Improve the performance of transfer learning without fine-tuning using dissimilarity-based multi-view learning for breast cancer histology images

Breast cancer is one of the most common types of cancer and leading cancer-related death causes for women. In the context of ICIAR 2018 Grand Challenge on Breast Cancer Histology Images, we compare one handcrafted feature extractor and five transfer learning feature extractors based on deep learning. We find out that the deep learning networks pretrained on ImageNet have better performance than the popular handcrafted features used for breast cancer histology images. The best feature extractor achieves an average accuracy of 79.30%. To improve the classification performance, a random forest dissimilarity based integration method is used to combine different feature groups together. When the five deep learning feature groups are combined, the average accuracy is improved to 82.90% (best accuracy 85.00%). When handcrafted features are combined with the five deep learning feature groups, the average accuracy is improved to 87.10% (best accuracy 93.00%)

Associations of stunting in early childhood with cardiometabolic risk factors in adulthood

Abstract Early life stunting may have long-term effects on body composition, resulting in obesity-related comorbidities. We tested the hypothesis that individuals stunted in early childhood may be at higher cardiometabolic risk later in adulthood. 1753 men and 1781 women participating in the 1982 Pelotas (Brazil) birth cohort study had measurements of anthropometry, body composition, lipids, glucose, blood pressure, and other cardiometabolic traits at age 30 years. Early stunting was defined as height-for-age Z-score at age 2 years below -2 against the World Health Organization growth standards. Linear regression models were performed controlling for sex, maternal race/ethnicity, family income at birth, and birthweight. Analyses were stratified by sex when p-interaction<0.05. Stunted individuals were shorter (β=-0.71 s.d.; 95% CI: -0.78 to -0.64), had lower BMI (β=-0.14 s.d.; 95%CI: -0.25 to -0.03), fat mass (β=-0.28 s.d.; 95%CI: -0.38 to -0.17), SAFT (β=-0.16 s.d.; 95%CI: -0.26 to -0.06), systolic (β=-0.12 s.d.; 95%CI: -0.21 to -0.02) and diastolic blood pressure (β=-0.11 s.d.; 95%CI: -0.22 to -0.01), and higher VFT/SAFT ratio (β=0.15 s.d.; 95%CI: 0.06 to 0.24), in comparison with non-stunted individuals. In addition, early stunting was associated with lower fat free mass in both men (β=-0.39 s.d.; 95%CI: -0.47 to -0.31) and women (β=-0.37 s.d.; 95%CI: -0.46 to -0.29) after adjustment for potential confounders. Our results suggest that early stunting has implications on attained height, body composition and blood pressure. The apparent tendency of stunted individuals to accumulate less fat-free mass and subcutaneous fat might predispose them towards increased metabolic risks in later life.The last phase of the 1982 Pelotas (Brazil) birth cohort study was supported by the Wellcome Trust and the Fundação de Aparo à Pesquisa do Estado do Rio Grande do Sul; Brazil (Edital 04/2012 – PQG; Processo 12/2185-9). Earlier phases were funded by the International Development Research Centre (Canada), the WHO (Department of Child and Adolescent Health and Development and Human Reproduction Programme) to BLH, the Overseas Development Administration (currently the Department for International Development, United Kingdom), the European Union, the United Nations Development Fund for Women, the National Program for Centres of Excellence, the Pastorate of the Child (Brazil), the National Council for Scientific and Technological Development (CNPq; Brazil), and the Ministry of Health (Brazil). GVAF was supported by the Brazilian Coordination of Improvement of Higher Education Personnel (scholarship process BEX 5077/13-3). EDLR and KKO are supported by the Medical Research Council [Unit Programme number MC_UU_12015/2]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Decay of correlations for maps with uniformly contracting fibers and logarithm law for singular hyperbolic attractors

We consider two dimensional maps preserving a foliation which is uniformly contracting and a one dimensional associated quotient map having exponential convergence to equilibrium (iterates of Lebesgue measure converge exponentially fast to physical measure). We prove that these maps have exponential decay of correlations over a large class of observables. We use this result to deduce exponential decay of correlations for the Poincare maps of a large class of singular hyperbolic flows. From this we deduce logarithm laws for these flows.Comment: 39 pages; 03 figures; proof of Theorem 1 corrected; many typos corrected; improvements on the statements and comments suggested by a referee. Keywords: singular flows, singular-hyperbolic attractor, exponential decay of correlations, exact dimensionality, logarithm la

Deep Convolutional Neural Networks for Breast Cancer Histology Image Analysis

Breast cancer is one of the main causes of cancer death worldwide. Early diagnostics significantly increases the chances of correct treatment and survival, but this process is tedious and often leads to a disagreement between pathologists. Computer-aided diagnosis systems showed potential for improving the diagnostic accuracy. In this work, we develop the computational approach based on deep convolution neural networks for breast cancer histology image classification. Hematoxylin and eosin stained breast histology microscopy image dataset is provided as a part of the ICIAR 2018 Grand Challenge on Breast Cancer Histology Images. Our approach utilizes several deep neural network architectures and gradient boosted trees classifier. For 4-class classification task, we report 87.2% accuracy. For 2-class classification task to detect carcinomas we report 93.8% accuracy, AUC 97.3%, and sensitivity/specificity 96.5/88.0% at the high-sensitivity operating point. To our knowledge, this approach outperforms other common methods in automated histopathological image classification. The source code for our approach is made publicly available at https://github.com/alexander-rakhlin/ICIAR2018Comment: 8 pages, 4 figure

