Low-dimensional embeddings are widely used as visual summaries of high-dimensional data and to enable downstream scientific discoveries. Yet, popular nonlinear dimension reduction methods, such as t-SNE and UMAP, are often selected based on visual appeal alone and without rigorous quantitative validation. A major reason is that manifold embeddings typically do not provide an out-of-sample map nor an inverse back to the original feature space; this makes held-out validation, the gold standard in supervised learning, all but impossible. To address these challenges, we develop a novel framework, MEDAL (Manifold Embedding Distillation via Autoencoder Learning), which distills a fitted manifold embedding into a reusable encoder--decoder model. MEDAL trains a constrained autoencoder whose bottleneck exactly matches any teacher embedding while the decoder reconstructs the original input; this yields an explicit map for new samples, an approximate inverse, and a pointwise reconstruction-based measure of distortion in the manifold space. This converts static manifold embeddings into models that can be evaluated on held-out data, enabling quantitative validation including comparing different dimension reduction methods as well as hyperparameter tuning. Across multiple benchmark and scientific case studies, we show that MEDAL enables held-out validation to determine optimal manifold embeddings and hyperparameters, reveals biologically coherent regions that are difficult to preserve in two dimensional embeddings, and detects distribution shift when new samples are mapped into a fixed reference manifold. MEDAL provides a general validation wrapper to any existing dimension reduction technique that will improve the rigor and

Single-cell RNA-seq data analysis typically requires representations that capture heterogeneous local structure across multiple scales while remaining stable and interpretable. In this work, we propose a hierarchical sheaf spectral embedding (HSSE) framework that constructs informative cell-level features based on persistent sheaf Laplacian analysis. Starting from scale-dependent low-dimensional embeddings, we define cell-centered local neighborhoods at multiple resolutions. For each local neighborhood, we construct a data-driven cellular sheaf that encodes local relationships among cells. We then compute persistent sheaf Laplacians over sampled filtration intervals and extract spectral statistics that summarize the evolution of local relational structure across scales. These spectral descriptors are aggregated into a unified feature vector for each cell and can be directly used in downstream learning tasks without additional model training. We evaluate HSSE on twelve benchmark single-cell RNA-seq datasets covering diverse biological systems and data scales. Under a consistent classification protocol, HSSE achieves competitive or improved performance compared with existing multiscale and classical embedding-based methods across multiple evaluation metrics. The results demonstrate that sheaf spectral representations provide a robust and interpretable approach for single-cell RNA-seq data representation learning.

To reduce annotation costs, it is common in crowdsourcing to collect only a few noisy labels from different crowd workers for each instance. However, the limited noisy labels restrict the performance of label integration algorithms in inferring the unknown true label for the instance. Recent works have shown that leveraging neighbor instances can help alleviate this problem. Yet, these works all assume that each instance has the same neighborhood size, which defies common sense. To address this gap, we propose a novel label integration algorithm called K-free nearest neighbor (KFNN). In KFNN, the neighborhood size of each instance is automatically determined based on its attributes and noisy labels.

The success of graph neural networks (GNNs) largely relies on the process of aggregating information from neighbors defined by the input graph structures. Notably, message passing based GNNs, e.g., graph convolutional networks, leverage the immediate neighbors of each node during the aggregation process, and recently, graph diffusion convolution (GDC) is proposed to expand the propagation neighborhood by leveraging generalized graph diffusion. However, the neighborhood size in GDC is manually tuned for each graph by conducting grid search over the validation set, making its generalization practically limited. To address this issue, we propose the adaptive diffusion convolution (ADC) strategy to automatically learn the optimal neighborhood size from the data. Furthermore, we break the conventional assumption that all GNN layers and feature channels (dimensions) should use the same neighborhood for propagation. We design strategies to enable ADC to learn a dedicated propagation neighborhood for each GNN layer and each feature channel, making the GNN architecture fully coupled with graph structures---the unique property that differs GNNs from traditional neural networks. By directly plugging ADC into existing GNNs, we observe consistent and significant outperformance over both GDC and their vanilla versions across various datasets, demonstrating the improved model capacity brought by automatically learning unique neighborhood size per layer and per channel in GNNs.