Charles Zheng

Lukas Muttenthaler, Charles Y. Zheng, Patrick McClure et al.

A central goal in the cognitive sciences is the development of numerical models for mental representations of object concepts. This paper introduces Variational Interpretable Concept Embeddings (VICE), an approximate Bayesian method for embedding object concepts in a vector space using data collected from humans in a triplet odd-one-out task. VICE uses variational inference to obtain sparse, non-negative representations of object concepts with uncertainty estimates for the embedding values. These estimates are used to automatically select the dimensions that best explain the data. We derive a PAC learning bound for VICE that can be used to estimate generalization performance or determine a sufficient sample size for experimental design. VICE rivals or outperforms its predecessor, SPoSE, at predicting human behavior in the triplet odd-one-out task. Furthermore, VICE's object representations are more reproducible and consistent across random initializations, highlighting the unique advantage of using VICE for deriving interpretable embeddings from human behavior.

Yenho Chen, Carl W. Harris, Xiaoyu Ma et al.

We propose a decoding-based approach to detect context effects on neural codes in longitudinal neural recording data. The approach is agnostic to how information is encoded in neural activity, and can control for a variety of possible confounding factors present in the data. We demonstrate our approach by determining whether it is possible to decode location encoding from prefrontal cortex in the mouse and, further, testing whether the encoding changes due to task engagement.

Charles Y. Zheng, Francisco Pereira, Chris I. Baker et al.

To study how mental object representations are related to behavior, we estimated sparse, non-negative representations of objects using human behavioral judgments on images representative of 1,854 object categories. These representations predicted a latent similarity structure between objects, which captured most of the explainable variance in human behavioral judgments. Individual dimensions in the low-dimensional embedding were found to be highly reproducible and interpretable as conveying degrees of taxonomic membership, functionality, and perceptual attributes. We further demonstrated the predictive power of the embeddings for explaining other forms of human behavior, including categorization, typicality judgments, and feature ratings, suggesting that the dimensions reflect human conceptual representations of objects beyond the specific task.

Patrick McClure, Nao Rho, John A. Lee et al.

In this paper, we describe a Bayesian deep neural network (DNN) for predicting FreeSurfer segmentations of structural MRI volumes, in minutes rather than hours. The network was trained and evaluated on a large dataset (n = 11,480), obtained by combining data from more than a hundred different sites, and also evaluated on another completely held-out dataset (n = 418). The network was trained using a novel spike-and-slab dropout-based variational inference approach. We show that, on these datasets, the proposed Bayesian DNN outperforms previously proposed methods, in terms of the similarity between the segmentation predictions and the FreeSurfer labels, and the usefulness of the estimate uncertainty of these predictions. In particular, we demonstrated that the prediction uncertainty of this network at each voxel is a good indicator of whether the network has made an error and that the uncertainty across the whole brain can predict the manual quality control ratings of a scan. The proposed Bayesian DNN method should be applicable to any new network architecture for addressing the segmentation problem.

Patrick McClure, Charles Y. Zheng, Jakub R. Kaczmarzyk et al.

Collecting the large datasets needed to train deep neural networks can be very difficult, particularly for the many applications for which sharing and pooling data is complicated by practical, ethical, or legal concerns. However, it may be the case that derivative datasets or predictive models developed within individual sites can be shared and combined with fewer restrictions. Training on distributed data and combining the resulting networks is often viewed as continual learning, but these methods require networks to be trained sequentially. In this paper, we introduce distributed weight consolidation (DWC), a continual learning method to consolidate the weights of separate neural networks, each trained on an independent dataset. We evaluated DWC with a brain segmentation case study, where we consolidated dilated convolutional neural networks trained on independent structural magnetic resonance imaging (sMRI) datasets from different sites. We found that DWC led to increased performance on test sets from the different sites, while maintaining generalization performance for a very large and completely independent multi-site dataset, compared to an ensemble baseline.

Charles Zheng, Rakesh Achanta, Yuval Benjamini

The difficulty of multi-class classification generally increases with the number of classes. Using data from a subset of the classes, can we predict how well a classifier will scale with an increased number of classes? Under the assumptions that the classes are sampled identically and independently from a population, and that the classifier is based on independently learned scoring functions, we show that the expected accuracy when the classifier is trained on k classes is the (k-1)st moment of a certain distribution that can be estimated from data. We present an unbiased estimation method based on the theory, and demonstrate its application on a facial recognition example.

