Showing papers by "University of Illinois at Urbana–Champaign published in 2015"

Single image super-resolution from transformed self-exemplars

Abstract: Self-similarity based super-resolution (SR) algorithms are able to produce visually pleasing results without extensive training on external databases. Such algorithms exploit the statistical prior that patches in a natural image tend to recur within and across scales of the same image. However, the internal dictionary obtained from the given image may not always be sufficiently expressive to cover the textural appearance variations in the scene. In this paper, we extend self-similarity based SR to overcome this drawback. We expand the internal patch search space by allowing geometric variations. We do so by explicitly localizing planes in the scene and using the detected perspective geometry to guide the patch search process. We also incorporate additional affine transformations to accommodate local shape variations. We propose a compositional model to simultaneously handle both types of transformations. We extensively evaluate the performance in both urban and natural scenes. Even without using any external training databases, we achieve significantly superior results on urban scenes, while maintaining comparable performance on natural scenes as other state-of-the-art SR algorithms.

Hierarchical Convolutional Features for Visual Tracking

Abstract: Visual object tracking is challenging as target objects often undergo significant appearance changes caused by deformation, abrupt motion, background clutter and occlusion. In this paper, we exploit features extracted from deep convolutional neural networks trained on object recognition datasets to improve tracking accuracy and robustness. The outputs of the last convolutional layers encode the semantic information of targets and such representations are robust to significant appearance variations. However, their spatial resolution is too coarse to precisely localize targets. In contrast, earlier convolutional layers provide more precise localization but are less invariant to appearance changes. We interpret the hierarchies of convolutional layers as a nonlinear counterpart of an image pyramid representation and exploit these multiple levels of abstraction for visual tracking. Specifically, we adaptively learn correlation filters on each convolutional layer to encode the target appearance. We hierarchically infer the maximum response of each layer to locate targets. Extensive experimental results on a largescale benchmark dataset show that the proposed algorithm performs favorably against state-of-the-art methods.

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

Abstract: The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

Combined Measurement of the Higgs Boson Mass in pp Collisions at √s=7 and 8 TeV with the ATLAS and CMS Experiments

Abstract: A measurement of the Higgs boson mass is presented based on the combined data samples of the ATLAS and CMS experiments at the CERN LHC in the H→γγ and H→ZZ→4l decay channels. The results are obtained from a simultaneous fit to the reconstructed invariant mass peaks in the two channels and for the two experiments. The measured masses from the individual channels and the two experiments are found to be consistent among themselves. The combined measured mass of the Higgs boson is mH=125.09±0.21 (stat)±0.11 (syst) GeV.

EDC-2: The Endocrine Society's Second Scientific Statement on Endocrine-Disrupting Chemicals

Abstract: The Endocrine Society's first Scientific Statement in 2009 provided a wake-up call to the scientific community about how environmental endocrine-disrupting chemicals (EDCs) affect health and disease. Five years later, a substantially larger body of literature has solidified our understanding of plausible mechanisms underlying EDC actions and how exposures in animals and humans-especially during development-may lay the foundations for disease later in life. At this point in history, we have much stronger knowledge about how EDCs alter gene-environment interactions via physiological, cellular, molecular, and epigenetic changes, thereby producing effects in exposed individuals as well as their descendants. Causal links between exposure and manifestation of disease are substantiated by experimental animal models and are consistent with correlative epidemiological data in humans. There are several caveats because differences in how experimental animal work is conducted can lead to difficulties in drawing broad conclusions, and we must continue to be cautious about inferring causality in humans. In this second Scientific Statement, we reviewed the literature on a subset of topics for which the translational evidence is strongest: 1) obesity and diabetes; 2) female reproduction; 3) male reproduction; 4) hormone-sensitive cancers in females; 5) prostate; 6) thyroid; and 7) neurodevelopment and neuroendocrine systems. Our inclusion criteria for studies were those conducted predominantly in the past 5 years deemed to be of high quality based on appropriate negative and positive control groups or populations, adequate sample size and experimental design, and mammalian animal studies with exposure levels in a range that was relevant to humans. We also focused on studies using the developmental origins of health and disease model. No report was excluded based on a positive or negative effect of the EDC exposure. The bulk of the results across the board strengthen the evidence for endocrine health-related actions of EDCs. Based on this much more complete understanding of the endocrine principles by which EDCs act, including nonmonotonic dose-responses, low-dose effects, and developmental vulnerability, these findings can be much better translated to human health. Armed with this information, researchers, physicians, and other healthcare providers can guide regulators and policymakers as they make responsible decisions.

