skscope: Fast Sparsity-Constrained Optimization in Python

Applying iterative solvers on sparsity-constrained optimization (SCO) requires tedious mathematical deduction and careful programming/debugging that hinders these solvers' broad impact. In the paper, the library skscope is introduced to overcome such an obstacle. With skscope, users can solve the SCO by just programming the objective function. The convenience of skscope is demonstrated through two examples in the paper, where sparse linear regression and trend filtering are addressed with just four lines of code. More importantly, skscope's efficient implementation allows state-of-the-art solvers to quickly attain the sparse solution regardless of the high dimensionality of parameter space. Numerical experiments reveal the available solvers in skscope can achieve up to 80x speedup on the competing relaxation solutions obtained via the benchmarked convex solver. skscope is published on the Python Package Index (PyPI) and Conda, and its source code is available at: https://github.com/abess-team/skscope.

A Consistent and Scalable Algorithm for Best Subset Selection in Single Index Models

Analysis of high-dimensional data has led to increased interest in both single index models (SIMs) and best subset selection. SIMs provide an interpretable and flexible modeling framework for high-dimensional data, while best subset selection aims to find a sparse model from a large set of predictors. However, best subset selection in high-dimensional models is known to be computationally intractable. Existing methods tend to relax the selection, but do not yield the best subset solution. In this paper, we directly tackle the intractability by proposing the first provably scalable algorithm for best subset selection in high-dimensional SIMs. Our algorithmic solution enjoys the subset selection consistency and has the oracle property with a high probability. The algorithm comprises a generalized information criterion to determine the support size of the regression coefficients, eliminating the model selection tuning. Moreover, our method does not assume an error distribution or a specific link function and hence is flexible to apply. Extensive simulation results demonstrate that our method is not only computationally efficient but also able to exactly recover the best subset in various settings (e.g., linear regression, Poisson regression, heteroscedastic models).

Best-Subset Selection in Generalized Linear Models: A Fast and Consistent Algorithm via Splicing Technique

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.

Simultaneous Best Subset Selection and Dimension Reduction via Primal-Dual Iterations

Sparse reduced rank regression is an essential statistical learning method. In the contemporary literature, estimation is typically formulated as a nonconvex optimization that often yields to a local optimum in numerical computation. Yet, their theoretical analysis is always centered on the global optimum, resulting in a discrepancy between the statistical guarantee and the numerical computation. In this research, we offer a new algorithm to address the problem and establish an almost optimal rate for the algorithmic solution. We also demonstrate that the algorithm achieves the estimation with a polynomial number of iterations. In addition, we present a generalized information criterion to simultaneously ensure the consistency of support set recovery and rank estimation. Under the proposed criterion, we show that our algorithm can achieve the oracle reduced rank estimation with a significant probability. The numerical studies and an application in the ovarian cancer genetic data demonstrate the effectiveness and scalability of our approach.

Best Subset Selection in Reduced Rank Regression

Sparse reduced rank regression is an essential statistical learning method. In the contemporary literature, estimation is typically formulated as a nonconvex optimization that often yields to a local optimum in numerical computation. Yet, their theoretical analysis is always centered on the global optimum, resulting in a discrepancy between the statistical guarantee and the numerical computation. In this research, we offer a new algorithm to address the problem and establish an almost optimal rate for the algorithmic solution. We also demonstrate that the algorithm achieves the estimation with a polynomial number of iterations. In addition, we present a generalized information criterion to simultaneously ensure the consistency of support set recovery and rank estimation. Under the proposed criterion, we show that our algorithm can achieve the oracle reduced rank estimation with a significant probability. The numerical studies and an application in the ovarian cancer genetic data demonstrate the effectiveness and scalability of our approach.

