Saliency Benchmarking Made Easy: Separating Models, Maps and Metrics

Dozens of new models on fixation prediction are published every year and compared on open benchmarks such as MIT300 and LSUN. However, progress in the field can be difficult to judge because models are compared using a variety of inconsistent metrics. Here we show that no single saliency map can perform well under all metrics. Instead, we propose a principled approach to solve the benchmarking problem by separating the notions of saliency models, maps and metrics. Inspired by Bayesian decision theory, we define a saliency model to be a probabilistic model of fixation density prediction and a saliency map to be a metric-specific prediction derived from the model density which maximizes the expected performance on that metric given the model density. We derive these optimal saliency maps for the most commonly used saliency metrics (AUC, sAUC, NSS, CC, SIM, KL-Div) and show that they can be computed analytically or approximated with high precision. We show that this leads to consistent rankings in all metrics and avoids the penalties of using one saliency map for all metrics. Our method allows researchers to have their model compete on many different metrics with state-of-the-art in those metrics: "good" models will perform well in all metrics.Comment: published at ECCV 201

Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution

It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons (“exon-intron marking”), linking chromatin structure and function to co-transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing

Considering the Case for Biodiversity Cycles: Reexamining the Evidence for Periodicity in the Fossil Record

Medvedev and Melott (2007) have suggested that periodicity in fossil biodiversity may be induced by cosmic rays which vary as the Solar System oscillates normal to the galactic disk. We re-examine the evidence for a 62 million year (Myr) periodicity in biodiversity throughout the Phanerozoic history of animal life reported by Rohde & Mueller (2005), as well as related questions of periodicity in origination and extinction. We find that the signal is robust against variations in methods of analysis, and is based on fluctuations in the Paleozoic and a substantial part of the Mesozoic. Examination of origination and extinction is somewhat ambiguous, with results depending upon procedure. Origination and extinction intensity as defined by RM may be affected by an artifact at 27 Myr in the duration of stratigraphic intervals. Nevertheless, when a procedure free of this artifact is implemented, the 27 Myr periodicity appears in origination, suggesting that the artifact may ultimately be based on a signal in the data. A 62 Myr feature appears in extinction, when this same procedure is used. We conclude that evidence for a periodicity at 62 Myr is robust, and evidence for periodicity at approximately 27 Myr is also present, albeit more ambiguous.Comment: Minor modifications to reflect final published versio

Object Detection Through Exploration With A Foveated Visual Field

We present a foveated object detector (FOD) as a biologically-inspired alternative to the sliding window (SW) approach which is the dominant method of search in computer vision object detection. Similar to the human visual system, the FOD has higher resolution at the fovea and lower resolution at the visual periphery. Consequently, more computational resources are allocated at the fovea and relatively fewer at the periphery. The FOD processes the entire scene, uses retino-specific object detection classifiers to guide eye movements, aligns its fovea with regions of interest in the input image and integrates observations across multiple fixations. Our approach combines modern object detectors from computer vision with a recent model of peripheral pooling regions found at the V1 layer of the human visual system. We assessed various eye movement strategies on the PASCAL VOC 2007 dataset and show that the FOD performs on par with the SW detector while bringing significant computational cost savings.Comment: An extended version of this manuscript was published in PLOS Computational Biology (October 2017) at https://doi.org/10.1371/journal.pcbi.100574

Colonoscopic screening for colorectal cancer improves quality of life measures: a population-based screening study

BACKGROUND: Screening asymptomatic individuals for neoplasia can have adverse consequences on quality of life. Colon cancer screening is widespread but the quality of life (QOL) consequences are unknown. This study determined the impact of screening colonoscopy on QOL measures in asymptomatic average-risk participants. METHODS: Asymptomatic male and female participants aged 55–74 years were randomly selected from the Australian Electoral Roll or six primary care physicians' databases. Participants completed the Short-Form (SF-36) Quality of Life Assessment at baseline and at a mean of 39 days after colonoscopy. Outcome measures were (i) significant changes in raw scores in any of the eight SF-36 domains assessed following colonoscopic screening and (ii) improvements or declines in previously validated categories, representing clinically significant changes, within any of the eight SF-36 domains. RESULTS: Baseline QOL measures were similar to those of a matched general population sample. Role Limitations due to Emotions, Mental Health and Vitality raw scores significantly improved following colonoscopy (P < 0.05, 2-tailed t-test). Health ratings according to Category were similar (same clinical status) in the majority of participants. However, 30% participants recorded clinically significant improvement in the Mental Health and Vitality domains (P < 0.05, Wilcoxon Signed-Ranks test). This improvement was not offset by declines in other domains or in other participants. Improvement in QOL was not related to colonoscopy results. CONCLUSION: Average-risk persons benefit significantly from colon cancer screening with colonoscopy, improving in Mental Health and Vitality domains of Quality of Life. This improvement is not offset by declines in other domains