Chromatin architecture reorganization during stem cell differentiation

Abstract: Higher-order chromatin structure is emerging as an important regulator of gene expression. Although dynamic chromatin structures have been identified in the genome, the full scope of chromatin dynamics during mammalian development and lineage specification remains to be determined. By mapping genome-wide chromatin interactions in human embryonic stem (ES) cells and four human ES-cell-derived lineages, we uncover extensive chromatin reorganization during lineage specification. We observe that although self-associating chromatin domains are stable during differentiation, chromatin interactions both within and between domains change in a striking manner, altering 36% of active and inactive chromosomal compartments throughout the genome. By integrating chromatin interaction maps with haplotype-resolved epigenome and transcriptome data sets, we find widespread allelic bias in gene expression correlated with allele-biased chromatin states of linked promoters and distal enhancers. Our results therefore provide a global view of chromatin dynamics and a resource for studying long-range control of gene expression in distinct human cell lineages.

Trust in Automation: Integrating Empirical Evidence on Factors That Influence Trust

Abstract: Objective:We systematically review recent empirical research on factors that influence trust in automation to present a three-layered trust model that synthesizes existing knowledge.Background:Much...

Joint Analysis of BICEP2/Keck Array and Planck Data

Abstract: We report the results of a joint analysis of data from BICEP2/Keck Array and Planck. BICEP2 and Keck Array have observed the same approximately 400 deg2 patch of sky centered on RA 0h, Dec. −57.5deg. The combined maps reach a depth of 57 nK deg in Stokes Q and U in a band centered at 150 GHz. Planck has observed the full sky in polarization at seven frequencies from 30 to 353 GHz, but much less deeply in any given region (1.2 μK deg in Q and U at 143 GHz). We detect 150×353 cross-correlation in B-modes at high significance. We fit the single- and cross-frequency power spectra at frequencies above 150 GHz to a lensed-ΛCDM model that includes dust and a possible contribution from inflationary gravitational waves (as parameterized by the tensor-to-scalar ratio r). We probe various model variations and extensions, including adding a synchrotron component in combination with lower frequency data, and find that these make little difference to the r constraint. Finally we present an alternative analysis which is similar to a map-based cleaning of the dust contribution, and show that this gives similar constraints. The final result is expressed as a likelihood curve for r, and yields an upper limit r0.05<0.12 at 95% confidence. Marginalizing over dust and r, lensing B-modes are detected at 7.0σ significance.

Strong Loophole-Free Test of Local Realism.

Abstract: We present a loophole-free violation of local realism using entangled photon pairs. We ensure that all relevant events in our Bell test are spacelike separated by placing the parties far enough apart and by using fast random number generators and high-speed polarization measurements. A high-quality polarization-entangled source of photons, combined with high-efficiency, low-noise, single-photon detectors, allows us to make measurements without requiring any fair-sampling assumptions. Using a hypothesis test, we compute p values as small as 5.9×10^{-9} for our Bell violation while maintaining the spacelike separation of our events. We estimate the degree to which a local realistic system could predict our measurement choices. Accounting for this predictability, our smallest adjusted p value is 2.3×10^{-7}. We therefore reject the hypothesis that local realism governs our experiment.

Big data: Astronomical or genomical?

Abstract: Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a “four-headed beast”—it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the “genomical” challenges of the next decade.

