4,422 research outputs found
Conjunctive Bayesian networks
Conjunctive Bayesian networks (CBNs) are graphical models that describe the
accumulation of events which are constrained in the order of their occurrence.
A CBN is given by a partial order on a (finite) set of events. CBNs generalize
the oncogenetic tree models of Desper et al. by allowing the occurrence of an
event to depend on more than one predecessor event. The present paper studies
the statistical and algebraic properties of CBNs. We determine the maximum
likelihood parameters and present a combinatorial solution to the model
selection problem. Our method performs well on two datasets where the events
are HIV mutations associated with drug resistance. Concluding with a study of
the algebraic properties of CBNs, we show that CBNs are toric varieties after a
coordinate transformation and that their ideals possess a quadratic Gr\"{o}bner
basis.Comment: Published in at http://dx.doi.org/10.3150/07-BEJ6133 the Bernoulli
(http://isi.cbs.nl/bernoulli/) by the International Statistical
Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm
Systems approaches and algorithms for discovery of combinatorial therapies
Effective therapy of complex diseases requires control of highly non-linear
complex networks that remain incompletely characterized. In particular, drug
intervention can be seen as control of signaling in cellular networks.
Identification of control parameters presents an extreme challenge due to the
combinatorial explosion of control possibilities in combination therapy and to
the incomplete knowledge of the systems biology of cells. In this review paper
we describe the main current and proposed approaches to the design of
combinatorial therapies, including the empirical methods used now by clinicians
and alternative approaches suggested recently by several authors. New
approaches for designing combinations arising from systems biology are
described. We discuss in special detail the design of algorithms that identify
optimal control parameters in cellular networks based on a quantitative
characterization of control landscapes, maximizing utilization of incomplete
knowledge of the state and structure of intracellular networks. The use of new
technology for high-throughput measurements is key to these new approaches to
combination therapy and essential for the characterization of control
landscapes and implementation of the algorithms. Combinatorial optimization in
medical therapy is also compared with the combinatorial optimization of
engineering and materials science and similarities and differences are
delineated.Comment: 25 page
Cheating for Problem Solving: A Genetic Algorithm with Social Interactions
We propose a variation of the standard genetic algorithm that incorporates
social interaction between the individuals in the population. Our goal is to
understand the evolutionary role of social systems and its possible application
as a non-genetic new step in evolutionary algorithms. In biological
populations, ie animals, even human beings and microorganisms, social
interactions often affect the fitness of individuals. It is conceivable that
the perturbation of the fitness via social interactions is an evolutionary
strategy to avoid trapping into local optimum, thus avoiding a fast convergence
of the population. We model the social interactions according to Game Theory.
The population is, therefore, composed by cooperator and defector individuals
whose interactions produce payoffs according to well known game models
(prisoner's dilemma, chicken game, and others). Our results on Knapsack
problems show, for some game models, a significant performance improvement as
compared to a standard genetic algorithm.Comment: 7 pages, 5 Figures, 5 Tables, Proceedings of Genetic and Evolutionary
Computation Conference (GECCO 2009), Montreal, Canad
Artificial and Natural Genetic Information Processing
Conventional methods of genetic engineering and more recent genome editing techniques focus on identifying genetic target sequences for manipulation. This is a result of historical concept of the gene which was also the main assumption of the ENCODE project designed to identify all functional elements in the human genome sequence.
However, the theoretical core concept changed dramatically. The old concept of genetic sequences which can be assembled and manipulated like molecular bricks has problems in explaining the natural genome-editing competences of viruses and RNA consortia that are able to insert or delete, combine and recombine genetic sequences
more precisely than random-like into cellular host organisms according to adaptational needs or even generate sequences de novo. Increasing knowledge about natural genome editing questions the traditional narrative of mutations (error replications) as essential for generating genetic diversity and genetic content arrangements in biological systems. This may have far-reaching consequences for our understanding
of artificial genome editing
Data Science and Ebola
Data Science---Today, everybody and everything produces data. People produce
large amounts of data in social networks and in commercial transactions.
Medical, corporate, and government databases continue to grow. Sensors continue
to get cheaper and are increasingly connected, creating an Internet of Things,
and generating even more data. In every discipline, large, diverse, and rich
data sets are emerging, from astrophysics, to the life sciences, to the
behavioral sciences, to finance and commerce, to the humanities and to the
arts. In every discipline people want to organize, analyze, optimize and
understand their data to answer questions and to deepen insights. The science
that is transforming this ocean of data into a sea of knowledge is called data
science. This lecture will discuss how data science has changed the way in
which one of the most visible challenges to public health is handled, the 2014
Ebola outbreak in West Africa.Comment: Inaugural lecture Leiden Universit
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