An Empirical Study of Graphormer on Large-Scale Molecular Modeling Datasets

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}.

Towards Open-Set Text Recognition via Label-to-Prototype Learning

Scene text recognition is a popular topic and can benefit various tasks. Although many methods have been proposed for the close-set text recognition challenges, they cannot be directly applied to open-set scenarios, where the evaluation set contains novel characters not appearing in the training set. Conventional methods require collecting new data and retraining the model to handle these novel characters, which is an expensive and tedious process. In this paper, we propose a label-to-prototype learning framework to handle novel characters without retraining the model. In the proposed framework, novel characters are effectively mapped to their corresponding prototypes with a label-to-prototype learning module. This module is trained on characters with seen labels and can be easily generalized to novel characters. Additionally, feature-level rectification is conducted via topology-preserving transformation, resulting in better alignments between visual features and constructed prototypes while having a reasonably small impact on model speed. A lot of experiments show that our method achieves promising performance on a variety of zero-shot, close-set, and open-set text recognition datasets.

Benchmarking Graphormer on Large-Scale Molecular Modeling Datasets

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.

A Survey for Solving Mixed Integer Programming via Machine Learning

This paper surveys the trend of leveraging machine learning to solve mixed integer programming (MIP) problems. Theoretically, MIP is an NP-hard problem, and most of the combinatorial optimization (CO) problems can be formulated as the MIP. Like other CO problems, the human-designed heuristic algorithms for MIP rely on good initial solutions and cost a lot of computational resources. Therefore, we consider applying machine learning methods to solve MIP, since ML-enhanced approaches can provide the solution based on the typical patterns from the historical data. In this paper, we first introduce the formulation and preliminaries of MIP and several traditional algorithms to solve MIP. Then, we advocate further promoting the different integration of machine learning and MIP and introducing related learning-based methods, which can be classified into exact algorithms and heuristic algorithms. Finally, we propose the outlook for learning-based MIP solvers, direction towards more combinatorial optimization problems beyond MIP, and also the mutual embrace of traditional solvers and machine learning components.

Bayesian Sequential Stacking Algorithm for Concurrently Designing Molecules and Synthetic Reaction Networks

In the last few years, de novo molecular design using machine learning has made great technical progress but its practical deployment has not been as successful. This is mostly owing to the cost and technical difficulty of synthesizing such computationally designed molecules. To overcome such barriers, various methods for synthetic route design using deep neural networks have been studied intensively in recent years. However, little progress has been made in designing molecules and their synthetic routes simultaneously. Here, we formulate the problem of simultaneously designing molecules with the desired set of properties and their synthetic routes within the framework of Bayesian inference. The design variables consist of a set of reactants in a reaction network and its network topology. The design space is extremely large because it consists of all combinations of purchasable reactants, often in the order of millions or more. In addition, the designed reaction networks can adopt any topology beyond simple multistep linear reaction routes. To solve this hard combinatorial problem, we present a powerful sequential Monte Carlo algorithm that recursively designs a synthetic reaction network by sequentially building up single-step reactions. In a case study of designing drug-like molecules based on commercially available compounds, compared with heuristic combinatorial search methods, the proposed method shows overwhelming performance in terms of computational efficiency and coverage and novelty with respect to existing compounds.

Orientation-Discriminative Feature Representation for Decentralized Pedestrian Tracking

This paper focuses on the problem of decentralized pedestrian tracking using a sensor network. Traditional works on pedestrian tracking usually use a centralized framework, which becomes less practical for robotic applications due to limited communication bandwidth. Our paper proposes a communication-efficient, orientation-discriminative feature representation to characterize pedestrian appearance information, that can be shared among sensors. Building upon that representation, our work develops a cross-sensor track association approach to achieve decentralized tracking. Extensive evaluations are conducted on publicly available datasets and results show that our proposed approach leads to improved performance in multi-sensor tracking.

Time-Frequency Mask Aware Bi-directional LSTM: A Deep Learning Approach for Underwater Acoustic Signal Separation

The underwater acoustic signals separation is a key technique for the underwater communications. The existing methods are mostly model-based, and could not accurately characterise the practical underwater acoustic communication environment. They are only suitable for binary signal separation, but cannot handle multivariate signal separation. On the other hand, the recurrent neural network (RNN) shows powerful capability in extracting the features of the temporal sequences. Inspired by this, in this paper, we present a data-driven approach for underwater acoustic signals separation using deep learning technology. We use the Bi-directional Long Short-Term Memory (Bi-LSTM) to explore the features of Time-Frequency (T-F) mask, and propose a T-F mask aware Bi-LSTM for signal separation. Taking advantage of the sparseness of the T-F image, the designed Bi-LSTM network is able to extract the discriminative features for separation, which further improves the separation performance. In particular, this method breaks through the limitations of the existing methods, not only achieves good results in multivariate separation, but also effectively separates signals when mixed with 40dB Gaussian noise signals. The experimental results show that this method can achieve a $97\%$ guarantee ratio (PSR), and the average similarity coefficient of the multivariate signal separation is stable above 0.8 under high noise conditions.

Predictive Beamforming for Integrated Sensing and Communication in Vehicular Networks: A Deep Learning Approach

The implementation of integrated sensing and communication (ISAC) highly depends on the effective beamforming design exploiting accurate instantaneous channel state information (ICSI). However, channel tracking in ISAC requires large amount of training overhead and prohibitively large computational complexity. To address this problem, in this paper, we focus on ISAC-assisted vehicular networks and exploit a deep learning approach to implicitly learn the features of historical channels and directly predict the beamforming matrix for the next time slot to maximize the average achievable sum-rate of system, thus bypassing the need of explicit channel tracking for reducing the system signaling overhead. To this end, a general sum-rate maximization problem with Cramer-Rao lower bounds-based sensing constraints is first formulated for the considered ISAC system. Then, a historical channels-based convolutional long short-term memory network is designed for predictive beamforming that can exploit the spatial and temporal dependencies of communication channels to further improve the learning performance. Finally, simulation results show that the proposed method can satisfy the requirement of sensing performance, while its achievable sum-rate can approach the upper bound obtained by a genie-aided scheme with perfect ICSI available.

Direct Molecular Conformation Generation

Molecular conformation generation aims to generate three-dimensional coordinates of all the atoms in a molecule and is an important task in bioinformatics and pharmacology. Previous distance-based methods first predict interatomic distances and then generate conformations based on them, which could result in conflicting distances. In this work, we propose a method that directly predicts the coordinates of atoms. We design a dedicated loss function for conformation generation, which is invariant to roto-translation of coordinates of conformations and permutation of symmetric atoms in molecules. We further design a backbone model that stacks multiple blocks, where each block refines the conformation generated by its preceding block. Our method achieves state-of-the-art results on four public benchmarks: on small-scale GEOM-QM9 and GEOM-Drugs which have $200$K training data, we can improve the previous best matching score by $3.5\%$ and $28.9\%$; on large-scale GEOM-QM9 and GEOM-Drugs which have millions of training data, those two improvements are $47.1\%$ and $36.3\%$. This shows the effectiveness of our method and the great potential of the direct approach. Our code is released at \url{https://github.com/DirectMolecularConfGen/DMCG}.

Crystal structure prediction with machine learning-based element substitution

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.