Generative AI, in particular large transformer models, are increasingly driving HPC system design in science and industry. We analyze performance characteristics of such transformer models and discuss their sensitivity to the transformer type, parallelization strategy, and HPC system features (accelerators and interconnects). We utilize a performance model that allows us to explore this complex design space and highlight its key components. We find that different transformer types demand different parallelism and system characteristics at different training regimes. Large Language Models are performant with 3D parallelism and amplify network needs only at pre-training scales with reduced dependence on accelerator capacity and bandwidth. On the other hand, long-sequence transformers, representative of scientific foundation models, place a more uniform dependence on network and capacity with necessary 4D parallelism. Our analysis emphasizes the need for closer performance modeling of different transformer types keeping system features in mind and demonstrates a path towards this. Our code is available as open-source.
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We introduce a generative model for protein backbone design utilizing geometric products and higher order message passing. In particular, we propose Clifford Frame Attention (CFA), an extension of the invariant point attention (IPA) architecture from AlphaFold2, in which the backbone residue frames and geometric features are represented in the projective geometric algebra. This enables to construct geometrically expressive messages between residues, including higher order terms, using the bilinear operations of the algebra. We evaluate our architecture by incorporating it into the framework of FrameFlow, a state-of-the-art flow matching model for protein backbone generation. The proposed model achieves high designability, diversity and novelty, while also sampling protein backbones that follow the statistical distribution of secondary structure elements found in naturally occurring proteins, a property so far only insufficiently achieved by many state-of-the-art generative models.
Iterative solvers are frequently used in scientific applications and engineering computations. However, the memory-bound Sparse Matrix-Vector (SpMV) kernel computation hinders the efficiency of iterative algorithms. As modern hardware increasingly supports low-precision computation, the mixed-precision optimization of iterative algorithms has garnered widespread attention. Nevertheless, existing mixed-precision methods pose challenges, including format conversion overhead, tight coupling between storage and computation representation, and the need to store multiple precision copies of data. This paper proposes a floating-point representation based on the group-shared exponent and segmented storage of the mantissa, enabling higher bit utilization of the representation vector and fast switches between different precisions without needing multiple data copies. Furthermore, a stepped mixed-precision iterative algorithm is proposed. Our experimental results demonstrate that, compared with existing floating-point formats, our approach significantly improves iterative algorithms' performance and convergence residuals.
Existing knowledge graph (KG) embedding models have primarily focused on static KGs. However, real-world KGs do not remain static, but rather evolve and grow in tandem with the development of KG applications. Consequently, new facts and previously unseen entities and relations continually emerge, necessitating an embedding model that can quickly learn and transfer new knowledge through growth. Motivated by this, we delve into an expanding field of KG embedding in this paper, i.e., lifelong KG embedding. We consider knowledge transfer and retention of the learning on growing snapshots of a KG without having to learn embeddings from scratch. The proposed model includes a masked KG autoencoder for embedding learning and update, with an embedding transfer strategy to inject the learned knowledge into the new entity and relation embeddings, and an embedding regularization method to avoid catastrophic forgetting. To investigate the impacts of different aspects of KG growth, we construct four datasets to evaluate the performance of lifelong KG embedding. Experimental results show that the proposed model outperforms the state-of-the-art inductive and lifelong embedding baselines.
Graph Neural Networks (GNNs) have shown promising results on a broad spectrum of applications. Most empirical studies of GNNs directly take the observed graph as input, assuming the observed structure perfectly depicts the accurate and complete relations between nodes. However, graphs in the real world are inevitably noisy or incomplete, which could even exacerbate the quality of graph representations. In this work, we propose a novel Variational Information Bottleneck guided Graph Structure Learning framework, namely VIB-GSL, in the perspective of information theory. VIB-GSL advances the Information Bottleneck (IB) principle for graph structure learning, providing a more elegant and universal framework for mining underlying task-relevant relations. VIB-GSL learns an informative and compressive graph structure to distill the actionable information for specific downstream tasks. VIB-GSL deduces a variational approximation for irregular graph data to form a tractable IB objective function, which facilitates training stability. Extensive experimental results demonstrate that the superior effectiveness and robustness of VIB-GSL.
Recently, graph neural networks (GNNs) have been widely used for document classification. However, most existing methods are based on static word co-occurrence graphs without sentence-level information, which poses three challenges:(1) word ambiguity, (2) word synonymity, and (3) dynamic contextual dependency. To address these challenges, we propose a novel GNN-based sparse structure learning model for inductive document classification. Specifically, a document-level graph is initially generated by a disjoint union of sentence-level word co-occurrence graphs. Our model collects a set of trainable edges connecting disjoint words between sentences and employs structure learning to sparsely select edges with dynamic contextual dependencies. Graphs with sparse structures can jointly exploit local and global contextual information in documents through GNNs. For inductive learning, the refined document graph is further fed into a general readout function for graph-level classification and optimization in an end-to-end manner. Extensive experiments on several real-world datasets demonstrate that the proposed model outperforms most state-of-the-art results, and reveal the necessity to learn sparse structures for each document.
