Subject clustering (i.e., the use of measured features to cluster subjects, such as patients or cells, into multiple groups) is a problem of great interest. In recent years, many approaches were proposed, among which unsupervised deep learning (UDL) has received a great deal of attention. Two interesting questions are (a) how to combine the strengths of UDL and other approaches, and (b) how these approaches compare to one other. We combine Variational Auto-Encoder (VAE), a popular UDL approach, with the recent idea of Influential Feature PCA (IF-PCA), and propose IF-VAE as a new method for subject clustering. We study IF-VAE and compare it with several other methods (including IF-PCA, VAE, Seurat, and SC3) on $10$ gene microarray data sets and $8$ single-cell RNA-seq data sets. We find that IF-VAE significantly improves over VAE, but still underperforms IF-PCA. We also find that IF-PCA is quite competitive, which slightly outperforms Seurat and SC3 over the $8$ single-cell data sets. IF-PCA is conceptually simple and permits delicate analysis. We demonstrate that IF-PCA is capable of achieving the phase transition in a Rare/Weak model. Comparatively, Seurat and SC3 are more complex and theoretically difficult to analyze (for these reasons, their optimality remains unclear).
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This paper presents the design and development of an Anderson Accelerated Preconditioned Modified Hermitian and Skew-Hermitian Splitting (AA-PMHSS) method for solving complex-symmetric linear systems with application to electromagnetics problems, such as wave scattering and eddy currents. While it has been shown that the Anderson Acceleration of real linear systems is essentially equivalent to GMRES, we show here that the formulation using Anderson acceleration leads to a more performant method. We show relatively good robustness compared to existing preconditioned GMRES methods and significantly better performance due to the faster evaluation of the preconditioner. In particular, AA-PMHSS can be applied to solve problems and equations arising from electromagnetics, such as time-harmonic eddy current simulations discretized with the Finite Element Method. We also evaluate three test systems present in previous literature. We show that the method is competitive with two types of preconditioned GMRES. One of the significant advantages of these methods is that the convergence rate is independent of the discretization size.
In high-dimensional generalized linear models, it is crucial to identify a sparse model that adequately accounts for response variation. Although the best subset section has been widely regarded as the Holy Grail of problems of this type, achieving either computational efficiency or statistical guarantees is challenging. In this article, we intend to surmount this obstacle by utilizing a fast algorithm to select the best subset with high certainty. We proposed and illustrated an algorithm for best subset recovery in regularity conditions. Under mild conditions, the computational complexity of our algorithm scales polynomially with sample size and dimension. In addition to demonstrating the statistical properties of our method, extensive numerical experiments reveal that it outperforms existing methods for variable selection and coefficient estimation. The runtime analysis shows that our implementation achieves approximately a fourfold speedup compared to popular variable selection toolkits like glmnet and ncvreg.
In recent years, there has been a growing interest in understanding complex microstructures and their effect on macroscopic properties. In general, it is difficult to derive an effective constitutive law for such microstructures with reasonable accuracy and meaningful parameters. One numerical approach to bridge the scales is computational homogenization, in which a microscopic problem is solved at every macroscopic point, essentially replacing the effective constitutive model. Such approaches are, however, computationally expensive and typically infeasible in multi-query contexts such as optimization and material design. To render these analyses tractable, surrogate models that can accurately approximate and accelerate the microscopic problem over a large design space of shapes, material and loading parameters are required. In previous works, such models were constructed in a data-driven manner using methods such as Neural Networks (NN) or Gaussian Process Regression (GPR). However, these approaches currently suffer from issues, such as need for large amounts of training data, lack of physics, and considerable extrapolation errors. In this work, we develop a reduced order model based on Proper Orthogonal Decomposition (POD), Empirical Cubature Method (ECM) and a geometrical transformation method with the following key features: (i) large shape variations of the microstructure are captured, (ii) only relatively small amounts of training data are necessary, and (iii) highly non-linear history-dependent behaviors are treated. The proposed framework is tested and examined in two numerical examples, involving two scales and large geometrical variations. In both cases, high speed-ups and accuracies are achieved while observing good extrapolation behavior.
Pattern discovery is a machine learning technique that aims to find sets of items, subsequences, or substructures that are present in a dataset with a higher frequency value than a manually set threshold. This process helps to identify recurring patterns or relationships within the data, allowing for valuable insights and knowledge extraction. In this work, we propose Information Gained Subgroup Discovery (IGSD), a new SD algorithm for pattern discovery that combines Information Gain (IG) and Odds Ratio (OR) as a multi-criteria for pattern selection. The algorithm tries to tackle some limitations of state-of-the-art SD algorithms like the need for fine-tuning of key parameters for each dataset, usage of a single pattern search criteria set by hand, usage of non-overlapping data structures for subgroup space exploration, and the impossibility to search for patterns by fixing some relevant dataset variables. Thus, we compare the performance of IGSD with two state-of-the-art SD algorithms: FSSD and SSD++. Eleven datasets are assessed using these algorithms. For the performance evaluation, we also propose to complement standard SD measures with IG, OR, and p-value. Obtained results show that FSSD and SSD++ algorithms provide less reliable patterns and reduced sets of patterns than IGSD algorithm for all datasets considered. Additionally, IGSD provides better OR values than FSSD and SSD++, stating a higher dependence between patterns and targets. Moreover, patterns obtained for one of the datasets used, have been validated by a group of domain experts. Thus, patterns provided by IGSD show better agreement with experts than patterns obtained by FSSD and SSD++ algorithms. These results demonstrate the suitability of the IGSD as a method for pattern discovery and suggest that the inclusion of non-standard SD metrics allows to better evaluate discovered patterns.