Testing general relativity with present and future astrophysical observations

Abstract: One century after its formulation, Einstein's general relativity (GR) has made remarkable predictions and turned out to be compatible with all experimental tests. Most of these tests probe the theory in the weak-field regime, and there are theoretical and experimental reasons to believe that GR should be modified when gravitational fields are strong and spacetime curvature is large. The best astrophysical laboratories to probe strong-field gravity are black holes and neutron stars, whether isolated or in binary systems. We review the motivations to consider extensions of GR. We present a (necessarily incomplete) catalog of modified theories of gravity for which strong-field predictions have been computed and contrasted to Einstein's theory, and we summarize our current understanding of the structure and dynamics of compact objects in these theories. We discuss current bounds on modified gravity from binary pulsar and cosmological observations, and we highlight the potential of future gravitational wave measurements to inform us on the behavior of gravity in the strong-field regime.

Flickr30k Entities: Collecting Region-to-Phrase Correspondences for Richer Image-to-Sentence Models

Abstract: The Flickr30k dataset has become a standard benchmark for sentence-based image description. This paper presents Flickr30k Entities, which augments the 158k captions from Flickr30k with 244k coreference chains linking mentions of the same entities in images, as well as 276k manually annotated bounding boxes corresponding to each entity. Such annotation is essential for continued progress in automatic image description and grounded language understanding. We present experiments demonstrating the usefulness of our annotations for text-to-image reference resolution, or the task of localizing textual entity mentions in an image, and for bidirectional image-sentence retrieval. These experiments confirm that we can further improve the accuracy of state-of-the-art retrieval methods by training with explicit region-to-phrase correspondence, but at the same time, they show that accurately inferring this correspondence given an image and a caption remains really challenging.

Expectations of brilliance underlie gender distributions across academic disciplines

Abstract: The gender imbalance in STEM subjects dominates current debates about women's underrepresentation in academia. However, women are well represented at the Ph.D. level in some sciences and poorly represented in some humanities (e.g., in 2011, 54% of U.S. Ph.D.'s in molecular biology were women versus only 31% in philosophy). We hypothesize that, across the academic spectrum, women are underrepresented in fields whose practitioners believe that raw, innate talent is the main requirement for success, because women are stereotyped as not possessing such talent. This hypothesis extends to African Americans' underrepresentation as well, as this group is subject to similar stereotypes. Results from a nationwide survey of academics support our hypothesis (termed the field-specific ability beliefs hypothesis) over three competing hypotheses.

Food Insecurity And Health Outcomes

Abstract: Almost fifty million people are food insecure in the United States, which makes food insecurity one of the nation's leading health and nutrition issues. We examine recent research evidence of the health consequences of food insecurity for children, nonsenior adults, and seniors in the United States. For context, we first provide an overview of how food insecurity is measured in the country, followed by a presentation of recent trends in the prevalence of food insecurity. Then we present a survey of selected recent research that examined the association between food insecurity and health outcomes. We show that the literature has consistently found food insecurity to be negatively associated with health. For example, after confounding risk factors were controlled for, studies found that food-insecure children are at least twice as likely to report being in fair or poor health and at least 1.4 times more likely to have asthma, compared to food-secure children; and food-insecure seniors have limitations in activities of daily living comparable to those of food-secure seniors fourteen years older. The Supplemental Nutrition Assistance Program (SNAP) substantially reduces the prevalence of food insecurity and thus is critical to reducing negative health outcomes.

The dominant role of semi-arid ecosystems in the trend and variability of the land CO2 sink

Abstract: The growth rate of atmospheric carbon dioxide (CO2) concentrations since industrialization is characterized by large interannual variability, mostly resulting from variability in CO2 uptake by terrestrial ecosystems (typically termed carbon sink). However, the contributions of regional ecosystems to that variability are not well known. Using an ensemble of ecosystem and land-surface models and an empirical observation-based product of global gross primary production, we show that the mean sink, trend, and interannual variability in CO2 uptake by terrestrial ecosystems are dominated by distinct biogeographic regions. Whereas the mean sink is dominated by highly productive lands (mainly tropical forests), the trend and interannual variability of the sink are dominated by semi-arid ecosystems whose carbon balance is strongly associated with circulation-driven variations in both precipitation and temperature.

