Entropy-scaling search of massive biological data

Many datasets exhibit a well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here, we introduce a framework for similarity search based on characterizing a dataset's entropy and fractal dimension. We prove that searching scales in time with metric entropy (number of covering hyperspheres), if the fractal dimension of the dataset is low, and scales in space with the sum of metric entropy and information-theoretic entropy (randomness of the data). Using these ideas, we present accelerated versions of standard tools, with no loss in specificity and little loss in sensitivity, for use in three domains---high-throughput drug screening (Ammolite, 150x speedup), metagenomics (MICA, 3.5x speedup of DIAMOND [3,700x BLASTX]), and protein structure search (esFragBag, 10x speedup of FragBag). Our framework can be used to achieve "compressive omics," and the general theory can be readily applied to data science problems outside of biology.Comment: Including supplement: 41 pages, 6 figures, 4 tables, 1 bo

Recurrence-based time series analysis by means of complex network methods

Complex networks are an important paradigm of modern complex systems sciences which allows quantitatively assessing the structural properties of systems composed of different interacting entities. During the last years, intensive efforts have been spent on applying network-based concepts also for the analysis of dynamically relevant higher-order statistical properties of time series. Notably, many corresponding approaches are closely related with the concept of recurrence in phase space. In this paper, we review recent methodological advances in time series analysis based on complex networks, with a special emphasis on methods founded on recurrence plots. The potentials and limitations of the individual methods are discussed and illustrated for paradigmatic examples of dynamical systems as well as for real-world time series. Complex network measures are shown to provide information about structural features of dynamical systems that are complementary to those characterized by other methods of time series analysis and, hence, substantially enrich the knowledge gathered from other existing (linear as well as nonlinear) approaches.Comment: To be published in International Journal of Bifurcation and Chaos (2011

One-class classifiers based on entropic spanning graphs

One-class classifiers offer valuable tools to assess the presence of outliers in data. In this paper, we propose a design methodology for one-class classifiers based on entropic spanning graphs. Our approach takes into account the possibility to process also non-numeric data by means of an embedding procedure. The spanning graph is learned on the embedded input data and the outcoming partition of vertices defines the classifier. The final partition is derived by exploiting a criterion based on mutual information minimization. Here, we compute the mutual information by using a convenient formulation provided in terms of the $\alpha$-Jensen difference. Once training is completed, in order to associate a confidence level with the classifier decision, a graph-based fuzzy model is constructed. The fuzzification process is based only on topological information of the vertices of the entropic spanning graph. As such, the proposed one-class classifier is suitable also for data characterized by complex geometric structures. We provide experiments on well-known benchmarks containing both feature vectors and labeled graphs. In addition, we apply the method to the protein solubility recognition problem by considering several representations for the input samples. Experimental results demonstrate the effectiveness and versatility of the proposed method with respect to other state-of-the-art approaches.Comment: Extended and revised version of the paper "One-Class Classification Through Mutual Information Minimization" presented at the 2016 IEEE IJCNN, Vancouver, Canad

Similarity-Based Models of Word Cooccurrence Probabilities

In many applications of natural language processing (NLP) it is necessary to determine the likelihood of a given word combination. For example, a speech recognizer may need to determine which of the two word combinations ``eat a peach'' and ``eat a beach'' is more likely. Statistical NLP methods determine the likelihood of a word combination from its frequency in a training corpus. However, the nature of language is such that many word combinations are infrequent and do not occur in any given corpus. In this work we propose a method for estimating the probability of such previously unseen word combinations using available information on ``most similar'' words. We describe probabilistic word association models based on distributional word similarity, and apply them to two tasks, language modeling and pseudo-word disambiguation. In the language modeling task, a similarity-based model is used to improve probability estimates for unseen bigrams in a back-off language model. The similarity-based method yields a 20% perplexity improvement in the prediction of unseen bigrams and statistically significant reductions in speech-recognition error. We also compare four similarity-based estimation methods against back-off and maximum-likelihood estimation methods on a pseudo-word sense disambiguation task in which we controlled for both unigram and bigram frequency to avoid giving too much weight to easy-to-disambiguate high-frequency configurations. The similarity-based methods perform up to 40% better on this particular task.Comment: 26 pages, 5 figure