Persistent homology is a methodology central to topological data analysis that extracts and summarizes the topological features within a dataset as a persistence diagram; it has recently gained much popularity from its myriad successful applications to many domains. However, its algebraic construction induces a metric space of persistence diagrams with a highly complex geometry. In this paper, we prove convergence of the $k$-means clustering algorithm on persistence diagram space and establish theoretical properties of the solution to the optimization problem in the Karush--Kuhn--Tucker framework. Additionally, we perform numerical experiments on various representations of persistent homology, including embeddings of persistence diagrams as well as diagrams themselves and their generalizations as persistence measures; we find that clustering performance directly on persistence diagrams and measures outperform their vectorized representations.
Gender inequity is one of the biggest challenges facing the STEM workforce. While there are many studies that look into gender disparities within STEM and academia, the majority of these have been designed and executed by those unfamiliar with research in sociology and gender studies. They adopt a normative view of gender as a binary choice of 'male' or 'female,' leaving individuals whose genders do not fit within that model out of such research entirely. This especially impacts those experiencing multiple axes of marginalization, such as race, disability, and socioeconomic status. For STEM fields to recruit and retain members of historically excluded groups, a new paradigm must be developed. Here, we collate a new dataset of the methods used in 119 past studies of gender equity, and recommend better survey practices and institutional policies based on a more complex and accurate approach to gender. We find that problematic approaches to gender in surveys can be classified into 5 main themes - treating gender as white, observable, discrete, as a statistic, and as inconsequential. We recommend allowing self-reporting of gender and never automating gender assignment within research. This work identifies the key areas of development for studies of gender-based inclusion within STEM, and provides recommended solutions to support the methodological uplift required for this work to be both scientifically sound and fully inclusive.
The research detailed in this paper scrutinizes Principal Component Analysis (PCA), a seminal method employed in statistics and machine learning for the purpose of reducing data dimensionality. Singular Value Decomposition (SVD) is often employed as the primary means for computing PCA, a process that indispensably includes the step of centering - the subtraction of the mean location from the data set. In our study, we delve into a detailed exploration of the influence of this critical yet often ignored or downplayed data centering step. Our research meticulously investigates the conditions under which two PCA embeddings, one derived from SVD with centering and the other without, can be viewed as aligned. As part of this exploration, we analyze the relationship between the first singular vector and the mean direction, subsequently linking this observation to the congruity between two SVDs of centered and uncentered matrices. Furthermore, we explore the potential implications arising from the absence of centering in the context of performing PCA via SVD from a spectral analysis standpoint. Our investigation emphasizes the importance of a comprehensive understanding and acknowledgment of the subtleties involved in the computation of PCA. As such, we believe this paper offers a crucial contribution to the nuanced understanding of this foundational statistical method and stands as a valuable addition to the academic literature in the field of statistics.
Artificial Intelligence (AI) and its applications have sparked extraordinary interest in recent years. This achievement can be ascribed in part to advances in AI subfields including Machine Learning (ML), Computer Vision (CV), and Natural Language Processing (NLP). Deep learning, a sub-field of machine learning that employs artificial neural network concepts, has enabled the most rapid growth in these domains. The integration of vision and language has sparked a lot of attention as a result of this. The tasks have been created in such a way that they properly exemplify the concepts of deep learning. In this review paper, we provide a thorough and an extensive review of the state of the arts approaches, key models design principles and discuss existing datasets, methods, their problem formulation and evaluation measures for VQA and Visual reasoning tasks to understand vision and language representation learning. We also present some potential future paths in this field of research, with the hope that our study may generate new ideas and novel approaches to handle existing difficulties and develop new applications.
Small data challenges have emerged in many learning problems, since the success of deep neural networks often relies on the availability of a huge amount of labeled data that is expensive to collect. To address it, many efforts have been made on training complex models with small data in an unsupervised and semi-supervised fashion. In this paper, we will review the recent progresses on these two major categories of methods. A wide spectrum of small data models will be categorized in a big picture, where we will show how they interplay with each other to motivate explorations of new ideas. We will review the criteria of learning the transformation equivariant, disentangled, self-supervised and semi-supervised representations, which underpin the foundations of recent developments. Many instantiations of unsupervised and semi-supervised generative models have been developed on the basis of these criteria, greatly expanding the territory of existing autoencoders, generative adversarial nets (GANs) and other deep networks by exploring the distribution of unlabeled data for more powerful representations. While we focus on the unsupervised and semi-supervised methods, we will also provide a broader review of other emerging topics, from unsupervised and semi-supervised domain adaptation to the fundamental roles of transformation equivariance and invariance in training a wide spectrum of deep networks. It is impossible for us to write an exclusive encyclopedia to include all related works. Instead, we aim at exploring the main ideas, principles and methods in this area to reveal where we are heading on the journey towards addressing the small data challenges in this big data era.
With the rapid increase of large-scale, real-world datasets, it becomes critical to address the problem of long-tailed data distribution (i.e., a few classes account for most of the data, while most classes are under-represented). Existing solutions typically adopt class re-balancing strategies such as re-sampling and re-weighting based on the number of observations for each class. In this work, we argue that as the number of samples increases, the additional benefit of a newly added data point will diminish. We introduce a novel theoretical framework to measure data overlap by associating with each sample a small neighboring region rather than a single point. The effective number of samples is defined as the volume of samples and can be calculated by a simple formula $(1-\beta^{n})/(1-\beta)$, where $n$ is the number of samples and $\beta \in [0,1)$ is a hyperparameter. We design a re-weighting scheme that uses the effective number of samples for each class to re-balance the loss, thereby yielding a class-balanced loss. Comprehensive experiments are conducted on artificially induced long-tailed CIFAR datasets and large-scale datasets including ImageNet and iNaturalist. Our results show that when trained with the proposed class-balanced loss, the network is able to achieve significant performance gains on long-tailed datasets.
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