Self-Consistency Training for Hamiltonian Prediction

Hamiltonian prediction is a versatile formulation to leverage machine learning for solving molecular science problems. Yet, its applicability is limited by insufficient labeled data for training. In this work, we highlight that Hamiltonian prediction possesses a self-consistency principle, based on which we propose an exact training method that does not require labeled data. This merit addresses the data scarcity difficulty, and distinguishes the task from other property prediction formulations with unique benefits: (1) self-consistency training enables the model to be trained on a large amount of unlabeled data, hence substantially enhances generalization; (2) self-consistency training is more efficient than labeling data with DFT for supervised training, since it is an amortization of DFT calculation over a set of molecular structures. We empirically demonstrate the better generalization in data-scarce and out-of-distribution scenarios, and the better efficiency from the amortization. These benefits push forward the applicability of Hamiltonian prediction to an ever larger scale.

M-OFDFT: Overcoming the Barrier of Orbital-Free Density Functional Theory for Molecular Systems Using Deep Learning

Orbital-free density functional theory (OFDFT) is a quantum chemistry formulation that has a lower cost scaling than the prevailing Kohn-Sham DFT, which is increasingly desired for contemporary molecular research. However, its accuracy is limited by the kinetic energy density functional, which is notoriously hard to approximate for non-periodic molecular systems. In this work, we propose M-OFDFT, an OFDFT approach capable of solving molecular systems using a deep-learning functional model. We build the essential nonlocality into the model, which is made affordable by the concise density representation as expansion coefficients under an atomic basis. With techniques to address unconventional learning challenges therein, M-OFDFT achieves a comparable accuracy with Kohn-Sham DFT on a wide range of molecules untouched by OFDFT before. More attractively, M-OFDFT extrapolates well to molecules much larger than those in training, which unleashes the appealing scaling for studying large molecules including proteins, representing an advancement of the accuracy-efficiency trade-off frontier in quantum chemistry.

An ensemble of VisNet, Transformer-M, and pretraining models for molecular property prediction in OGB Large-Scale Challenge @ NeurIPS 2022

In the technical report, we provide our solution for OGB-LSC 2022 Graph Regression Task. The target of this task is to predict the quantum chemical property, HOMO-LUMO gap for a given molecule on PCQM4Mv2 dataset. In the competition, we designed two kinds of models: Transformer-M-ViSNet which is an geometry-enhanced graph neural network for fully connected molecular graphs and Pretrained-3D-ViSNet which is a pretrained ViSNet by distilling geomeotric information from optimized structures. With an ensemble of 22 models, ViSNet Team achieved the MAE of 0.0723 eV on the test-challenge set, dramatically reducing the error by 39.75% compared with the best method in the last year competition.

Multi-View Substructure Learning for Drug-Drug Interaction Prediction

Drug-drug interaction (DDI) prediction provides a drug combination strategy for systemically effective treatment. Previous studies usually model drug information constrained on a single view such as the drug itself, leading to incomplete and noisy information, which limits the accuracy of DDI prediction. In this work, we propose a novel multi- view drug substructure network for DDI prediction (MSN-DDI), which learns chemical substructures from both the representations of the single drug (intra-view) and the drug pair (inter-view) simultaneously and utilizes the substructures to update the drug representation iteratively. Comprehensive evaluations demonstrate that MSN-DDI has almost solved DDI prediction for existing drugs by achieving a relatively improved accuracy of 19.32% and an over 99% accuracy under the transductive setting. More importantly, MSN-DDI exhibits better generalization ability to unseen drugs with a relatively improved accuracy of 7.07% under more challenging inductive scenarios. Finally, MSN-DDI improves prediction performance for real-world DDI applications to new drugs.

Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model

Understanding protein sequences is vital and urgent for biology, healthcare, and medicine. Labeling approaches are expensive yet time-consuming, while the amount of unlabeled data is increasing quite faster than that of the labeled data due to low-cost, high-throughput sequencing methods. In order to extract knowledge from these unlabeled data, representation learning is of significant value for protein-related tasks and has great potential for helping us learn more about protein functions and structures. The key problem in the protein sequence representation learning is to capture the co-evolutionary information reflected by the inter-residue co-variation in the sequences. Instead of leveraging multiple sequence alignment as is usually done, we propose a novel method to capture this information directly by pre-training via a dedicated language model, i.e., Pairwise Masked Language Model (PMLM). In a conventional masked language model, the masked tokens are modeled by conditioning on the unmasked tokens only, but processed independently to each other. However, our proposed PMLM takes the dependency among masked tokens into consideration, i.e., the probability of a token pair is not equal to the product of the probability of the two tokens. By applying this model, the pre-trained encoder is able to generate a better representation for protein sequences. Our result shows that the proposed method can effectively capture the inter-residue correlations and improves the performance of contact prediction by up to 9% compared to the MLM baseline under the same setting. The proposed model also significantly outperforms the MSA baseline by more than 7% on the TAPE contact prediction benchmark when pre-trained on a subset of the sequence database which the MSA is generated from, revealing the potential of the sequence pre-training method to surpass MSA based methods in general.

