6 papers · 1 filter
ORBIT-FMIB: Tracking Order-Resolved Epistatic Information Through ESM-2
Maryam Rahimimovassagh, Ivan Garibay, Niloofar Yousefi
Protein foundation models support mutation-effect and structural prediction, but predictive performance alone does not reveal which forms of biological interaction information rema…
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…
MotifRole-Diff: Risk-Optimal Role-Aware Corruption for Masked Molecular Graph Diffusion
Tasfia Nuzhat Ornee, Elias Hossain, Ivan Garibay +1
Masked discrete diffusion for molecular graph generation typically applies a uniform corruption schedule to all tokens in a lossless graph-to-sequence representation, implicitly tr…
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…
ConRetroBert: EMA Stabilized Dual Encoders for Template-Based Single-Step Retrosynthesis
Mohammad Jahid Ibna Basher, Ali Khodabandeh Yalabadi, Ivan Garibay +1
Template based single step retrosynthesis predicts reactants by selecting and applying an explicit reaction template, making each prediction traceable to a chemical transformation…
When Policies Cannot Be Retrained: A Unified Closed-Form View of Post-Training Steering in Offline Reinforcement Learning
Elias Hossain, Mohammad Jahid Ibna Basher, Ivan Garibay +2
Offline reinforcement learning (RL) can learn effective policies from fixed datasets, but deployment objectives may change after training, and in many applications the trained acto…