Matthew Scicluna

Andrew J Steindl, João Felipe Rocha, Brian Tshilengi Di Bassinga et al.

High-dimensional point cloud data arise across many scientific domains, especially single-cell biology. The shapes or topologies of these datasets determine the types of information that can be extracted. For example, clustered data supports cell-type identification, trajectory structures support transition analysis, and archetypal structures capture continua of cellular behaviors. Existing analysis pipelines often assume a specific shape. The standard Seurat pipeline combines UMAP visualization with Louvain clustering and therefore assumes clustered data, while tools such as Monocle and SPADE assume tree-like structures, and flow-based models such as MIOFlow and Conditional Flow Matching target trajectories. Choosing which pipeline to apply is therefore often left to bioinformaticians who visually inspect datasets before selecting an analysis strategy. With the rise of agentic AI scientists, automating shape detection is increasingly important for selecting downstream analysis pipelines. To address this problem, we introduce scShapeBench, a benchmark dataset for shape detection containing both synthetic and expert-annotated single-cell datasets. Synthetic datasets are sampled from ground-truth skeleton graphs with controlled variance. Real single-cell datasets are curated from diverse sources and annotated by experts into four categories: clusters, single trajectory, multi-branching, and archetypal. We additionally introduce scReebTower, a baseline method that uses diffusion geometry to extract Reeb graphs and connect visualization with pipeline selection. We provide topology-aware evaluation metrics and compare scReebTower against PAGA and Mapper on synthetic and real data. Our results indicate that scReebTower outperforms existing baselines. Overall, our contributions span benchmarks, evaluation metrics, and a baseline for automated shape detection in single-cell data.

Brady Neal, Sarthak Mittal, Aristide Baratin et al.

The bias-variance tradeoff tells us that as model complexity increases, bias falls and variances increases, leading to a U-shaped test error curve. However, recent empirical results with over-parameterized neural networks are marked by a striking absence of the classic U-shaped test error curve: test error keeps decreasing in wider networks. This suggests that there might not be a bias-variance tradeoff in neural networks with respect to network width, unlike was originally claimed by, e.g., Geman et al. (1992). Motivated by the shaky evidence used to support this claim in neural networks, we measure bias and variance in the modern setting. We find that both bias and variance can decrease as the number of parameters grows. To better understand this, we introduce a new decomposition of the variance to disentangle the effects of optimization and data sampling. We also provide theoretical analysis in a simplified setting that is consistent with our empirical findings.