$\textbf{Motivation:}$ Small $p$-values are often required to be accurately estimated in large-scale genomic studies for the adjustment of multiple hypothesis tests and the ranking of genomic features based on their statistical significance. For those complicated test statistics whose cumulative distribution functions are analytically intractable, existing methods usually do not work well with small $p$-values due to lack of accuracy or computational restrictions. We propose a general approach for accurately and efficiently estimating small $p$-values for a broad range of complicated test statistics based on the principle of the cross-entropy method and Markov chain Monte Carlo sampling techniques. $\textbf{Results:}$ We evaluate the performance of the proposed algorithm through simulations and demonstrate its application to three real-world examples in genomic studies. The results show that our approach can accurately evaluate small to extremely small $p$-values (e.g. $10^{-6}$ to $10^{-100}$). The proposed algorithm is helpful for the improvement of some existing test procedures and the development of new test procedures in genomic studies.
Classical wisdom in machine learning holds that the generalization error can be decomposed into bias and variance, and these two terms exhibit a \emph{trade-off}. However, in this paper, we show that for an ensemble of deep learning based classification models, bias and variance are \emph{aligned} at a sample level, where squared bias is approximately \emph{equal} to variance for correctly classified sample points. We present empirical evidence confirming this phenomenon in a variety of deep learning models and datasets. Moreover, we study this phenomenon from two theoretical perspectives: calibration and neural collapse. We first show theoretically that under the assumption that the models are well calibrated, we can observe the bias-variance alignment. Second, starting from the picture provided by the neural collapse theory, we show an approximate correlation between bias and variance.
Originating from the diffusion phenomenon in physics that describes particle movement, the diffusion generative models inherit the characteristics of stochastic random walk in the data space along the denoising trajectory. However, the intrinsic mutual interference among image regions contradicts the need for practical downstream application scenarios where the preservation of low-level pixel information from given conditioning is desired (e.g., customization tasks like personalized generation and inpainting based on a user-provided single image). In this work, we investigate the diffusion (physics) in diffusion (machine learning) properties and propose our Cyclic One-Way Diffusion (COW) method to control the direction of diffusion phenomenon given a pre-trained frozen diffusion model for versatile customization application scenarios, where the low-level pixel information from the conditioning needs to be preserved. Notably, unlike most current methods that incorporate additional conditions by fine-tuning the base text-to-image diffusion model or learning auxiliary networks, our method provides a novel perspective to understand the task needs and is applicable to a wider range of customization scenarios in a learning-free manner. Extensive experiment results show that our proposed COW can achieve more flexible customization based on strict visual conditions in different application settings.
Tensor-valued data arise frequently from a wide variety of scientific applications, and many among them can be translated into an alteration detection problem of tensor dependence structures. In this article, we formulate the problem under the popularly adopted tensor-normal distributions and aim at two-sample correlation/partial correlation comparisons of tensor-valued observations. Through decorrelation and centralization, a separable covariance structure is employed to pool sample information from different tensor modes to enhance the power of the test. Additionally, we propose a novel Sparsity-Exploited Reranking Algorithm (SERA) to further improve the multiple testing efficiency. The algorithm is approached through reranking of the p-values derived from the primary test statistics, by incorporating a carefully constructed auxiliary tensor sequence. Besides the tensor framework, SERA is also generally applicable to a wide range of two-sample large-scale inference problems with sparsity structures, and is of independent interest. The asymptotic properties of the proposed test are derived and the algorithm is shown to control the false discovery at the pre-specified level. We demonstrate the efficacy of the proposed method through intensive simulations and two scientific applications.
Despite the recent advances in abstractive text summarization, current summarization models still suffer from generating factually inconsistent summaries, reducing their utility for real-world application. We argue that the main reason for such behavior is that the summarization models trained with maximum likelihood objective assign high probability to plausible sequences given the context, but they often do not accurately rank sequences by their consistency. In this work, we solve this problem by calibrating the likelihood of model generated sequences to better align with a consistency metric measured by natural language inference (NLI) models. The human evaluation study and automatic metrics show that the calibrated models generate more consistent and higher-quality summaries. We also show that the models trained using our method return probabilities that are better aligned with the NLI scores, which significantly increase reliability of summarization models.
Covariate shift occurs prevalently in practice, where the input distributions of the source and target data are substantially different. Despite its practical importance in various learning problems, most of the existing methods only focus on some specific learning tasks and are not well validated theoretically and numerically. To tackle this problem, we propose a unified analysis of general nonparametric methods in a reproducing kernel Hilbert space (RKHS) under covariate shift. Our theoretical results are established for a general loss belonging to a rich loss function family, which includes many commonly used methods as special cases, such as mean regression, quantile regression, likelihood-based classification, and margin-based classification. Two types of covariate shift problems are the focus of this paper and the sharp convergence rates are established for a general loss function to provide a unified theoretical analysis, which concurs with the optimal results in literature where the squared loss is used. Extensive numerical studies on synthetic and real examples confirm our theoretical findings and further illustrate the effectiveness of our proposed method.
Most of the current hypergraph learning methodologies and benchmarking datasets in the hypergraph realm are obtained by lifting procedures from their graph analogs, simultaneously leading to overshadowing hypergraph network foundations. This paper attempts to confront some pending questions in that regard: Can the concept of homophily play a crucial role in Hypergraph Neural Networks (HGNNs), similar to its significance in graph-based research? Is there room for improving current hypergraph architectures and methodologies? (e.g. by carefully addressing the specific characteristics of higher-order networks) Do existing datasets provide a meaningful benchmark for HGNNs? Diving into the details, this paper proposes a novel conceptualization of homophily in higher-order networks based on a message passing scheme; this approach harmonizes the analytical frameworks of datasets and architectures, offering a unified perspective for exploring and interpreting complex, higher-order network structures and dynamics. Further, we propose MultiSet, a novel message passing framework that redefines HGNNs by allowing hyperedge-dependent node representations, as well as introduce a novel architecture MultiSetMixer that leverages a new hyperedge sampling strategy. Finally, we provide an extensive set of experiments that contextualize our proposals and lead to valuable insights in hypergraph representation learning.
