arXiv subjects

Zhihui Qi

Publications and source records attributed to Zhihui Qi.

4 recordsLinked to original sources

arXiv2026

VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design

Protein design aims to compose amino-acid sequences that fold into stable three-dimensional structures while satisfying targeted functional properties. The field is increasingly shifting toward vibe protein design, where a single model is expected to generate novel sequences, engineer existing proteins, and reason about protein characteristics through flexible natural-language constraints. Large language models (LLMs) have emerged as a leading paradigm in this space. However, existing evaluation benchmarks often limit their scope to a partial aspect of protein design, while others restrict design objectives to structured input schemas, lacking an integrated framework that evaluates the broad spectrum of protein design competence under open-ended intents. To this end, we present Vibe Protein design Benchmark (VibeProteinBench), a language-interfaced benchmark that probes generalist capabilities through three complementary stages mirroring a computational protein design workflow: recognition, engineering, and generation. Each stage is grounded in expert-curated mechanistic rationales and multi-faceted in silico validation, to computationally verify whether model outputs are biologically plausible. Evaluations across diverse general-purpose and domain-specialized LLMs reveal that no model achieves strong performance across all three stages, suggesting that generalist protein design remains a substantial open challenge for current LLMs.

q-bio.QM↗

arXiv2025

ScholarSearch: Benchmarking Scholar Searching Ability of LLMs

Large Language Models (LLMs)' search capabilities have garnered significant attention. Existing benchmarks, such as OpenAI's BrowseComp, primarily focus on general search scenarios and fail to adequately address the specific demands of academic search. These demands include deeper literature tracing and organization, professional support for academic databases, the ability to navigate long-tail academic knowledge, and ensuring academic rigor. Here, we proposed ScholarSearch, the first dataset specifically designed to evaluate the complex information retrieval capabilities of Large Language Models (LLMs) in academic research. ScholarSearch possesses the following key characteristics: Academic Practicality, where question content closely mirrors real academic learning and research environments, avoiding deliberately misleading models; High Difficulty, with answers that are challenging for single models (e.g., Grok DeepSearch or Gemini Deep Research) to provide directly, often requiring at least three deep searches to derive; Concise Evaluation, where limiting conditions ensure answers are as unique as possible, accompanied by clear sources and brief solution explanations, greatly facilitating subsequent audit and verification, surpassing the current lack of analyzed search datasets both domestically and internationally; and Broad Coverage, as the dataset spans at least 15 different academic disciplines. Through ScholarSearch, we expect to more precisely measure and promote the performance improvement of LLMs in complex academic information retrieval tasks. The data is available at: https://huggingface.co/datasets/PKU-DS-LAB/ScholarSearch

cs.IR↗

arXiv2025

Point2Quad: Generating Quad Meshes from Point Clouds via Face Prediction

Quad meshes are essential in geometric modeling and computational mechanics. Although learning-based methods for triangle mesh demonstrate considerable advancements, quad mesh generation remains less explored due to the challenge of ensuring coplanarity, convexity, and quad-only meshes. In this paper, we present Point2Quad, the first learning-based method for quad-only mesh generation from point clouds. The key idea is learning to identify quad mesh with fused pointwise and facewise features. Specifically, Point2Quad begins with a k-NN-based candidate generation considering the coplanarity and squareness. Then, two encoders are followed to extract geometric and topological features that address the challenge of quad-related constraints, especially by combining in-depth quadrilaterals-specific characteristics. Subsequently, the extracted features are fused to train the classifier with a designed compound loss. The final results are derived after the refinement by a quad-specific post-processing. Extensive experiments on both clear and noise data demonstrate the effectiveness and superiority of Point2Quad, compared to baseline methods under comprehensive metrics.

cs.CV↗

arXiv2022

Two improvements of the foliation based quad meshing method

Quadrilateral meshes with high level structure and feature preserving property benefit industrial applications the most. Generation of such quad mesh remains a challenge. Quad meshes generated using surface foliation have the highest level structure, however they lack of the feature preserving ability. In this paper, we analyze the boundary curvature with Gauss-Bonnet theorem to determine whether a boundary rectangle corner preserving foliation based method exists. When it exists, we adopt a modified double cover technique together with surface foliation method to generate a corner feature preserving quad mesh. The experiments demonstrate the efficacy of our algorithm.

cs.CG↗