F-measure Maximization in Multi-Label Classification with Conditionally Independent Label Subsets

We discuss a method to improve the exact F-measure maximization algorithm called GFM, proposed in (Dembczynski et al. 2011) for multi-label classification, assuming the label set can be can partitioned into conditionally independent subsets given the input features. If the labels were all independent, the estimation of only $m$ parameters ($m$ denoting the number of labels) would suffice to derive Bayes-optimal predictions in $O(m^2)$ operations. In the general case, $m^2+1$ parameters are required by GFM, to solve the problem in $O(m^3)$ operations. In this work, we show that the number of parameters can be reduced further to $m^2/n$, in the best case, assuming the label set can be partitioned into $n$ conditionally independent subsets. As this label partition needs to be estimated from the data beforehand, we use first the procedure proposed in (Gasse et al. 2015) that finds such partition and then infer the required parameters locally in each label subset. The latter are aggregated and serve as input to GFM to form the Bayes-optimal prediction. We show on a synthetic experiment that the reduction in the number of parameters brings about significant benefits in terms of performance

Distributional fixed point equations for island nucleation in one dimension: a retrospective approach for capture zone scaling

The distributions of inter-island gaps and captures zones for islands nucleated on a one-dimensional substrate during submonolayer deposition are considered using a novel retrospective view. This provides an alternative perspective on why scaling occurs in this continuously evolving system. Distributional fixed point equations for the gaps are derived both with and without a mean field approximation for nearest neighbour gap size correlation. Solutions to the equations show that correct consideration of fragmentation bias justifies the mean field approach which can be extended to provide closed-from equations for the capture zones. Our results compare favourably to Monte Carlo data for both point and extended islands using a range of critical island size $i=0,1,2,3$. We also find satisfactory agreement with theoretical models based on more traditional fragmentation theory approaches.Comment: 9 pages, 7 figures and 1 tabl

Using integrated absorption to calibrate optical cavity spectrometers

Sensitive absorption techniques using optical cavities (such as CEAS or ICOS) generally need the spectrometer response to be calibrated for quantitative measurements. Most calibrations are based on the instrument response to a known, steady state absorption. Such calibrations often have drawbacks in terms of cost, complexity, or convenience, especially for field measurements. In this paper, we show that the relationship between the integrated absorption and a known amount of absorber provides an alternative calibration strategy that yields a highly linear calibration curve and has a low uncertainty. This method is straightforward to implement and offers a practical alternative to other calibration strategies

The process of irreversible nucleation in multilayer growth. II. Exact results in one and two dimensions

We study irreversible dimer nucleation on top of terraces during epitaxial growth in one and two dimensions, for all values of the step-edge barrier. The problem is solved exactly by transforming it into a first passage problem for a random walker in a higher-dimensional space. The spatial distribution of nucleation events is shown to differ markedly from the mean-field estimate except in the limit of very weak step-edge barriers. The nucleation rate is computed exactly, including numerical prefactors.Comment: 22 pages, 10 figures. To appear in Phys. Rev.

Spatio-temporal distribution of nucleation events during crystal growth

We consider irreversible second-layer nucleation that occurs when two adatoms on a terrace meet. We solve the problem analytically in one dimension for zero and infinite step-edge barriers, and numerically for any value of the barriers in one and two dimensions. For large barriers, the spatial distribution of nucleation events strongly differs from $\rho^2$, where $\rho$ is the stationary adatom density in the presence of a constant flux. The probability $Q(t)$ that nucleation occurs at time $t$ after the deposition of the second adatom, decays for short time as a power law [$Q(t)\sim t^{-1/2}$] in $d=1$ and logarithmically [$Q(t)\sim 1/\ln(t/t_0)$] in $d=2$; for long time it decays exponentially. Theories of the nucleation rate $\omega$ based on the assumption that it is proportional to $\rho^2$ are shown to overestimate $\omega$ by a factor proportional to the number of times an adatom diffusing on the terrace visits an already visited lattice site.Comment: 4 pages, 3 figures; accepted for publication on PR

Island nucleation in the presence of step edge barriers: Theory and applications

We develop a theory of nucleation on top of two-dimensional islands bordered by steps with an additional energy barrier $\Delta E_S$ for descending atoms. The theory is based on the concept of the residence time of an adatom on the island,and yields an expression for the nucleation rate which becomes exact in the limit of strong step edge barriers. This expression differs qualitatively and quantitatively from that obtained using the conventional rate equation approach to nucleation [J. Tersoff et al., Phys. Rev. Lett.72, 266 (1994)]. We argue that rate equation theory fails because nucleation is dominated by the rare instances when two atoms are present on the island simultaneously. The theory is applied to two distinct problems: The onset of second layer nucleation in submonolayer growth, and the distribution of the sizes of top terraces of multilayer mounds under conditions of strong step edge barriers. Application to homoepitaxial growth on Pt(111) yields the estimate $\Delta E_S \geq 0.33$ eV for the additional energy barrier at CO-decorated steps.Comment: 13 pages, 3 figure

