8 papers · ranked by Valyu relevance
Jackie Rao, Muntadher Jihad, Giulia Biffi, Paul D.W. Kirk
Identifying cell types from single-cell RNA sequencing (scRNA-seq) data typically requires several separate and often uninterpretable steps: dimensionality reduction, batch-correction, clustering, marker-gene identification and the discovery of finer-grained structure. Here we introduce scFLAME (single-cell Factor…
Shanti Prasad Khanal, Chitra Bahadur Budhathoki, Bhimsen Devkota, Shyam Krishna Maharjan + 1 more
Background: Evidence indicates a lack of school-based interventions targeting adolescents' health literacy. To date, no structured, theory-driven, Delphi-guided health literacy intervention has been designed for Nepalese adolescents. Objective: This study aims to report the systematic development of a context-specific…
Francesco Carli, Polina Rusina, Lun Ai, Leonie Küchenhoff + 7 more
Language models and agents are increasingly used in biomedicine, but current benchmarks reward correct answers even when the underlying reasoning is flawed. Here we introduce Karenina, an open-source framework that turns expert knowledge into multi-dimensional evaluations of questions, conversations and autonomous…
Jennifer E. Harris, Emma Rice, Carolyn Lowry, Estelle Couradeau + 1 more
Mixing plant functional groups can boost plant productivity, but the underlying rhizosphere microbial dynamics remain unclear. We tested when to expect divergence from additive expectations by measuring plant traits and active and total rhizosphere microbiomes (via BONCAT-FACS and 16S rRNA gene amplicon sequencing) in…
Xiaoqian Dong, Nandan Chen, Cuilan Dong, Xingxing Wang + 5 more
Internal consistency was estimated using Cronbach’s α coefficient, while reproducibility was examined through split-half reliability and test-retest reliability . Following recent methodological recommendations, recognizing the limitations of Cronbach’s α (e.g., tau-equivalence assumption) , we further evaluated the…
Linsui Deng, Kejun He, Xianyang Zhang
Mendelian randomization (MR) has been widely used to infer causal relationships between exposures and outcomes in epidemiological studies. However, classical MR assumptions can be violated when genetic variants are associated with outcomes through pathways other than the exposure, leading to uncorrelated and/or…
Amélie Barozet, Vincent Cabeli, Jean Ogier du Terrail, Alexey Rukhovich + 6 more
The development of climate-resilient crops would be greatly accelerated by models able to reason directly over plant genomic sequences and to pinpoint trait-associated regions or loci. Anticipating the impact of DNA base changes (variants) remains challenging, and understanding regulatory mechanisms is still an active…
Abdullah İyigün, Göker Yurdakul, Alper Dünki, Mehmet Ali Yayla
4.1### Rank-Order Alignment and the Limits of Categorical Agreement The moderate-to-strong Spearman correlations confirm that the rank ordering of item endorsement by these models is broadly consistent with that of the expert panel, and this is consistent with prior evaluations of language models against clinical…