Search results for "Theoretical Computer Science"
showing 10 items of 1151 documents
Verification of scope-dependent hierarchical state machines
2008
AbstractA hierarchical state machine (Hsm) is a finite state machine where a vertex can either expand to another hierarchical state machine (box) or be a basic vertex (node). Each node is labeled with atomic propositions. We study an extension of such model which allows atomic propositions to label also boxes (Shsm). We show that Shsms can be exponentially more succinct than Shsms and verification is in general harder by an exponential factor. We carefully establish the computational complexity of reachability, cycle detection, and model checking against general Ltl and Ctl specifications. We also discuss some natural and interesting restrictions of the considered problems for which we can …
Verifying a medical protocol with temporal graphs: the case of a nosocomial disease.
2014
Abstract Objective Our contribution focuses on the implementation of a formal verification approach for medical protocols with graphical temporal reasoning paths to facilitate the understanding of verification steps. Materials and methods Formal medical guideline specifications and background knowledge are represented through conceptual graphs, and reasoning is based on graph homomorphism. These materials explain the underlying principles or rationale that guide the functioning of verifications. Results An illustration of this proposal is made using a medical protocol defining guidelines for the monitoring and prevention of nosocomial infections. Such infections, which are acquired in the h…
A heuristic for problem formalization in agent based simulation studies
2015
Agent Based Modeling and Simulation (ABMS) is considered an effective approach for conducting simulation studies in many fields. In order to develop high quality simulation models, methodological approaches are demanded. In such direction we are moving by proposing a heuristic for the formalization of agent based simulation problems. The proposed heuristic is based on some guidelines developed for identifying the main elements of the problem domain description by analysing verbs and their common taxonomy in grammar.
What place does molecular topology have in today’s drug discovery?
2020
Introduction: Most methods in molecular and drug design are currently based on physicochemical descriptors. However, molecular topology, which relies on topological descriptors, has also shown value for molecular design even if it does not take into account the physical or chemical properties of ligands and receptors, including the ligand-receptor interaction itself. Areas covered: Herein, the authors provide new insights into the importance of molecular topology according to some of the latest discoveries in physics and chemistry. Furthermore, the authors report on the most significant achievements in drug design using molecular topology over the last 5 years and give their expert perspect…
On the contribution of molecular topology to drug design and discovery.
2010
Abstract The role of molecular topology (MT) in the design and selection of new drugs is discussed. After an overview of the different in silico molecular design current technologies, the QSAR analysis is dealt in detail with particular emphasis in the use of topological indices as molecular descriptors. The results of the application of MT in drug design and discovery are described and finally a possible explanation is given about some of the key reasons explaining it's the extraordinary performance.
Exploiting a list of protein sequences
2007
Abstract: We describe a software program to help exploit a database of aligned protein sequences. In addition to the classical lists of sequences, a graphical representation is used to get a better overview of the information. As natural parameters, the type of amino acid and sequence position are used. Various plots or 3D representations are then updated. Examples are shown based on globin sequences from various species and on the abnormal human hemoglobins. The software should be of interest to protein engineers who need to know what variants are already known.
General topological patterns of known drugs.
2001
Abstract Discriminating “drug-like” from “non-drug-like” compounds is a relatively emerging topic within the drug research. The basic assumption is that it is possible to obtain relevant information from structural features common to the known drugs, in order to discard a huge number of candidate chemical structures with low probability of becoming drugs. A graph-theoretical contribution to this subject is reported in this paper, by making exclusive use of linear relationships. The results suggest that it is possible to achieve a pattern of general pharmacological activity based on molecular topology. Conclusions are tentative pending verification of the results with larger compound librari…
Protein knot server: detection of knots in protein structures
2007
KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regul…
Posets That Locally Resemble Distributive Lattices
2000
Abstract Let P be a graded poset with 0 and 1 and rank at least 3. Assume that every rank 3 interval is a distributive lattice and that, for every interval of rank at least 4, the interval minus its endpoints is connected. It is shown that P is a distributive lattice, thus resolving an issue raised by Stanley. Similar theorems are proven for semimodular, modular, and complemented modular lattices. As a corollary, a theorem of Stanley for Boolean lattices is obtained, as well as a theorem of Grabiner (conjectured by Stanley) for products of chains. Applications to incidence geometry and connections with the theory of buildings are discussed.
Distributed evolutionary approach to data clustering and modeling
2014
In this article we describe a framework (DEGA-Gen) for the application of distributed genetic algorithms for detection of communities in networks. The framework proposes efficient ways of encoding the network in the chromosomes, greatly optimizing the memory use and computations, resulting in a scalable framework. Different objective functions may be used for producing division of network into communities. The framework is implemented using open source implementation of MapReduce paradigm, Hadoop. We validate the framework by developing community detection algorithm, which uses modularity as measure of the division. Result of the algorithm is the network, partitioned into non-overlapping co…