Dynamic order Markov model for categorical sequence clustering

Markov models are extensively used for categorical sequence clustering and classification due to their inherent ability to capture complex chronological dependencies hidden in sequential data. Existing Markov models are based on an implicit assumption that the probability of the next state depends on the preceding context/pattern which is consist of consecutive states. This restriction hampers the models since some patterns, disrupted by noise, may be not frequent enough in a consecutive form, but frequent in a sparse form, which can not make use of the information hidden in the sequential data. A sparse pattern corresponds to a pattern in which one or some of the state(s) between the first and last one in the pattern is/are replaced by wildcard(s) that can be matched by a subset of values in the state set. In this paper, we propose a new model that generalizes the conventional Markov approach making it capable of dealing with the sparse pattern and handling the length of the sparse patterns adaptively, i.e. allowing variable length pattern with variable wildcards. The model, named Dynamic order Markov model (DOMM), allows deriving a new similarity measure between a sequence and a set of sequences/cluster. DOMM builds a sparse pattern from sub-frequent patterns that contain significant statistical information veiled by the noise. To implement DOMM, we propose a sparse pattern detector (SPD) based on the probability suffix tree (PST) capable of discovering both sparse and consecutive patterns, and then we develop a divisive clustering algorithm, named DMSC, for Dynamic order Markov model for categorical sequence clustering. Experimental results on real-world datasets demonstrate the promising performance of the proposed model.

Two kinds of memory signals in neurons of the human hippocampus

Some studies of the neural representation of memory in the human hippocampus have identified memory signals reflecting the categorical status of test items (novel vs. repeated). Others have identified pattern-separated, episodic memory signals reflecting recognition of particular test items. Here, we report that both kinds of memory signals can be found in the hippocampus, and we consider their possible functions. We recorded single-unit activity from four brain regions (hippocampus, amygdala, anterior cingulate, and prefrontal cortex) of epilepsy patients as they performed a continuous recognition task. The generic signal was found in all four regions, whereas the sparse, pattern-separated signal was limited to the hippocampus, as predicted by longstanding computational models.

Enhanced Infrared Sparse Pattern Extraction and Usage for Impact Evaluation of Basalt-Carbon Hybrid Composites by Pulsed Thermography

Nowadays, infrared thermography, as a widely used non-destructive testing method, is increasingly studied for impact evaluation of composite structures. Sparse pattern extraction is attracting increasing attention as an advanced post-processing method. In this paper, an enhanced sparse pattern extraction framework is presented for thermographic sequence processing and defect detection. This framework adapts cropping operator and typical component extraction as a preprocessing step to reduce the dimensions of raw data and applies sparse pattern extraction algorithms to enhance the contrast on the defect area. Different cases are studied involving several defects in four basalt-carbon hybrid fiber-reinforced polymer composite laminates. Finally, comparative analysis with intensity distribution is carried out to verify the effectiveness of contrast enhancement using this framework.

A two-enzyme adaptive unit within bacterial folate metabolism

Metabolic enzyme function and evolution is influenced by the larger context of a biochemical pathway – deleterious mutations or perturbations in one enzyme can often be compensated by mutations to others. To explore strategies for mapping adaptive dependencies between enzymes, we used a combination of comparative genomics and experiments to examine interactions with the model metabolic enzyme Dihydrofolate Reductase (DHFR). Biochemically, DHFR shares a metabolic intermediate with numerous folate metabolic enzymes. In contrast, comparative genomics analyses of synteny and gene co-occurrence indicate a sparse pattern of evolutionary couplings in which DHFR is coupled to the enzyme thymidylate synthase (TYMS), but is relatively independent from the rest of folate metabolism. To test this apparent modularity, we used quantitative growth rate measurements and forward evolution inE. colito demonstrate that the two enzymes are coupled to one another, and can adapt independently from the remainder of the genome. Mechanistically, the coupling between DHFR and TYMS is driven by a constraint wherein TYMS activity must not greatly exceed that of DHFR – both to avoid depletion of reduced folates and prevent accumulation of the metabolic intermediate dihydrofolate. Extending our comparative genomics analyses genome-wide reveals over 200 gene pairs with statistical signatures similar to DHFR/TYMS, suggesting the possibility that cellular pathways might be decomposed into small adaptive units.