17 papers
Response Magnitude as a Dominant Signal for Held-Out CRISPRi Perturbation Effect Prediction
Mehrdad Shoeibi, Niloofar Yousefi
Predicting the magnitude of a CRISPRi perturbation's transcriptomic effect on held-out target genes is an important open problem in single-cell biology. Recent work has documented…
BRIDGE: Bottleneck-Aware Regulator-Set Inference and Diagnosis for Cooperative Gene Regulatory Recovery
Maryam Rahimimovassagh, Clayton Thomas Barham, Ivan Garibay +1
Cooperative gene regulation often depends on groups of regulators acting jointly, but most gene regulatory network (GRN) inference methods output pairwise regulator-target rankings…
Adaptive Multi-Expert Graph Transformer for Interpretable EEG-Based Diagnostics
Maryam Rahimimovassagh, Md Elias Hossain, Ivan Garibay +1
Electroencephalographic (EEG) abnormalities arise from dynamic changes in neural synchrony across spatial and temporal scales, yet many computational approaches reduce these dynami…
MedBayes-Lite: A Clinical Uncertainty Governance Layer for Risk-Aware Medical Decision Support
Elias Hossain, Md Mehedi Hasan Nipu, Maleeha Sheikh +5
Clinical language models often assign high confidence to incorrect predictions, particularly in high-severity and out-of-distribution cases. We present MedBayes-Lite, a retraining-…
Right Knowledge, Wrong Answer: Characterizing Parametric Temporal Conflict in Open-Weight Language Models
Elias Hossain, Sourav Saha, Tasfia Nuzhat Ornee +5
Language models may encode both outdated facts and their newer replacements. We introduce Parametric Temporal Conflict (PTC), where the newer fact is present and recoverable, but t…
NEXUS: Structured Runtime Safety for Tool-Using LLM Agents
Elias Hossain, Md Mehedi Hasan Nipu, Tasfia Nuzhat Ornee +2
Tool-using LLM agents increasingly execute high-impact actions, making runtime safety monitoring essential. We present NEXUS (Neural EXecution Utility and Safety), a structured-pla…