arXiv subjects

Wenda Wang

Publications and source records attributed to Wenda Wang.

8 recordsLinked to original sources

arXiv2026

AbFlow : End-to-end Paratope-Centric Antibody Design by Interaction Enhanced Flow Matching

Antigen-antibody binding is a critical process in the immune response. Although recent progress has advanced antibody design, current methods lack a generative framework for end-to-end modeling of full-atom antibody structures and struggle to fully exploit antigen-specific geometric information for optimizing local binding interfaces and global structures. To overcome these limitations, we introduce AbFlow, a paratope-restricted one-step flow-matching framework for designing full-atom antibodies end-to-end. AbFlow incorporates an extended velocity field network featuring an equivariant Surface Multi-channel Encoder, which uses surface-level antigen interaction data to refine the antibody structure, particularly the CDR-H3 region. Extensive experiments in paratope-centric antibody design, multi-CDRs and full-atom antibody design, binding affinity optimization, and complex structure prediction show that AbFlow produces superior antigen-antibody complexes, especially at the contact interface, and markedly improves the binding affinity of generated antibodies.

q-bio.QM↗

arXiv2026

MolSight: A Graph-Aware Vision-Language Model for Unified Chemical Image Understanding

Using molecular large language models (LLMs) as a unified framework for understanding molecular structures and functions is emerging as a new trend in tasks such as molecular design and drug discovery. However, these models struggle to fully capture the visual representation of molecular structures, limiting their potential. While existing molecular vision-language models (VLMs) show promise, they still face challenges in structural alignment and lack the necessary topological modeling for accurate molecular understanding. To address this, we propose MolSight, a graph-aware vision-language model framework designed to enhance the understanding of molecular images by VLMs. MolSight integrates a Molecular Topology Module to inject chemical-bond adjacency information into vision tokens, and a Molecular Grounding Module to align visual features with chemical symbolic semantics. Our experiments demonstrate that MolSight significantly outperforms existing VLMs, molecular LLMs, and task-specific models across multiple chemical visual understanding tasks, achieving a new level of molecular image reasoning in complex chemical scenarios.

cs.CV↗

arXiv2026

Back to Basics: Improving Molecular Understanding in LLMs via SMILES-Graph Translation

Recent advances in molecular large language models have led to strong performance on molecular understanding and generation tasks, yet these gains often come without reliable structural grounding. In particular, existing approaches conflict with the chemistry principle that structure determines function: despite their downstream success, current molecular LLMs perform poorly on basic structure recognition, suggesting that they fail to capture molecular graphs from canonical SMILES. To remedy this, we propose MolBasic, a structure-first framework that strengthens structural comprehension via SMILES-Graph translation. MolBasic is built around a multi-level structure perception benchmark, where bidirectional SMILES-Graph conversion serves as the core task to align sequential and topological representations. On top of this foundation, we employ a progressive learning scheme with a standardized Chain-of-Thought (CoT) to steer models from structure acquisition toward higher-level molecular reasoning. Experiments show that MolBasic substantially improves structural understanding and yields robust gains on downstream tasks, including property prediction and objective optimization, supporting our structure-first paradigm.

cs.LG↗

arXiv2026

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval

Identifying enzymes that catalyze target biochemical reactions is a key step in computational enzyme discovery and biocatalyst design. Recent representation-learning methods formulate this problem as enzyme--reaction matching, where paired enzymes and reactions are embedded into a shared space. However, most existing approaches primarily rely on pairwise enzyme--reaction supervision and make limited use of the relationships within reaction sets or enzyme families. This work introduces a multi-alignment contrastive learning framework for biochemical retrieval. The framework jointly models cross-domain compatibility between enzymes and reactions and within-domain relationships induced by functional annotations. In addition, a Gromov--Wasserstein-inspired regularization objective encourages geometric consistency between the learned enzyme and reaction representation spaces. By combining pairwise catalytic supervision with higher-order relational alignment, the model captures both direct enzyme--reaction associations and broader functional organization. We evaluate the approach on enzyme virtual screening and bidirectional enzyme--reaction retrieval tasks. Experiments on EnzymeMap show improved early-recognition performance under BEDROC and enrichment-factor metrics compared with strong contrastive baselines. On ReactZyme, the method achieves consistent gains across time-based, enzyme-similarity, and reaction-similarity splits, demonstrating robustness to unseen enzymes and unseen reactions. Ablation studies further indicate that within-domain alignment, functional supervision, and the geometric regularization term each contribute to the observed improvements. These results suggest that modeling multiple forms of alignment can improve contrastive retrieval models for enzyme discovery, reaction annotation, and related computational biology applications.

q-bio.BM↗

arXiv2026

Sketch2MinSurf: Vision-Language Guided Generation of Editable Minimal Surfaces from Hand-Drawn Sketches

