Kangyu Zheng

Kangyu Zheng, Yingzhou Lu, Zaixi Zhang et al.

Currently, the field of structure-based drug design is dominated by three main types of algorithms: search-based algorithms, deep generative models, and reinforcement learning. While existing works have typically focused on comparing models within a single algorithmic category, cross-algorithm comparisons remain scarce. In this paper, to fill the gap, we establish a benchmark to evaluate the performance of sixteen models across these different algorithmic foundations by assessing the pharmaceutical properties of the generated molecules and their docking affinities with specified target proteins. We highlight the unique advantages of each algorithmic approach and offer recommendations for the design of future SBDD models. We emphasize that 1D/2D ligand-centric drug design methods can be used in SBDD by treating the docking function as a black-box oracle, which is typically neglected. The empirical results show that 1D/2D methods achieve competitive performance compared with 3D-based methods that use the 3D structure of the target protein explicitly. Also, AutoGrow4, a 2D molecular graph-based genetic algorithm, dominates SBDD in terms of optimization ability. The relevant code is available in https://github.com/zkysfls/2024-sbdd-benchmark.

Kangyu Zheng, Tianfan Fu, Zhiding Liang

The biomedical field is beginning to explore the use of quantum machine learning (QML) for tasks traditionally handled by classical machine learning, especially in predicting ADME (absorption, distribution, metabolism, and excretion) properties, which are essential in drug evaluation. However, ADME tasks pose unique challenges for existing quantum computing systems (QCS) frameworks, as they involve both classification with unbalanced dataset and regression problems. These dual requirements make it necessary to adapt and refine current QCS frameworks to effectively address the complexities of ADME predictions. We propose a novel training-free scoring mechanism to evaluate QML circuit performance on imbalanced classification and regression tasks. Our mechanism demonstrates significant correlation between scoring metrics and test performance on imbalanced classification tasks. Additionally, we develop methods to quantify continuous similarity relationships between quantum states, enabling performance prediction for regression tasks. This represents the first comprehensive approach to searching and evaluating QCS circuits specifically for regression applications. Validation on representative ADME tasks-one imbalanced classification and one regression-demonstrates moderate positive correlation between our scoring metrics and circuit performance, significantly outperforming baseline scoring methods that show negligible correlation.

Che Liu, Zhongwei Wan, Yuqi Wang et al.

Automatic radiology report generation holds significant potential to streamline the labor-intensive process of report writing by radiologists, particularly for 3D radiographs such as CT scans. While CT scans are critical for clinical diagnostics, they remain less explored compared to 2D radiographs. To date, there has been no comprehensive benchmark for 3D radiograph report generation (3DRRG), nor sufficient investigation into the optimal training strategies for Vision Language Models (VLMs) in this context, particularly with respect to vision encoder choices, visual token compression, and model scaling. In this work, we make three key contributions. We curate **CT-3DRRG**, the largest **publicly** available 3D CT-report dataset, establishing a robust and diverse benchmark for evaluating VLM performance on 3DRRG. Furthermore, we propose a comprehensive training recipe for building high-performing VLMs for 3DRRG, exploring key factors such as vision encoder pretraining strategies, visual token compression, and the impact of data & model scale. Guided by these findings, we introduce **Argus**, a state-of-the-art family of VLMs that achieve superior performance across different model sizes and input 3D medical image resolutions, efficiently processing high-resolution 3D images up to $512 \times 512 \times 256$[^1].