arXiv:2602.19455v1 Announce Type: cross Abstract: Time-series diagnostic reasoning is essential for many applications, yet existing solutions face a persistent gap: general reasoning large language models (GRLMs) possess strong reasoning skills but lack the domain-specific knowledge to understand complex time-series patterns. Conversely, fine-tuned time-series LLMs (TSLMs) understand these patterns but lack the capacity to generalize reasoning for more complicated questions. To bridge this gap, we propose a hybrid knowledge-injection framework that injects TSLM-generated insights directly into GRLM's reasoning trace, thereby achieving strong time-series reasoning with in-domain knowledge. As collecting data for knowledge injection fine-tuning is costly, we further leverage a reinforcement learning-based approach with verifiable rewards (RLVR) to elicit knowledge-rich traces without human supervision, then transfer such an in-domain thinking trace into GRLM for efficient knowledge injection. We further release SenTSR-Bench, a multivariate time-series-based diagnostic reasoning benchmark collected from real-world industrial operations. Across SenTSR-Bench and other public datasets, our method consistently surpasses TSLMs by 9.1%-26.1% and GRLMs by 7.9%-22.4%, delivering robust, context-aware time-series diagnostic insights.

arXiv:2602.19685v1 Announce Type: cross Abstract: Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot be observed both before and after a perturbation. Thus, perturbation prediction requires mapping unpaired control and perturbed populations. Existing models address this by learning maps between distributions, but typically assume a single fixed response distribution when conditioned on observed cellular context (e.g., cell type) and the perturbation type. In reality, responses vary systematically due to unobservable latent factors such as microenvironmental fluctuations and complex batch effects, forming a manifold of possible distributions for the same observed conditions. To account for this variability, we introduce PerturbDiff, which shifts modeling from individual cells to entire distributions. By embedding distributions as points in a Hilbert space, we define a diffusion-based generative process operating directly over probability distributions. This allows PerturbDiff to capture population-level response shifts across hidden factors. Benchmarks on established datasets show that PerturbDiff achieves state-of-the-art performance in single-cell response prediction and generalizes substantially better to unseen perturbations. See our project page (https://katarinayuan.github.io/PerturbDiff-ProjectPage/), where code and data will be made publicly available (https://github.com/DeepGraphLearning/PerturbDiff).