[PDF] Top 20 Learning Boolean logic models of signaling networks with ASP
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Learning Boolean logic models of signaling networks with ASP
... list of ASP applications in systems ...problem of representing and reasoning about signaling networks ...question of pruning or identification of biological ... Voir le document complet
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Comparing Signaling Networks between Normal and Transformed Hepatocytes Using Discrete Logical Models
... Because Boolean models lack continuous parameters (akin to the rate constants in an differential equation network), it is not necessarily true that training will yield a model having a substantially better ... Voir le document complet
21
Reasoning on the response of logical signaling networks with answer set programming
... cope with multi-objective optimization is to transform it into a single-objective ...power of the ...scales of measurements that need to be ...context logic models providing high ... Voir le document complet
155
Reasoning on the response of logical signaling networks with Answer Set Programming
... all models found can explain the data similarly or equally well if one take into account the experimental ...execution of the algorithm which is not necessarily the global ...incompleteness of ... Voir le document complet
47
CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms
... complicated models if they explain the data equally ...the Boolean state predicted by the ...associated with a mismatch with the Boolean output of the ...part of the model ... Voir le document complet
15
Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming
... view of the space of solutions, we investigated the role of the model size over the optimization ...choice of a model of minimal size -according to a parsimonious principle- by a free ... Voir le document complet
22
Fixing monotone Boolean networks asynchronously
... in networks f which can be fixed in polynomial time, ...F of n-component ...members of F are ...length of a shortest word fixing ...result of this kind was given in [15], where it is ... Voir le document complet
22
Topological fixed points in Boolean networks
... point of G ...vertex of G has a predecessor and at most one unsigned predecessor, and G has no undirected negative ...component of ˜ G induces an interaction graph that satisfies the conditions ... Voir le document complet
6
Conformance Checking with Constraint Logic Programming: The Case of Feature Models
... checking of Product Line Models ...topic of Systems Engineering that requires adequate models, meta-models, methods, and ...kind of consistency verification called conformance ... Voir le document complet
11
Epistemic boolean games based on a logic of visibility and control
... epistemic boolean games in a compu- tationally grounded dynamic epistemic ...values of atoms. We provide an axiomatisa- tion of the logic, establish that the model checking problem is in PS ... Voir le document complet
9
Boolean Networks: Beyond Generalized Asynchronicity
... Abstract. Boolean networks are commonly used in systems biology to model dynamics of biochemical networks by abstracting away many (and often unknown) parameters related to speed and species ... Voir le document complet
15
Feasibility and reliability of sequential logic with gene regulatory networks
... Simple boolean functions have been routinely implemented with gene regulatory networks (GRNs) for the last two decades [ 1 – 10 ...most of them, the output signal depends only on the current ... Voir le document complet
20
Algorithms for the Sequential Reprogramming of Boolean Networks
... Most of the existing computational methods for controlling which attractor (steady state) the cell will reach focus on finding mutations to apply to the initial ...dynamics of the system prepares the ... Voir le document complet
12
Note on models of polarised intuitionistic logic
... model of linear logic V gives rise to a model of intuitionistic logic in the Kleisli category V ! ; the latter is equipped with the dual of a thunk which we call a runnable ... Voir le document complet
10
Isomorphic Boolean networks and dense interaction graphs
... no networks f such that G(f ) only contains the complete ...all networks f with n ≥ 5 ...network with n ≥ 5 components, then |G(f )| = 1 if and only if f = id or f = ... Voir le document complet
14
A reduction method for noisy Boolean networks
... B of a NBN is geometri with mean 1/npα , we negle t transitions of order 1 from transient states as well as transitions of order 2 or more (transitions from transient or attra tor states due ... Voir le document complet
49
Validation of biological models with Temporal logic and Timed Hybrid Petri nets
... understanding of the functioning of a biological system like the cell, taking into account not only molecular phenomena but also structuration of the cells, communication channels and exchanges ... Voir le document complet
7
Learning aspect models with partially labeled data
... some of the errors in the translation generated by the RBMT ...consisting of initial output from the RBMT system on a given source-language text in parallel with a version of this output that ... Voir le document complet
7
Quantum half-adder Boolean logic gate with a nano-graphene molecule and graphene nano-electrodes
... molecule Boolean 1/2-adder is designed and the XOR and AND truth table calculated at ...functions with level re- pulsion and destructive interferences effects using 4 molecule electronic states in a quantum ... Voir le document complet
22
Supervised Reconstruction of Biological Networks with Local Models
... reconstruction of protein networks using a variety of available genomic ...sets of pertinent biological information about the known enzymes, such as gene expression data, phylogenetic data and ... Voir le document complet
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