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Molecular property prediction is an important problem in drug discovery and materials science. As geometric structures have been demonstrated necessary for molecular property prediction, 3D information has been combined with various graph learning methods to boost prediction performance. However, obtaining the geometric structure of molecules is not feasible in many real-world applications due to the high computational cost. In this work, we propose a novel 3D pre-training framework (dubbed 3D PGT), which pre-trains a model on 3D molecular graphs, and then fine-tunes it on molecular graphs without 3D structures. Based on fact that bond length, bond angle, and dihedral angle are three basic geometric descriptors corresponding to a complete molecular 3D conformer, we first develop a multi-task generative pre-train framework based on these three attributes. Next, to automatically fuse these three generative tasks, we design a surrogate metric using the \textit{total energy} to search for weight distribution of the three pretext task since total energy corresponding to the quality of 3D conformer.Extensive experiments on 2D molecular graphs are conducted to demonstrate the accuracy, efficiency and generalization ability of the proposed 3D PGT compared to various pre-training baselines.

Additional file 3: File S1. The top-5 motifs of FaCINs for each chromosome.

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Additional file 1: Fig. S1. AUROC of DSB-GNN on each chromosome for NHEK cell line and performance comparison. Fig. S2. The distribution of the importance score of all node features and the top 10 k-mer features. Fig. S3. The comparison between the numbers of direct chromatin interactions and neck interactions for a prediction site on average. Fig. S4. Details for FaCIN’s bottleneck pattern. Fig. S5. An illustration for betweenness centrality and the comparison between neck neighbours and other neighbours in terms of betweenness centrality. Fig. S6. Results of subgraph search on FaCIN and random graph. Fig. S7. A schematic comparison between bottleneck and cycle patterns. Fig. S8. The 1D genomic length spanned by FaCIN’s interactions for 1-hop and 2-hop interactions. Fig. S9. The description of hypergeometric test for neck interactions and loop interactions.Fig. S10. Neck interactions in TAD boundaries. Fig. S11. The average length and intensity of neck interactions at DSB and non-DSB sites. Fig. S12. Percentage for neck neighbours of DSB prediction sites. Fig. S13. Statistics of the raw Hi-C contact counts. Fig. S14. A schematic for GNNExplainer masking approach to identify important edges.

Tabular data prediction (TDP) is one of the most popular industrial applications, and various methods have been designed to improve the prediction performance. However, existing works mainly focus on feature interactions and ignore sample relations, e.g., users with the same education level might have a similar ability to repay the debt. In this work, by explicitly and systematically modeling sample relations, we propose a novel framework TabGNN based on recently popular graph neural networks (GNN). Specifically, we firstly construct a multiplex graph to model the multifaceted sample relations, and then design a multiplex graph neural network to learn enhanced representation for each sample. To integrate TabGNN with the tabular solution in our company, we concatenate the learned embeddings and the original ones, which are then fed to prediction models inside the solution. Experiments on eleven TDP datasets from various domains, including classification and regression ones, show that TabGNN can consistently improve the performance compared to the tabular solution AutoFE in 4Paradigm.

The Adam algorithm has become extremely popular for large-scale machine learning. Under convexity condition, it has been proved to enjoy a data-dependant $O(\sqrt{T})$ regret bound where $T$ is the time horizon. However, whether strong convexity can be utilized to further improve the performance remains an open problem. In this paper, we give an affirmative answer by developing a variant of Adam (referred to as SAdam) which achieves a data-dependant $O(\log T)$ regret bound for strongly convex functions. The essential idea is to maintain a faster decaying yet under controlled step size for exploiting strong convexity. In addition, under a special configuration of hyperparameters, our SAdam reduces to SC-RMSprop, a recently proposed variant of RMSprop for strongly convex functions, for which we provide the first data-dependent logarithmic regret bound. Empirical results on optimizing strongly convex functions and training deep networks demonstrate the effectiveness of our method., 19 pages, 9 figures

To meet the standard of differential privacy, noise is usually added into the original data, which inevitably deteriorates the predicting performance of subsequent learning algorithms. In this paper, motivated by the success of improving predicting performance by ensemble learning, we propose to enhance privacy-preserving logistic regression by stacking. We show that this can be done either by sample-based or feature-based partitioning. However, we prove that when privacy-budgets are the same, feature-based partitioning requires fewer samples than sample-based one, and thus likely has better empirical performance. As transfer learning is difficult to be integrated with a differential privacy guarantee, we further combine the proposed method with hypothesis transfer learning to address the problem of learning across different organizations. Finally, we not only demonstrate the effectiveness of our method on two benchmark data sets, i.e., MNIST and NEWS20, but also apply it into a real application of cross-organizational diabetes prediction from RUIJIN data set, where privacy is of significant concern.