maandag 25 juni 2012

The spatial range of contour integration deficits in schizophrenia

 
 

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Abstract  
Contour integration (CI) refers to the process that represents spatially separated elements as a unified edge or closed shape. Schizophrenia is a psychiatric disorder characterized by symptoms such as hallucinations, delusions, disorganized thinking, inappropriate affect, and social withdrawal. Persons with schizophrenia are impaired at CI, but the specific mechanisms underlying the deficit are still not clear. Here, we explored the hypothesis that poor patient performance owes to reduced feedback or impaired longer-range lateral connectivity within early visual cortex—functionally similar to that found in 5- to 6-year old children. This hypothesis predicts that as target element spacing increases from .7 to 1.4° of visual angle, patient impairments will become more pronounced. As a test of the prediction, 25 healthy controls and 36 clinically stable, asymptomatic persons with schizophrenia completed a CI task that involved determining whether a subset of Gabor elements formed a leftward or rightward pointing shape. Adjacent shape elements were spaced at either .7 or 1.4° of visual angle. Difficulty in each spacing condition depended on the number of noise elements present. Patients performed worse than controls overall, both groups performed worse with the larger spacing, and the magnitude of the between-group difference was not amplified at the larger spacing. These results show that CI deficits in schizophrenia cannot be explained in terms of a reduced spatial range of integration, at least not when the shape elements are spaced within 1.5°. Later-developing, low-level integrative mechanisms of lateral connectivity and feedback appear not to be differentially impaired in the illness.

  • Content Type Journal Article
  • Category Research Article
  • Pages 1-9
  • DOI 10.1007/s00221-012-3134-4
  • Authors
    • Brian P. Keane, Division of Schizophrenia Research, University Behavioral HealthCare, University of Medicine and Dentistry of New Jersey, 151 Centennial Ave, Piscataway, NJ 08854, USA
    • Steven M. Silverstein, Division of Schizophrenia Research, University Behavioral HealthCare, University of Medicine and Dentistry of New Jersey, 151 Centennial Ave, Piscataway, NJ 08854, USA
    • Deanna M. Barch, Departments of Psychology, Psychiatry, and Radiology, Washington University in St. Louis, One Brookings Drive, Box 1125, St. Louis, MO 63130, USA
    • Cameron S. Carter, University of California, Davis, 4701 X Street, Sacramento, CA 95817, USA
    • James M. Gold, Maryland Psychiatric Research Center, University of Maryland School of Medicine, P.O. Box 21247, Baltimore, MD 21228, USA
    • Ilona Kovács, Department of Cognitive Science, Budapest University of Technology and Economics, 1 Egry J. u., Bldg T., Budapest, 1111 Hungary
    • Angus W. MacDonald III, Department of Psychology, University of Minnesota, N426 Elliott Hall, 75 E. River Rd., Minneapolis, MN 55455, USA
    • J. Daniel Ragland, University of California, Davis, 4701 X Street, Sacramento, CA 95817, USA
    • Milton E. Strauss, Department of Psychological Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-7123, USA

 
 

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dinsdag 19 juni 2012

On the quality of academic software

This is an interesting and, in my opinion, very valid view on coding in academia. Especially imporant is the concept of "code review" which we should try and do in the lab, I believe.

 
 

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per Daniel Lemire's blog autorius Daniel Lemire 12.6.18

Software is eating the world. Despite a poor year, Facebook has a market capitalization of $65 billion. This little company with barely 2000 developers is worth as much as a car marker.

Students should take notice. I would expect countless students to come to college demanding top-notch software training. I would expect graduate students to be gorgeous software programs.

Yet software produced in universities and colleges is awful, and it is not getting better. I have an explanation:

  • Most professors spent little time programming. And because they don't program, they do not enforce good practices such as code reviews and unit testing. Don't believe me? Try to look up your favorite professor on GitHub. Does he proudly display the code he produced?
  • Because few professors program, it should not come as a surprise that there are few, if any, publication outlets for academic researchers who want to present their software products. In turn, it means that if you produce high quality software, few of your academic peers will even know about it.
  • Most academic software is written by students who lack the experience and the incentives to produce good software. You would think that after spending four years in college and attending countless classes where they have programming assignments, most computer science and engineering students would be decent programmers. That is not my experience. And part of the reason is that schooling is a process by which you emulate your teachers. I am sure that if you attend four years of schooling with Linus Torvalds, you would become a decent kernel programmer. However, Linus is not, nor is he ever likely to be, a college professor. College professors don't spend much time programming and neither do their students.

