113 research outputs found
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Predictive Entropy Search for Bayesian optimization with unknown constraints
Unknown constraints arise in many types of expensive black-box optimization
problems. Several methods have been proposed recently for performing Bayesian
optimization with constraints, based on the expected improvement (EI)
heuristic. However, EI can lead to pathologies when used with constraints. For
example, in the case of decoupled constraints---i.e., when one can
independently evaluate the objective or the constraints---EI can encounter a
pathology that prevents exploration. Additionally, computing EI requires a
current best solution, which may not exist if none of the data collected so far
satisfy the constraints. By contrast, information-based approaches do not
suffer from these failure modes. In this paper, we present a new
information-based method called Predictive Entropy Search with Constraints
(PESC). We analyze the performance of PESC and show that it compares favorably
to EI-based approaches on synthetic and benchmark problems, as well as several
real-world examples. We demonstrate that PESC is an effective algorithm that
provides a promising direction towards a unified solution for constrained
Bayesian optimization.José Miguel Hernández-Lobato acknowledges support
from the Rafael del Pino Foundation. Zoubin Ghahramani
acknowledges support from Google Focused Research
Award and EPSRC grant EP/I036575/1. Matthew
W. Hoffman acknowledges support from EPSRC grant
EP/J012300/1.This is the final published version. It first appeared at http://jmlr.org/proceedings/papers/v37/hernandez-lobatob15.html
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A General Framework for Constrained Bayesian Optimization using Information-based Search
We present an information-theoretic framework for solving global black-box optimization problems that also have black-box constraints. Of particular interest to us is to efficiently solve problems with constraints, in which subsets of the objective and constraint functions may be evaluated independently. For example, when the objective is evaluated on a CPU and the constraints are evaluated independently on a GPU. These problems require an acquisition function that can be separated into the contributions of the individual function evaluations. We develop one such acquisition function and call it Predictive Entropy Search with Constraints (PESC). PESC is an approximation to the expected information gain criterion and it compares favorably to alternative approaches based on improvement in several synthetic and real-world problems. In addition to this, we consider problems with a mix of functions that are fast and slow to evaluate. These problems require balancing the amount of time spent in the meta-computation of PESC and in the actual evaluation of the target objective. We take a bounded rationality approach and develop a partial update for PESC which trades off accuracy against speed. We then propose a method for adaptively switching between the partial and full updates for PESC. This allows us to interpolate between versions of PESC that are efficient in terms of function evaluations and those that are efficient in terms of wall-clock time. Overall, we demonstrate that PESC is an effective algorithm that provides a promising direction towards a unified solution for constrained Bayesian optimization.Rafael del Pino Foundation, Google Focused Research Award, Engineering and Physical Sciences Research Council (Grant IDs: EP/I036575/1, EP/J012300/1
Lattice-gas simulations of Domain Growth, Saturation and Self-Assembly in Immiscible Fluids and Microemulsions
We investigate the dynamical behavior of both binary fluid and ternary
microemulsion systems in two dimensions using a recently introduced
hydrodynamic lattice-gas model of microemulsions. We find that the presence of
amphiphile in our simulations reduces the usual oil-water interfacial tension
in accord with experiment and consequently affects the non-equilibrium growth
of oil and water domains. As the density of surfactant is increased we observe
a crossover from the usual two-dimensional binary fluid scaling laws to a
growth that is {\it slow}, and we find that this slow growth can be
characterized by a logarithmic time scale. With sufficient surfactant in the
system we observe that the domains cease to grow beyond a certain point and we
find that this final characteristic domain size is inversely proportional to
the interfacial surfactant concentration in the system.Comment: 28 pages, latex, embedded .eps figures, one figure is in colour, all
in one uuencoded gzip compressed tar file, submitted to Physical Review
Counterion Condensation and Fluctuation-Induced Attraction
We consider an overall neutral system consisting of two similarly charged
plates and their oppositely charged counterions and analyze the electrostatic
interaction between the two surfaces beyond the mean-field Poisson-Boltzmann
approximation. Our physical picture is based on the fluctuation-driven
counterion condensation model, in which a fraction of the counterions is
allowed to ``condense'' onto the charged plates. In addition, an expression for
the pressure is derived, which includes fluctuation contributions of the whole
system. We find that for sufficiently high surface charges, the distance at
which the attraction, arising from charge fluctuations, starts to dominate can
be large compared to the Gouy-Chapmann length. We also demonstrate that
depending on the valency, the system may exhibit a novel first-order binding
transition at short distances.Comment: 15 pages, 8 figures, to appear in PR
Partially Annealed Disorder and Collapse of Like-Charged Macroions
Charged systems with partially annealed charge disorder are investigated
using field-theoretic and replica methods. Charge disorder is assumed to be
confined to macroion surfaces surrounded by a cloud of mobile neutralizing
counterions in an aqueous solvent. A general formalism is developed by assuming
that the disorder is partially annealed (with purely annealed and purely
quenched disorder included as special cases), i.e., we assume in general that
the disorder undergoes a slow dynamics relative to fast-relaxing counterions
making it possible thus to study the stationary-state properties of the system
using methods similar to those available in equilibrium statistical mechanics.
