newsletter/2017/04 (Link Bibliography)

“newsletter/​2017/​04” links:


  2. 03

  3. newsletter

  4. Changelog


  6. Water

  7. ⁠, Daniel R. Schrider, Andrew D. Kern (2017-04-27):

    The degree to which adaptation in recent human evolution shapes genetic variation remains controversial. This is in part due to the limited evidence in humans for classic “hard selective sweeps,” wherein a novel beneficial mutation rapidly sweeps through a population to ⁠. However, positive selection may often proceed via “soft sweeps” acting on mutations already present within a population. Here we examine recent positive selection across six human populations using a powerful machine learning approach that is sensitive to both hard and soft sweeps. We found evidence that soft sweeps are widespread and account for the vast majority of recent human adaptation. Surprisingly, our results also suggest that linked positive selection affects patterns of variation across much of the genome, and may increase the frequencies of deleterious mutations. Our results also reveal insights into the role of ⁠, cancer risk, and central nervous system development in recent human evolution.

  8. ⁠, Constantina Theofanopoulou, Simone Gastaldon, Thomas O’Rourke, Bridget D. Samuels, Angela Messner, Pedro Tiago Martins, Francesco Delogu, Saleh Alamri, Boeckx Cedric (2017-04-09):

    This study identifies and analyzes statistically-significant overlaps between selective sweep screens in anatomically modern humans and several domesticated species. The results obtained suggest that (paleo-) genomic data can be exploited to complement the fossil record and support the idea of self-domestication in Homo sapiens, a process that likely intensified as our species populated its niche. Our analysis lends support to attempts to capture the “domestication syndrome” in terms of alterations to certain signaling pathways and cell lineages, such as the neural crest.

  9. 2017-owers.pdf

  10. ⁠, Arslan A. Zaidi, Brooke C. Mattern, Peter Claes, Brian McEcoy, Cris Hughes, Mark D. Shriver (2017-02-03):

    The evolutionary reasons for variation in nose shape across human populations have been subject to continuing debate. An import function of the nose and nasal cavity is to condition inspired air before it reaches the lower respiratory tract. For this reason, it is thought the observed differences in nose shape among populations are not simply the result of ⁠, but may be adaptations to climate. To address the question of whether local adaptation to climate is responsible for nose shape divergence across populations, we use Qst–Fst comparisons to show that nares width and alar base width are more differentiated across populations than expected under genetic drift alone. To test whether this differentiation is due to climate adaptation, we compared the spatial distribution of these variables with the global distribution of temperature, absolute humidity, and relative humidity. We find that width of the nares is correlated with temperature and absolute humidity, but not with relative humidity. We conclude that some aspects of nose shape may indeed have been driven by local adaptation to climate. However, we think that this is a simplified explanation of a very complex evolutionary history, which possibly also involved other non-neutral forces such as sexual selection.

    Author summary:

    The study of human adaptation is essential to our understanding of disease etiology. Evolutionary investigations into why certain disease phenotypes such as sickle-cell anemia and lactose intolerance occur at different rates in different populations have led to a better understanding of the genetic and environmental risk factors involved. Similarly, research into the geographical distribution of skin pigmentation continues to yield important clues regarding risk of vitamin D deficiency and skin cancer. Here, we investigate whether variation in the shape of the external nose across populations has been driven by regional differences in climate. We find that variation in both nares width and alar base width appear to have experienced accelerated divergence across human populations. We also find that the geospatial distribution of nares width is correlated with temperature, and absolute humidity, but not with relative humidity. Our results support the claim that local adaptation to climate may have had a role in the evolution of nose shape differences across human populations.

  11. 2017-librado.pdf


  13. ⁠, Anna R. Docherty, Arden Moscati, Danielle Dick, Jeanne E. Savage, Jessica E. Salvatore, Megan Cooke, Fazil Aliev, Ashlee A. Moore, Alexis C. Edwards, Brien P. Riley, Daniel E. Adkins, Roseann Peterson, Bradley T. Webb, Silviu A. Bacanu, and Kenneth S. Kendler (2017-11-27):

    Background: Identifying genetic relationships between complex traits in emerging adulthood can provide useful etiological insights into risk for psychopathology. College-age individuals are under-represented in genomic analyses thus far, and the majority of work has focused on the clinical disorder or cognitive abilities rather than normal-range behavioral outcomes.

    Methods: This study examined a sample of emerging adults 18–22 years of age (n = 5947) to construct an atlas of polygenic risk for 33 traits predicting relevant phenotypic outcomes. 28 hypotheses were tested based on the previous literature on samples of European ancestry, and the availability of rich assessment data allowed for polygenic predictions across 55 psychological and medical phenotypes.

