In the expansive realm of drug discovery, with approximately 15,000 known drugs and only around 4,200 approved, the combinatorial nature of the chemical space presents a formidable challenge. While Artificial Intelligence (AI) has emerged as a powerful ally, traditional AI frameworks face significant hurdles. This manuscript introduces CardiGraphormer, a groundbreaking approach that synergizes self-supervised learning (SSL), Graph Neural Networks (GNNs), and Cardinality Preserving Attention to revolutionize drug discovery. CardiGraphormer, a novel combination of Graphormer and Cardinality Preserving Attention, leverages SSL to learn potent molecular representations and employs GNNs to extract molecular fingerprints, enhancing predictive performance and interpretability while reducing computation time. It excels in handling complex data like molecular structures and performs tasks associated with nodes, pairs of nodes, subgraphs, or entire graph structures. CardiGraphormer's potential applications in drug discovery and drug interactions are vast, from identifying new drug targets to predicting drug-to-drug interactions and enabling novel drug discovery. This innovative approach provides an AI-enhanced methodology in drug development, utilizing SSL combined with GNNs to overcome existing limitations and pave the way for a richer exploration of the vast combinatorial chemical space in drug discovery.

翻译：在药物发现的广阔领域中，已知药物约15,000种，而获批准的仅约4,200种，化学空间的组合性质构成了巨大挑战。尽管人工智能（AI）已成为有力助手，但传统AI框架仍面临显著障碍。本文介绍CardGraphormer，一种开创性方法，将自监督学习（SSL）、图神经网络（GNN）与基数保持注意力机制相结合，以革新药物发现。CardGraphormer是Graphormer与基数保持注意力机制的新颖结合，利用SSL学习有效的分子表征，并采用GNN提取分子指纹，从而提升预测性能与可解释性，同时减少计算时间。它在处理分子结构等复杂数据方面表现卓越，可执行与节点、节点对、子图或整个图结构相关的任务。CardGraphormer在药物发现与药物相互作用中的潜在应用极为广泛，涵盖从识别新药物靶点到预测药物间相互作用以及实现新药发现。这种创新方法为药物开发提供了增强型AI方法论，通过利用SSL与GNN相结合来克服现有局限性，为更深入地探索药物发现中庞大的组合化学空间铺平道路。