Tactical Voting in Plurality Elections

How often will elections end in landslides? What is the probability for a head-to-head race? Analyzing ballot results from several large countries rather anomalous and yet unexplained distributions have been observed. We identify tactical voting as the driving ingredient for the anomalies and introduce a model to study its effect on plurality elections, characterized by the relative strength of the feedback from polls and the pairwise interaction between individuals in the society. With this model it becomes possible to explain the polarization of votes between two candidates, understand the small margin of victories frequently observed for different elections, and analyze the polls' impact in American, Canadian, and Brazilian ballots. Moreover, the model reproduces, quantitatively, the distribution of votes obtained in the Brazilian mayor elections with two, three, and four candidates.Comment: 7 pages, 4 figure

Communication skills in Brazilian pharmaceutical education: a documentary analysis

Objective: To characterize the inclusion of the teaching of communication skills in the curriculum of Pharmacy Schools of Federal Institutions of Higher Education. Methods: An exploratory study of documental analysis of curriculum of Pharmacy Schools was carried out. A convenience sample was selected from undergraduate pharmacy courses of Federal Institutions of Higher Education (IFES). The variables collected were related to the identification of the course, its nature (elective or mandatory), workload, semester, and program content. Results: Among the 49 undergraduate pharmacy courses of IFES, 35 (71.4%) had their curriculum available online. The teaching of communication in health was identified in 26 (74.3%) curriculum. In this study, three courses (7.2%) specifically aimed at teaching communication skills, while 39 (92.9%) had content related to this subject. Most courses (22; 52.4%) belonged to the field of Social, Behavioral, and Administrative Sciences. As for the course period, there was a concentration in the third (19%) and fourth (28.6%) years. The main content present in the curriculum was related to the principles and techniques of health communication (42.8%). Conclusions: Data obtained enabled the identification of gaps in the curricula of undergraduate courses in pharmacy concerning the inclusion of the teaching of communication skills. These results can be used to reflect the current models adopted in Brazil for the teaching of this skills, especially after the recent publication of the new curricular guidelines for undergraduate pharmacy courses

Climate change and outdoor regional living plant collections: an example from mainland Portugal

Original PaperClimate change threatens not only plant species occurring naturally, but also impacts on regional living plant collections, which play an important role in ex situ conservation strategies. In the last few years, several global circulation models have been used to predict different global climate change scenarios. Due to their coarse resolutions, and while more detailed regional approaches are not available, downscaling techniques have been proposed, as a very simple first approach to increase detail. We analysed seven sites on mainland Portugal with potential for species conservation (four botanic gardens and three universities), in the light of downscaled climate change scenarios, using an environmental envelope approach and a predefined bioclimatic neighbourhood for each site. Thresholds for the bioclimatic neighbourhood were based on Rivas-Martı´nez’s Bioclimatic Classification of the Earth. For each site, the expected geographical shift of its original bioclimatic neighbourhood (1950–2000) was mapped for 2020, 2050 and 2080. Analysing those shifts enabled us to delineate knowledge-transfer paths between sites, according to the analysed scenarios. We concluded that, according to the Intergovernmental Panel on Climate Change A2 scenario, all considered sites will be outside the predefined bioclimatic neighbourhood by 2080, while according to the B2 scenario all of them will be inside that neighbourhood, although sometimes marginally so. Therefore, the implementation of global sustainability measures as considered in the B2 scenario family can be of great importance in order to delay significantly the impacts of climate change, giving extra time for the adaptation of the outdoor regional living plant collectionsinfo:eu-repo/semantics/publishedVersio

Fracturing ranked surfaces

Discretized landscapes can be mapped onto ranked surfaces, where every element (site or bond) has a unique rank associated with its corresponding relative height. By sequentially allocating these elements according to their ranks and systematically preventing the occupation of bridges, namely elements that, if occupied, would provide global connectivity, we disclose that bridges hide a new tricritical point at an occupation fraction $p=p_{c}$, where $p_{c}$ is the percolation threshold of random percolation. For any value of $p$ in the interval $p_{c}< p \leq 1$, our results show that the set of bridges has a fractal dimension $d_{BB} \approx 1.22$ in two dimensions. In the limit $p \rightarrow 1$, a self-similar fracture is revealed as a singly connected line that divides the system in two domains. We then unveil how several seemingly unrelated physical models tumble into the same universality class and also present results for higher dimensions

Shifting Global Invasive Potential of European Plants with Climate Change

Global climate change and invasions by nonnative species rank among the top concerns for agents of biological loss in coming decades. Although each of these themes has seen considerable attention in the modeling and forecasting communities, their joint effects remain little explored and poorly understood. We developed ecological niche models for 1804 species from the European flora, which we projected globally to identify areas of potential distribution, both at present and across 4 scenarios of future (2055) climates. As expected from previous studies, projections based on the CGCM1 climate model were more extreme than those based on the HadCM3 model, and projections based on the a2 emissions scenario were more extreme than those based on the b2 emissions scenario. However, less expected were the highly nonlinear and contrasting projected changes in distributional areas among continents: increases in distributional potential in Europe often corresponded with decreases on other continents, and species seeing expanding potential on one continent often saw contracting potential on others. In conclusion, global climate change will have complex effects on invasive potential of plant species. The shifts and changes identified in this study suggest strongly that biological communities will see dramatic reorganizations in coming decades owing to shifting invasive potential by nonnative species