Interpretable travel distance on the county-wise COVID-19 by sequence to sequence with attention

Background: Travel restrictions as a means of intervention in the COVID-19 epidemic have reduced the spread of outbreaks using epidemiological models. We introduce the attention module in the sequencing model to assess the effects of the different classes of travel distances. Objective: To establish a direct relationship between the number of travelers for various travel distances and the COVID-19 trajectories. To improve the prediction performance of sequencing model. Setting: Counties from all over the United States. Participants: New confirmed cases and deaths have been reported in 3158 counties across the United States. Measurements: Outcomes included new confirmed cases and deaths in the 30 days preceding November 13, 2021. The daily number of trips taken by the population for various classes of travel distances and the geographical information of infected counties are assessed. Results: There is a spatial pattern of various classes of travel distances across the country. The varying geographical effects of the number of people travelling for different distances on the epidemic spread are demonstrated. Limitation: We examined data up to November 13, 2021, and the weights of each class of travel distances may change accordingly as the data evolves. Conclusion: Given the weights of people taking trips for various classes of travel distances, the epidemics could be mitigated by reducing the corresponding class of travellers.

abess: A Fast Best Subset Selection Library in Python and R

We introduce a new library named abess that implements a unified framework of best-subset selection for solving diverse machine learning problems, e.g., linear regression, classification, and principal component analysis. Particularly, the abess certifiably gets the optimal solution within polynomial times under the linear model. Our efficient implementation allows abess to attain the solution of best-subset selection problems as fast as or even 100x faster than existing competing variable (model) selection toolboxes. Furthermore, it supports common variants like best group subset selection and $\ell_2$ regularized best-subset selection. The core of the library is programmed in C++. For ease of use, a Python library is designed for conveniently integrating with scikit-learn, and it can be installed from the Python library Index. In addition, a user-friendly R library is available at the Comprehensive R Archive Network. The source code is available at: https://github.com/abess-team/abess.

Certifiably Polynomial Algorithm for Best Group Subset Selection

Best group subset selection aims to choose a small part of non-overlapping groups to achieve the best interpretability on the response variable. It is practically attractive for group variable selection; however, due to the computational intractability in high dimensionality setting, it doesn't catch enough attention. To fill the blank of efficient algorithms for best group subset selection, in this paper, we propose a group-splicing algorithm that iteratively detects effective groups and excludes the helpless ones. Moreover, coupled with a novel Bayesian group information criterion, an adaptive algorithm is developed to determine the true group subset size. It is certifiable that our algorithms enable identifying the optimal group subset in polynomial time under mild conditions. We demonstrate the efficiency and accuracy of our proposal by comparing state-of-the-art algorithms on both synthetic and real-world datasets.

Computational analysis of pathological image enables interpretable prediction for microsatellite instability

Microsatellite instability (MSI) is associated with several tumor types and its status has become increasingly vital in guiding patient treatment decisions. However, in clinical practice, distinguishing MSI from its counterpart is challenging since the diagnosis of MSI requires additional genetic or immunohistochemical tests. In this study, interpretable pathological image analysis strategies are established to help medical experts to automatically identify MSI. The strategies only require ubiquitous Haematoxylin and eosin-stained whole-slide images and can achieve decent performance in the three cohorts collected from The Cancer Genome Atlas. The strategies provide interpretability in two aspects. On the one hand, the image-level interpretability is achieved by generating localization heat maps of important regions based on the deep learning network; on the other hand, the feature-level interpretability is attained through feature importance and pathological feature interaction analysis. More interestingly, both from the image-level and feature-level interpretability, color features and texture characteristics are shown to contribute the most to the MSI predictions. Therefore, the classification models under the proposed strategies can not only serve as an efficient tool for predicting the MSI status of patients, but also provide more insights to pathologists with clinical understanding.

A Fast and Effective Method of Macula Automatic Detection for Retina Images

Retina image processing is one of the crucial and popular topics of medical image processing. The macula fovea is responsible for sharp central vision, which is necessary for human behaviors where visual detail is of primary importance, such as reading, writing, driving, etc. This paper proposes a novel method to locate the macula through a series of morphological processing. On the premise of maintaining high accuracy, our approach is simpler and faster than others. Furthermore, for the hospital's real images, our method is also able to detect the macula robustly.