Interpretable Diabetic Retinopathy Diagnosis based on Biomarker Activation Map

Deep learning classifiers provide the most accurate means of automatically diagnosing diabetic retinopathy (DR) based on optical coherence tomography (OCT) and its angiography (OCTA). The power of these models is attributable in part to the inclusion of hidden layers that provide the complexity required to achieve a desired task. However, hidden layers also render algorithm outputs difficult to interpret. Here we introduce a novel biomarker activation map (BAM) framework based on generative adversarial learning that allows clinicians to verify and understand classifiers decision-making. A data set including 456 macular scans were graded as non-referable or referable DR based on current clinical standards. A DR classifier that was used to evaluate our BAM was first trained based on this data set. The BAM generation framework was designed by combing two U-shaped generators to provide meaningful interpretability to this classifier. The main generator was trained to take referable scans as input and produce an output that would be classified by the classifier as non-referable. The BAM is then constructed as the difference image between the output and input of the main generator. To ensure that the BAM only highlights classifier-utilized biomarkers an assistant generator was trained to do the opposite, producing scans that would be classified as referable by the classifier from non-referable scans. The generated BAMs highlighted known pathologic features including nonperfusion area and retinal fluid. A fully interpretable classifier based on these highlights could help clinicians better utilize and verify automated DR diagnosis.Comment: 12 pages, 8 figure

Update of ∣Vcb∣|V_{cb}| from the Bˉ→D∗ℓνˉ\bar{B}\to D^*\ell\bar{\nu} form factor at zero recoil with three-flavor lattice QCD

We compute the zero-recoil form factor for the semileptonic decay $\bar{B}^0\to D^{*+}\ell^-\bar{\nu}$ (and modes related by isospin and charge conjugation) using lattice QCD with three flavors of sea quarks. We use an improved staggered action for the light valence and sea quarks (the MILC \asqtad\ configurations), and the Fermilab action for the heavy quarks. Our calculations incorporate higher statistics, finer lattice spacings, and lighter quark masses than our 2008 work. As a byproduct of tuning the new data set, we obtain the $D_s$ and $B_s$ hyperfine splittings with few-MeV accuracy. For the zero-recoil form factor, we obtain $\mathcal{F}(1)=0.906(4)(12)$, where the first error is statistical and the second is the sum in quadrature of all systematic errors. With the latest HFAG average of experimental results and a cautious treatment of QED effects, we find $|V_{cb}| = (39.04 \pm 0.49_\text{expt} \pm 0.53_\text{QCD} \pm 0.19_\text{QED})\times10^{-3}$. The QCD error is now commensurate with the experimental error.Comment: 53 pages, 12 figures; expanded discussion of correlator fits, typos corrected, conforms to version published in PR

A soluble model of evolution and extinction dynamics in a rugged fitness landscape

We consider a continuum version of a previously introduced and numerically studied model of macroevolution (PRL 75, 2055, (1995)) in which agents evolve by an optimization process in a rugged fitness landscape and die due to their competitive interactions. We first formulate dynamical equations for the fitness distribution and the survival probability. Secondly we analytically derive the $t^{-2}$ law which characterizes the life time distribution of biological genera. Thirdly we discuss other dynamical properties of the model such as the rate of extinction and conclude with a brief discussion.Comment: 6 pages LaTeX source with 2 figures. Submitted to PRL (Jan. 97

Neutral B-meson mixing from three-flavor lattice QCD: Determination of the SU(3)-breaking ratio \xi

We study SU(3)-breaking effects in the neutral B_d-\bar B_d and B_s-\bar B_s systems with unquenched N_f=2+1 lattice QCD. We calculate the relevant matrix elements on the MILC collaboration's gauge configurations with asqtad-improved staggered sea quarks. For the valence light-quarks (u, d, and s) we use the asqtad action, while for b quarks we use the Fermilab action. We obtain \xi=f_{B_s}\sqrt{B_{B_s}}/f_{B_d}\sqrt{B_{B_d}}=1.268+-0.063. We also present results for the ratio of bag parameters B_{B_s}/B_{B_d} and the ratio of CKM matrix elements |V_{td}|/|V_{ts}|. Although we focus on the calculation of \xi, the strategy and techniques described here will be employed in future extended studies of the B mixing parameters \Delta M_{d,s} and \Delta\Gamma_{d,s} in the Standard Model and beyond.Comment: 36 pages, 7 figure