Converting hand-drawn sketches into structured 3D geometries remains challenging due to the difficulty of representing non-Euclidean surfaces and maintaining topological consistency. Existing generative models such as GANs, NeRFs, and diffusion architectures often fail to produce editable manifolds directly usable in downstream design workflows. We present Sketch2MinSurf, a hybrid vision-language and geometric optimization framework that integrates vision-language guidance with minimal-surface theory to generate smooth and editable 3D surfaces from hand-drawn sketches. The core of our approach is a spatial-topological encoding that represents geometry as tuples of node coordinates and real/virtual edge skeletons, enabling stable topological control during generation. We further introduce the Sketch2MinSurf Structural Loss (S2MS-Loss), a reward-modulated objective that jointly constrains geometric reconstruction and topological coherence. On a test set of 100 sketches, Sketch2MinSurf achieves a topological similarity score of 0.844, outperforming existing sketch-to-shape baselines. The generated manifolds are directly editable and free from non-manifold artifacts. A public art installation at a university showcases the method's potential for human-intent-driven 3D form generation. The dataset and code are available at https://anonymous.4open.science/r/Sketch2MinSurf/.

cs.CV↗

arXiv2026

ArchSIBench: Benchmarking the Architectural Spatial Intelligence of Vision-Language Models

Architectural spatial intelligence, the ability to recognize and infer architectural space, is fundamental to tasks such as robot navigation, embodied interaction, and 3D scene understanding and generation. Although extensive research has evaluated the basic spatial skills of Vision-Language Models (VLMs) such as relative orientation, distance comparison, and object counting, these tasks cover only the most elementary levels of spatial cognition and largely overlook higher-level cognition of architectural space, including layout understanding, circulation patterns, and functional zoning. In this work, we present ArchSIBench, a Benchmark for Architectural Spatial Intelligence based on the perspectives from architecture, cognitive science, and psychology. ArchSIBench covers five core dimensions: perception, reasoning, navigation, transformation, and configuration, comprising 17 fine-grained subtasks. Through careful manual annotation by experts with architectural backgrounds, we construct 3,000 question-answer pairs to enable comprehensive evaluation of architectural spatial intelligence. Based on ArchSIBench, we evaluate various VLMs and find that the architectural spatial intelligence of most models shows significant differences from human baselines; additionally, models exhibit substantial variability across capability dimensions. Some state-of-the-art models can approach the level of human evaluators without architectural training. However, a clear gap remains compared to human evaluators with architectural training, particularly in spatial transformation and configuration reasoning. We believe that ArchSIBench will provide important insights and systematic resources for measuring and advancing the architectural spatial intelligence of VLMs. The dataset and code are available at https://huggingface.co/datasets/ArchSIBench/ArchSIBench.

cs.CV↗

arXiv2024

DCI: An Accurate Quality Assessment Criteria for Protein Complex Structure Models

The structure of proteins is the basis for studying protein function and drug design. The emergence of AlphaFold 2 has greatly promoted the prediction of protein 3D structures, and it is of great significance to give an overall and accurate evaluation of the predicted models, especially the complex models. Among the existing methods for evaluating multimer structures, DockQ is the most commonly used. However, as a more suitable metric for complex docking, DockQ cannot provide a unique and accurate evaluation in the non-docking situation. Therefore, it is necessary to propose an evaluation strategy that can directly evaluate the whole complex without limitation and achieve good results. In this work, we proposed DCI score, a new evaluation strategy for protein complex structure models, which only bases on distance map and CI (contact-interface) map, DCI focuses on the prediction accuracy of the contact interface based on the overall evaluation of complex structure, is not inferior to DockQ in the evaluation accuracy according to CAPRI classification, and is able to handle the non-docking situation better than DockQ. Besides, we calculated DCI score on CASP datasets and compared it with CASP official assessment, which obtained good results. In addition, we found that DCI can better evaluate the overall structure deviation caused by interface prediction errors in the case of multi-chains. Our DCI is available at \url{https://gitee.com/WendaWang/DCI-score.git}, and the online-server is available at \url{http://mialab.ruc.edu.cn/DCIServer/}.

q-bio.BM↗

arXiv2017

Learning from Simulated and Unsupervised Images through Adversarial Training

With recent progress in graphics, it has become more tractable to train models on synthetic images, potentially avoiding the need for expensive annotations. However, learning from synthetic images may not achieve the desired performance due to a gap between synthetic and real image distributions. To reduce this gap, we propose Simulated+Unsupervised (S+U) learning, where the task is to learn a model to improve the realism of a simulator's output using unlabeled real data, while preserving the annotation information from the simulator. We develop a method for S+U learning that uses an adversarial network similar to Generative Adversarial Networks (GANs), but with synthetic images as inputs instead of random vectors. We make several key modifications to the standard GAN algorithm to preserve annotations, avoid artifacts, and stabilize training: (i) a 'self-regularization' term, (ii) a local adversarial loss, and (iii) updating the discriminator using a history of refined images. We show that this enables generation of highly realistic images, which we demonstrate both qualitatively and with a user study. We quantitatively evaluate the generated images by training models for gaze estimation and hand pose estimation. We show a significant improvement over using synthetic images, and achieve state-of-the-art results on the MPIIGaze dataset without any labeled real data.

cs.CV↗