Empowering AI drug discovery with explicit and implicit knowledge

Motivation: Recently, research on independently utilizing either explicit knowledge from knowledge graphs or implicit knowledge from biomedical literature for AI drug discovery has been growing rapidly. These approaches have greatly improved the prediction accuracy of AI models on multiple downstream tasks. However, integrating explicit and implicit knowledge independently hinders their understanding of molecules. Results: We propose DeepEIK, a unified deep learning framework that incorporates both explicit and implicit knowledge for AI drug discovery. We adopt feature fusion to process the multi-modal inputs, and leverage the attention mechanism to denoise the text information. Experiments show that DeepEIK significantly outperforms state-of-the-art methods on crucial tasks in AI drug discovery including drug-target interaction prediction, drug property prediction and protein-protein interaction prediction. Further studies show that benefiting from explicit and implicit knowledge, our framework achieves a deeper understanding of molecules and shows promising potential in facilitating drug discovery applications.

DAIR-V2X: A Large-Scale Dataset for Vehicle-Infrastructure Cooperative 3D Object Detection

Autonomous driving faces great safety challenges for a lack of global perspective and the limitation of long-range perception capabilities. It has been widely agreed that vehicle-infrastructure cooperation is required to achieve Level 5 autonomy. However, there is still NO dataset from real scenarios available for computer vision researchers to work on vehicle-infrastructure cooperation-related problems. To accelerate computer vision research and innovation for Vehicle-Infrastructure Cooperative Autonomous Driving (VICAD), we release DAIR-V2X Dataset, which is the first large-scale, multi-modality, multi-view dataset from real scenarios for VICAD. DAIR-V2X comprises 71254 LiDAR frames and 71254 Camera frames, and all frames are captured from real scenes with 3D annotations. The Vehicle-Infrastructure Cooperative 3D Object Detection problem (VIC3D) is introduced, formulating the problem of collaboratively locating and identifying 3D objects using sensory inputs from both vehicle and infrastructure. In addition to solving traditional 3D object detection problems, the solution of VIC3D needs to consider the temporal asynchrony problem between vehicle and infrastructure sensors and the data transmission cost between them. Furthermore, we propose Time Compensation Late Fusion (TCLF), a late fusion framework for the VIC3D task as a benchmark based on DAIR-V2X. Find data, code, and more up-to-date information at https://thudair.baai.ac.cn/index and https://github.com/AIR-THU/DAIR-V2X.

CogDL: An Extensive Toolkit for Deep Learning on Graphs

Graph representation learning aims to learn low-dimensional node embeddings for graphs. It is used in several real-world applications such as social network analysis and large-scale recommender systems. In this paper, we introduce CogDL, an extensive research toolkit for deep learning on graphs that allows researchers and developers to easily conduct experiments and build applications. It provides standard training and evaluation for the most important tasks in the graph domain, including node classification, link prediction, graph classification, and other graph tasks. For each task, it offers implementations of state-of-the-art models. The models in our toolkit are divided into two major parts, graph embedding methods and graph neural networks. Most of the graph embedding methods learn node-level or graph-level representations in an unsupervised way and preserves the graph properties such as structural information, while graph neural networks capture node features and work in semi-supervised or self-supervised settings. All models implemented in our toolkit can be easily reproducible for leaderboard results. Most models in CogDL are developed on top of PyTorch, and users can leverage the advantages of PyTorch to implement their own models. Furthermore, we demonstrate the effectiveness of CogDL for real-world applications in AMiner, which is a large academic database and system.