arXiv Machine Learning

Score Distributions, Not Cells: Evaluating Single-Cell Perturbations Under Class Overlap

arXiv:2607. 04595v1 Announce Type: new Abstract: Most classification problems assume the classes are roughly separable, so that an individual sample can usually be assigned to one class.

arXiv Machine Learning
Sep 22

Rethinking Class Imbalance for Single-Cell Foundation Models: A Systematic Benchmark Across Architectures and Long-Tail Loss Functions

The paper benchmarks six long‑tail loss functions—cross‑entropy, weighted CE, class‑balanced loss, focal loss, LDAM, and logit‑adjusted softmax—across three single‑cell foundation model architectures (scGPT, scBERT, Geneformer) and three datasets (Multiple Sclerosis, Zheng68K, human Pancreas). It shows that overall accuracy masks systematic failures on rare, disease‑relevant cell types, with a consistent gap between overall accuracy, Macro‑F1, and rare‑class recall under plain cross‑entropy. The study identifies two distinct regimes of rare‑class failure, predicts reweighting efficacy by absolute training‑set size, and finds class‑balanced loss and LDAM to be the most reliable across all settings.

By Zeyu Dong, Jiahui Zhong
arXiv Machine Learning
Sep 11

When do cheap embeddings beat protein language models? A theoretically-grounded hashing sketch for biological sequence classification

The paper introduces Murmur2Vec, a lightweight, alignment‑free embedding that uses k‑mer counts hashed with MurmurHash to create a compact representation for biological sequences. It provides a full theoretical analysis, including bias/variance formulas, a Johnson–Lindenstrauss‑style concentration bound, and an excess‑risk bound that clarifies the trade‑off between hash‑table size and classifier performance. Empirically, Murmur2Vec matches or surpasses a fine‑tuned 650M‑parameter ESM‑2 protein language model across several classification tasks, including SARS‑CoV‑2 spike lineage and HIV‑1 Env subtype identification.

By Sarwan Ali, Taslim Murad, Imdadullah Khan, Safi Faizullah
arXiv Machine Learning
Jun 18

Not Just How Much, But Where: Decomposing Epistemic Uncertainty into Per-Class Contributions

arXiv:2602. 21160v3 Announce Type: replace-cross Abstract: In safety-critical classification, the cost of failure is often asymmetric, yet Bayesian deep learning summarises epistemic uncertainty with a single scalar, mutual information (MI), that cannot distinguish whether a model's ignorance involves a benign or safety-critical class.

By Mame Diarra Toure, David A. Stephens