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May 25

HR-VILAGE-3K3M: A Human Respiratory Viral Immunization Longitudinal Gene Expression Dataset for Systems Immunity

Respiratory viral infections pose a global health burden, yet the cellular immune responses driving protection or pathology remain unclear. Natural infection cohorts often lack pre-exposure baseline data and structured temporal sampling. In contrast, inoculation and vaccination trials generate insightful longitudinal transcriptomic data. However, the scattering of these datasets across platforms, along with inconsistent metadata and preprocessing procedure, hinders AI-driven discovery. To address these challenges, we developed the Human Respiratory Viral Immunization LongitudinAl Gene Expression (HR-VILAGE-3K3M) repository: an AI-ready, rigorously curated dataset that integrates 14,136 RNA-seq profiles from 3,178 subjects across 66 studies encompassing over 2.56 million cells. Spanning vaccination, inoculation, and mixed exposures, the dataset includes microarray, bulk RNA-seq, and single-cell RNA-seq from whole blood, PBMCs, and nasal swabs, sourced from GEO, ImmPort, and ArrayExpress. We harmonized subject-level metadata, standardized outcome measures, applied unified preprocessing pipelines with rigorous quality control, and aligned all data to official gene symbols. To demonstrate the utility of HR-VILAGE-3K3M, we performed predictive modeling of vaccine responders and evaluated batch-effect correction methods. Beyond these initial demonstrations, it supports diverse systems immunology applications and benchmarking of feature selection and transfer learning algorithms. Its scale and heterogeneity also make it ideal for pretraining foundation models of the human immune response and for advancing multimodal learning frameworks. As the largest longitudinal transcriptomic resource for human respiratory viral immunization, it provides an accessible platform for reproducible AI-driven research, accelerating systems immunology and vaccine development against emerging viral threats.

  • 17 authors
·
May 19, 2025

Representation-Aware Unlearning via Activation Signatures: From Suppression to Knowledge-Signature Erasure

Selective knowledge erasure from LLMs is critical for GDPR compliance and model safety, yet current unlearning methods conflate behavioral suppression with true knowledge removal, allowing latent capabilities to persist beneath surface-level refusals. In this work, we address this challenge by introducing Knowledge Immunization Framework (KIF), a representation-aware architecture that distinguishes genuine erasure from obfuscation by targeting internal activation signatures rather than surface outputs. Our approach combines dynamic suppression of subject-specific representations with parameter-efficient adaptation, enabling durable unlearning without full model retraining. KIF achieves near-oracle erasure (FQ approx 0.99 vs. 1.00) while preserving utility at oracle levels (MU = 0.62), effectively breaking the stability-erasure tradeoff that has constrained all prior work. We evaluate both standard foundation models (Llama and Mistral) and reasoning-prior models (Qwen and DeepSeek) across 3B to 14B parameters. Our observation shows that standard models exhibit scale-independent true erasure (<3% utility drift), while reasoning-prior models reveal fundamental architectural divergence. Our comprehensive dual-metric evaluation protocol, combining surface-level leakage with latent trace persistence, operationalizes the obfuscation - erasure distinction and enables the first systematic diagnosis of mechanism-level forgetting behavior across model families and scales.

  • 8 authors
·
Mar 16