Integration and analysis of multi-omics data provide valuable insights for cancer subtype classification. However, such data are inherently heterogeneous, high-dimensional, and exhibit complex intra- and inter-modality dependencies. Recent advances in graph neural networks (GNNs) offer powerful tools for modeling such structure. Yet, most existing methods rely on prior knowledge or predefined similarity networks to construct graphs, which are often undirected or unweighted, failing to capture the directionality and strength of biological interactions. Interpretability at both the modality and feature levels also remains limited. To address these challenges, we propose TF-DWGNet, a novel Graph Neural Network framework that combines tree-based Directed Weighted graph construction with Tensor Fusion for multiclass cancer subtype classification. TF-DWGNet introduces two key innovations: a supervised tree-based approach for constructing directed, weighted graphs tailored to each omics modality, and a tensor fusion mechanism that captures unimodal, bimodal, and trimodal interactions using low-rank decomposition for efficiency. TF-DWGNet enables modality-specific representation learning, joint embedding fusion, and interpretable subtype prediction. Experiments on real-world cancer datasets show that TF-DWGNet consistently outperforms state-of-the-art baselines across multiple metrics and statistical tests. Moreover, it provides biologically meaningful insights by ranking influential features and modalities. These results highlight TF-DWGNet's potential for effective and interpretable multi-omics integration in cancer research.

Communication scheduling has been shown to be effective in accelerating distributed training, which enables all-reduce communications to be overlapped with backpropagation computations. This has been commonly adopted in popular distributed deep learning frameworks. However, there exist two fundamental problems: (1) excessive startup latency proportional to the number of workers for each all-reduce operation; (2) it only achieves sub-optimal training performance due to the dependency and synchronization requirement of the feed-forward computation in the next iteration. We propose a novel scheduling algorithm, DeAR, that decouples the all-reduce primitive into two continuous operations, which overlaps with both backpropagation and feed-forward computations without extra communications. We further design a practical tensor fusion algorithm to improve the training performance. Experimental results with five popular models show that DeAR achieves up to 83% and 15% training speedup over the state-of-the-art solutions on a 64-GPU cluster with 10Gb/s Ethernet and 100Gb/s InfiniBand interconnects, respectively.

Accurate protein structure prediction can significantly accelerate the development of life science. The accuracy of AlphaFold2, a frontier end-to-end structure prediction system, is already close to that of the experimental determination techniques. Due to the complex model architecture and large memory consumption, it requires lots of computational resources and time to implement the training and inference of AlphaFold2 from scratch. The cost of running the original AlphaFold2 is expensive for most individuals and institutions. Therefore, reducing this cost could accelerate the development of life science. We implement AlphaFold2 using PaddlePaddle, namely HelixFold, to improve training and inference speed and reduce memory consumption. The performance is improved by operator fusion, tensor fusion, and hybrid parallelism computation, while the memory is optimized through Recompute, BFloat16, and memory read/write in-place. Compared with the original AlphaFold2 (implemented with Jax) and OpenFold (implemented with PyTorch), HelixFold needs only 7.5 days to complete the full end-to-end training and only 5.3 days when using hybrid parallelism, while both AlphaFold2 and OpenFold take about 11 days. HelixFold saves 1x training time. We verified that HelixFold's accuracy could be on par with AlphaFold2 on the CASP14 and CAMEO datasets. HelixFold's code is available on GitHub for free download: https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold, and we also provide stable web services on https://paddlehelix.baidu.com/app/drug/protein/forecast.

Growing amounts of online user data motivate the need for automated processing techniques. In case of user ratings, one interesting option is to use neural networks for learning to predict ratings given an item and a user. While training for prediction, such an approach at the same time learns to map each user to a vector, a so-called user embedding. Such embeddings can for example be valuable for estimating user similarity. However, there are various ways how item and user information can be combined in neural networks, and it is unclear how the way of combining affects the resulting embeddings. In this paper, we run an experiment on movie ratings data, where we analyze the effect on embedding quality caused by several fusion strategies in neural networks. For evaluating embedding quality, we propose a novel measure, Pair-Distance Correlation, which quantifies the condition that similar users should have similar embedding vectors. We find that the fusion strategy affects results in terms of both prediction performance and embedding quality. Surprisingly, we find that prediction performance not necessarily reflects embedding quality. This suggests that if embeddings are of interest, the common tendency to select models based on their prediction ability should be reconsidered.