Jiansheng Wu

Yueming Yin, Haifeng Hu, Zhen Yang et al.

Computational discovery of ideal lead compounds is a critical process for modern drug discovery. It comprises multiple stages: hit screening, molecular property prediction, and molecule optimization. Current efforts are disparate, involving the establishment of models for each stage, followed by multi-stage multi-model integration. However, this is non-ideal, as clumsy integration of incompatible models increases research overheads, and may even reduce success rates in drug discovery. Facilitating compatibilities requires establishing inherent model consistencies across lead discovery stages. Towards that effect, we propose an open deep graph learning (DGL) based pipeline: generative adversarial feature subspace enhancement (GAFSE), which first unifies the modeling of these stages into one learning framework. GAFSE also offers standardized modular design and streamlined interfaces for future expansions and community support. GAFSE combines adversarial/generative learning, graph attention network, graph reconstruction network, and optimizes the classification/regression loss, adversarial/generative loss, and reconstruction loss simultaneously. Convergence analysis theoretically guarantees model generalization performance. Exhaustive benchmarking demonstrates that the GAFSE pipeline achieves excellent performance across almost all lead discovery stages, while also providing valuable model interpretability. Hence, we believe this tool will enhance the efficiency and productivity of drug discovery researchers.

Fuxiang Sun, Xi Jiang, Jiansheng Wu et al.

Multimodal Large Language Models (MLLMs) show promise for general industrial quality inspection, but fall short in complex scenarios, such as Printed Circuit Board (PCB) inspection. PCB inspection poses unique challenges due to densely packed components, complex wiring structures, and subtle defect patterns that require specialized domain expertise. However, a high-quality, unified vision-language benchmark for quantitatively evaluating MLLMs across PCB inspection tasks remains absent, stemming not only from limited data availability but also from fragmented datasets and inconsistent standardization. To fill this gap, we propose UniPCB, the first unified vision-language benchmark for open-ended PCB quality inspection. UniPCB is built via a systematic pipeline that curates and standardizes data from disparate sources across three annotated scenarios. Furthermore, we introduce PCB-GPT, an MLLM trained on a new instruction dataset generated by this pipeline, utilizing a novel progressive curriculum that mimics the learning process of human experts. Evaluations on the UniPCB benchmark show that while existing MLLMs falter on domain-specific tasks, PCB-GPT establishes a new baseline. Notably, it more than doubles the performance on fine-grained defect localization compared to the strongest competitors, with significant advantages in localization and analysis. We will release the instruction data, benchmark, and model to facilitate future research.

Yiheng Zhu, Mingyang Li, Junlong Liu et al.

Structure-based drug discovery (SBDD) is a systematic scientific process that develops new drugs by leveraging the detailed physical structure of the target protein. Recent advancements in pre-trained models for biomolecules have demonstrated remarkable success across various biochemical applications, including drug discovery and protein engineering. However, in most approaches, the pre-trained models primarily focus on the characteristics of either small molecules or proteins, without delving into their binding interactions which are essential cross-domain relationships pivotal to SBDD. To fill this gap, we propose a general-purpose foundation model named BIT (an abbreviation for Biomolecular Interaction Transformer), which is capable of encoding a range of biochemical entities, including small molecules, proteins, and protein-ligand complexes, as well as various data formats, encompassing both 2D and 3D structures. Specifically, we introduce Mixture-of-Domain-Experts (MoDE) to handle the biomolecules from diverse biochemical domains and Mixture-of-Structure-Experts (MoSE) to capture positional dependencies in the molecular structures. The proposed mixture-of-experts approach enables BIT to achieve both deep fusion and domain-specific encoding, effectively capturing fine-grained molecular interactions within protein-ligand complexes. Then, we perform cross-domain pre-training on the shared Transformer backbone via several unified self-supervised denoising tasks. Experimental results on various benchmarks demonstrate that BIT achieves exceptional performance in downstream tasks, including binding affinity prediction, structure-based virtual screening, and molecular property prediction.