Charles Y. Zheng, Yuval Benjamini

Multivariate pattern analyses approaches in neuroimaging are fundamentally concerned with investigating the quantity and type of information processed by various regions of the human brain; typically, estimates of classification accuracy are used to quantify information. While a extensive and powerful library of methods can be applied to train and assess classifiers, it is not always clear how to use the resulting measures of classification performance to draw scientific conclusions: e.g. for the purpose of evaluating redundancy between brain regions. An additional confound for interpreting classification performance is the dependence of the error rate on the number and choice of distinct classes obtained for the classification task. In contrast, mutual information is a quantity defined independently of the experimental design, and has ideal properties for comparative analyses. Unfortunately, estimating the mutual information based on observations becomes statistically infeasible in high dimensions without some kind of assumption or prior. In this paper, we construct a novel classification-based estimator of mutual information based on high-dimensional asymptotics. We show that in a particular limiting regime, the mutual information is an invertible function of the expected $k$-class Bayes error. While the theory is based on a large-sample, high-dimensional limit, we demonstrate through simulations that our proposed estimator has superior performance to the alternatives in problems of moderate dimensionality.

Charles Y. Zheng, Rakesh Achanta, Yuval Benjamini

The difficulty of multi-class classification generally increases with the number of classes. Using data from a subset of the classes, can we predict how well a classifier will scale with an increased number of classes? Under the assumption that the classes are sampled exchangeably, and under the assumption that the classifier is generative (e.g. QDA or Naive Bayes), we show that the expected accuracy when the classifier is trained on $k$ classes is the $k-1$st moment of a \emph{conditional accuracy distribution}, which can be estimated from data. This provides the theoretical foundation for performance extrapolation based on pseudolikelihood, unbiased estimation, and high-dimensional asymptotics. We investigate the robustness of our methods to non-generative classifiers in simulations and one optical character recognition example.

Charles Zheng, Franco Pestilli, Ariel Rokem

Diffusion-weighted MR imaging (DWI) is the only method we currently have to measure connections between different parts of the human brain in vivo. To elucidate the structure of these connections, algorithms for tracking bundles of axonal fibers through the subcortical white matter rely on local estimates of the fiber orientation distribution function (fODF) in different parts of the brain. These functions describe the relative abundance of populations of axonal fibers crossing each other in each location. Multiple models exist for estimating fODFs. The quality of the resulting estimates can be quantified by means of a suitable measure of distance on the space of fODFs. However, there are multiple distance metrics that can be applied for this purpose, including smoothed $L_p$ distances and the Wasserstein metrics. Here, we give four reasons for the use of the Earth Mover's Distance (EMD) equipped with the arc-length, as a distance metric. (continued)

Charles Zheng, Franco Pestilli, Ariel Rokem

Diffusion-weighted magnetic resonance imaging (DWI) and fiber tractography are the only methods to measure the structure of the white matter in the living human brain. The diffusion signal has been modelled as the combined contribution from many individual fascicles of nerve fibers passing through each location in the white matter. Typically, this is done via basis pursuit, but estimation of the exact directions is limited due to discretization. The difficulties inherent in modeling DWI data are shared by many other problems involving fitting non-parametric mixture models. Ekanadaham et al. proposed an approach, continuous basis pursuit, to overcome discretization error in the 1-dimensional case (e.g., spike-sorting). Here, we propose a more general algorithm that fits mixture models of any dimensionality without discretization. Our algorithm uses the principles of L2-boost, together with refitting of the weights and pruning of the parameters. The addition of these steps to L2-boost both accelerates the algorithm and assures its accuracy. We refer to the resulting algorithm as elastic basis pursuit, or EBP, since it expands and contracts the active set of kernels as needed. We show that in contrast to existing approaches to fitting mixtures, our boosting framework (1) enables the selection of the optimal bias-variance tradeoff along the solution path, and (2) scales with high-dimensional problems. In simulations of DWI, we find that EBP yields better parameter estimates than a non-negative least squares (NNLS) approach, or the standard model used in DWI, the tensor model, which serves as the basis for diffusion tensor imaging (DTI). We demonstrate the utility of the method in DWI data acquired in parts of the brain containing crossings of multiple fascicles of nerve fibers.