The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics

Abstract: P granules and other RNA/protein bodies are membrane-less organelles that may assemble by intracellular phase separation, similar to the condensation of water vapor into droplets. However, the molecular driving forces and the nature of the condensed phases remain poorly understood. Here, we show that the Caenorhabditis elegans protein LAF-1, a DDX3 RNA helicase found in P granules, phase separates into P granule-like droplets in vitro. We adapt a microrheology technique to precisely measure the viscoelasticity of micrometer-sized LAF-1 droplets, revealing purely viscous properties highly tunable by salt and RNA concentration. RNA decreases viscosity and increases molecular dynamics within the droplet. Single molecule FRET assays suggest that this RNA fluidization results from highly dynamic RNA–protein interactions that emerge close to the droplet phase boundary. We demonstrate than an N-terminal, arginine/glycine rich, intrinsically disordered protein (IDP) domain of LAF-1 is necessary and sufficient for both phase separation and RNA–protein interactions. In vivo, RNAi knockdown of LAF-1 results in the dissolution of P granules in the early embryo, with an apparent submicromolar phase boundary comparable to that measured in vitro. Together, these findings demonstrate that LAF-1 is important for promoting P granule assembly and provide insight into the mechanism by which IDP-driven molecular interactions give rise to liquid phase organelles with tunable properties.

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes.

Abstract: MOTIVATION The estimation of species phylogenies requires multiple loci, since different loci can have different trees due to incomplete lineage sorting, modeled by the multi-species coalescent model. We recently developed a coalescent-based method, ASTRAL, which is statistically consistent under the multi-species coalescent model and which is more accurate than other coalescent-based methods on the datasets we examined. ASTRAL runs in polynomial time, by constraining the search space using a set of allowed 'bipartitions'. Despite the limitation to allowed bipartitions, ASTRAL is statistically consistent. RESULTS We present a new version of ASTRAL, which we call ASTRAL-II. We show that ASTRAL-II has substantial advantages over ASTRAL: it is faster, can analyze much larger datasets (up to 1000 species and 1000 genes) and has substantially better accuracy under some conditions. ASTRAL's running time is [Formula: see text], and ASTRAL-II's running time is [Formula: see text], where n is the number of species, k is the number of loci and X is the set of allowed bipartitions for the search space. AVAILABILITY AND IMPLEMENTATION ASTRAL-II is available in open source at https://github.com/smirarab/ASTRAL and datasets used are available at http://www.cs.utexas.edu/~phylo/datasets/astral2/. CONTACT smirarab@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

The dark energy camera

Abstract: The Dark Energy Camera is a new imager with a 2.2-degree diameter field of view mounted at the prime focus of the Victor M. Blanco 4-meter telescope on Cerro Tololo near La Serena, Chile. The camera was designed and constructed by the Dark Energy Survey Collaboration, and meets or exceeds the stringent requirements designed for the wide-field and supernova surveys for which the collaboration uses it. The camera consists of a five element optical corrector, seven filters, a shutter with a 60 cm aperture, and a CCD focal plane of 250 micron thick fully-depleted CCDs cooled inside a vacuum Dewar. The 570 Mpixel focal plane comprises 62 2kx4k CCDs for imaging and 12 2kx2k CCDs for guiding and focus. The CCDs have 15 microns x15 microns pixels with a plate scale of 0.263 arc sec per pixel. A hexapod system provides state-of-the-art focus and alignment capability. The camera is read out in 20 seconds with 6-9 electrons readout noise. This paper provides a technical description of the camera's engineering, construction, installation, and current status.