So, academic software is awful because academic folks aren't that great at programming. But there are also other factors involved:

  • Programming can be as easy as cooking eggs or building a bird house. That is, it is not very difficult to write a PHP script to display the content of a database inside a browser. But producing novel software requires the programmer to act as creator. While your programming classes might teach you how to cook an egg (metaphorically speaking), they fall short of teaching you how to design a new dish for a 4-star restaurant.

    And the bar for novelty is lower than you might expect. Given an algorithm taken out from a research paper, dozens of implementations are possible, most of them inefficient. It takes a lot of work and experience to come up with the right design even if the full pseudo-code is provided to you. And making sure you implemented it properly can be much harder than one expects.

    There is very little appreciation for this fact among theoreticians who often believe that the hard part is designing an algorithm with nice theoretical properties. They fail to recognize that there might be orders of magnitude differences in speed between two algorithms having the same computational complexity.

    In effect, suppose you were provided a summary of Stephen King's next novel. Could you beat King to it and produce as good a novel? Doubtful. Software is similar. Execution is everything. A clever plot is worthless.

  • Most academic researchers write software for themselves. As Cook put it: "People who have only written software for their own use have no idea how much work goes into writing software for others." Cooking your own food is a lot easier than being a chef in a restaurant. The difference between the two is at least an order of magnitude, if not two.

    There is very little appreciation for this fact in academia. The default is to write throw-away code: you write the code, you use it and you forget about it. Issues like maintenance and documentation are discussed at length in some classes, but it is rarely put in practice within academia.

So, what about the future? I remain pessimistic regarding academic software. There will always be exceptions, but as a rule, I expect mediocrity to remain. Hence, when I review a research paper or a thesis, I expect the software supporting it to be awful. And I expect whoever hires new programmers to think the same. And there is a practical consequence to my pessimism: perhaps if you hope to get a job as a Facebook engineer, you ought to spend more time on GitHub and less time in the classroom. If you are lucky, you might convince your school to grant you a few credits for your open source work.

Further reading: In a recent blog post, Google's Matt Welsh states that he wasted millions of dollars as a Harvard professor. How? By producing software prototypes that were later thrown away. Maybe his code could have stood the test of time if only the university had better supported its commercialization. I have my doubts.

You might also want to read In the long run… by Suresh Venkat for a description of the distance between software practice and theoretical computer science.


 
 

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donderdag 14 juni 2012

An exploration of eye movements when reading texts with atypical spatial lay...

 
 

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via i-Perception by Pion on 6/12/12

In two experiments we explored eye movements that people make when looking at texts with an atypical spatial layout. In the first experiment, participants repeatedly viewed the same piece of text, containing sections in different languages and printed using different fonts and reading directions, while they answered different questions about what they saw. In agreement with earlier studies showing significant differences in gaze patterns across different tasks, we found that reading was strongly influenced by the questions that participants tried to answer. In the second experiment, we examined gaze patterns for different types of poems while participants performed a single task: To rate their appreciation of the poem. Poems were either in the typical form, with short lines all aligned to the left, or they were in an atypical form ("graphical poem"), with the text dispersed across the page, in different fonts, reading directions, and size. Half of the poems were from an artist known for his graphical poems, the other half were from different authors who posted their poems on a webpage. All these poems were presented in a typical and an atypical form. Participants rated the poems from the web more highly, but took less time to inspect them. Whether the poem was in a typical or an atypical layout did not influence the ratings, even though longer inspection times were found for the atypical forms. Eye movement parameters, such as fixation duration and saccade amplitude, were relatively unaffected by the layout of the poems, although some additional larger amplitude saccades could be observed for the atypical forms.    

