arXiv:2607. 19426v2 Announce Type: replace-cross Abstract: Large single-cell datasets are expensive to store, curate, and repeatedly reuse for model training.
arXiv:2607. 19426v1 Announce Type: cross Abstract: Single-cell datasets are increasingly costly to store, audit, and reuse for model training.
arXiv:2608. 00985v1 Announce Type: new Abstract: The rapid growth of single-cell transcriptomic data has enabled the development of foundation models pretrained primarily by reconstructing masked expression values.
CellMSA introduces a novel single‑cell representation learning framework that leverages a multiple‑sequence‑alignment‑inspired context model. For each target cell, it retrieves relevant cells across batches and related cell types, summarizing cross‑cell patterns into a context‑dependent gene‑pair representation that is fed into a pair‑aware encoder. Pretraining on a massive human single‑cell corpus (≈109 million cells) and subsequent benchmarks demonstrate consistent performance gains over existing methods.
arXiv:2607. 04987v1 Announce Type: new Abstract: Cell-type deconvolution, the task of estimating the proportions of constituent cell types in a heterogeneous biological sample, is a core problem in computational biology.
arXiv:2607. 29043v1 Announce Type: cross Abstract: Single-cell RNA sequencing (scRNA-seq) has become an essential tool in modern cellular biology, and generating accurate synthetic scRNA-seq data is becoming increasingly important.
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.
arXiv:2609.09863v1 Announce Type: new Abstract: Choosing a deep learning architecture for label-free single-cell classification remains an open question, with microscopy benchmarks reporting conflict...
arXiv:2606. 07760v1 Announce Type: new Abstract: Understanding cellular phenotypes and how they respond to perturbations is critical for disease biology and therapeutic design.
The paper introduces scTrilemma, a latent-bottleneck variational autoencoder designed to address the representation trilemma in single‑cell RNA‑seq data: preserving biological identity and state, remaining robust to nuisance context, and retaining gene‑level variation for expression analysis. scTrilemma routes expression‑derived variation to the embedding, decoder, or prior, gating gene tokens by expression and conditioning the prior on unlabeled pseudo‑bulk context, all under a single reconstruction objective without target annotations. In zero‑shot evaluations on successive CZ CELLxGENE Census releases, scTrilemma simultaneously satisfies all three demands, maintaining biological state, differential‑expression, and pathway structure across multiple disease settings, and latent interventions show context can be removed with minimal impact on other demands.
arXiv:2607. 27712v1 Announce Type: new Abstract: Standard masked-language-model fine-tuning applies a uniform masking probability across every token position, assuming reconstruction difficulty is position-agnostic.
arXiv:2607. 14070v1 Announce Type: cross Abstract: Genomic foundation models such as Evo 2 learn rich sequence representations, but their value for biosecurity screening is largely unexplored.
arXiv:2606. 27752v1 Announce Type: new Abstract: Single-cell perturbation models can reduce costly wet-lab screening by predicting how cells respond transcriptionally to interventions.