arXiv:2606. 08816v1 Announce Type: cross Abstract: Predicting the effect of an unseen gene knockout perturbation on transcriptomic gene expression remains a highly challenging problem for virtual cell models.
arXiv:2606. 01042v1 Announce Type: cross Abstract: Perturbation experiments are central to understanding cellular mechanisms, but remain costly and sparse, motivating prediction of gene expression responses for unobserved conditions.
arXiv:2608. 16419v1 Announce Type: cross Abstract: Large language models can describe mechanisms, yet scalable post-training still depends on costly, manually curated biological reasoning traces.
arXiv:2607. 18777v1 Announce Type: new Abstract: Evaluating machine learning in scientific domains requires separating correct predictions from correct reasons under realistic distribution shifts.
arXiv:2608. 12906v1 Announce Type: cross Abstract: RNA-Protein Interactions (RPIs) are critical for regulating cellular functions.
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.
The paper proposes a three‑stage training pipeline that begins with procedural pretraining on abstract, procedurally generated data, followed by molecular pretraining on SMILES, and finally downstream fine‑tuning for molecular property prediction. Experiments show that procedural pretraining improves downstream performance—e.g., a 4.8% error reduction on Lipophilicity—especially when labeled data are scarce, and that the benefit peaks at an intermediate procedural training budget. Analysis indicates that transferable knowledge resides mainly in attention layers, while feed‑forward layers may over‑specialize.
The paper introduces LitEm, a neural regression model that allows transductive knowledge graph embedding models to predict numerical attributes. LitEm achieves top or near‑top performance on most attributes across datasets such as FB15K‑237, YAGO15K, DB15K, and Mutagenesis. A co‑training framework further improves link prediction for bilinear models while enabling them to predict numerical attributes, demonstrating literal‑aware encoding of attribute information.
arXiv:2606. 08147v1 Announce Type: cross Abstract: DNA cis-regulatory elements (CREs) such as enhancers control gene expression levels.
arXiv:2608. 05928v1 Announce Type: new Abstract: Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes.
arXiv:2603. 10395v2 Announce Type: replace Abstract: Graph generation is a fundamental task with broad applications, such as drug discovery.
arXiv:2602. 07832v3 Announce Type: replace-cross Abstract: Process rewards have been widely used in deep reinforcement learning to improve training efficiency, reduce variance, and prevent reward hacking.
arXiv:2609.06779v1 Announce Type: cross Abstract: Drug repurposing aims to identify new therapeutic uses for existing compounds and, compared with de novo drug discovery, offers a faster and more cos...