 
 

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Chromatic properties of texture-shape and of texture-surround suppression of...

 
 

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via Journal of Vision recent issues by Gheorghiu, E., Kingdom, F. A. A. on 6/12/12

Abstract Contour-shape coding is color selective (Gheorghiu Kingdom & Prins, 2009). These two findings raise two questions: (1) is texture-surround suppression of contour shape color selective, and (2) is texture-shape processing color selective? To answer these questions, we measured the shape-frequency aftereffect using contours constructed from strings of Gabors defined along the red-green, blue-yellow, and luminance axes of cardinal color space. The stimuli were either single sinusoidal-shaped contours or textures made of sinusoidal-shaped contours arranged in parallel. We measured aftereffects for (A) single-contour adaptors and single-contour tests defined along the same versus different cardinal directions, (B) texture adaptors and single-contour tests in which the central-adaptor contour/single-contour test and surround adaptor contours were defined along the same versus different cardinal directions, and (C) texture adaptors and texture tests defined along same versus different cardinal directions. We found that color selectivity was most prominent for contour-shape processing, weaker for texture-surround suppression of contour-shape processing, and absent for texture-shape processing.

 
 

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Illusory contour formation survives crowding

 
 

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via Journal of Vision recent issues by Lau, J. S. F., Cheung, S.-H. on 6/12/12

Abstract Flanked objects are difficult to identify using peripheral vision due to visual crowding, which limits conscious access to target identity. Nonetheless, certain types of visual information have been shown to survive crowding. Such resilience to crowding provides valuable information about the underlying neural mechanism of crowding. Here we ask whether illusory contour formation survives crowding of the inducers. We manipulated the presence of illusory contours through the (mis)alignment of the four inducers of a Kanizsa square. In the inducer-aligned condition, the observers judged the perceived shape (thin vs. fat) of the illusory Kanizsa square, manipulated by small rotations of the inducers. In the inducer-misaligned condition, three of the four inducers (all except the upper-left) were rotated 90°. The observers judged the orientation of the upper-left inducer. Crowding of the inducers worsened observers' performance significantly only in the inducer-misaligned condition. Our findings suggest that information for illusory contour formation survives crowding of the inducers. Crowding happens at a stage where the low-level featural information is integrated for inducer orientation discrimination, but not at a stage where the same information is used for illusory contour formation.

 
 

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woensdag 13 juni 2012

Members only: PeerJ promises new approach to open-access

 
 

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via cognitive science and more door Sebastiaan Mathôt op 13-6-12

New open-access journals aplenty, usually nothing to get too excited about. Just a few minutes ago, I received an invitation to submit a paper for a special issue of the open-access International Journal of Advanced Robotic Systems. For just E850 I would have the honour of contributing to this 0.33 impact factor journal (somewhat surprisingly it has an impact factor)—A clear case of straight-to-spam.

Yet today I read an article on the Nature website about a new open-access initiative that seems very promising. It is called PeerJ, and is founded by Peter Binfield and Jason Hoyt. These are credible names, previously linked to PLoS ONE, the most successfull open-access journal, and Mendeley, a free reference management service.

Essentially, PeerJ is a members-only peer-reviewed open-access journal. Members-only, because in order to submit you have to become a member of the journal. Peer-reviewed, because papers are refereed by experts. And open-access, because all papers are freely released under a Creative Commons license.


 
 

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maandag 11 juni 2012

Cortical oscillations and sensory predictions

Feed: TRENDS IN COGNITIVE SCIENCES
Posted on: vrijdag 8 juni 2012 2:00
Author: TRENDS IN COGNITIVE SCIENCES
Subject: Cortical oscillations and sensory predictions

 

Luc H. Arnal, Anne-Lise Giraud. Many theories of perception are anchored in the central notion that the brain continuously updates an internal model of the world to infer the probable causes of sensory events. In this framework,....


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dinsdag 5 juni 2012

for the next M-exhibition?

http://coolsciencenews.blogspot.be/2012/06/3d-mapping-will-allow-us-to-look-inside.html
--
Suggested reading by Ervin
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