An information-based approach to handle various types of uncertainty in fuzzy bodies of evidence.

Fuzzy evidence theory, or fuzzy Dempster-Shafer Theory captures all three types of uncertainty, i.e. fuzziness, non-specificity, and conflict, which are usually contained in a piece of information within one framework. Therefore, it is known as one of the most promising approaches for practical applications. Quantifying the difference between two fuzzy bodies of evidence becomes important when this framework is used in applications. This work is motivated by the fact that while dissimilarity measures have been surveyed in the fields of evidence theory and fuzzy set theory, no comprehensive survey is yet available for fuzzy evidence theory. We proposed a modification to a set of the most discriminative dissimilarity measures (smDDM)-as the minimum set of dissimilarity with the maximal power of discrimination in evidence theory- to handle all types of uncertainty in fuzzy evidence theory. The generalized smDDM (FsmDDM) together with the one previously introduced as fuzzy measures make up a set of measures that is comprehensive enough to collectively address all aspects of information conveyed by the fuzzy bodies of evidence. Experimental results are presented to validate the method and to show the efficiency of the proposed method.

Coincidence Detection within the Excitable Rat Olfactory Bulb Granule Cell Spines.

In the mammalian olfactory bulb, the inhibitory axonless granule cells (GCs) feature reciprocal synapses that interconnect them with the principal neurons of the bulb, mitral, and tufted cells. These synapses are located within large excitable spines that can generate local action potentials (APs) upon synaptic input ("spine spike"). Moreover, GCs can fire global APs that propagate throughout the dendrite. Strikingly, local postsynaptic Ca2+ entry summates mostly linearly with Ca2+ entry due to coincident global APs generated by glomerular stimulation, although some underlying conductances should be inactivated. We investigated this phenomenon by constructing a compartmental GC model to simulate the pairing of local and global signals as a function of their temporal separation Δt. These simulations yield strongly sublinear summation of spine Ca2+ entry for the case of perfect coincidence Δt = 0 ms. Summation efficiency (SE) sharply rises for both positive and negative Δt. The SE reduction for coincident signals depends on the presence of voltage-gated Na+ channels in the spine head, while NMDARs are not essential. We experimentally validated the simulated SE in slices of juvenile rat brain (both sexes) by pairing two-photon uncaging of glutamate at spines and APs evoked by somatic current injection at various intervals Δt while imaging spine Ca2+ signals. Finally, the latencies of synaptically evoked global APs and EPSPs were found to correspond to Δt ≈ 10 ms, explaining the observed approximately linear summation of synaptic local and global signals. Our results provide additional evidence for the existence of the GC spine spike.SIGNIFICANCE STATEMENT Here we investigate the interaction of local synaptic inputs and global activation of a neuron by a backpropagating action potential within a dendritic spine with respect to local Ca2+ signaling. Our system of interest, the reciprocal spine of the olfactory bulb granule cell, is known to feature a special processing mode, namely, a synaptically triggered action potential that is restricted to the spine head. Therefore, coincidence detection of local and global signals follows different rules than in more conventional synapses. We unravel these rules using both simulations and experiments and find that signals coincident within ≈±7 ms around 0 ms result in sublinear summation of Ca2+ entry because of synaptic activation of voltage-gated Na+ channels within the spine.

Evidence theoretic protein fold classification based on the concept of hyperfold.

In current computational biology, assigning a protein domain to a fold class is a complicated and controversial task. It can be more challenging in the much harder task of correct identification of protein domain fold pattern solely through using extracted information from protein sequence. To deal with such a challenging problem, the concepts of hyperfold and interlaced folds are introduced for the first time. Each hyperfold is a set of interlaced folds with a centroid fold. These concepts are used to construct a framework for handling the uncertainty involved with the fold classification problem. In this approach, an unknown query protein is assigned to a hyperfold rather than a single fold. Ten different sequence based features are used to predicting the correct hyperfold. This architecture is featured by the Dempster-Shafer theory of evidence through the bodies of evidence and Dempster's rule of combination to combine the hyperfolds. The classification architecture thus developed was applied for identifying protein folds among the 27 famous SCOP fold patterns from a stringent well-known dataset. Compared with the existing predictors tested by the same benchmark dataset, our approach might achieve the better results.

Dynamical analysis of yeast protein interaction network during the sake brewing process.

Proteins interact with each other for performing essential functions of an organism. They change partners to get involved in various processes at different times or locations. Studying variations of protein interactions within a specific process would help better understand the dynamic features of the protein interactions and their functions. We studied the protein interaction network of Saccharomyces cerevisiae (yeast) during the brewing of Japanese sake. In this process, yeast cells are exposed to several stresses. Analysis of protein interaction networks of yeast during this process helps to understand how protein interactions of yeast change during the sake brewing process. We used gene expression profiles of yeast cells for this purpose. Results of our experiments revealed some characteristics and behaviors of yeast hubs and non-hubs and their dynamical changes during the brewing process. We found that just a small portion of the proteins (12.8 to 21.6%) is responsible for the functional changes of the proteins in the sake brewing process. The changes in the number of edges and hubs of the yeast protein interaction networks increase in the first stages of the process and it then decreases at the final stages.

