scHelix: Asymmetric Dual-Stream Integration via Explicit Gene-Level Disentanglement

A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest heterogeneously across genes, most existing methods process the transcriptome uniformly, frequently resulting in over-correction and loss of subtle biological signals. To address this, we present scHelix, a dataset-adaptive framework that fundamentally changes how features are processed by explicitly partitioning genes into domain-invariant Anchors and domain-sensitive Variants at the input level. scHelix utilizes a dual-stream sparse diffusion encoder equipped with stop-gradient graph caching to efficiently learn multi-scale structural representations. The core of our approach is a novel asymmetric Align-Refine-Fuse protocol: the unstable Variant stream is first aligned to the robust topology of the Anchor stream, followed by a conservative refinement phase where the Anchor stream absorbs denoised details via bounded residual gating. This divide-and-conquer architecture prevents shortcut learning and ensures robust batch removal without compromising the integrity of biological clusters. Extensive benchmarking demonstrates that scHelix outperforms state-of-the-art methods.

Classroom Final Exam: An Instructor-Tested Reasoning Benchmark

We introduce \CFE{} (\textbf{C}lassroom \textbf{F}inal \textbf{E}xam), a multimodal benchmark for evaluating the reasoning capabilities of large language models across more than 20 STEM domains. \CFE{} is curated from repeatedly used, authentic university homework and exam problems, together with reference solutions provided by course instructors. \CFE{} presents a significant challenge even for frontier models: the newly released Gemini-3.1-pro-preview achieves an overall accuracy of 59.69\%, while the second-best model, Gemini-3-flash-preview, reaches 55.46\%, leaving considerable room for improvement. Beyond leaderboard results, we perform a diagnostic analysis by decomposing reference solutions into reasoning flows. We find that although frontier models can often answer intermediate sub-questions correctly, they struggle to reliably derive and maintain correct intermediate states throughout multi-step solutions. We further observe that model-generated solutions typically have more reasoning steps than those provided by the instructor, indicating suboptimal step efficiency and a higher risk of error accumulation. The data and code are available at https://github.com/Analogy-AI/CFE_Bench.