arXiv:2607. 19426v1 Announce Type: cross Abstract: Single-cell datasets are increasingly costly to store, audit, and reuse for model training.
arXiv:2607. 19426v2 Announce Type: replace-cross Abstract: Large single-cell datasets are expensive to store, curate, and repeatedly reuse for model training.
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: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.
The study evaluates whether a portfolio of compact, semantically named descriptor blocks can match the performance of a 2048‑dimensional CheMeleon embedding in low‑data molecular assays. Using a fixed 11‑dimensional physicochemical base and greedily adding provenance‑screened blocks, the portfolio achieves a mean test AUC of 0.762 across nine ADME/Tox assays, comparable to CheMeleon’s 0.764 and better than Mordred’s 0.756. The results meet a predeclared pooled parity threshold but not all per‑assay thresholds, and further analysis confirms the competitiveness of the auditable representation while highlighting unresolved assay‑level differences.
arXiv:2602. 00423v3 Announce Type: replace Abstract: Single-cell integration workflows often construct low-dimensional cell embeddings and then refine them with post-hoc methods to reduce batch effects.
TopU-LBVS is a new multi‑target benchmark for ligand‑based virtual screening that addresses shortcomings of existing datasets by using hard‑negative decoys and a fixed 1:40 active‑to‑decoy ratio. It covers 93 protein targets across seven classes, provides three evaluation protocols (full, low‑data, and mini), and includes curated ChEMBL‑35 bioactivity data with property‑matched, structurally similar decoys. The benchmark demonstrates that performance drops sharply when moving from random‑decoy to hard‑negative evaluation, and it releases data, splits, code, and baseline implementations for reproducible comparison.
arXiv:2607. 17671v1 Announce Type: new Abstract: Large-scale single-cell perturbation atlases make it possible to ask an inverse question: given an observed transcriptional response, which annotated targets and compounds in a fixed library are most consistent with that response?
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:2512. 22240v5 Announce Type: replace-cross Abstract: Machine learning models are primarily judged by predictive performance, especially in applied genomics, where explanations are read as biological findings.
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.
TopU-LBVS is a new multi‑target benchmark for ligand‑based virtual screening that addresses shortcomings of previous datasets by using hard‑negative decoys and a fixed 1:40 active‑to‑decoy ratio. It covers 93 protein targets across seven classes, provides three evaluation protocols (full, low‑data, and mini), and includes curated ChEMBL‑35 bioactivity data with property‑matched, structurally similar decoys to reduce shortcut learning. The benchmark comes with released data, fixed splits, evaluation code, and baseline implementations for reproducible comparison of LBVS and molecular representation methods.
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.