Learning to Select Features with Manifold Deep Unfolding PCA

Unsupervised feature selection seeks a compact subset of informative features without access to class labels, making feature utility difficult to define. Existing UFS methods therefore rely on indirect structural criteria, such as similarity preservation, locality, sparsity, cluster geometry, or reconstruction quality. In this paper, we instead study UFS through representation consistency and propose Inverted Contrastive Learning for Unsupervised Feature Selection (ICLFS), a feature-wise contrastive framework that reformulates UFS as a representation learning problem over features rather than samples. ICLFS first inverts the data matrix so that each feature is represented by its sample-profile vector, then constructs multiple masked positive views together with a shuffled negative view, and learns projector-space representations that remain consistent across these structured perturbations under an InfoNCE-based objective. Motivated by recent findings that cosine-based and InfoNCE-based training affect embedding norms, we use projector-space embedding magnitude as the saliency signal for ranking features. The resulting norm-based ranking is subsequently refined through Laplacian-Gated Ranking Correction, which suppresses locally redundant candidates while preserving salient ones. Extensive experiments on 12 benchmark datasets show that ICLFS achieves the best clustering accuracy on 10 datasets against both classical and neural baselines under the standard clustering-based UFS evaluation protocol, while remaining competitive on the other two. These results show that feature-wise contrastive representation consistency provides a strong and effective alternative to neighborhood, cluster, and reconstruction-based UFS formulations.

Unsupervised learning of high-dimensional data is challenging due to irrelevant or noisy features obscuring underlying structures. It's common that only a few features, called the influential features, meaningfully define the clusters. Recovering these influential features is helpful in data interpretation and clustering. We propose i-IF-Learn, an iterative unsupervised framework that jointly performs feature selection and clustering. Our core innovation is an adaptive feature selection statistic that effectively combines pseudo-label supervision with unsupervised signals, dynamically adjusting based on intermediate label reliability to mitigate error propagation common in iterative frameworks. Leveraging low-dimensional embeddings (PCA or Laplacian eigenmaps) followed by $k$-means, i-IF-Learn simultaneously outputs influential feature subset and clustering labels. Numerical experiments on gene microarray and single-cell RNA-seq datasets show that i-IF-Learn significantly surpasses classical and deep clustering baselines. Furthermore, using our selected influential features as preprocessing substantially enhances downstream deep models such as DeepCluster, UMAP, and VAE, highlighting the importance and effectiveness of targeted feature selection. Code is available at: [https://github.com/mc25800852/i_if_learn].

Feature selection is one of the most important and fundamental tasks in data mining, tackled by a family of methods with an established set of evaluation techniques to measure the quality of a specific method. Most of the methods commonly used for the unsupervised evaluation of feature selection algorithms suffer from critical design flaws which question their unsupervised nature. In this paper, we provide a critical discussion on the established allegedly unsupervised evaluation techniques, and shed light on the reasons why they are not truly unsupervised but, at best, supervised evaluation under an unsupervised downstream task. We also propose a novel, truly unsupervised evaluation framework to measure the quality of the feature selection algorithms without any form of information about the labels. The proposed framework utilizes unsupervised Principal Component Analysis, and optimal transport to measure the quality of the feature selection methods in a truly unsupervised manner.