Yanhao Zhu

Jiahao Chen, Letian Gao, Yanhao Zhu et al.

Recent advances in generative modeling have enabled significant progress in structure-based drug design (SBDD). Existing methods typically condition molecule generation on empty binding pockets from holo complexes, overlooking informative components such as the filler (ligands and solvent). Here, we leverage low-resolution electron density (ED) derived from the filler as a physically grounded condition for \textit{de novo} drug design. We consider two types of ED, calculated and cryo-EM/X-ray, obtainable from computational or experimental sources, supporting unified pre-training and experimental integration. Compared with rigid pocket representations, experimental ED naturally captures conformational flexibility and provides a more faithful description of the binding environment. Based on this, we introduce EDMolGPT, a decoder-only autoregressive framework that generates molecules from low-resolution ED point clouds. By grounding generation in physically meaningful density signals, EDMolGPT mitigates structural bias and produces molecules with 3D conformations. Evaluations on 101 biological targets verify the effectiveness. Our project page: https://jiahaochen1.github.io/EDMolGPT_Page/.

Wei Feng, Lvwei Wang, Zaiyun Lin et al.

Generative models for molecules based on sequential line notation (e.g. SMILES) or graph representation have attracted an increasing interest in the field of structure-based drug design, but they struggle to capture important 3D spatial interactions and often produce undesirable molecular structures. To address these challenges, we introduce Lingo3DMol, a pocket-based 3D molecule generation method that combines language models and geometric deep learning technology. A new molecular representation, fragment-based SMILES with local and global coordinates, was developed to assist the model in learning molecular topologies and atomic spatial positions. Additionally, we trained a separate noncovalent interaction predictor to provide essential binding pattern information for the generative model. Lingo3DMol can efficiently traverse drug-like chemical spaces, preventing the formation of unusual structures. The Directory of Useful Decoys-Enhanced (DUD-E) dataset was used for evaluation. Lingo3DMol outperformed state-of-the-art methods in terms of drug-likeness, synthetic accessibility, pocket binding mode, and molecule generation speed.

Junjun Hu, Yanhao Zhu, Bo Zhao et al.

One of the challenges of logo recognition lies in the diversity of forms, such as symbols, texts or a combination of both; further, logos tend to be extremely concise in design while similar in appearance, suggesting the difficulty of learning discriminative representations. To investigate the variety and representation of logo, we introduced Makeup216, the largest and most complex logo dataset in the field of makeup, captured from the real world. It comprises of 216 logos and 157 brands, including 10,019 images and 37,018 annotated logo objects. In addition, we found that the marginal background around the pure logo can provide a important context information and proposed an adversarial attention representation framework (AAR) to attend on the logo subject and auxiliary marginal background separately, which can be combined for better representation. Our proposed framework achieved competitive results on Makeup216 and another large-scale open logo dataset, which could provide fresh thinking for logo recognition. The dataset of Makeup216 and the code of the proposed framework will be released soon.

Yanhao Zhu, Zhineng Chen, Shuai Zhao et al.

Nowadays U-net-like FCNs predominate various biomedical image segmentation applications and attain promising performance, largely due to their elegant architectures, e.g., symmetric contracting and expansive paths as well as lateral skip-connections. It remains a research direction to devise novel architectures to further benefit the segmentation. In this paper, we develop an ACE-net that aims to enhance the feature representation and utilization by augmenting the contracting and expansive paths. In particular, we augment the paths by the recently proposed advanced techniques including ASPP, dense connection and deep supervision mechanisms, and novel connections such as directly connecting the raw image to the expansive side. With these augmentations, ACE-net can utilize features from multiple sources, scales and reception fields to segment while still maintains a relative simple architecture. Experiments on two typical biomedical segmentation tasks validate its effectiveness, where highly competitive results are obtained in both tasks while ACE-net still runs fast at inference.