Colloquium : Theory of intertwined orders in high temperature superconductors

Abstract: Understanding high temperature superconductors is a central problem in condensed matter physics. Many experiments have uncovered ordering tendencies which are responsible for the complex phase diagram of high temperature superconductors. This Colloquium discusses the interplay between different order parameters in these materials. Considering the intertwining of these orders leads to new experimentally observable consequences, shedding new light into the physics of these fascinating materials.

Causal reasoning with forces

Abstract: Causal composition allows people to generate new causal relations by combining existing causal knowledge. We introduce a new computational model of such reasoning, the force theory, which holds that people compose causal relations by simulating the processes that join forces in the world, and compare this theory with the mental model theory (Khemlani, Barbey, & Johnson-Laird, 2014) and the causal model theory (Sloman, Barbey, & Hotaling, 2009), which explain causal composition on the basis of mental models and structural equations, respectively. In one experiment, the force theory was uniquely able to account for people’s ability to compose causal relationships from complex animations of real-world events. In three additional experiments, the force theory did as well as or better than the other two theories in explaining the causal compositions people generated from linguistically presented causal relations. Implications for causal learning and the hierarchical structure of causal knowledge are discussed.

Framing Image Description as a Ranking Task: Data, Models and Evaluation Metrics (Extended Abstract)

Abstract: In [Hodosh et al., 2013], we establish a rankingbased framework for sentence-based image description and retrieval. We introduce a new dataset of images paired with multiple descriptive captions that was specifically designed for these tasks. We also present strong KCCA-based baseline systems for description and search, and perform an in-depth study of evaluation metrics for these two tasks. Our results indicate that automatic evaluation metrics for our ranking-based tasks are more accurate and robust than those proposed for generation-based image description.

Fat, fibre and cancer risk in African Americans and rural Africans

Abstract: Rates of colon cancer are much higher in African Americans (65:100,000) than in rural South Africans (<5:100,000). The higher rates are associated with higher animal protein and fat, and lower fibre consumption, higher colonic secondary bile acids, lower colonic short-chain fatty acid quantities and higher mucosal proliferative biomarkers of cancer risk in otherwise healthy middle-aged volunteers. Here we investigate further the role of fat and fibre in this association. We performed 2-week food exchanges in subjects from the same populations, where African Americans were fed a high-fibre, low-fat African-style diet and rural Africans a high-fat, low-fibre western-style diet, under close supervision. In comparison with their usual diets, the food changes resulted in remarkable reciprocal changes in mucosal biomarkers of cancer risk and in aspects of the microbiota and metabolome known to affect cancer risk, best illustrated by increased saccharolytic fermentation and butyrogenesis, and suppressed secondary bile acid synthesis in the African Americans.

Assembly of micro/nanomaterials into complex, three-dimensional architectures by compressive buckling

Abstract: Complex three-dimensional (3D) structures in biology (e.g., cytoskeletal webs, neural circuits, and vasculature networks) form naturally to provide essential functions in even the most basic forms of life. Compelling opportunities exist for analogous 3D architectures in human-made devices, but design options are constrained by existing capabilities in materials growth and assembly. We report routes to previously inaccessible classes of 3D constructs in advanced materials, including device-grade silicon. The schemes involve geometric transformation of 2D micro/nanostructures into extended 3D layouts by compressive buckling. Demonstrations include experimental and theoretical studies of more than 40 representative geometries, from single and multiple helices, toroids, and conical spirals to structures that resemble spherical baskets, cuboid cages, starbursts, flowers, scaffolds, fences, and frameworks, each with single- and/or multiple-level configurations.

Entity Linking with a Knowledge Base: Issues, Techniques, and Solutions

Abstract: The large number of potential applications from bridging web data with knowledge bases have led to an increase in the entity linking research. Entity linking is the task to link entity mentions in text with their corresponding entities in a knowledge base. Potential applications include information extraction, information retrieval, and knowledge base population. However, this task is challenging due to name variations and entity ambiguity. In this survey, we present a thorough overview and analysis of the main approaches to entity linking, and discuss various applications, the evaluation of entity linking systems, and future directions.