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Social Foraging
Dynamics of Social Interaction
Curated by Ashish Umre
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Harvard cracks DNA storage, crams 700 terabytes of data into a single gram

Harvard cracks DNA storage, crams 700 terabytes of data into a single gram | Social Foraging | Scoop.it

A bioengineer and geneticist at Harvard's Wyss Institute have successfully stored 5.5 petabits of data -- around 700 terabytes -- in a single gram of DNA, smashing the previous DNA data density record by a thousand times.

 

The work, carried out by George Church and Sri Kosuri, basically treats DNA as just another digital storage device. Instead of binary data being encoded as magnetic regions on a hard drive platter, strands of DNA that store 96 bits are synthesized, with each of the bases (TGAC) representing a binary value (T and G = 1, A and C = 0).

 

To read the data stored in DNA, you simply sequence it — just as if you were sequencing the human genome — and convert each of the TGAC bases back into binary. To aid with sequencing, each strand of DNA has a 19-bit address block at the start (the red bits in the image below) — so a whole vat of DNA can be sequenced out of order, and then sorted into usable data using the addresses.

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Ngozi Odochi (Godwell) Nwokocha's comment, August 19, 2012 2:41 PM
Thanks for posting!
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Maintaining a Cognitive Map in Darkness: The Need to Fuse Boundary Knowledge with Path Integration

Maintaining a Cognitive Map in Darkness: The Need to Fuse Boundary Knowledge with Path Integration | Social Foraging | Scoop.it

Spatial navigation requires the processing of complex, disparate and often ambiguous sensory data. The neurocomputations underpinning this vital ability remain poorly understood. Controversy remains as to whether multimodal sensory information must be combined into a unified representation, consistent with Tolman's “cognitive map”, or whether differential activation of independent navigation modules suffice to explain observed navigation behaviour. Here we demonstrate that key neural correlates of spatial navigation in darkness cannot be explained if the path integration system acted independently of boundary (landmark) information. In vivo recordings demonstrate that the rodent head direction (HD) system becomes unstable within three minutes without vision. In contrast, rodents maintain stable place fields and grid fields for over half an hour without vision.

 

Using a simple HD error model, we show analytically that idiothetic path integration (iPI) alone cannot be used to maintain any stable place representation beyond two to three minutes. We then use a measure of place stability based on information theoretic principles to prove that featureless boundaries alone cannot be used to improve localization above chance level. Having shown that neither iPI nor boundaries alone are sufficient, we then address the question of whether their combination is sufficient and – we conjecture – necessary to maintain place stability for prolonged periods without vision. We addressed this question in simulations and robot experiments using a navigation model comprising of a particle filter and boundary map. The model replicates published experimental results on place field and grid field stability without vision, and makes testable predictions including place field splitting and grid field rescaling if the true arena geometry differs from the acquired boundary map. We discuss our findings in light of current theories of animal navigation and neuronal computation, and elaborate on their implications and significance for the design, analysis and interpretation of experiments.

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One extinction leads to another

One extinction leads to another | Social Foraging | Scoop.it

When a carnivore becomes extinct, other predatory species could soon follow, according to new research. Scientists have previously put forward this theory, but a University of Exeter team has now carried out the first experiment to prove it. Published August 15, 2012 in the Royal Society journal Biology Letters, the study shows how the demise of one carnivore species can indirectly cause another to become extinct. The University of Exeter team believes any extinction can create a ripple effect across a food web, with far-reaching consequences for many other animals.

 

The research adds weight to growing evidence that a 'single species' approach to conservation, for example in fisheries management, is misguided. Instead the focus needs to be holistic, encompassing species across an entire ecosystem.

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When it comes to food, chimps only think of themselves

When it comes to food, chimps only think of themselves | Social Foraging | Scoop.it

A sense of fairness is an important part of human behaviour, yet a research team involving Queen Mary, University of London (UK) found it did not evolve from our closest living relatives.

 

The study, published in the journal Biology Letters today (15 August) tested whether our great ape relatives, the chimpanzees and bonobos, have a sense of fairness like humans.

