A holistic miRNA-mRNA module discovery.

The regulatory role of the Micro-RNAs (miRNAs) in the messenger RNAs (mRNAs) gene expression is well understood by the biologists since some decades, even though the delving into specific aspects is in progress. In this paper we will focus on miRNA-mRNA modules, where regulation jointly occurs in miRNA-mRNA pairs. Namely, we propose a holistic procedure to identify miRNA-mRNA modules within a population of candidate pairs. Since current methods still leave open issues, we adopt the strategy of postponing any decision on the value of the module ingredients exactly at the end, i.e. at the moment of biologically exploiting the results. This diverts chains of statistical tests into sequences of specially-devised-evolving metrics on the possible solutions. This strategy is rather expensive under a computational perspective, so needing implementations on HPC. The reward stands in the discovery of new modules, possibly hosting non differentially expressed miRNAs and mRNAs and pairs containing genes that currently are considered not targeted. In the paper we implement the procedure on a Multiple Myeloma dataset publicly available on GEO platform, as a template of a cancer instance analysis, and hazard some biological issues. These results, jointly with the normal manageability of the computations, suggest that the discovery procedure may be profitably extended to a wide spectrum of diseases where miRNA-mRNA interactions play a relevant role.

Inferring statistical trends of the COVID19 pandemic from current data. Where probability meets fuzziness.

We introduce unprecedented tools to infer approximate evolution features of the COVID19 outbreak when these features are altered by containment measures. In this framework we present: (1) a basic tool to deal with samples that are both truncated and non independently drawn, and (2) a two-phase random variable to capture a game changer along a process evolution. To overcome these challenges we lie in an intermediate domain between probability models and fuzzy sets, still maintaining probabilistic features of the employed statistics as the reference KPI of the tools. This research uses as a benchmark the daily cumulative death numbers of COVID19 in two countries, with no any ancillary data. Numerical results show: (i) the model capability of capturing the inflection point and forecasting the end-of-infection time and related outbreak size, and (ii) the out-performance of the model inference method according to conventional indicators.

Mobility timing for agent communities, a cue for advanced connectionist systems.

We introduce a wait-and-chase scheme that models the contact times between moving agents within a connectionist construct. The idea that elementary processors move within a network to get a proper position is borne out both by biological neurons in the brain morphogenesis and by agents within social networks. From the former, we take inspiration to devise a medium-term project for new artificial neural network training procedures where mobile neurons exchange data only when they are close to one another in a proper space (are in contact). From the latter, we accumulate mobility tracks experience. We focus on the preliminary step of characterizing the elapsed time between neuron contacts, which results from a spatial process fitting in the family of random processes with memory, where chasing neurons are stochastically driven by the goal of hitting target neurons. Thus, we add an unprecedented mobility model to the literature in the field, introducing a distribution law of the intercontact times that merges features of both negative exponential and Pareto distribution laws. We give a constructive description and implementation of our model, as well as a short analytical form whose parameters are suitably estimated in terms of confidence intervals from experimental data. Numerical experiments show the model and related inference tools to be sufficiently robust to cope with two main requisites for its exploitation in a neural network: the nonindependence of the observed intercontact times and the feasibility of the model inversion problem to infer suitable mobility parameters.

A feed-forward neural logic based on synaptic and volume transmission.

We consider a homeostatic mechanism to maintain a plastic layer of a feed-forward neural network reactive to a long sequence of signals, with neither falling in a fixed point of the state space nor undergoing in overfitting. Homeostasis is achieved without asking the neural network to be able to pursue an offset through local feedbacks. Rather, each neuron evolves monotonically in the direction increasing its own parameter, while a global feedback emerges from volume transmission of a homostatic signal. Namely: 1) each neuron is triggered to increase its own parameter in order to exceed the mean value of all of the other neurons' parameters, and 2) a global feedback on the population emerges from the composition of the single neurons behavior paired with a reasonable rule through which surrounding neurons in the same layer are activated. We provide a formal description of the model that we implement in an ad hoc version of pi-calculus. Some numerical simulations will depict some typical behaviors that seem to show a plausible biological interpretation.

A general framework for learning rules from data.

With the aim of getting understandable symbolic rules to explain a given phenomenon, we split the task of learning these rules from sensory data in two phases: a multilayer perceptron maps features into propositional variables and a set of subsequent layers operated by a PAC-like algorithm learns Boolean expressions on these variables. The special features of this procedure are that: i) the neural network is trained to produce a Boolean output having the principal task of discriminating between classes of inputs; ii) the symbolic part is directed to compute rules within a family that is not known a priori; iii) the welding point between the two learning systems is represented by a feedback based on a suitability evaluation of the computed rules. The procedure we propose is based on a computational learning paradigm set up recently in some papers in the fields of theoretical computer science, artificial intelligence and cognitive systems. The present article focuses on information management aspects of the procedure. We deal with the lack of prior information about the rules through learning strategies that affect both the meaning of the variables and the description length of the rules into which they combine. The paper uses the task of learning to formally discriminate among several emotional states as both a working example and a test bench for a comparison with previous symbolic and subsymbolic methods in the field.

Learning fuzzy decision trees.

We present a recurrent neural network which learns to suggest the next move during the descent along the branches of a decision tree. More precisely, given a decision instance represented by a node in the decision tree, the network provides the degree of membership of each possible move to the fuzzy set z.Lt;good movez.Gt;. These fuzzy values constitute the core of the probability of selecting the move out of the set of the children of the current node.This results in a natural way for driving the sharp discrete-state process running along the decision tree by means of incremental methods on the continuous-valued parameters of the neural network. The bulk of the learning problem consists in stating useful links between the local decisions about the next move and the global decisions about the suitability of the final solution. The peculiarity of the learning task is that the network has to deal explicitly with the twofold charge of lighting up the best solution and generating the move sequence that leads to that solution. We tested various options for the learning procedure on the problem of disambiguating natural language sentences.

Learning by Asymmetric Parallel Boltzmann Machines.

We consider the Little, Shaw, Vasudevan model as a parallel asymmetric Boltzmann machine, in the sense that we extend to this model the entropic learning rule first studied by Ackley, Hinton, and Sejnowski in the case of a sequentially activated network with symmetric synaptic matrix. The resulting Hebbian learning rule for the parallel asymmetric model draws the signal for the updating of synaptic weights from time averages of the discrepancy between expected and actual transitions along the past history of the network. As we work without the hypothesis of symmetry of the weights, we can include in our analysis also feedforward networks, for which the entropic learning rule turns out to be complementary to the error backpropagation rule, in that it "rewards the correct behavior" instead of "penalizing the wrong answers."