Molecular identification of Palearctic members of Anopheles maculipennis in northern Iran

BACKGROUND: Members of Anopheles maculipennis complex are effective malaria vectors in Europe and the Caspian Sea region in northern Iran, where malaria has been re-introduced since 1994. The current study has been designed in order to provide further evidence on the status of species composition and to identify more accurately the members of the maculipennis complex in northern Iran. METHODS: The second internal transcribed spacer of ribosomal DNA (rDNA-ITS2) was sequenced in 28 out of 235 specimens that were collected in the five provinces of East Azerbayjan, Ardebil, Guilan, Mazandaran and Khorassan in Iran. RESULTS: The length of the ITS2 ranged from 283 to 302 bp with a GC content of 49.33 – 54.76%. No intra-specific variations were observed. Construction of phylogenetic tree based on the ITS2 sequence revealed that the six Iranian members of the maculipennis complex could be easily clustered into three groups: the An. atroparvus – Anopheles labranchiae group; the paraphyletic group of An. maculipennis, An. messeae, An. persiensis; and An. sacharovi as the third group. CONCLUSION: Detection of three species of the An. maculipennis complex including An. atroparvus, An. messae and An. labranchiae, as shown as new records in northern Iran, is somehow alarming. A better understanding of the epidemiology of malaria on both sides of the Caspian Sea may be provided by applying the molecular techniques to the correct identification of species complexes, to the detection of Plasmodium composition in Anopheles vectors and to the status of insecticide resistance by looking to related genes

How to look next? A data-driven approach for scanpath prediction

By and large, current visual attention models mostly rely, when considering static stimuli, on the following procedure. Given an image, a saliency map is computed, which, in turn, might serve the purpose of predicting a sequence of gaze shifts, namely a scanpath instantiating the dynamics of visual attention deployment. The temporal pattern of attention unfolding is thus confined to the scanpath generation stage, whilst salience is conceived as a static map, at best conflating a number of factors (bottom-up information, top-down, spatial biases, etc.). In this note we propose a novel sequential scheme that consists of a three-stage processing relying on a center-bias model, a context/layout model, and an object-based model, respectively. Each stage contributes, at different times, to the sequential sampling of the final scanpath. We compare the method against classic scanpath generation that exploits state-of-the-art static saliency model. Results show that accounting for the structure of the temporal unfolding leads to gaze dynamics close to human gaze behaviour

Problems with Saliency Maps

Despite the popularity that saliency models have gained in the computer vision community, they are most often conceived, exploited and benchmarked without taking heed of a number of problems and subtle issues they bring about. When saliency maps are used as proxies for the likelihood of fixating a location in a viewed scene, one such issue is the temporal dimension of visual attention deployment. Through a simple simulation it is shown how neglecting this dimension leads to results that at best cast shadows on the predictive performance of a model and its assessment via benchmarking procedures

Peptidases compartmentalized to the Ascaris suum intestinal lumen and apical intestinal membrane

The nematode intestine is a tissue of interest for developing new methods of therapy and control of parasitic nematodes. However, biological details of intestinal cell functions remain obscure, as do the proteins and molecular functions located on the apical intestinal membrane (AIM), and within the intestinal lumen (IL) of nematodes. Accordingly, methods were developed to gain a comprehensive identification of peptidases that function in the intestinal tract of adult female Ascaris suum. Peptidase activity was detected in multiple fractions of the A. suum intestine under pH conditions ranging from 5.0 to 8.0. Peptidase class inhibitors were used to characterize these activities. The fractions included whole lysates, membrane enriched fractions, and physiological- and 4 molar urea-perfusates of the intestinal lumen. Concanavalin A (ConA) was confirmed to bind to the AIM, and intestinal proteins affinity isolated on ConA-beads were compared to proteins from membrane and perfusate fractions by mass spectrometry. Twenty-nine predicted peptidases were identified including aspartic, cysteine, and serine peptidases, and an unexpectedly high number (16) of metallopeptidases. Many of these proteins co-localized to multiple fractions, providing independent support for localization to specific intestinal compartments, including the IL and AIM. This unique perfusion model produced the most comprehensive view of likely digestive peptidases that function in these intestinal compartments of A. suum, or any nematode. This model offers a means to directly determine functions of these proteins in the A. suum intestine and, more generally, deduce the wide array functions that exist in these cellular compartments of the nematode intestine