 

The scientists, involving Professor Keith Jensen, from Queen Mary's School of Biological and Chemical Sciences, put the apes through a series of ultimatum games.

 

One against the other, they had to choose whether to steal or leave the other's grapes. The games were set up in a variety of different ways involving equal proportions of grapes and others were split with a higher proportion given to one over the other.

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Karate black belts' white matter shows how a powerful punch comes from the brain

Karate black belts' white matter shows how a powerful punch comes from the brain | Social Foraging | Scoop.it

Brain scans have revealed distinctive features in the brain structure of karate experts, which could be linked to their ability to punch powerfully from close range. Researchers from Imperial College London and UCL (University College London) found that differences in the structure of white matter -- the connections between brain regions -- were correlated with how black belts and novices performed in a test of punching ability.

 

Karate experts are able to generate extremely powerful forces with their punches, but how they do this is not fully understood. Previous studies have found that the force generated in a karate punch is not determined by muscular strength, suggesting that factors related to the control of muscle movement by the brain might be important.

 

The study, published in the journal Cerebral Cortex, looked for differences in brain structure between 12 karate practitioners with a black belt rank and an average of 13.8 years' karate experience, and 12 control subjects of similar age who exercised regularly but did not have any martial arts experience.

 

The researchers tested how powerfully the subjects could punch, but to make useful comparisons with the punching of novices they restricted the task to punching from short range -- a distance of 5 centimetres. The subjects wore infrared markers on their arms and torso to capture the speed of their movements.

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An algorithm for tracking viruses (and Twitter rumors) to their source

An algorithm for tracking viruses (and Twitter rumors) to their source | Social Foraging | Scoop.it

A team of Swiss researchers thinks it has created an algorithm capable of tracking almost anything -- from computer viruses to terrorist attacks to epidemics -- back to the source using a minimal amount of data. The trick is focusing on time to figure out who “infected” whom.

 

No, Vanilla Ice isn’t dead — and if he had access to a new algorithm from Swiss researcher Pedro Pinto, the Ice Man could go all techno-ninja and track down who started the rumor claiming he was. That’s because Pinto and his colleagues at the Ecole Polytechnique Fédérale de Lausanne have developed an algorithm for finding the source of such rumors, as well as viruses (physical and digital) and other maladies, even across highly complex networks.

 

Their method, according to an abstract of a paper just published in Physical Review Letters, is ideal for situations where there is relatively little data to work with, and is “based on the principles used by telecommunication towers to pinpoint cell phone users.” Essentially, the algorithm starts by looking at a small collection of points within a network and working back from there to determine the origin, kind of like how investigators can zero in on a cell phone’s location using triangulation. The more connections, or observers, a particular point has, the fewer that are needed to track down the source point.

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How Algorithmically Created Content will Transform Publishing

How Algorithmically Created Content will Transform Publishing | Social Foraging | Scoop.it

A recent conversation with Fred Zimmerman, a long time friend and publishing entrepreneur, woke me up to the fact that the a part of the publishing industry that has long resisted technology may finally be ripe for transformation. The key question is: Does algorithmic content creation that uses machine learning and automation have a role to play in content creation?

 

The first impulse of most people like me, who have spent much of their careers writing for love and money, is to loudly answer NO WAY. I firmly believe that it is impossible to replace the creativity of the human mind and the skill of writing learned over years with an algorithm.

 

But Zimmerman, who is CEO of Nimble Books, is pioneering a new technique he calls combinatorial publishing that can create a book that is useful in seconds for pennies. He persuasively argues that algorithmic content creation has an important role to play, even if the virtuosity of the human will always be the beating heart of content creation.

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Boeing showcase drones that behave like swarm of insects

Boeing showcase drones that behave like swarm of insects | Social Foraging | Scoop.it

Boeing engineers have successfully demonstrated new technology that enables drones to function like a ‘swarm of insects’ where they can communicate and carry out tasks together mid-air.

 

In June, engineers and researchers from Johns Hopkins University tested their technology on two ScanEagle drones in Oregon, Boeing revealed.

