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Microarray datasets are highly dimensional, with a small number of collected samples in comparison to thousands of features. This poses a significant challenge that affects the interpretation, applicability and validation of the analytical results. Matrix factorizations have proven to be a useful method for describing data in terms of a small number of meta-features, which reduces noise, while still capturing the essential features of the data. Three novel and mutually relevant methods are presented in this paper: 1) gradient-based matrix factorization with two adaptive learning rates (in accordance with the number of factor matrices) and their automatic updates; 2) nonparametric criterion for the selection of the number of factors; and 3) nonnegative version of the gradient-based matrix factorization which doesn't require any extra computational costs in difference to the existing methods. We demonstrate effectiveness of the proposed methods to the supervised classification of gene expression data.

Working memory mechanisms in spiking neural networks consisting of leaky integrate-and-fire neurons with adaptive threshold and synaptic plasticity are studied in this work. Moderate size networks including thousands of neurons were explored. Working memory is a network ability to keep in its state the information about recent stimuli presented to the network such that this information is sufficient to determine which stimulus has been presented. In this study, network state is defined as the current characteristics of network activity only — without internal state of its neurons. In order to discover the neuronal structures serving as a possible substrate of the memory mechanism, optimization of the network parameters and structure using genetic algorithm was carried out. Two kinds of neuronal structures with the desired properties were found. These are neuron pairs mutually connected by strong synaptic links and long tree-like neuronal ensembles. It was shown that only the neuron pairs are suitable for efficient and reliable implementation of working memory. Properties of such memory units and structures formed by them are explored in the present study. It is shown that characteristics of the studied two-neuron memory units can be set easily by the respective choice of the parameters of its neurons and synaptic connections. Besides that, this work demonstrates that ensembles of these structures can provide the network with capability of unsupervised learning to recognize patterns in the input signal.

The probabilistic topic model of a text document collection finds two matrices: a matrix of conditional probabilities of topics in documents and a matrix of conditional probabilities of words in topics. Each document is represented by a multiset of words also called the “bag of words”, thus assuming that the order of words is not important for revealing the latent topics of the document. Under this assumption, the problem is reduced to a low-rank non-negative matrix factorization governed by likelihood maximization. In general, this problem is ill-posed having an infinite set of solutions. In order to regularize the solution, a weighted sum of optimization criteria is added to the log-likelihood. When modeling large text collections, storing the first matrix seems to be impractical, since its size is proportional to the number of documents in the collection. At the same time, the topical vector representation (embedding) of documents is necessary for solving many text analysis tasks, such as information retrieval, clustering, classification, and summarization of texts. In practice, the topical embedding is calculated for a document “on-the-fly”, which may require dozens of iterations over all the words of the document. In this paper, we propose a way to calculate a topical embedding quickly, by one pass over document words. For this, an additional constraint is introduced into the model in the form of an equation, which calculates the first matrix from the second one in linear time. Although formally this constraint is not an optimization criterion, in fact it plays the role of a regularizer and can be used in combination with other regularizers within the additive regularization framework ARTM. Experiments on three text collections have shown that the proposed method improves the model in terms of sparseness, difference, logLift and coherence measures of topic quality. The open source libraries BigARTM and TopicNet were used for the experiments.