Zooplankton Gut Passage Mobilizes Lithogenic Iron for Ocean Productivity

Iron is an essential nutrient for phytoplankton, but low concentrations limit primary production and associated atmospheric carbon drawdown in large parts of the world’s oceans [1 and 2]. Lithogenic particles deriving from aeolian dust deposition, glacial runoff, or river discharges can form an important source if the attached iron becomes dissolved and therefore bioavailable [3, 4 and 5]. Acidic digestion by zooplankton is a potential mechanism for iron mobilization [6], but evidence is lacking. Here we show that Antarctic krill sampled near glacial outlets at the island of South Georgia (Southern Ocean) ingest large amounts of lithogenic particles and contain 3-fold higher iron concentrations in their muscle than specimens from offshore, which confirms mineral dissolution in their guts. About 90% of the lithogenic and biogenic iron ingested by krill is passed into their fecal pellets, which contain ∼5-fold higher proportions of labile (reactive) iron than intact diatoms. The mobilized iron can be released in dissolved form directly from krill or via multiple pathways involving microbes, other zooplankton, and krill predators. This can deliver substantial amounts of bioavailable iron and contribute to the fertilization of coastal waters and the ocean beyond. In line with our findings, phytoplankton blooms downstream of South Georgia are more intensive and longer lasting during years with high krill abundance on-shelf. Thus, krill crop phytoplankton but boost new production via their nutrient supply. Understanding and quantifying iron mobilization by zooplankton is essential to predict ocean productivity in a warming climate where lithogenic iron inputs from deserts, glaciers, and rivers are increasing [7, 8, 9 and 10]

Characterizing Ranked Chinese Syllable-to-Character Mapping Spectrum: A Bridge Between the Spoken and Written Chinese Language

One important aspect of the relationship between spoken and written Chinese is the ranked syllable-to-character mapping spectrum, which is the ranked list of syllables by the number of characters that map to the syllable. Previously, this spectrum is analyzed for more than 400 syllables without distinguishing the four intonations. In the current study, the spectrum with 1280 toned syllables is analyzed by logarithmic function, Beta rank function, and piecewise logarithmic function. Out of the three fitting functions, the two-piece logarithmic function fits the data the best, both by the smallest sum of squared errors (SSE) and by the lowest Akaike information criterion (AIC) value. The Beta rank function is the close second. By sampling from a Poisson distribution whose parameter value is chosen from the observed data, we empirically estimate the $p$-value for testing the two-piece-logarithmic-function being better than the Beta rank function hypothesis, to be 0.16. For practical purposes, the piecewise logarithmic function and the Beta rank function can be considered a tie.Comment: 15 pages, 4 figure

"They just come, pick and go." The Acceptability of Integrated Medication Adherence Clubs for HIV and Non Communicable Disease (NCD) Patients in Kibera, Kenya

Introduction The number of people on antiretroviral therapy (ART) for the long-term management of HIV in low- and middle-income countries (LMICs) is continuing to increase, along with the prevalence of Non-Communicable Diseases (NCDs). The need to provide large volumes of HIV patients with ART has led to significant adaptations in how medication is delivered, but access to NCD care remains limited in many contexts. Medication Adherence Clubs (MACs) were established in Kibera, Kenya to address the large numbers of patients requiring chronic HIV and/or NCD care. Stable NCD and HIV patients can now collect their chronic medication every three months through a club, rather than through individual clinic appointments. METHODOLOGY: We conducted a qualitative research study to assess patient and health-care worker perceptions and experiences of MACs in the urban informal settlement of Kibera, Kenya. A total of 106 patients (with HIV and/or other NCDs) and health-care workers were purposively sampled and included in the study. Ten focus groups and 19 in-depth interviews were conducted and 15 sessions of participant observation were carried out at the clinic where the MACs took place. Thematic data analysis was conducted using NVivo software, and coding focussed on people's experiences of MACs, the challenges they faced and their perceptions about models of care for chronic conditions. RESULTS: MACs were considered acceptable to patients and health-care workers because they saved time, prevented unnecessary queues in the clinic and provided people with health education and group support whilst they collected their medication. Some patients and health-care workers felt that MACs reduced stigma for HIV positive patients by treating HIV as any other chronic condition. Staff and patients reported challenges recruiting patients into MACs, including patients not fully understanding the eligibility criteria for the clubs. There were also some practical challenges during the implementation of the clubs, but MACs have shown that it is possible to learn from ART provision and enable stable HIV and NCD patients to collect chronic medication together in a group. CONCLUSIONS: Extending models of care previously only offered to HIV-positive cohorts to NCD patients can help to de-stigmatise HIV, allow for the efficient clinical management of co-morbidities and enable patients to benefit from peer support. Through MACs, we have demonstrated that an integrated approach to providing medication for chronic diseases including HIV can be implemented in resource-poor settings and could thus be rolled out in other similar contexts

Continuous and correlated nucleation during nonstandard island growth at Ag/Si(111)-7x7 heteroepitaxy

We present a combined experimental and theoretical study of submonolayer heteroepitaxial growth of Ag on Si(111)-7x7 at temperatures from 420 K to 550 K when Ag atoms can easily diffuse on the surface and the reconstruction 7x7 remains stable. STM measurements for coverages from 0.05 ML to 0.6 ML show that there is an excess of smallest islands (each of them fills up just one half-unit cell - HUC) in all stages of growth. Formation of 2D wetting layer proceeds by continuous nucleation of the smallest islands in the proximity of larger 2D islands (extended over several HUCs) and following coalescence with them. Such a growth scenario is verified by kinetic Monte Carlo simulation which uses a coarse-grained model based on a limited capacity of HUC and a mechanism which increases nucleation probability in a neighbourhood of already saturated HUCs (correlated nucleation). The model provides a good fit for experimental dependences of the relative number of Ag-occupied HUCs and the preference in occupation of faulted HUCs on temperature and amount of deposited Ag. Parameters obtained for the hopping of Ag adatoms between HUCs agree with those reported earlier for initial stages of growth. The model provides two new parameters - maximum number of Ag atoms inside HUC, and on HUC boundary.Comment: LaTeX2e, BibTeX, 9 pages, 7 images, accepted to Phys. Rev.