    Results: Polygenic risk for (SZ) in emerging adults predicted anxiety, depression, nicotine use, trauma, and family history of psychological disorders. Polygenic risk for neuroticism predicted anxiety, depression, phobia, panic, neuroticism, and was correlated with polygenic risk for cardiovascular disease.

    Conclusions: These results demonstrate the extensive impact of genetic risk for SZ, neuroticism, and major depression on a range of health outcomes in early adulthood. Minimal cross-ancestry replication of these phenomic patterns of polygenic influence underscores the need for more of non-European populations.


  15. 2017-mcconnell.pdf



  18. ⁠, Silvia Chiappa, Sébastien Racaniere, Daan Wierstra, Shakir Mohamed (2017-04-07):

    Models that can simulate how environments change in response to actions can be used by agents to plan and act efficiently. We improve on previous environment simulators from high-dimensional pixel observations by introducing recurrent neural networks that are able to make temporally and spatially coherent predictions for hundreds of time-steps into the future. We present an in-depth analysis of the factors affecting performance, providing the most extensive attempt to advance the understanding of the properties of these models. We address the issue of computationally inefficiency with a model that does not need to generate a high-dimensional image at each time-step. We show that our approach can be used to improve exploration and is adaptable to many diverse environments, namely 10 Atari games, a 3D car racing environment, and complex 3D mazes.


  20. ⁠, Ruth Fong, Walter Scheirer, David Cox (2017-03-16):

    Machine learning is a field of computer science that builds algorithms that learn. In many cases, machine learning algorithms are used to recreate a human ability like adding a caption to a photo, driving a car, or playing a game. While the human brain has long served as a source of inspiration for machine learning, little effort has been made to directly use data collected from working brains as a guide for machine learning algorithms. Here we demonstrate a new paradigm of “neurally-weighted” machine learning, which takes fMRI measurements of human brain activity from subjects viewing images, and infuses these data into the training process of an object recognition learning algorithm to make it more consistent with the human brain. After training, these neurally-weighted classifiers are able to classify images without requiring any additional neural data. We show that our neural-weighting approach can lead to large performance gains when used with traditional machine vision features, as well as to significant improvements with already high-performing convolutional neural network features. The effectiveness of this approach points to a path forward for a new class of hybrid machine learning algorithms which take both inspiration and direct constraints from neuronal data.

  21. 2017-jouppi.pdf

  22. ⁠, H. Brendan McMahan, Eider Moore, Daniel Ramage, Seth Hampson, Blaise Agüera y Arcas (2016-02-17):

    Modern mobile devices have access to a wealth of data suitable for learning models, which in turn can greatly improve the user experience on the device. For example, language models can improve speech recognition and text entry, and image models can automatically select good photos. However, this rich data is often privacy sensitive, large in quantity, or both, which may preclude logging to the data center and training there using conventional approaches. We advocate an alternative that leaves the training data distributed on the mobile devices, and learns a shared model by aggregating locally-computed updates. We term this decentralized approach Federated Learning.

    We present a practical method for the federated learning of deep networks based on iterative model averaging, and conduct an extensive empirical evaluation, considering five different model architectures and four datasets. These experiments demonstrate the approach is robust to the unbalanced and non-IID data distributions that are a defining characteristic of this setting. Communication costs are the principal constraint, and we show a reduction in required communication rounds by 10–100× as compared to synchronized ⁠.

  23. ⁠, Jing Liao, Yuan Yao, Lu Yuan, Gang Hua, Sing Bing Kang (2017-05-02):

    We propose a new technique for visual attribute transfer across images that may have very different appearance but have perceptually similar semantic structure. By visual attribute transfer, we mean transfer of visual information (such as color, tone, texture, and style) from one image to another. For example, one image could be that of a painting or a sketch while the other is a photo of a real scene, and both depict the same type of scene.

    Our technique finds semantically-meaningful dense correspondences between two input images. To accomplish this, it adapts the notion of “image analogy” with features extracted from a Deep Convolutional Neutral Network for matching; we call our technique Deep Image Analogy. A coarse-to-fine strategy is used to compute the nearest-neighbor field for generating the results. We validate the effectiveness of our proposed method in a variety of cases, including style/​​​​texture transfer, color/​​​​style swap, sketch/​​​​painting to photo, and time lapse.


  25. ⁠, Ning Xie, Hirotaka Hachiya, Masashi Sugiyama (2012-06-18):

    Oriental ink painting, called Sumi-e, is one of the most appealing painting styles that has attracted artists around the world. Major challenges in computer-based Sumi-e simulation are to abstract complex scene information and draw smooth and natural brush strokes. To automatically find such strokes, we propose to model the brush as a agent, and learn desired brush-trajectories by maximizing the sum of rewards in the policy search framework. We also provide elaborate design of actions, states, and rewards tailored for a Sumi-e agent. The effectiveness of our proposed approach is demonstrated through simulated Sumi-e experiments.

