8 papers
Stable-Shift: Biologically Structured Prediction of Transcriptional Responses to Unseen Gene Perturbations
Sajib Acharjee Dip, Liqing Zhang
Predicting transcriptional responses to genetic perturbations could reduce the experimental burden of functional genomics, but extrapolation to genes that were never perturbed duri…
Think Again or Think Longer? Selective Verification for Budget-Aware Reasoning
Sajib Acharjee Dip, Dawei Zhou, Liqing Zhang
Test-time reasoning is increasingly used as a serving-time control knob, but extra reasoning is not uniformly valuable: it can repair failed attempts, waste compute on already-corr…
BenSyc: Benchmarking Conversational Sycophancy and Human Alignment in LLMs for Bengali Contexts
Kazi Noshin, Sajib Acharjee Dip, Ranat Das Prangon +4
Large language models (LLMs) increasingly participate in emotionally sensitive social conversations, where responses may shift from balanced support toward excessive validation or…
PlantMarkerBench: A Multi-Species Benchmark for Evidence-Grounded Plant Marker Reasoning
Sajib Acharjee Dip, Song Li, Liqing Zhang
Cell-type-specific marker genes are fundamental to plant biology, yet existing resources primarily rely on curated databases or high-throughput studies without explicitly modeling…
LLM4Cell: A Survey of Large Language and Agentic Models for Single-Cell Biology
Sajib Acharjee Dip, Adrika Zafor, Bikash Kumar Paul +4
Large language models (LLMs) and emerging agentic frameworks are beginning to transform single-cell biology by enabling natural-language reasoning, generative annotation, and multi…
CFM-GP: Unified Conditional Flow Matching to Learn Gene Perturbation Across Cell Types
Abrar Rahman Abir, Sajib Acharjee Dip, Liqing Zhang
Understanding gene perturbation effects across diverse cellular contexts is a central challenge in functional genomics, with important implications for therapeutic discovery and pr…