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Register a new userReducing Boolean Networks with Backward Boolean Equivalence
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Added by
Georgios Argyris
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Boolean Networks (BNs) are established models to qualitatively describe biological systems. The analysis of BNs might be infeasible for medium to large BNs due to the state-space explosion problem. We propose a novel reduction technique called emph{Backward Boolean Equivalence} (BBE), which preserves some properties of interest of BNs. In particular, reduced BNs provide a compact representation by grouping variables that, if initialized equally, are always updated equally. The resulting reduced state space is a subset of the original one, restricted to identical initialization of grouped variables. The corresponding trajectories of the original BN can be exactly restored. We show the effectiveness of BBE by performing a large-scale validation on the whole GINsim BN repository. In selected cases, we show how our method enables analyses that would be otherwise intractable. Our method complements, and can be combined with, other reduction methods found in the literature.
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Boolean networks are discrete dynamical systems for modeling regulation and signaling in living cells. We investigate a particular class of Boolean functions with inhibiting inputs exerting a veto (forced zero) on the output. We give analytical expressions for the sensitivity of these functions and provide evidence for their role in natural systems. In an intracellular signal transduction network [Helikar et al., PNAS (2008)], the functions with veto are over-represented by a factor exceeding the over-representation of threshold functions and canalyzing functions in the same system. In Boolean networks for control of the yeast cell cycle [Fangting Li et al., PNAS (2004), Davidich et al., PLoS One (2009)], none or minimal changes to the wiring diagrams are necessary to formulate their dynamics in terms of the veto functions introduced here.
While on some natural distributions, neural-networks are trained efficiently using gradient-based algorithms, it is known that learning them is computationally hard in the worst-case. To separate hard from easy to learn distributions, we observe the property of local correlation: correlation between local patterns of the input and the target label. We focus on learning deep neural-networks using a gradient-based algorithm, when the target function is a tree-structured Boolean circuit. We show that in this case, the existence of correlation between the gates of the circuit and the target label determines whether the optimization succeeds or fails. Using this result, we show that neural-networks can learn the (log n)-parity problem for most product distributions. These results hint that local correlation may play an important role in separating easy/hard to learn distributions. We also obtain a novel depth separation result, in which we show that a shallow network cannot express some functions, while there exists an efficient gradient-based algorithm that can learn the very same functions using a deep network. The negative expressivity result for shallow networks is obtained by a reduction from results in communication complexity, that may be of independent interest.
Observabililty is an important topic of Boolean control networks (BCNs). In this paper, we propose a new type of observability named online observability to present the sufficient and necessary condition of determining the initial states of BCNs, when their initial states cannot be reset. And we design an algorithm to decide whether a BCN has the online observability. Moreover, we prove that a BCN is identifiable iff it satisfies controllability and the online observability, which reveals the essence of identification problem of BCNs.
A new analytical framework consisting of two phenomena: single sample and multiple samples, is proposed to deal with the identification problem of Boolean control networks (BCNs) systematically and comprehensively. Under this framework, the existing works on identification can be categorized as special cases of these two phenomena. Several effective criteria for determining the identifiability and the corresponding identification algorithms are proposed. Three important results are derived: (1) If a BN is observable, it is uniquely identifiable; (2) If a BCN is O1-observable, it is uniquely identifiable, where O1-observability is the most general form of the existing observability terms; (3) A BN or BCN may be identifiable, but not observable. In addition, remarks present some challenging future research and contain a preliminary attempt about how to identify unobservable systems.
We study the stable attractors of a class of continuous dynamical systems that may be idealized as networks of Boolean elements, with the goal of determining which Boolean attractors, if any, are good approximations of the attractors of generic continuous systems. We investigate the dynamics in simple rings and rings with one additional self-input. An analysis of switching characteristics and pulse propagation explains the relation between attractors of the continuous systems and their Boolean approximations. For simple rings, reliable Boolean attractors correspond to stable continuous attractors. For networks with more complex logic, the qualitative features of continuous attractors are influenced by inherently non-Boolean characteristics of switching events.
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