arXiv:2510.16082v5 Announce Type: replace-cross Abstract: Interpreting gene clusters from RNA sequencing (RNA-seq) remains challenging, especially in antimicrobial resistance studies where mechanistic insight is important for hypothesis generation. Existing pathway enrichment methods can summarize co-expressed modules, but they often provide limited cluster-specific explanations and weak connections to supporting literature. We present BIOGEN, an evidence-grounded multi-agent framework for post hoc interpretation of RNA-seq transcriptional modules. BIOGEN combines biomedical retrieval, structured reasoning, and multi-critic verification to generate traceable cluster-level explanations with explicit evidence and confidence labels. On a primary Salmonella enterica dataset, BIOGEN achieved strong biological grounding, including BERTScore 0.689, Semantic Alignment Score 0.715, KEGG Functional Similarity 0.342, and a hallucination rate of 0.000, compared with 0.100 for an LLM-only baseline. Across four additional bacterial RNA-seq datasets, BIOGEN also maintained zero hallucination under the same fixed pipeline. In comparisons with representative open-source agentic AI baselines, BIOGEN was the only framework that consistently preserved zero hallucination across all five datasets. These findings suggest that retrieval alone is not enough for reliable biological interpretation, and that evidence-grounded orchestration is important for transparent and source-traceable transcriptomic reasoning.

arXiv:2511.16625v2 Announce Type: replace Abstract: We propose MedBayes-Lite, a lightweight Bayesian enhancement for transformer-based clinical language models that improves reliability through uncertainty-aware prediction. The framework operates without retraining, architectural modification, or additional trainable parameters, and integrates three components: Bayesian Embedding Calibration via Monte Carlo dropout, Uncertainty-Weighted Attention for reliability-aware token aggregation, and Confidence-Guided Decision Shaping for abstention under uncertainty. Across MedQA, PubMedQA, and MIMIC-III, MedBayes-Lite improves calibration and trustworthiness, reducing overconfidence by 32--48\%. In simulated clinical settings, it further supports safer decision-making by flagging uncertain predictions for human review, particularly under distribution shift. For closed API models, the framework remains applicable through sampling-based predictive uncertainty and confidence-guided abstention, while full embedding- and attention-level uncertainty propagation is evaluated on open-weight transformer models.