Bs→KℓνB_s \to K \ell\nu form factors with 2+1 flavors

Using the MILC 2+1 flavor asqtad quark action ensembles, we are calculating the form factors $f_0$ and $f_+$ for the semileptonic $B_s \rightarrow K \ell\nu$ decay. A total of six ensembles with lattice spacing from $\approx0.12$ to 0.06 fm are being used. At the coarsest and finest lattice spacings, the light quark mass $m'_l$ is one-tenth the strange quark mass $m'_s$. At the intermediate lattice spacing, the ratio $m'_l/m'_s$ ranges from 0.05 to 0.2. The valence $b$ quark is treated using the Sheikholeslami-Wohlert Wilson-clover action with the Fermilab interpretation. The other valence quarks use the asqtad action. When combined with (future) measurements from the LHCb and Belle II experiments, these calculations will provide an alternate determination of the CKM matrix element $|V_{ub}|$.Comment: 8 pages, 6 figures, to appear in the Proceedings of Lattice 2017, June 18-24, Granada, Spai

Origins of the Greenland shark (Somniosus microcephalus): Impacts of ice-olation and introgression

Herein, we use genetic data from 277 sleeper sharks to perform coalescent-based modeling to test the hypothesis of early Quaternary emergence of the Greenland shark (Somniosus microcephalus) from ancestral sleeper sharks in the Canadian Arctic-Subarctic region. Our results show that morphologically cryptic somniosids S. microcephalus and Somniosus pacificus can be genetically distinguished using combined mitochondrial and nuclear DNA markers. Our data confirm the presence of genetically admixed individuals in the Canadian Arctic and sub-Arctic, and temperate Eastern Atlantic regions, suggesting introgressive hybridization upon secondary contact following the initial species divergence. Conservative substitution rates fitted to an Isolation with Migration (IM) model indicate a likely species divergence time of 2.34 Ma, using the mitochondrial sequence DNA, which in conjunction with the geographic distribution of admixtures and Pacific signatures likely indicates speciation associated with processes other than the closing of the Isthmus of Panama. This time span coincides with further planetary cooling in the early Quaternary period followed by the onset of oscillating glacial-interglacial cycles. We propose that the initial S. microcephalus–S. pacificus split, and subsequent hybridization events, were likely associated with the onset of Pleistocene glacial oscillations, whereby fluctuating sea levels constrained connectivity among Arctic oceanic basins, Arctic marginal seas, and the North Atlantic Ocean. Our data demonstrates support for the evolutionary consequences of oscillatory vicariance via transient oceanic isolation with subsequent secondary contact associated with fluctuating sea levels throughout the Quaternary period—which may serve as a model for the origins of Arctic marine fauna on a broad taxonomic scale

Hypertension in Pregnancy Is a Risk Factor for Microalbuminuria Later in Life

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/99687/1/jch12116.pd

B→Kl+l−B\to Kl^+l^- decay form factors from three-flavor lattice QCD

We compute the form factors for the $B \to Kl^+l^-$ semileptonic decay process in lattice QCD using gauge-field ensembles with 2+1 flavors of sea quark, generated by the MILC Collaboration. The ensembles span lattice spacings from 0.12 to 0.045 fm and have multiple sea-quark masses to help control the chiral extrapolation. The asqtad improved staggered action is used for the light valence and sea quarks, and the clover action with the Fermilab interpretation is used for the heavy $b$ quark. We present results for the form factors $f_+(q^2)$, $f_0(q^2)$, and $f_T(q^2)$, where $q^2$ is the momentum transfer, together with a comprehensive examination of systematic errors. Lattice QCD determines the form factors for a limited range of $q^2$, and we use the model-independent $z$ expansion to cover the whole kinematically allowed range. We present our final form-factor results as coefficients of the $z$ expansion and the correlations between them, where the errors on the coefficients include statistical and all systematic uncertainties. We use this complete description of the form factors to test QCD predictions of the form factors at high and low $q^2$. We also compare a Standard-Model calculation of the branching ratio for $B \to Kl^+l^-$ with experimental data.Comment: V2: Fig.7 added. Typos text corrected. Reference added. Version published in Phys. Rev.