 

The drone development could lead to lower costs and less risk in military welfare, Boeing said in a statement.

 

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Soft autonomous robot inches along like an earthworm

Soft autonomous robot inches along like an earthworm | Social Foraging | Scoop.it

Earthworms creep along the ground by alternately squeezing and stretching muscles along the length of their bodies, inching forward with each wave of contractions. Snails and sea cucumbers also use this mechanism, called peristalsis, to get around, and our own gastrointestinal tracts operate by a similar action, squeezing muscles along the esophagus to push food to the stomach.

 

Now researchers at MIT, Harvard University and Seoul National University have engineered a soft autonomous robot that moves via peristalsis, crawling across surfaces by contracting segments of its body, much like an earthworm. The robot, made almost entirely of soft materials, is remarkably resilient: Even when stepped upon or bludgeoned with a hammer, the robot is able to inch away, unscathed.

 

Sangbae Kim, the Esther and Harold E. Edgerton Assistant Professor of Mechanical Engineering at MIT, says such a soft robot may be useful for navigating rough terrain or squeezing through tight spaces.

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Pesticides cause bees to lose their bearings

Pesticides cause bees to lose their bearings | Social Foraging | Scoop.it

If they eat the wrong thing, bees cannot find their way home. Two new studies confirm that a group of widely used pesticides subtly affect the insects' behaviour, and may be partly to blame for their falling populations.

 

Neonicotinoid pesticides are used around the world to protect major crops like oilseed rape (canola). But studies have suggested that they are harmful to bees – they make them more susceptible to gut parasites, for example.

 

In field tests of 75 colonies of buff-tailed bumblebees (Bombus terrestris), David Goulson at the University of Stirling, UK, and colleagues found that food treated with realistic levels of one neonicotinoid, called imidacloprid, dramatically slows their spring population growth.

 

Dosed colonies also produced 85 per cent fewer queens than control colonies – a major problem as only the new queens survive the winter to found new colonies the following year.

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Supercomputer-level millisecond-scale sampling for protein simulation on a desktop computer

Supercomputer-level millisecond-scale sampling for protein simulation on a desktop computer | Social Foraging | Scoop.it

Computer scientists and biochemists at the University of California, San Diego, have developed advanced GPU accelerated software and demonstrated for the first time that they could sample biological events that occur on the millisecond timescale using only an upgraded desktop computer equipped with a relatively inexpensive graphics processing card.

 

These results have the potential to bring millisecond-scale sampling, now available only on a multi-million dollar supercomputer, to all researchers, and could significantly impact the study of protein dynamics with key implications for improved drug and biocatalyst development.

 

With some innovative coding, a GPU (graphics processing unit) that retails for about $500, and the widely used software package of molecular simulations called Amber (Assisted Model Building with Energy Refinement), the researchers were able to run a simulation showing the same five long-lived structural states of a specific protein as observed in a simulation conducted by D.E. Shaw Research’s Anton, a purpose-built molecular dynamics (MD) supercomputer.

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Derek123's comment, August 20, 2012 2:27 PM
Very interesting, and exciting for researchers. Our solution is in-memory computing (SAP HANA) which achieves the similar results by holding the entire sequence in-memory. Here are two short videos on this subject. http://www.youtube.com/watch?v=m4bulUhHAx4 ,
http://www.sap-tv.com/video/7678.
Ashish, please reach out if you would like to discuss.
Derek
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Graph spectra and the detectability of community structure in networks

We study networks that display community structure -- groups of nodes within which connections are unusually dense. Using methods from random matrix theory, we calculate the spectra of such networks in the limit of large size, and hence demonstrate the presence of a phase transition in matrix methods for community detection, such as the popular modularity maximization method. The transition separates a regime in which such methods successfully detect the community structure from one in which the structure is present but is not detected. By comparing these results with recent analyses of maximum-likelihood methods we are able to show that spectral modularity maximization is an optimal detection method in the sense that no other method will succeed in the regime where the modularity method fails.

