Yu Shi, Shuxin Zheng, Guolin Ke et al. · microsoft-research, tsinghua
This technical note describes the recent updates of Graphormer, including architecture design modifications, and the adaption to 3D molecular dynamics simulation. With these simple modifications, Graphormer could attain better results on large-scale molecular modeling datasets than the vanilla one, and the performance gain could be consistently obtained on 2D and 3D molecular graph modeling tasks. In addition, we show that with a global receptive field and an adaptive aggregation strategy, Graphormer is more powerful than classic message-passing-based GNNs. Empirically, Graphormer could achieve much less MAE than the originally reported results on the PCQM4M quantum chemistry dataset used in KDD Cup 2021. In the meanwhile, it greatly outperforms the competitors in the recent Open Catalyst Challenge, which is a competition track on NeurIPS 2021 workshop, and aims to model the catalyst-adsorbate reaction system with advanced AI models. All codes could be found at https://github.com/Microsoft/Graphormer.
Shuxin Zheng, Jiyan He, Chang Liu et al. · microsoft-research
Advances in deep learning have greatly improved structure prediction of molecules. However, many macroscopic observations that are important for real-world applications are not functions of a single molecular structure, but rather determined from the equilibrium distribution of structures. Traditional methods for obtaining these distributions, such as molecular dynamics simulation, are computationally expensive and often intractable. In this paper, we introduce a novel deep learning framework, called Distributional Graphormer (DiG), in an attempt to predict the equilibrium distribution of molecular systems. Inspired by the annealing process in thermodynamics, DiG employs deep neural networks to transform a simple distribution towards the equilibrium distribution, conditioned on a descriptor of a molecular system, such as a chemical graph or a protein sequence. This framework enables efficient generation of diverse conformations and provides estimations of state densities. We demonstrate the performance of DiG on several molecular tasks, including protein conformation sampling, ligand structure sampling, catalyst-adsorbate sampling, and property-guided structure generation. DiG presents a significant advancement in methodology for statistically understanding molecular systems, opening up new research opportunities in molecular science.
This technical note describes the recent updates of Graphormer, including architecture design modifications, and the adaption to 3D molecular dynamics simulation. The "Graphormer-V2" could attain better results on large-scale molecular modeling datasets than the vanilla one, and the performance gain could be consistently obtained on downstream tasks. In addition, we show that with a global receptive field and an adaptive aggregation strategy, Graphormer is more powerful than classic message-passing-based GNNs. Graphormer-V2 achieves much less MAE than the vanilla Graphormer on the PCQM4M quantum chemistry dataset used in KDD Cup 2021, where the latter one won the first place in this competition. In the meanwhile, Graphormer-V2 greatly outperforms the competitors in the recent Open Catalyst Challenge, which is a competition track on NeurIPS 2021 workshop, and aims to model the catalyst-adsorbate reaction system with advanced AI models. All models could be found at \url{https://github.com/Microsoft/Graphormer}.
Single-modal object detection tasks often experience performance degradation when encountering diverse scenarios. In contrast, multimodal object detection tasks can offer more comprehensive information about object features by integrating data from various modalities. Current multimodal object detection methods generally use various fusion techniques, including conventional neural networks and transformer-based models, to implement feature fusion strategies and achieve complementary information. However, since multimodal images are captured by different sensors, there are often misalignments between them, making direct matching challenging. This misalignment hinders the ability to establish strong correlations for the same object across different modalities. In this paper, we propose a novel approach called the CrOss-Mamba interaction and Offset-guided fusion (COMO) framework for multimodal object detection tasks. The COMO framework employs the cross-mamba technique to formulate feature interaction equations, enabling multimodal serialized state computation. This results in interactive fusion outputs while reducing computational overhead and improving efficiency. Additionally, COMO leverages high-level features, which are less affected by misalignment, to facilitate interaction and transfer complementary information between modalities, addressing the positional offset challenges caused by variations in camera angles and capture times. Furthermore, COMO incorporates a global and local scanning mechanism in the cross-mamba module to capture features with local correlation, particularly in remote sensing images. To preserve low-level features, the offset-guided fusion mechanism ensures effective multiscale feature utilization, allowing the construction of a multiscale fusion data cube that enhances detection performance.
The prediction of energetically stable crystal structures formed by a given chemical composition is a central problem in solid-state physics. In principle, the crystalline state of assembled atoms can be determined by optimizing the energy surface, which in turn can be evaluated using first-principles calculations. However, performing the iterative gradient descent on the potential energy surface using first-principles calculations is prohibitively expensive for complex systems, such as those with many atoms per unit cell. Here, we present a unique methodology for crystal structure prediction (CSP) that relies on a machine learning algorithm called metric learning. It is shown that a binary classifier, trained on a large number of already identified crystal structures, can determine the isomorphism of crystal structures formed by two given chemical compositions with an accuracy of approximately 96.4\%. For a given query composition with an unknown crystal structure, the model is used to automatically select from a crystal structure database a set of template crystals with nearly identical stable structures to which element substitution is to be applied. Apart from the local relaxation calculation of the identified templates, the proposed method does not use ab initio calculations. The potential of this substation-based CSP is demonstrated for a wide variety of crystal systems.
Simulation of the real-world traffic can be used to help validate the transportation policies. A good simulator means the simulated traffic is similar to real-world traffic, which often requires dense traffic trajectories (i.e., with a high sampling rate) to cover dynamic situations in the real world. However, in most cases, the real-world trajectories are sparse, which makes simulation challenging. In this paper, we present a novel framework ImInGAIL to address the problem of learning to simulate the driving behavior from sparse real-world data. The proposed architecture incorporates data interpolation with the behavior learning process of imitation learning. To the best of our knowledge, we are the first to tackle the data sparsity issue for behavior learning problems. We investigate our framework on both synthetic and real-world trajectory datasets of driving vehicles, showing that our method outperforms various baselines and state-of-the-art methods.