Ruqi Zhang
Publications
SE(3)-MeanFlow: Few-Step Protein Backbone Generation on Lie Groups
Generative modeling of protein backbones promises the de novo design of proteins with prescribed structural and functional properties. Existing diffusion and flow-matching models produce high-quality backbones on SE(3)^N, but inference requires numerically integrating an ODE over hundreds of network evaluations, each involving a Lie group exponential map - a bottleneck for high-throughput design campaigns. We introduce SE(3)-MeanFlow, a few-step generative framework that extends MeanFlow from Euclidean space to the Lie group geometry of protein frames. Working natively in the Lie algebra so(3) and in R^3, we derive closed-form average-velocity identities for rotations and translations, giving simulation-free training targets. We further introduce an SE(3) alpha-Flow objective that removes the Jacobian-vector product from the rotation branch and serves as a warm-up stage, after which training switches to a small-t stabilized MeanFlow loss that is used for the remainder of pretraining and for rectification-based post-training. In protein backbone generation, SE(3)-MeanFlow matches or exceeds flow-matching baselines that use several times more sampling steps, and its advantage widens in the few-step regime, where rectification lets it lead at every matched budget - at a modest cost in diversity.
Learning From Developers: Towards Reliable Patch Validation at Scale for Linux
Patch reviewing is critical for software development, especially in distributed open-source development, which highly depends on voluntary work, such as Linux. This paper studies the past 10 years of patch reviews of the Linux memory management subsystem to characterize the challenges involved in patch reviewing at scale. Our study reveals that the review process is still primarily reliant on human effort despite a wide-range of automatic checking tools. Although kernel developers strive to review all patch proposals, they struggle to keep up with the increasing volume of submissions and depend significantly on a few developers for these reviews. To help scale the patch review process, we introduce FLINT, a patch validation system framework that synthesizes insights from past discussions among developers and automatically analyzes patch proposals for compliance. FLINT employs a rule-based analysis informed by past discussions among developers and an LLM that does not require training or fine-tuning on new data, and can continuously improve with minimum human effort. FLINT uses a multi-stage approach to efficiently distill the essential information from past discussions. Later, when a patch proposal needs review, FLINT retrieves the relevant validation rules for validation and generates a reference-backed report that developers can easily interpret and validate. FLINT targets bugs that traditional tools find hard to detect, ranging from maintainability issues, e.g., design choices and naming conventions, to complex concurrency issues, e.g., deadlocks and data races. FLINT detected 2 new issues in Linux v6.18 development cycle and 7 issues in previous versions. FLINT achieves 21% and 14% of higher ground-truth coverage on concurrency bugs than the baseline with LLM only. Moreover, FLINT achieves a 35% false positive rate, which is lower than the baseline.