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Mixup is a widely adopted strategy for training deep networks, where additional samples are augmented by interpolating inputs and labels of training pairs. Mixup has shown to improve classification performance, network calibration, and out-of-distribution generalisation. While effective, a cornerstone of Mixup, namely that networks learn linear behaviour patterns between classes, is only indirectly enforced since the output interpolation is performed at the probability level. This paper seeks to address this limitation by mixing the classifiers directly instead of mixing the labels for each mixed pair. We propose to define the target of each augmented sample as a uniquely new classifier, whose parameters are a linear interpolation of the classifier vectors of the input pair. The space of all possible classifiers is continuous and spans all interpolations between classifier pairs. To make optimisation tractable, we propose a dual-contrastive Infinite Class Mixup loss, where we contrast the classifier of a mixed pair to both the classifiers and the predicted outputs of other mixed pairs in a batch. Infinite Class Mixup is generic in nature and applies to many variants of Mixup. Empirically, we show that it outperforms standard Mixup and variants such as RegMixup and Remix on balanced, long-tailed, and data-constrained benchmarks, highlighting its broad applicability.

With the fast-growing and evolving omics data, the demand for streamlined and adaptable tools to handle the analysis continues to grow. In response to this need, we introduce Auto Bioinformatics Analysis (AutoBA), an autonomous AI agent based on a large language model designed explicitly for conventional omics data analysis. AutoBA simplifies the analytical process by requiring minimal user input while delivering detailed step-by-step plans for various bioinformatics tasks. Through rigorous validation by expert bioinformaticians, AutoBA's robustness and adaptability are affirmed across a diverse range of omics analysis cases, including whole genome sequencing (WGS), RNA sequencing (RNA-seq), single-cell RNA-seq, ChIP-seq, and spatial transcriptomics. AutoBA's unique capacity to self-design analysis processes based on input data variations further underscores its versatility. Compared with online bioinformatic services, AutoBA deploys the analysis locally, preserving data privacy. Moreover, different from the predefined pipeline, AutoBA has adaptability in sync with emerging bioinformatics tools. Overall, AutoBA represents a convenient tool, offering robustness and adaptability for complex omics data analysis.

Coded computing is a method for mitigating straggling workers in a centralized computing network, by using erasure-coding techniques. Federated learning is a decentralized model for training data distributed across client devices. In this work we propose approximating the inverse of an aggregated data matrix, where the data is generated by clients; similar to the federated learning paradigm, while also being resilient to stragglers. To do so, we propose a coded computing method based on gradient coding. We modify this method so that the coordinator does not access the local data at any point; while the clients access the aggregated matrix in order to complete their tasks. The network we consider is not centrally administrated, and the communications which take place are secure against potential eavesdroppers.

Stationary graph process models are commonly used in the analysis and inference of data sets collected on irregular network topologies. While most of the existing methods represent graph signals with a single stationary process model that is globally valid on the entire graph, in many practical problems, the characteristics of the process may be subject to local variations in different regions of the graph. In this work, we propose a locally stationary graph process (LSGP) model that aims to extend the classical concept of local stationarity to irregular graph domains. We characterize local stationarity by expressing the overall process as the combination of a set of component processes such that the extent to which the process adheres to each component varies smoothly over the graph. We propose an algorithm for computing LSGP models from realizations of the process, and also study the approximation of LSGPs locally with WSS processes. Experiments on signal interpolation problems show that the proposed process model provides accurate signal representations competitive with the state of the art.

In order to characterize complex higher-order interactions among variables in a system, we introduce a new framework for decomposing the information entropy of variables in a system, termed System Information Decomposition (SID). Diverging from Partial Information Decomposition (PID) correlation methods, which quantify the interaction between a single target variable and a collection of source variables, SID extends those approaches by equally examining the interactions among all system variables. Specifically, we establish the robustness of the SID framework by proving all the information atoms are symmetric, which detaches the unique, redundant, and synergistic information from the specific target variable, empowering them to describe the relationship among variables. Additionally, we analyze the relationship between SID and existing information measures and propose several properties that SID quantitative methods should follow. Furthermore, by employing an illustrative example, we demonstrate that SID uncovers a higher-order interaction relationships among variables that cannot be captured by current measures of probability and information and provide two approximate calculation methods verified by this case. This advance in higher-order measures enables SID to explain why Holism posits that some systems cannot be decomposed without loss of characteristics under existing measures, and offers a potential quantitative framework for higher-order relationships across a broad spectrum of disciplines.