Equivariant vector field network for many-body system modeling

Modeling many-body systems has been a long-standing challenge in science, from classical and quantum physics to computational biology. Equivariance is a critical physical symmetry for many-body dynamic systems, which enables robust and accurate prediction under arbitrary reference transformations. In light of this, great efforts have been put on encoding this symmetry into deep neural networks, which significantly boosts the prediction performance of down-streaming tasks. Some general equivariant models which are computationally efficient have been proposed, however, these models have no guarantee on the approximation power and may have information loss. In this paper, we leverage insights from the scalarization technique in differential geometry to model many-body systems by learning the gradient vector fields, which are SE(3) and permutation equivariant. Specifically, we propose the Equivariant Vector Field Network (EVFN), which is built on a novel tuple of equivariant basis and the associated scalarization and vectorization layers. Since our tuple equivariant basis forms a complete basis, learning the dynamics with our EVFN has no information loss and no tensor operations are involved before the final vectorization, which reduces the complex optimization on tensors to a minimum. We evaluate our method on predicting trajectories of simulated Newton mechanics systems with both full and partially observed data, as well as the equilibrium state of small molecules (molecular conformation) evolving as a statistical mechanics system. Experimental results across multiple tasks demonstrate that our model achieves best or competitive performance on baseline models in various types of datasets.

Improved Drug-target Interaction Prediction with Intermolecular Graph Transformer

The identification of active binding drugs for target proteins (termed as drug-target interaction prediction) is the key challenge in virtual screening, which plays an essential role in drug discovery. Although recent deep learning-based approaches achieved better performance than molecular docking, existing models often neglect certain aspects of the intermolecular information, hindering the performance of prediction. We recognize this problem and propose a novel approach named Intermolecular Graph Transformer (IGT) that employs a dedicated attention mechanism to model intermolecular information with a three-way Transformer-based architecture. IGT outperforms state-of-the-art approaches by 9.1% and 20.5% over the second best for binding activity and binding pose prediction respectively, and shows superior generalization ability to unseen receptor proteins. Furthermore, IGT exhibits promising drug screening ability against SARS-CoV-2 by identifying 83.1% active drugs that have been validated by wet-lab experiments with near-native predicted binding poses.

Defending Model Inversion and Membership Inference Attacks via Prediction Purification

Neural networks are susceptible to data inference attacks such as the model inversion attack and the membership inference attack, where the attacker could infer the reconstruction and the membership of a data sample from the confidence scores predicted by the target classifier. In this paper, we propose a common approach, namely purification framework, to defend data inference attacks. It purifies the confidence score vectors predicted by the target classifier, with the goal of removing redundant information that could be exploited by the attacker to perform the inferences. Specifically, we design a purifier model which takes a confidence score vector as input and reshapes it to meet the defense goals. It does not retrain the target classifier. The purifier can be used to mitigate the model inversion attack, the membership inference attack or both attacks. We evaluate our approach on deep neural networks using benchmark datasets. We show that the purification framework can effectively defend the model inversion attack and the membership inference attack, while introducing negligible utility loss to the target classifier (e.g., less than 0.3% classification accuracy drop). Moreover, we also empirically show that it is possible to defend data inference attacks with negligible change to the generalization ability of the classification function.

SEEK: Segmented Embedding of Knowledge Graphs

In recent years, knowledge graph embedding becomes a pretty hot research topic of artificial intelligence and plays increasingly vital roles in various downstream applications, such as recommendation and question answering. However, existing methods for knowledge graph embedding can not make a proper trade-off between the model complexity and the model expressiveness, which makes them still far from satisfactory. To mitigate this problem, we propose a lightweight modeling framework that can achieve highly competitive relational expressiveness without increasing the model complexity. Our framework focuses on the design of scoring functions and highlights two critical characteristics: 1) facilitating sufficient feature interactions; 2) preserving both symmetry and antisymmetry properties of relations. It is noteworthy that owing to the general and elegant design of scoring functions, our framework can incorporate many famous existing methods as special cases. Moreover, extensive experiments on public benchmarks demonstrate the efficiency and effectiveness of our framework. Source codes and data can be found at \url{https://github.com/Wentao-Xu/SEEK}.

Hallucinating very low-resolution and obscured face images

Most of the face hallucination methods are designed for complete inputs. They will not work well if the inputs are very tiny or contaminated by large occlusion. Inspired by this fact, we propose an obscured face hallucination network(OFHNet). The OFHNet consists of four parts: an inpainting network, an upsampling network, a discriminative network, and a fixed facial landmark detection network. The inpainting network restores the low-resolution(LR) obscured face images. The following upsampling network is to upsample the output of inpainting network. In order to ensure the generated high-resolution(HR) face images more photo-realistic, we utilize the discriminative network and the facial landmark detection network to better the result of upsampling network. In addition, we present a semantic structure loss, which makes the generated HR face images more pleasing. Extensive experiments show that our framework can restore the appealing HR face images from 1/4 missing area LR face images with a challenging scaling factor of 8x.