25 papers
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…
One pool, many targets: a conservation layer and what archival data can identify
Zahra Khodagholi, Niloofar Yousefi
Pairwise guide--transcript scores do not enforce conservation of a finite guide-loaded RISC pool when they are interpreted independently as occupancies. We formulate a differentiab…
Representable but Unlearned: Encoding Rank and the Interaction-Prediction Floor
Zahra Khodagholi, Niloofar Yousefi
Input encodings can restrict which measured contrasts a predictor can jointly reproduce, even when no single contrast is forced to vanish. We compute the attainable contrast space…
Agreement Overstates Evidence: Error Dependence in LLM Judge Consensus
Elias Hossain, Niloofar Yousefi, Ser-Nam Lim
Consensus among LLM judges is often taken as strong evidence that a decision is correct. This assumes that judges make their errors independently. In practice, LLM judges are often…
A Decision-Support Audit Protocol for Supervision Drift in Proxy-Labeled Credit-Risk Prediction
Mehrdad Shoeibi, Muhammad Shabanpour, Waldemar Karwowski +1
Credit-risk models are trained on proxy labels and deployed under temporal and segment change, yet no single transfer metric separates base-rate shift, probability-scale shift, and…
Can We Trust In-Distribution Success? Locked Evaluation Reveals Transfer Failure and Sampling-Depth Entanglement in CRISPRi Perturbation Prediction
Mehrdad Shoeibi, Niloofar Yousefi
AI evaluation can support the wrong inference when an in-domain benchmark success does not survive distribution shift, or when the benchmark endpoint is entangled with a design fac…
Beyond Tokens: Probing Higher-Order Epistasis in Learned Protein Representations
Maryam Rahimimovassagh, Ivan Garibay, Niloofar Yousefi
Protein fitness landscapes contain nonlinear interactions in which mutation effects depend on other residues. We introduce ORBIT, an Order-Resolved Benchmarking of Interaction Tran…
Pre-Registered External Evaluation Yields a Consistent Partial-Replication Category across Three Transcriptomic Foundation Models
Mehrdad Shoeibi, Niloofar Yousefi
Transcriptomic foundation models are increasingly used as reusable cell and gene representations, but validating them on new data under weak supervision and distribution shift is h…
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…
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…
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…
BioDivergence: A Benchmark and Evaluation Framework for Hidden Contextual Contradictions in Biomedical Abstracts
Elias Hossain, Sanjeda Sara Jennifer, Sabera Akter Bushra +1
Biomedical findings often seem to conflict across studies, but many of these differences are context-dependent rather than true contradictions. Variations in cohort, geography, ass…
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…
UAT-LITE: Inference-Time Uncertainty-Aware Attention for Pretrained Transformers
Elias Hossain, Shubhashis Roy Dipta, Subash Neupane +4
Neural NLP models are often miscalibrated and overconfident, assigning high confidence to incorrect predictions and failing to express uncertainty during internal evidence aggregat…
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-…
BIOGEN: Evidence-Grounded Multi-Agent Reasoning Framework for Transcriptomic Interpretation in Antimicrobial Resistance
Elias Hossain, Mehrdad Shoeibi, Ivan Garibay +1
Interpreting gene clusters from RNA sequencing (RNA-seq) remains challenging, especially in antimicrobial resistance studies where mechanistic insight is important for hypothesis g…
Explainable Detection of Implicit Influential Patterns in Conversations via Data Augmentation
Sina Abdidizaji, Md Kowsher, Niloofar Yousefi +1
In the era of digitalization, as individuals increasingly rely on digital platforms for communication and news consumption, various actors employ linguistic strategies to influence…
FlowNIB: An Information Bottleneck Analysis of Bidirectional vs. Unidirectional Language Models
Md Kowsher, Nusrat Jahan Prottasha, Shiyun Xu +4
Bidirectional language models have better context understanding and perform better than unidirectional models on natural language understanding tasks, yet the theoretical reasons b…
BnTTS: Few-Shot Speaker Adaptation in Low-Resource Setting
Mohammad Jahid Ibna Basher, Md Kowsher, Md Saiful Islam +8
This paper introduces BnTTS (Bangla Text-To-Speech), the first framework for Bangla speaker adaptation-based TTS, designed to bridge the gap in Bangla speech synthesis using minima…
Predicting Through Generation: Why Generation Is Better for Prediction
Md Kowsher, Nusrat Jahan Prottasha, Prakash Bhat +6
This paper argues that generating output tokens is more effective than using pooled representations for prediction tasks because token-level generation retains more mutual informat…
Does Self-Attention Need Separate Weights in Transformers?
Md Kowsher, Nusrat Jahan Prottasha, Chun-Nam Yu +2
The success of self-attention lies in its ability to capture long-range dependencies and enhance context understanding, but it is limited by its computational complexity and challe…
LLM-Mixer: Multiscale Mixing in LLMs for Time Series Forecasting
Md Kowsher, Md. Shohanur Islam Sobuj, Nusrat Jahan Prottasha +3
Time series forecasting remains a challenging task, particularly in the context of complex multiscale temporal patterns. This study presents LLM-Mixer, a framework that improves fo…