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Researchers unveil molecular details of how bacteria propagate antibiotic resistance

Fighting "superbugs" -- strains of pathogenic bacteria that are impervious to the antibiotics that subdued their predecessor generations -- has required physicians to seek new and more powerful drugs for their arsenals. Unfortunately, in time, these treatments also can fall prey to the same microbial ability to become drug resistant. Now, a research team at the University of North Carolina at Chapel Hill (UNC) may have found a way to break the cycle that doesn't demand the deployment of a next-generation medical therapy: preventing "superbugs" from genetically propagating drug resistance.

 

The team will present their findings at the annual meeting of the American Crystallographic Association (ACA), held July 28 -- Aug. 1 in Boston, Mass.

 

For years, the drug vancomycin has been the last-stand treatment for life-threatening cases of methicilin-resistant Staphylococcus aureus, or MRSA. A powerful antibiotic first isolated in 1953 from soil collected in the jungles of Borneo, vancomycin works by inhibiting formation of the S. aureus cell wall so that it cannot provide structural support and protection. In 2002, however, a strain of S. aureus was isolated from a diabetic kidney dialysis patient. This particular strain would not succumb to vancomycin. This was the first recorded instance in the United States of vancomycin-resistant Staphylococcus aureus, or VRSA, a deadly variant that many now consider one of the most dangerous bacteria in the world.

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Next-Generation Digital Information Storage in DNA

Digital information is accumulating at an astounding rate, straining our ability to store and archive it. DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. Here, we develop a strategy to encode arbitrary digital information in DNA, write a 5.27-megabit book using DNA microchips, and read the book using next-generation DNA sequencing.

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Locust Dynamics: Behavioral Phase Change and Swarming

Locust Dynamics: Behavioral Phase Change and Swarming | Social Foraging | Scoop.it

Locusts exhibit two interconvertible behavioral phases, solitarious and gregarious. While solitarious individuals are repelled from other locusts, gregarious insects are attracted to conspecifics and can form large aggregations such as marching hopper bands. Numerous biological experiments at the individual level have shown how crowding biases conversion towards the gregarious form. To understand the formation of marching locust hopper bands, we study phase change at the collective level, and in a quantitative framework. Specifically, we construct a partial integrodifferential equation model incorporating the interplay between phase change and spatial movement at the individual level in order to predict the dynamics of hopper band formation at the population level. Stability analysis of our model reveals conditions for an outbreak, characterized by a large scale transition to the gregarious phase. A model reduction enables quantification of the temporal dynamics of each phase, of the proportion of the population that will eventually gregarize, and of the time scale for this to occur. Numerical simulations provide descriptions of the aggregation's structure and reveal transiently traveling clumps of gregarious insects. Our predictions of aggregation and mass gregarization suggest several possible future biological experiments.

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Why do we assume economic algorithms are always right?

Why do we assume economic algorithms are always right? | Social Foraging | Scoop.it

I am writing this in the grips of a profound headache, largely brought on by my stumbling efforts to get a grip on where we are with our economies.

 

If our global economy were a commercial aircraft, and I one of the pilots, the entire instrument panel would be covered in flashing lights. But instead of sounding steady alarms, most would be stuttering on and off in apparently random patterns, making coherent responses very difficult. And that mental image had me racing back to the inquiry report on Air France 447, which disappeared en route from Rio de Janeiro to Charles de Gaulle on 1 June 2009.

 

Apart from routine fears of flying, those boarding the Airbus A330 would have had no reason to expect anything untoward. But, in the worst accident in French aviation history, the plane fell out of the sky into the Atlantic, killing all 228 people aboard. The causes were a mystery for air crash investigators, though early suspicions focused on the possible icing up of the critical airspeed monitoring devices called pitot tubes. It took Herculean efforts to retrieve the black boxes, but they provided a much clearer idea of what had gone so dramatically wrong.

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Twitter founders launch two sharing web sites (BRANCH & MEDIUM)

Twitter founders launch two sharing web sites (BRANCH & MEDIUM) | Social Foraging | Scoop.it

THE CHAPS behind Twitter have launched two sharing web sites that they hope will enjoy the same success.

