Selection of sequence motifs and generative Hopfield-Potts models for protein familiesilies

Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the three-dimensional structure of folded proteins, and about the effect of amino-acid substitutions in proteins. These models are typically requested to reproduce the one- and two-point statistics of the amino-acid usage in a protein family, {\em i.e.}~to capture the so-called residue conservation and covariation statistics of proteins of common evolutionary origin. Pairwise Potts models are the maximum-entropy models achieving this. While being successful, these models depend on huge numbers of {\em ad hoc} introduced parameters, which have to be estimated from finite amount of data and whose biophysical interpretation remains unclear. Here we propose an approach to parameter reduction, which is based on selecting collective sequence motifs. It naturally leads to the formulation of statistical sequence models in terms of Hopfield-Potts models. These models can be accurately inferred using a mapping to restricted Boltzmann machines and persistent contrastive divergence. We show that, when applied to protein data, even 20-40 patterns are sufficient to obtain statistically close-to-generative models. The Hopfield patterns form interpretable sequence motifs and may be used to clusterize amino-acid sequences into functional sub-families. However, the distributed collective nature of these motifs intrinsically limits the ability of Hopfield-Potts models in predicting contact maps, showing the necessity of developing models going beyond the Hopfield-Potts models discussed here.Comment: 26 pages, 16 figures, to app. in PR

Exploring non-stationarity patterns in schizophrenia: neural reorganization abnormalities in the alpha band

Producción CientíficaObjective. The aim of this paper was to characterize brain non-stationarity during an auditory oddball task in schizophrenia (SCH). The level of non-stationarity was measured in the baseline and response windows of relevant tones in SCH patients and healthy controls. Approach. Event-related potentials were recorded from 28 SCH patients and 51 controls. Non-stationarity was estimated in the conventional electroencephalography frequency bands by means of Kullback-Leibler divergence (KLD). Relative power (RP) was also computed to assess a possible complementarity with KLD. Main results. Results showed a widespread statistically significant increase in the level of non-stationarity from baseline to response in all frequency bands for both groups. Statistically significant differences in non-stationarity were found between SCH patients and controls in beta-2 and especially in the alpha band. SCH patients showed more non-stationarity in the left parieto-occipital region during the baseline window in the beta-2 band. A leave-one-out cross validation classification study with feature selection based on binary stepwise logistic regression to discriminate between SCH patients and controls provided an accuracy of 89.87% and area under ROC of 0.9510. Significance. KLD can characterize transient neural reorganization during an attentional task in response to novelty and relevance. Our findings suggest anomalous reorganization of neural dynamics in SCH during an oddball task. The abnormal frequency-dependent modulation found in SCH patients during relevant tones is in agreement with the hypothesis of aberrant salience detection in SCH. The increase in non-stationarity in the alpha band during the active task supports the notion that this band is involved in top-down processing. The baseline differences in the beta-2 band suggest that hyperactivation of the default mode network during attention tasks may be related to SCH symptoms. Furthermore, the binary stepwise logistic regression procedure selected features from both KLD and RP, supporting the idea that these measures can be complementary.This research project was supported in part by the projects TEC2014-53196-R of ‘Ministerio de Economía y Competitividad’ and FEDER; the project VA037U16 from the “Consejería de Educación de la Junta de Castilla y León”, the “Fondo de Investigaciones Sanitarias (Instituto de Salud Carlos III)” under projects FIS PI11/02203 and PI15/00299; and the “Gerencia Regional de Salud de Castilla y León” under projects GRS 932/A/14 and GRS 1134/A/15. P. Núñez was in receipt of a ‘Promoción de empleo joven e implantación de la Garantía Juvenil en I+D+i’ grant from ‘Ministerio de Economía y Competitividad’ and the University of Valladolid, A. Bachiller and J. Gomez-Pilar were in receipt of a PIF-UVA grant from the University of Valladolid. A. Lubeiro has a predoctoral scholarship from the “Junta de Castilla y León” and European Social Fund

“Structuration” by intellectual organization: the configuration of knowledge in relations among structural components in networks of science

Using aggregated journal–journal citation networks, the measurement of the knowledge base in empirical systems is factor-analyzed in two cases of interdisciplinary developments during the period 1995–2005: (i) the development of nanotechnology in the natural sciences and (ii) the development of communication studies as an interdiscipline between social psychology and political science. The results are compared with a case of stable development: the citation networks of core journals in chemistry. These citation networks are intellectually organized by networks of expectations in the knowledge base at the specialty (that is, above-journal) level. The “structuration” of structural components (over time) can be measured as configurational information. The latter is compared with the Shannon-type information generated in the interactions among structural components: the difference between these two measures provides us with a measure for the redundancy generated by the specification of a model in the knowledge base of the system. This knowledge base incurs (against the entropy law) to variable extents on the knowledge infrastructures provided by the observable networks of relations