from the HINT database (Das and Hint, 2012). We find evidence of a weak association between the latent community memberships of proteins defined with respect to binary interaction data and the latent community memberships of proteins defined with respect to co-complex association data. We also extend this proposal to the setting of a network with node covariates.

Lucy L. Gao, Jacob Bien, Daniela Witten

In the Pioneer 100 (P100) Wellness Project (Price and others, 2017), multiple types of data are collected on a single set of healthy participants at multiple timepoints in order to characterize and optimize wellness. One way to do this is to identify clusters, or subgroups, among the participants, and then to tailor personalized health recommendations to each subgroup. It is tempting to cluster the participants using all of the data types and timepoints, in order to fully exploit the available information. However, clustering the participants based on multiple data views implicitly assumes that a single underlying clustering of the participants is shared across all data views. If this assumption does not hold, then clustering the participants using multiple data views may lead to spurious results. In this paper, we seek to evaluate the assumption that there is some underlying relationship among the clusterings from the different data views, by asking the question: are the clusters within each data view dependent or independent? We develop a new test for answering this question, which we then apply to clinical, proteomic, and metabolomic data, across two distinct timepoints, from the P100 study. We find that while the subgroups of the participants defined with respect to any single data type seem to be dependent across time, the clustering among the participants based on one data type (e.g. proteomic data) appears not to be associated with the clustering based on another data type (e.g. clinical data).