Dynamic Control of Explore/Exploit Trade-Off In Bayesian Optimization

Bayesian optimization offers the possibility of optimizing black-box operations not accessible through traditional techniques. The success of Bayesian optimization methods such as Expected Improvement (EI) are significantly affected by the degree of trade-off between exploration and exploitation. Too much exploration can lead to inefficient optimization protocols, whilst too much exploitation leaves the protocol open to strong initial biases, and a high chance of getting stuck in a local minimum. Typically, a constant margin is used to control this trade-off, which results in yet another hyper-parameter to be optimized. We propose contextual improvement as a simple, yet effective heuristic to counter this - achieving a one-shot optimization strategy. Our proposed heuristic can be swiftly calculated and improves both the speed and robustness of discovery of optimal solutions. We demonstrate its effectiveness on both synthetic and real world problems and explore the unaccounted for uncertainty in the pre-determination of search hyperparameters controlling explore-exploit trade-off.Comment: Accepted for publication in the proceedings of 2018 Computing Conferenc

Swimming eukaryotic microorganisms exhibit a universal speed distribution.

One approach to quantifying biological diversity consists of characterizing the statistical distribution of specific properties of a taxonomic group or habitat. Microorganisms living in fluid environments, and for whom motility is key, exploit propulsion resulting from a rich variety of shapes, forms, and swimming strategies. Here, we explore the variability of swimming speed for unicellular eukaryotes based on published data. The data naturally partitions into that from flagellates (with a small number of flagella) and from ciliates (with tens or more). Despite the morphological and size differences between these groups, each of the two probability distributions of swimming speed are accurately represented by log-normal distributions, with good agreement holding even to fourth moments. Scaling of the distributions by a characteristic speed for each data set leads to a collapse onto an apparently universal distribution. These results suggest a universal way for ecological niches to be populated by abundant microorganisms.This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 682754 to EL), and from Established Career Fellowship EP/M017982/1 from the Engineering and Physical Sciences Research Council and Grant 7523 from the Gordon and Betty Moore Foundation (REG)

The non-Gaussian tops and tails of diffusing boomerangs

Experiments involving the two-dimensional passive diffusion of colloidal boomerangs tracked off their centre of mobility have shown striking non-Gaussian tails in their probability distribution function [Chakrabarty et al., Soft Matter, 2016, 12, 4318]. This in turn can lead to anomalous diffusion characteristics, including mean drift. In this paper, we develop a general theoretical explanation for these measurements. The idea relies on calculating the two-dimensional probability densities at the centre of mobility of the particle, where all distributions are Gaussian, and then transforming them to a different reference point. Our model clearly captures the experimental results, without any fitting parameters, and demonstrates that the one-dimensional probability distributions may also exhibit strongly non-Gaussian tops. These results indicate that the choice of tracking point can cause a considerable departure from Gaussian statistics, potentially causing some common modelling techniques to fail.This research was funded in part by an ERC grant to EL and a Mobility Plus Fellowship from the Polish Ministry of Science and Higher Education to ML

Phoretic flow induced by asymmetric confinement

Internal phoretic flows due to the interactions of solid boundaries with local chemical gradients may be created using chemical patterning. Alternatively, we demonstrate here that internal flows might also be induced by geometric asymmetries of chemically homogeneous surfaces. We characterise the circulatory flow created in a cavity enclosed between two eccentric cylindrical walls of uniform chemical activity. Local gradients of the diffusing solute induce a slip flow along the surface of the cylinders, leading to a circulatory bulk flow pattern which can be solved analytically in the diffusive limit. The flow strength can be controlled by adjusting the relative positions of the cylinders, and an optimal configuration is identified. These results provide a model system for tunable phoretic pumps.This work was funded in part by a David Crighton Fellowship at the University of Cambridge (ML), a Mobility Plus Fellowship from the Polish Ministry of Science and Higher Education (ML), the EU through a Marie-Curie CIG grant (EL) and the French Ministry of Defense DGA (SM).This is the author accepted manuscript. The final version is available from Cambridge University Press via http://dx.doi.org/10.1017/jfm.2016.40