 

Ev Williams and Biz Stone have launched Branch and Medium from their money fund, The Obvious Corporation, and expect them to have an immediate impact on the market.

 

Both web sites are destinations for sharing. Branch is billed as "a new way to talk to each other" and lets users create tree-like chat structures that take links and discussion in stride.

 

It is, as far as we can see, linked chats that rely on expert opinion, easier said than done in the online world. Branch has been around for a little while, but has now pulled out of beta and is open to new users. New users with something to say, that is. On paper it sounds not dissimilar to other services, like Google hangouts, for example, where users can chat and interact with experts.

 

Medium, which is introduced personally by Ev Williams, has an air of Tumblr about it, and is designed to make it easier for people to share things - images and links, for example - that they want to share.

 

Mediums can be open or closed, depending on the user, and the service is still in beta and not open to all.

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Babies may not have a 'moral compass' after all

Babies may not have a 'moral compass' after all | Social Foraging | Scoop.it

New research from New Zealand's University of Otago is casting doubt on a landmark US study that suggested infants as young as six months old possess an innate moral compass that allows them to evaluate individuals as 'good' or 'bad'.

 

The 2007 study by Yale University researchers provided the first evidence that 6- and 10-month-old infants could assess individuals based on their behaviour towards others, showing a preference for those who helped rather than hindered another individual.

 

Based on a series of experiments, researchers in the Department of Psychology at Otago have shown that the earlier findings may simply be the result of infants' preferences for interesting and attention grabbing events, rather than an ability to evaluate individuals based on their social interactions with others.

 

The Otago study was recently published in PLoS One, an international, peer-reviewed, open-access, online journal.

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Self-Evolvable Systems: Machine Learning in Social Media (Understanding Complex Systems)

Self-Evolvable Systems: Machine Learning in Social Media (Understanding Complex Systems) | Social Foraging | Scoop.it

This monograph presents key method to successfully manage the growing complexity of systems where conventional engineering and scientific methodologies and technologies based on learning and adaptability come to their limits and new ways are nowadays required. The transition from adaptable to evolvable and finally to self-evolvable systems is highlighted, self-properties such as self-organization, self-configuration, and self-repairing are introduced and challenges and limitations of the self-evolvable engineering systems are evaluated.

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How To Breed A Face

How To Breed A Face | Social Foraging | Scoop.it

The genetic algorithm is a way to create solutions to problems by mimicking the way that nature works. However, that doesn't mean it can't be fun! Pareidoloop is a program which uses a GA approach to create a face that satisfies a face recognition algorithm - and all using JavaScript.

 

The basic idea of the GA is simple enough. Start with a representation of a solution as a sequence of bits that can be combined in the same way as DNA, i.e. using exchange and mutation. Next set up a population of solutions and test them against the problem. Finally weed out the poor performers and allow the best of the rest to mix their genetic material to product the next generation of solutions.

 

If you go through enough generations the solutions should keep getting better as the population evolves towards a better fitness.

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New router enhances the precision of woodworking

New router enhances the precision of woodworking | Social Foraging | Scoop.it

Anyone who has tried to build a piece of furniture from scratch knows the frustration of painstakingly cutting pieces of wood, only to discover that they won’t fit together because the cutting was not quite accurate enough.

 

That’s exactly what happened to Alec Rivers, a PhD student in the Department of Electrical Engineering and Computer Science (EECS), when he attempted to build a simple picture frame using woodworking equipment he had inherited from his grandfather. Despite measuring and aligning his tools as best he could by hand, Rivers found that he could not produce shapes with enough precision to make them all fit together. “I was getting incredibly frustrated, because just as with any home project I would cut things out and they would look about right, but none of the pieces would line up,” Rivers says.

 

But rather than simply throwing the pieces of wood into the trash and settling for a store-bought picture frame, Rivers decided there had to be a better way. So he and colleagues Frédo Durand, an EECS associate professor and member of the Computer Science and Artificial Intelligence Laboratory (CSAIL), and Ilan Moyer, a graduate student in the Department of Mechanical Engineering, began developing a new kind of woodworking router — a drill-like cutting tool — that could automatically cut out accurate shapes from a piece of material by following a digital design. The result is a handheld device that can adjust its position to precisely follow a digital plan when the user moves the router roughly around the shape to be cut.