By focusing on the specific case of two planar surfaces of equal mean surface
charge and disorder variance, it is shown that partial annealing of the
quenched disorder leads to renormalization of the mean surface charge density
and thus a reduction of the inter-plate repulsion on the mean-field or
weak-coupling level. In the strong-coupling limit, charge disorder induces a
long-range attraction resulting in a continuous disorder-driven collapse
transition for the two surfaces as the disorder variance exceeds a threshold
value. Disorder annealing further enhances the attraction and, in the limit of
low screening, leads to a global attractive instability in the system.Comment: 21 pages, 2 figure
Screened non-bonded interactions in native proteins manipulate optimal paths for robust residue communication
A protein structure is represented as a network of residues whereby edges are
determined by intra-molecular contacts. We introduce inhomogeneity into these
networks by assigning each edge a weight that is determined by amino-acid pair
potentials. Two methodologies are utilized to calculate the average path
lengths (APLs) between pairs: To minimize (i) the maximum weight in the strong
APL, and (ii) the total weight in the weak APL. We systematically screen edges
that have higher than a cutoff potential and calculate the shortest APLs in
these reduced networks, while keeping chain connectivity. Therefore,
perturbations introduced at a selected region of the residue network propagate
to remote regions only along the non-screened edges that retain their ability
to disseminate the perturbation. The shortest APLs computed from the reduced
homogeneous networks with only the strongest few non-bonded pairs closely
reproduce the strong APLs from the weighted networks. The rate of change in the
APL in the reduced residue network as compared to its randomly connected
counterpart remains constant until a lower bound. Upon further link removal,
this property shows an abrupt increase, towards a random coil behavior. Under
different perturbation scenarios, diverse optimal paths emerge for robust
residue communication.Comment: 21 pages with 6 figure
A Facile Strategy for In Situ Core-Template-Functionalizing Siliceous Hollow Nanospheres for Guest Species Entrapment
The shell wall-functionalized siliceous hollow nanospheres (SHNs) with functional molecules represent an important class of nanocarriers for a rich range of potential applications. Herein, a self-templated approach has been developed for the synthesis of in situ functionalized SHNs, in which the biocompatible long-chain polycarboxylates (i.e., polyacrylate, polyaspartate, gelatin) provide the framework for silica precursor deposition by simply controlling chain conformation with divalent metal ions (i.e., Ca2+, Sr2+), without the intervention of any external templates. Metal ions play crucial roles in the formation of organic vesicle templates by modulating the long chains of polymers and preventing them from separation by washing process. We also show that, by in situ functionalizing the shell wall of SHNs, it is capable of entrapping nearly an eightfold quantity of vitamin Bc in comparison to the bare bulk silica nanospheres. These results confirm the feasibility of guest species entrapment in the functionalized shell wall, and SHNs are effective carriers of guest (bio-)molecules potentially for a variety of biomedical applications. By rationally choosing the functional (self-templating) molecules, this concept may represent a general strategy for the production of functionalized silica hollow structures
Caprin Controls Follicle Stem Cell Fate in the Drosophila Ovary
Adult stem cells must balance self-renewal and differentiation for tissue homeostasis. The Drosophila ovary has provided a wealth of information about the extrinsic niche signals and intrinsic molecular processes required to ensure appropriate germline stem cell renewal and differentiation. The factors controlling behavior of the more recently identified follicle stem cells of the ovary are less well-understood but equally important for fertility. Here we report that translational regulators play a critical role in controlling these cells. Specifically, the translational regulator Caprin (Capr) is required in the follicle stem cell lineage to ensure maintenance of this stem cell population and proper encapsulation of developing germ cells by follicle stem cell progeny. In addition, reduction of one copy of the gene fmr1, encoding the translational regulator Fragile X Mental Retardation Protein, exacerbates the Capr encapsulation phenotype, suggesting Capr and fmr1 are regulating a common process. Caprin was previously characterized in vertebrates as Cytoplasmic Activation/Proliferation-Associated Protein. Significantly, we find that loss of Caprin alters the dynamics of the cell cycle, and we present evidence that misregulation of CycB contributes to the disruption in behavior of follicle stem cell progeny. Our findings support the idea that translational regulators may provide a conserved mechanism for oversight of developmentally critical cell cycles such as those in stem cell populations
Filament Depolymerization Can Explain Chromosome Pulling during Bacterial Mitosis
Chromosome segregation is fundamental to all cells, but the force-generating mechanisms underlying chromosome translocation in bacteria remain mysterious. Caulobacter crescentus utilizes a depolymerization-driven process in which a ParA protein structure elongates from the new cell pole, binds to a ParB-decorated chromosome, and then retracts via disassembly, pulling the chromosome across the cell. This poses the question of how a depolymerizing structure can robustly pull the chromosome that disassembles it. We perform Brownian dynamics simulations with a simple, physically consistent model of the ParABS system. The simulations suggest that the mechanism of translocation is “self-diffusiophoretic”: by disassembling ParA, ParB generates a ParA concentration gradient so that the ParA concentration is higher in front of the chromosome than behind it. Since the chromosome is attracted to ParA via ParB, it moves up the ParA gradient and across the cell. We find that translocation is most robust when ParB binds side-on to ParA filaments. In this case, robust translocation occurs over a wide parameter range and is controlled by a single dimensionless quantity: the product of the rate of ParA disassembly and a characteristic relaxation time of the chromosome. This time scale measures the time it takes for the chromosome to recover its average shape after it is has been pulled. Our results suggest explanations for observed phenomena such as segregation failure, filament-length-dependent translocation velocity, and chromosomal compaction
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