Data augmentation, the artificial creation of training data for machine learning by transformations, is a widely studied research field across machine learning disciplines. While it is useful for increasing the generalization capabilities of a model, it can also address many other challenges and problems, from overcoming a limited amount of training data over regularizing the objective to limiting the amount data used to protect privacy. Based on a precise description of the goals and applications of data augmentation (C1) and a taxonomy for existing works (C2), this survey is concerned with data augmentation methods for textual classification and aims to achieve a concise and comprehensive overview for researchers and practitioners (C3). Derived from the taxonomy, we divided more than 100 methods into 12 different groupings and provide state-of-the-art references expounding which methods are highly promising (C4). Finally, research perspectives that may constitute a building block for future work are given (C5).
Federated Learning (FL) is a decentralized machine-learning paradigm, in which a global server iteratively averages the model parameters of local users without accessing their data. User heterogeneity has imposed significant challenges to FL, which can incur drifted global models that are slow to converge. Knowledge Distillation has recently emerged to tackle this issue, by refining the server model using aggregated knowledge from heterogeneous users, other than directly averaging their model parameters. This approach, however, depends on a proxy dataset, making it impractical unless such a prerequisite is satisfied. Moreover, the ensemble knowledge is not fully utilized to guide local model learning, which may in turn affect the quality of the aggregated model. Inspired by the prior art, we propose a data-free knowledge distillation} approach to address heterogeneous FL, where the server learns a lightweight generator to ensemble user information in a data-free manner, which is then broadcasted to users, regulating local training using the learned knowledge as an inductive bias. Empirical studies powered by theoretical implications show that, our approach facilitates FL with better generalization performance using fewer communication rounds, compared with the state-of-the-art.
Data augmentation has been widely used to improve generalizability of machine learning models. However, comparatively little work studies data augmentation for graphs. This is largely due to the complex, non-Euclidean structure of graphs, which limits possible manipulation operations. Augmentation operations commonly used in vision and language have no analogs for graphs. Our work studies graph data augmentation for graph neural networks (GNNs) in the context of improving semi-supervised node-classification. We discuss practical and theoretical motivations, considerations and strategies for graph data augmentation. Our work shows that neural edge predictors can effectively encode class-homophilic structure to promote intra-class edges and demote inter-class edges in given graph structure, and our main contribution introduces the GAug graph data augmentation framework, which leverages these insights to improve performance in GNN-based node classification via edge prediction. Extensive experiments on multiple benchmarks show that augmentation via GAug improves performance across GNN architectures and datasets.
The potential of graph convolutional neural networks for the task of zero-shot learning has been demonstrated recently. These models are highly sample efficient as related concepts in the graph structure share statistical strength allowing generalization to new classes when faced with a lack of data. However, knowledge from distant nodes can get diluted when propagating through intermediate nodes, because current approaches to zero-shot learning use graph propagation schemes that perform Laplacian smoothing at each layer. We show that extensive smoothing does not help the task of regressing classifier weights in zero-shot learning. In order to still incorporate information from distant nodes and utilize the graph structure, we propose an Attentive Dense Graph Propagation Module (ADGPM). ADGPM allows us to exploit the hierarchical graph structure of the knowledge graph through additional connections. These connections are added based on a node's relationship to its ancestors and descendants and an attention scheme is further used to weigh their contribution depending on the distance to the node. Finally, we illustrate that finetuning of the feature representation after training the ADGPM leads to considerable improvements. Our method achieves competitive results, outperforming previous zero-shot learning approaches.
Dynamic programming (DP) solves a variety of structured combinatorial problems by iteratively breaking them down into smaller subproblems. In spite of their versatility, DP algorithms are usually non-differentiable, which hampers their use as a layer in neural networks trained by backpropagation. To address this issue, we propose to smooth the max operator in the dynamic programming recursion, using a strongly convex regularizer. This allows to relax both the optimal value and solution of the original combinatorial problem, and turns a broad class of DP algorithms into differentiable operators. Theoretically, we provide a new probabilistic perspective on backpropagating through these DP operators, and relate them to inference in graphical models. We derive two particular instantiations of our framework, a smoothed Viterbi algorithm for sequence prediction and a smoothed DTW algorithm for time-series alignment. We showcase these instantiations on two structured prediction tasks and on structured and sparse attention for neural machine translation.
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