  26. ⁠, Wojciech Marian Czarnecki, Grzegorz Świrszcz, Max Jaderberg, Simon Osindero, Oriol Vinyals, Koray Kavukcuoglu (2017-03-01):

    When training neural networks, the use of Synthetic Gradients (SG) allows layers or modules to be trained without update locking—without waiting for a true error gradient to be backpropagated—resulting in Decoupled Neural Interfaces (DNIs). This unlocked ability of being able to update parts of a neural network asynchronously and with only local information was demonstrated to work empirically in Jaderberg et al 2016. However, there has been very little demonstration of what changes DNIs and SGs impose from a functional, representational, and learning dynamics point of view. In this paper, we study DNIs through the use of synthetic gradients on feed-forward networks to better understand their behaviour and elucidate their effect on optimisation. We show that the incorporation of SGs does not affect the representational strength of the learning system for a neural network, and prove the convergence of the learning system for linear and deep linear models. On practical problems we investigate the mechanism by which synthetic gradient estimators approximate the true loss, and, surprisingly, how that leads to drastically different layer-wise representations. Finally, we also expose the relationship of using synthetic gradients to other error approximation techniques and find a unifying language for discussion and comparison.

  27. ⁠, Bertr, Rouet-Leduc, Claudia Hulbert, Nicholas Lubbers, Kipton Barros, Colin Humphreys, Paul A. Johnson (2017-02-19):

    Forecasting fault failure is a fundamental but elusive goal in earthquake science. Here we show that by listening to the acoustic signal emitted by a laboratory fault, machine learning can predict the time remaining before it fails with great accuracy. These predictions are based solely on the instantaneous physical characteristics of the acoustical signal, and do not make use of its history. Surprisingly, machine learning identifies a signal emitted from the fault zone previously thought to be low-amplitude noise that enables failure forecasting throughout the laboratory quake cycle. We hypothesize that applying this approach to continuous seismic data may lead to significant advances in identifying currently unknown signals, in providing new insights into fault physics, and in placing bounds on fault failure times.






  33. 2017-adams.pdf

  34. 2016-caro.html




  38. ⁠, Stuart J. Ritchie, Simon R. Cox, Xueyi Shen, Michael V. Lombardo, Lianne M. Reus, Clara Alloza, Matthew A. Harris, Helen L. Alderson, Stuart Hunter, Emma Neilson, David C. M. Liewald, Bonnie Auyeung, Heather C. Whalley, Stephen M. Lawrie, Catharine R. Gale, Mark E. Bastin, Andrew M. McIntosh, Ian J. Deary (2017-04-04):

    Sex differences in human brain structure and function are of substantial scientific interest because of sex-differential susceptibility to psychiatric disorders [1,2,3] and because of the potential to explain sex differences in psychological traits [4]. Males are known to have larger brain volumes, though the patterns of differences across brain subregions have typically only been examined in small, inconsistent studies [5]. In addition, despite common findings of greater male variability in traits like intelligence [6], personality [7], and physical performance [8], differences in the brain have received little attention. Here we report the largest single-sample study of structural and functional sex differences in the human brain to date (2,750 female and 2,466 male participants aged 44–77 years). Males had higher cortical and sub-cortical volumes, cortical surface areas, and white matter diffusion directionality; females had thicker cortices and higher white matter tract complexity. Considerable overlap between the distributions for males and females was common, and subregional differences were smaller after accounting for global differences. There was generally greater male variance across structural measures. The modestly higher male score on two cognitive tests was partly mediated via structural differences. Functional connectome organization showed stronger connectivity for males in unimodal sensorimotor cortices, and stronger connectivity for females in the ⁠. This large-scale characterisation of neurobiological sex differences provides a foundation for attempts to understand the causes of sex differences in brain structure and function, and their associated psychological and psychiatric consequences.

  39. 2017-trepanowski.pdf: “Effect of Alternate-Day Fasting on Weight Loss, Weight Maintenance, and Cardioprotection Among Metabolically Healthy Obese AdultsA Randomized Clinical Trial”⁠, American Medical Association




  43. 2012-mannes.pdf







  50. 1999-kohn.pdf: “Medieval and Early Modern Coinage and its Problems”⁠, Meir Kohn


  52. Books#moondust-smith-2006


  54. Anime#the-tale-of-the-princess-kaguya


  56. Movies#dna-dreams