Humans perceive the world by concurrently processing and fusing high-dimensional inputs from multiple modalities such as vision and audio. Machine perception models, in stark contrast, are typically modality-specific and optimised for unimodal benchmarks, and hence late-stage fusion of final representations or predictions from each modality (`late-fusion') is still a dominant paradigm for multimodal video classification. Instead, we introduce a novel transformer based architecture that uses `fusion bottlenecks' for modality fusion at multiple layers. Compared to traditional pairwise self-attention, our model forces information between different modalities to pass through a small number of bottleneck latents, requiring the model to collate and condense the most relevant information in each modality and only share what is necessary. We find that such a strategy improves fusion performance, at the same time reducing computational cost. We conduct thorough ablation studies, and achieve state-of-the-art results on multiple audio-visual classification benchmarks including Audioset, Epic-Kitchens and VGGSound. All code and models will be released.

Graph neural networks (GNNs) have been widely used in representation learning on graphs and achieved state-of-the-art performance in tasks such as node classification and link prediction. However, most existing GNNs are designed to learn node representations on the fixed and homogeneous graphs. The limitations especially become problematic when learning representations on a misspecified graph or a heterogeneous graph that consists of various types of nodes and edges. In this paper, we propose Graph Transformer Networks (GTNs) that are capable of generating new graph structures, which involve identifying useful connections between unconnected nodes on the original graph, while learning effective node representation on the new graphs in an end-to-end fashion. Graph Transformer layer, a core layer of GTNs, learns a soft selection of edge types and composite relations for generating useful multi-hop connections so-called meta-paths. Our experiments show that GTNs learn new graph structures, based on data and tasks without domain knowledge, and yield powerful node representation via convolution on the new graphs. Without domain-specific graph preprocessing, GTNs achieved the best performance in all three benchmark node classification tasks against the state-of-the-art methods that require pre-defined meta-paths from domain knowledge.

Graph representation learning is to learn universal node representations that preserve both node attributes and structural information. The derived node representations can be used to serve various downstream tasks, such as node classification and node clustering. When a graph is heterogeneous, the problem becomes more challenging than the homogeneous graph node learning problem. Inspired by the emerging information theoretic-based learning algorithm, in this paper we propose an unsupervised graph neural network Heterogeneous Deep Graph Infomax (HDGI) for heterogeneous graph representation learning. We use the meta-path structure to analyze the connections involving semantics in heterogeneous graphs and utilize graph convolution module and semantic-level attention mechanism to capture local representations. By maximizing local-global mutual information, HDGI effectively learns high-level node representations that can be utilized in downstream graph-related tasks. Experiment results show that HDGI remarkably outperforms state-of-the-art unsupervised graph representation learning methods on both classification and clustering tasks. By feeding the learned representations into a parametric model, such as logistic regression, we even achieve comparable performance in node classification tasks when comparing with state-of-the-art supervised end-to-end GNN models.

We investigate a lattice-structured LSTM model for Chinese NER, which encodes a sequence of input characters as well as all potential words that match a lexicon. Compared with character-based methods, our model explicitly leverages word and word sequence information. Compared with word-based methods, lattice LSTM does not suffer from segmentation errors. Gated recurrent cells allow our model to choose the most relevant characters and words from a sentence for better NER results. Experiments on various datasets show that lattice LSTM outperforms both word-based and character-based LSTM baselines, achieving the best results.

The dominant sequence transduction models are based on complex recurrent or convolutional neural networks in an encoder-decoder configuration. The best performing models also connect the encoder and decoder through an attention mechanism. We propose a new simple network architecture, the Transformer, based solely on attention mechanisms, dispensing with recurrence and convolutions entirely. Experiments on two machine translation tasks show these models to be superior in quality while being more parallelizable and requiring significantly less time to train. Our model achieves 28.4 BLEU on the WMT 2014 English-to-German translation task, improving over the existing best results, including ensembles by over 2 BLEU. On the WMT 2014 English-to-French translation task, our model establishes a new single-model state-of-the-art BLEU score of 41.8 after training for 3.5 days on eight GPUs, a small fraction of the training costs of the best models from the literature. We show that the Transformer generalizes well to other tasks by applying it successfully to English constituency parsing both with large and limited training data.