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  1. Abstract

    Single-cell technologies characterize complex cell populations across multiple data modalities at unprecedented scale and resolution. Multi-omic data for single cell gene expression, in situ hybridization, or single cell chromatin states are increasingly available across diverse tissue types. When isolating specific cell types from a sample of disassociated cells or performing in situ sequencing in collections of heterogeneous cells, one challenging task is to select a small set of informative markers that robustly enable the identification and discrimination of specific cell types or cell states as precisely as possible. Given single cell RNA-seq data and a set of cellular labels to discriminate, scGeneFit selects gene markers that jointly optimize cell label recovery using label-aware compressive classification methods. This results in a substantially more robust and less redundant set of markers than existing methods, most of which identify markers that separate each cell label from the rest. When applied to a data set given a hierarchy of cell types as labels, the markers found by our method improves the recovery of the cell type hierarchy with fewer markers than existing methods using a computationally efficient and principled optimization.

     
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  2. Free, publicly-accessible full text available June 1, 2024
  3. Computing systems are omnipresent; their sustainability has become crucial for our society. A key aspect of this sustainability is the ability of computing systems to cope with the continuous change they face, ranging from dynamic operating conditions, to changing goals, and technological progress. While we are able to engineer smart computing systems that autonomously deal with various types of changes, handling unanticipated changes requires system evolution, which remains in essence a human-centered process. This will eventually become unmanageable. To break through the status quo, we put forward an arguable opinion for the vision of self-evolving computing systems that are equipped with an evolutionary engine enabling them to evolve autonomously. Specifically, when a self-evolving computing systems detects conditions outside its operational domain, such as an anomaly or a new goal, it activates an evolutionary engine that runs online experiments to determine how the system needs to evolve to deal with the changes, thereby evolving its architecture. During this process the engine can integrate new computing elements that are provided by computing warehouses. These computing elements provide specifications and procedures enabling their automatic integration. We motivate the need for self-evolving computing systems in light of the state of the art, outline a conceptual architecture of self-evolving computing systems, and illustrate the architecture for a future smart city mobility system that needs to evolve continuously with changing conditions. To conclude, we highlight key research challenges to realize the vision of self-evolving computing systems. 
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  4. State-of-the-art subspace clustering methods are based on the self-expressive model, which represents each data point as a linear combination of other data points. However, such methods are designed for a finite sample dataset and lack the ability to generalize to out-of-sample data. Moreover, since the number of self-expressive coefficients grows quadratically with the number of data points, their ability to handle large-scale datasets is often limited. In this paper, we propose a novel framework for subspace clustering, termed Self-Expressive Network (SENet), which employs a properly designed neural network to learn a self-expressive representation of the data. We show that our SENet can not only learn the self-expressive coefficients with desired properties on the training data, but also handle out-of-sample data. Besides, we show that SENet can also be leveraged to perform subspace clustering on large-scale datasets. Extensive experiments conducted on synthetic data and real world benchmark data validate the effectiveness of the proposed method. In particular, SENet yields highly competitive performance on MNIST, Fashion MNIST and Extended MNIST and state-of-the-art performance on CIFAR-10. 
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  5. Abstract Arguably, the two most popular accelerated or momentum-based optimization methods in machine learning are Nesterov’s accelerated gradient and Polyaks’s heavy ball, both corresponding to different discretizations of a particular second order differential equation with friction. Such connections with continuous-time dynamical systems have been instrumental in demystifying acceleration phenomena in optimization. Here we study structure-preserving discretizations for a certain class of dissipative (conformal) Hamiltonian systems, allowing us to analyse the symplectic structure of both Nesterov and heavy ball, besides providing several new insights into these methods. Moreover, we propose a new algorithm based on a dissipative relativistic system that normalizes the momentum and may result in more stable/faster optimization. Importantly, such a method generalizes both Nesterov and heavy ball, each being recovered as distinct limiting cases, and has potential advantages at no additional cost. 
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  6. null (Ed.)