156 research outputs found
Bio-logic: gene expression and the laws of combinatorial logic
Original article can be found at: http://www.mitpressjournals.org/ Copyright MIT Press DOI: 10.1162/artl.2008.14.1.121At the heart of the development of fertilized eggs into fully formed organisms and the adaptation of cells to changed conditions are genetic regulatory networks (GRNs). In higher multi-cellular organisms, signal selection and multiplexing is performed at the cis-regulatory domains of genes, where combinations of transcription factors (TFs) regulate the rates at which the genes are transcribed into mRNA. To be able to act as activators or repressors of gene transcription, TFs must first bind to target sequences on the regulatory domains. Two TFs that act in concert may bind entirely independently of each other, but more often binding of the first one will alter the affinity of the other for its binding site. This paper presents a systematic investigation into the effect of TF binding dependencies on the predicted regulatory function of this “bio-logic”. Four extreme scenarios, commonly used to classify enzyme activation and inhibition patterns, for the binding of two TFs were explored: independent (the TFs bind without affecting each other’s affinities), competitive (the TFs compete for the same binding site), ordered (the TFs bind in a compulsory order), and joint binding (the TFs either bind as a preformed complex, or binding of one is virtually impossible in the absence of the other). The conclusions are: 1) the laws of combinatorial logic hold only for systems with independently binding TFs; 2) systems formed according to the other scenarios can mimic the functions of their Boolean logical counterparts, but cannot be combined or decomposed in the same way; and 3) the continuously scaled output of systems consisting of competitively binding activators and repressors can be more robustly controlled than that of single TF or (quasi-) logical multi-TF systems. Keywords: Transcription regulation, Genetic regulatory networks, Enzyme kinetics, Combinatorial logic, Non-Boolean continuous logic, Modelling.Peer reviewe
Session Types in Abelian Logic
There was a PhD student who says "I found a pair of wooden shoes. I put a
coin in the left and a key in the right. Next morning, I found those objects in
the opposite shoes." We do not claim existence of such shoes, but propose a
similar programming abstraction in the context of typed lambda calculi. The
result, which we call the Amida calculus, extends Abramsky's linear lambda
calculus LF and characterizes Abelian logic.Comment: In Proceedings PLACES 2013, arXiv:1312.221
Parallel symbolic state-space exploration is difficult, but what is the alternative?
State-space exploration is an essential step in many modeling and analysis
problems. Its goal is to find the states reachable from the initial state of a
discrete-state model described. The state space can used to answer important
questions, e.g., "Is there a dead state?" and "Can N become negative?", or as a
starting point for sophisticated investigations expressed in temporal logic.
Unfortunately, the state space is often so large that ordinary explicit data
structures and sequential algorithms cannot cope, prompting the exploration of
(1) parallel approaches using multiple processors, from simple workstation
networks to shared-memory supercomputers, to satisfy large memory and runtime
requirements and (2) symbolic approaches using decision diagrams to encode the
large structured sets and relations manipulated during state-space generation.
Both approaches have merits and limitations. Parallel explicit state-space
generation is challenging, but almost linear speedup can be achieved; however,
the analysis is ultimately limited by the memory and processors available.
Symbolic methods are a heuristic that can efficiently encode many, but not all,
functions over a structured and exponentially large domain; here the pitfalls
are subtler: their performance varies widely depending on the class of decision
diagram chosen, the state variable order, and obscure algorithmic parameters.
As symbolic approaches are often much more efficient than explicit ones for
many practical models, we argue for the need to parallelize symbolic
state-space generation algorithms, so that we can realize the advantage of both
approaches. This is a challenging endeavor, as the most efficient symbolic
algorithm, Saturation, is inherently sequential. We conclude by discussing
challenges, efforts, and promising directions toward this goal
Applications of Nonclassical Logic Methods for Purposes of Knowledge Discovery and Data Mining
* The work is partially supported by Grant no. NIP917 of the Ministry of Science and Education – Republic of Bulgaria.Methods for solution of a large class of problems on the base of nonclassical, multiple-valued, and
probabilistic logics have been discussed. A theory of knowledge about changing knowledge, of defeasible
inference, and network approach to an analogous derivation have been suggested. A method for regularity
search, logic-axiomatic and logic-probabilistic methods for learning of terms and pattern recognition in the case of
multiple-valued logic have been described and generalized. Defeasible analogical inference and new forms of
inference using exclusions are considered. The methods are applicable in a broad range of intelligent systems
Automata & Sequential Machines, A Survey
Coordinated Science Laboratory was formerly known as Control Systems LaboratoryContract DA-36-039-TR US AMC 02208(E
- …