Hydrodynamic coupling and rotational mobilities near planar elastic membranes

We study theoretically and numerically the coupling and rotational hydrodynamic interactions between spherical particles near a planar elastic membrane that exhibits resistance towards shear and bending. Using a combination of the multipole expansion and Faxen's theorems, we express the frequency-dependent hydrodynamic mobility functions as a power series of the ratio of the particle radius to the distance from the membrane for the self mobilities, and as a power series of the ratio of the radius to the interparticle distance for the pair mobilities. In the quasi-steady limit of zero frequency, we find that the shear- and bending-related contributions to the particle mobilities may have additive or suppressive effects depending on the membrane properties in addition to the geometric configuration of the interacting particles relative to the confining membrane. To elucidate the effect and role of the change of sign observed in the particle self and pair mobilities, we consider an example involving a torque-free doublet of counterrotating particles near an elastic membrane. We find that the induced rotation rate of the doublet around its center of mass may differ in magnitude and direction depending on the membrane shear and bending properties. Near a membrane of only energetic resistance toward shear deformation, such as that of a certain type of elastic capsules, the doublet undergoes rotation of the same sense as observed near a no-slip wall. Near a membrane of only energetic resistance toward bending, such as that of a fluid vesicle, we find a reversed sense of rotation. Our analytical predictions are supplemented and compared with fully resolved boundary integral simulations where a very good agreement is obtained over the whole range of applied frequencies.Comment: 14 pages, 7 figures. Revised manuscript resubmitted to J. Chem. Phy

In silico analysis of gene expression in V3a and the superior occipital gyrus. Relevance for migraine

Introduction: Visual manifestations are the most prominent non-painful features of migraine. During the last decades, visual area V3a has gathered attention of headache scientists because of its apparent implication on aura initiation, photophobia and cortical hyper-responsiveness related to visual motion perception. In this hypothesis-generating study, we performed an in silico analysis of gene expression in left V3a and the cerebral gyrus that harbours it (left superior occipital gyrus (lSOG)) searching for transcriptomic patterns that could be linked with migraine’s pathophysiology. Materials and methods: Neurotransmitter receptor gene expression levels in left V3a were extracted from validated brain mRNA expression models using a probabilistic volumetric mask of this region. The primary visual cortex and other sensory cortices (auditory, olfactory and somatosensory) were used as comparators. Genome-wide transcriptomic differences between the gyrus harbouring left V3a (lSOG) and the rest of the cerebral cortex were assessed using the Allen Brain Institute Human RNA micro array atlas/database. Results: Adrenergic receptor β1, dopaminergic receptor D3 and serotoninergic receptors 1B, 1F and 2A, which have been previously implicated in migraine’s pathophysiology and/or treatment, showed significantly higher expression levels on left V3a. Transcriptomic differences between the lSOG harbouring V3a and the rest of the cortex comprise genes whose products are involved in neuronal excitability (SLC17A6, KCNS1, KCNG1 and GABRQ), activation of multiple signal transduction pathways (MET) and cell metabolism (SPHKAP via its interaction with cAMP-dependent protein kinase). Conclusions: Focal gene expression analysis of V3a suggests some clues about its implication in migraine. Further studies are warranted

Structural insights into crista junction formation by the Mic60-Mic19 complex

Mitochondrial cristae membranes are the oxidative phosphorylation sites in cells. Crista junctions (CJs) form the highly curved neck regions of cristae and are thought to function as selective entry gates into the cristae space. Little is known about how CJs are generated and maintained. We show that the central coiled-coil (CC) domain of the mitochondrial contact site and cristae organizing system subunit Mic60 forms an elongated, bow tie–shaped tetrameric assembly. Mic19 promotes Mic60 tetramerization via a conserved interface between the Mic60 mitofilin and Mic19 CHCH (CC-helix-CC-helix) domains. Dimerization of mitofilin domains exposes a crescent-shaped membrane-binding site with convex curvature tailored to interact with the curved CJ neck. Our study suggests that the Mic60-Mic19 subcomplex traverses CJs as a molecular strut, thereby controlling CJ architecture and function