As machine learning models are increasingly being employed to make consequential decisions in real-world settings, it becomes critical to ensure that individuals who are adversely impacted (e.g., loan denied) by the predictions of these models are provided with a means for recourse. While several approaches have been proposed to construct recourses for affected individuals, the recourses output by these methods either achieve low costs (i.e., ease-of-implementation) or robustness to small perturbations (i.e., noisy implementations of recourses), but not both due to the inherent trade-offs between the recourse costs and robustness. Furthermore, prior approaches do not provide end users with any agency over navigating the aforementioned trade-offs. In this work, we address the above challenges by proposing the first algorithmic framework which enables users to effectively manage the recourse cost vs. robustness trade-offs. More specifically, our framework Probabilistically ROBust rEcourse (\texttt{PROBE}) lets users choose the probability with which a recourse could get invalidated (recourse invalidation rate) if small changes are made to the recourse i.e., the recourse is implemented somewhat noisily. To this end, we propose a novel objective function which simultaneously minimizes the gap between the achieved (resulting) and desired recourse invalidation rates, minimizes recourse costs, and also ensures that the resulting recourse achieves a positive model prediction. We develop novel theoretical results to characterize the recourse invalidation rates corresponding to any given instance w.r.t. different classes of underlying models (e.g., linear models, tree based models etc.), and leverage these results to efficiently optimize the proposed objective. Experimental evaluation with multiple real world datasets demonstrates the efficacy of the proposed framework.
Deep learning models are known to exhibit a strong texture bias, while human tends to rely heavily on global shape for object recognition. The current benchmark for evaluating a model's shape bias is a set of style-transferred images with the assumption that resistance to the attack of style transfer is related to the development of shape sensitivity in the model. In this work, we show that networks trained with style-transfer images indeed learn to ignore style, but its shape bias arises primarily from local shapes. We provide a Distorted Shape Testbench (DiST) as an alternative measurement of global shape sensitivity. Our test includes 2400 original images from ImageNet-1K, each of which is accompanied by two images with the global shapes of the original image distorted while preserving its texture via the texture synthesis program. We found that (1) models that performed well on the previous shape bias evaluation do not fare well in the proposed DiST; (2) the widely adopted ViT models do not show significant advantages over Convolutional Neural Networks (CNNs) on this benchmark despite that ViTs rank higher on the previous shape bias tests. (3) training with DiST images bridges the significant gap between human and existing SOTA models' performance while preserving the models' accuracy on standard image classification tasks; training with DiST images and style-transferred images are complementary, and can be combined to train network together to enhance both the global and local shape sensitivity of the network. Our code will be host at: //github.com/leelabcnbc/DiST
The incredible development of federated learning (FL) has benefited various tasks in the domains of computer vision and natural language processing, and the existing frameworks such as TFF and FATE has made the deployment easy in real-world applications. However, federated graph learning (FGL), even though graph data are prevalent, has not been well supported due to its unique characteristics and requirements. The lack of FGL-related framework increases the efforts for accomplishing reproducible research and deploying in real-world applications. Motivated by such strong demand, in this paper, we first discuss the challenges in creating an easy-to-use FGL package and accordingly present our implemented package FederatedScope-GNN (FS-G), which provides (1) a unified view for modularizing and expressing FGL algorithms; (2) comprehensive DataZoo and ModelZoo for out-of-the-box FGL capability; (3) an efficient model auto-tuning component; and (4) off-the-shelf privacy attack and defense abilities. We validate the effectiveness of FS-G by conducting extensive experiments, which simultaneously gains many valuable insights about FGL for the community. Moreover, we employ FS-G to serve the FGL application in real-world E-commerce scenarios, where the attained improvements indicate great potential business benefits. We publicly release FS-G, as submodules of FederatedScope, at //github.com/alibaba/FederatedScope to promote FGL's research and enable broad applications that would otherwise be infeasible due to the lack of a dedicated package.
While existing work in robust deep learning has focused on small pixel-level $\ell_p$ norm-based perturbations, this may not account for perturbations encountered in several real world settings. In many such cases although test data might not be available, broad specifications about the types of perturbations (such as an unknown degree of rotation) may be known. We consider a setup where robustness is expected over an unseen test domain that is not i.i.d. but deviates from the training domain. While this deviation may not be exactly known, its broad characterization is specified a priori, in terms of attributes. We propose an adversarial training approach which learns to generate new samples so as to maximize exposure of the classifier to the attributes-space, without having access to the data from the test domain. Our adversarial training solves a min-max optimization problem, with the inner maximization generating adversarial perturbations, and the outer minimization finding model parameters by optimizing the loss on adversarial perturbations generated from the inner maximization. We demonstrate the applicability of our approach on three types of naturally occurring perturbations -- object-related shifts, geometric transformations, and common image corruptions. Our approach enables deep neural networks to be robust against a wide range of naturally occurring perturbations. We demonstrate the usefulness of the proposed approach by showing the robustness gains of deep neural networks trained using our adversarial training on MNIST, CIFAR-10, and a new variant of the CLEVR dataset.