A protein fold classifier formed by fusing different modes of pseudo amino acid composition via PSSM.

Protein function is related to its chemical reaction to the surrounding environment including other proteins. On the other hand, this depends on the spatial shape and tertiary structure of protein and folding of its constituent components in space. The correct identification of protein domain fold solely using extracted information from protein sequence is a complicated and controversial task in the current computational biology. In this article a combined classifier based on the information content of extracted features from the primary structure of protein has been introduced to face this challenging problem. In the first stage of our proposed two-tier architecture, there are several classifiers each of which is trained with a different sequence based feature vector. Apart from the application of the predicted secondary structure, hydrophobicity, van der Waals volume, polarity, polarizability, and different dimensions of pseudo-amino acid composition vectors in similar studies, the position specific scoring matrix (PSSM) has also been used to improve the correct classification rate (CCR) in this study. Using K-fold cross validation on training dataset related to 27 famous folds of SCOP, the 28 dimensional probability output vector from each evidence theoretic K-NN classifier is used to determine the information content or expertness of corresponding feature for discrimination in each fold class. In the second stage, the outputs of classifiers for test dataset are fused using Sugeno fuzzy integral operator to make better decision for target fold class. The expertness factor of each classifier in each fold class has been used to calculate the fuzzy integral operator weights. Results make it possible to provide deeper interpretation about the effectiveness of each feature for discrimination in target classes for query proteins.

Learning active fusion of multiple experts' decisions: an attention-based approach.

In this letter, we propose a learning system, active decision fusion learning (ADFL), for active fusion of decisions. Each decision maker, referred to as a local decision maker, provides its suggestion in the form of a probability distribution over all possible decisions. The goal of the system is to learn the active sequential selection of the local decision makers in order to consult with and thus learn the final decision based on the consultations. These two learning tasks are formulated as learning a single sequential decision-making problem in the form of a Markov decision process (MDP), and a continuous reinforcement learning method is employed to solve it. The states of this MDP are decisions of the attended local decision makers, and the actions are either attending to a local decision maker or declaring final decisions. The learning system is punished for each consultation and wrong final decision and rewarded for correct final decisions. This results in minimizing the consultation and decision-making costs through learning a sequential consultation policy where the most informative local decision makers are consulted and the least informative, misleading, and redundant ones are left unattended. An important property of this policy is that it acts locally. This means that the system handles any nonuniformity in the local decision maker's expertise over the state space. This property has been exploited in the design of local experts. ADFL is tested on a set of classification tasks, where it outperforms two well-known classification methods, Adaboost and bagging, as well as three benchmark fusion algorithms: OWA, Borda count, and majority voting. In addition, the effect of local experts design strategy on the performance of ADFL is studied, and some guidelines for the design of local experts are provided. Moreover, evaluating ADFL in some special cases proves that it is able to derive the maximum benefit from the informative local decision makers and to minimize attending to redundant ones.

Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae.

BACKGROUND: It has been understood that biological networks have modular organizations which are the sources of their observed complexity. Analysis of networks and motifs has shown that two types of hubs, party hubs and date hubs, are responsible for this complexity. Party hubs are local coordinators because of their high co-expressions with their partners, whereas date hubs display low co-expressions and are assumed as global connectors. However there is no mutual agreement on these concepts in related literature with different studies reporting their results on different data sets. We investigated whether there is a relation between the biological features of Saccharomyces Cerevisiae's proteins and their roles as non-hubs, intermediately connected, party hubs, and date hubs. We propose a classifier that separates these four classes. RESULTS: We extracted different biological characteristics including amino acid sequences, domain contents, repeated domains, functional categories, biological processes, cellular compartments, disordered regions, and position specific scoring matrix from various sources. Several classifiers are examined and the best feature-sets based on average correct classification rate and correlation coefficients of the results are selected. We show that fusion of five feature-sets including domains, Position Specific Scoring Matrix-400, cellular compartments level one, and composition pairs with two and one gaps provide the best discrimination with an average correct classification rate of 77%. CONCLUSIONS: We study a variety of known biological feature-sets of the proteins and show that there is a relation between domains, Position Specific Scoring Matrix-400, cellular compartments level one, composition pairs with two and one gaps of Saccharomyces Cerevisiae's proteins, and their roles in the protein interaction network as non-hubs, intermediately connected, party hubs and date hubs. This study also confirms the possibility of predicting non-hubs, party hubs and date hubs based on their biological features with acceptable accuracy. If such a hypothesis is correct for other species as well, similar methods can be applied to predict the roles of proteins in those species.