Internet Archive Search: Gillmor Gang
Archived version of the .mp3 podcast for Gillmor Gang
[1608.00462] Are Safer Looking Neighborhoods More Lively? A Multimodal Investigation into Urban Life
Authors: Marco De Nadai, Radu L. Vieriu, Gloria Zen, Stefan Dragicevic, Nikhil Naik, Michele Caraviello, Cesar A. Hidalgo, Nicu Sebe, Bruno Lepri
To appear in the Proceedings of ACM Multimedia Conference (MM), 2016. October 15 - 19, 2016, Amsterdam, Netherlands
Policy makers, urban planners, architects, sociologists, and economists are interested in creating urban areas that are both lively and safe. But are the safety and liveliness of neighborhoods independent characteristics? Or are they just two sides of the same coin? In a world where people avoid unsafe looking places, neighborhoods that look unsafe will be less lively, and will fail to harness the natural surveillance of human activity. But in a world where the preference for safe looking neighborhoods is small, the connection between the perception of safety and liveliness will be either weak or nonexistent. In this paper we explore the connection between the levels of activity and the perception of safety of neighborhoods in two major Italian cities by combining mobile phone data (as a proxy for activity or liveliness) with scores of perceived safety estimated using a Convolutional Neural Network trained on a dataset of Google Street View images scored using a crowdsourced visual perception survey. We find that: (i) safer looking neighborhoods are more active than what is expected from their population density, employee density, and distance to the city centre; and (ii) that the correlation between appearance of safety and activity is positive, strong, and significant, for females and people over 50, but negative for people under 30, suggesting that the behavioral impact of perception depends on the demographic of the population. Finally, we use occlusion techniques to identify the urban features that contribute to the appearance of safety, finding that greenery and street facing windows contribute to a positive appearance of safety (in agreement with Oscar Newman's defensible space theory). These results suggest that urban appearance modulates levels of human activity and, consequently, a neighborhood's rate of natural surveillance
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Deep learning for computational biology | Molecular Systems Biology
Technological advances in genomics and imaging have led to an explosion of molecular and cellular profiling data from large numbers of samples. This rapid increase in biological data dimension and acquisition rate is challenging conventional analysis strategies. Modern machine learning methods, such as deep learning, promise to leverage very large data sets for finding hidden structure within them, and for making accurate predictions. In this review, we discuss applications of this new breed of analysis approaches in regulatory genomics and cellular imaging. We provide background of what deep learning is, and the settings in which it can be successfully applied to derive biological insights. In addition to presenting specific applications and providing tips for practical use, we also highlight possible pitfalls and limitations to guide computational biologists when and how to make the most use of this new technology.
#CellularImaging, #ComputationalBiology, #DeepLearning, #MachineLearning, #RegulatoryGenomics
Mol Syst Biol. (2016) 12: 878
A statistical definition for reproducibility and replicability | bioRxiv
Everyone agrees that reproducibility and replicability are fundamental characteristics of scientific studies. These topics are attracting increasing attention, scrutiny, and debate both in the popular press and the scientific literature. But there are no formal statistical definitions for these concepts, which leads to confusion since the same words are used for different concepts by different people in different fields. We provide formal and informal definitions of scientific studies, reproducibility, and replicability that can be used to clarify discussions around these concepts in the scientific and popular press.
Network Neuroscience | MIT Press Journals
Network Neuroscience features innovative scientific work that significantly advances our understanding of network organization and function in the brain across all scales, from molecules and neurons to circuits and systems.
Positioned at the intersection of brain and network sciences, the journal covers empirical and computational studies that record, analyze or model relational data among elements of neurobiological systems, including neuronal signaling and information flow in circuits, patterns of functional connectivity recorded with electrophysiological or imaging methodology, studies of anatomical connections among neurons and brain regions, and interactions among biomolecules or genes.
Genetic variability in a frozen batch of MCF-7 cells invisible in routine authentication
Common recommendations for cell line authentication, annotation and quality control fall short addressing genetic heterogeneity. Within the Human Toxome Project, we demonstrate that there can be marked cellular and phenotypic heterogeneity in a single batch of the human breast adenocarcinoma cell line MCF-7 obtained directly from a cell bank that are invisible with the usual cell authentication by short tandem repeat (STR) markers. STR profiling just fulfills the purpose of authentication testing, which is to detect significant cross-contamination and cell line misidentification. Heterogeneity needs to be examined using additional methods. This heterogeneity can have serious consequences for reproducibility of experiments as shown by morphology, estrogenic growth dose-response, whole genome gene expression and untargeted mass-spectroscopy metabolomics for MCF-7 cells. Using Comparative Genomic Hybridization (CGH), differences were traced back to genetic heterogeneity already in the cells from the original frozen vials from the same ATCC lot, however, STR markers did not differ from ATCC reference for any sample. These findings underscore the need for additional quality assurance in Good Cell Culture Practice and cell characterization, especially using other methods such as CGH to reveal possible genomic heterogeneity and genetic drifts within cell lines.
Scientific #repeatability
Disconnected, fragmented, or united? a trans-disciplinary review of network science by Cesar Hidalgo
Hidalgo, C.A. Appl Netw Sci (2016) 1: 6. doi:10.1007/s41109-016-0010-3
Abstract
During decades the study of networks has been divided between the efforts of social scientists and natural scientists, two groups of scholars who often do not see eye to eye. In this review I present an effort to mutually translate the work conducted by scholars from both of these academic fronts hoping to continue to unify what has become a diverging body of literature. I argue that social and natural scientists fail to see eye to eye because they have diverging academic goals. Social scientists focus on explaining how context specific social and economic mechanisms drive the structure of networks and on how networks shape social and economic outcomes. By contrast, natural scientists focus primarily on modeling network characteristics that are independent of context, since their focus is to identify universal characteristics of systems instead of context specific mechanisms. In the following pages I discuss the differences between both of these literatures by summarizing the parallel theories advanced to explain link formation and the applications used by scholars in each field to justify their approach to network science. I conclude by providing an outlook on how these literatures can be further unified.