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Simple mathematical computations underlie brain circuits

Simple mathematical computations underlie brain circuits | Social Foraging | Scoop.it

The brain has billions of neurons, arranged in complex circuits that allow us to perceive the world, control our movements and make decisions. Deciphering those circuits is critical to understanding how the brain works and what goes wrong in neurological disorders.

 

MIT neuroscientists have now taken a major step toward that goal. In a new paper appearing in the Aug. 9 issue of Nature, they report that two major classes of brain cells repress neural activity in specific mathematical ways: One type subtracts from overall activation, while the other divides it.

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Why living in the moment is impossible: Decision-making memories stored in mysterious brain area known to be involved with vision

The sought-after equanimity of "living in the moment" may be impossible, according to neuroscientists who've pinpointed a brain area responsible for using past decisions and outcomes to guide future behavior. The study, based on research conducted at the University of Pittsburgh and published August 9 in the professional journal Neuron, is the first of its kind to analyze signals associated with metacognition -- a person's ability to monitor and control cognition (a term cleverly described by researchers as "thinking about thinking.")

 

"The brain has to keep track of decisions and the outcomes they produce," said Marc Sommer, who did his research for the study as a University of Pittsburgh neuroscience faculty member and is now on the faculty at Duke University. "You need that continuity of thought," Sommer continued. "We are constantly keeping decisions in mind as we move through life, thinking about other things. We guessed it was analogous to working memory, which would point toward the prefrontal cortex."

 

Sommer predicted that neuronal correlates of metacognition resided in the same brain areas responsible for cognition, including the frontal cortex -- a part of the brain linked with personality expression, decision making, and social behavior. Sommer worked with Paul G. Middlebrooks, who did his research for the study at Pitt before he received his Pitt PhD in neuroscience in 2011; Middlebrooks is now a postdoctoral fellow at Vanderbilt University. The research team studied single neurons in vivo in three frontal cortical regions of the brain: the frontal eye field (associated with visual attention and eye movements), the dorsolateral prefrontal cortex (responsible for motor planning, organization, and regulation), and the supplementary eye field (SEF) involved in the planning and control of saccadic eye movements, which are the extremely fast movements of the eye that allow it to continually refocus on an object.

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Spectra of random graphs with arbitrary expected degrees

We study random graphs with arbitrary distributions of expected degree and derive expressions for the spectra of their adjacency and modularity matrices. We give a complete prescription for calculating the spectra that is exact in the limit of large network size and large vertex degrees. We also study the effect on the spectra of hubs in the network, vertices of unusually high degree, and show that these produce isolated eigenvalues outside the main spectral band, akin to impurity states in condensed matter systems, with accompanying eigenvectors that are strongly localized around the hubs. We also give numerical results that confirm our analytic expressions.

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Inquire — The intelligent textbook that helps students learn

Inquire — The intelligent textbook that helps students learn | Social Foraging | Scoop.it

Want to know more about your subject? Type in your own question and artificially intelligent software will construct a new page to answer your query

 

SITTING down with the Inquire system is, at first, a lot like trying to cosy up to an intimidatingly dense biology textbook. Sure, its presentation on the iPad is slick, but that can't hide the fact that you are in for a tough old read.

 

That is until you highlight the first bit of particularly impenetrable text. Suddenly a list of questions pops up in the right-hand margin. Touch one and you are whisked away to a Wikipedia-like page full of information specific to the concept you are stuck on. Terms like "chloroplast" and "plasma membrane" are succinctly defined, and the page explains how each concept fits into the wider field of biology.

 

Want to know more? Type in your own question and artificially intelligent software will construct a new page to answer your query.

The aim of Inquire is to provide students with the world's first intelligent textbook, says its creator David Gunning of Seattle-based Vulcan. At first glance, the system just looks like an electronic version of Campbell Biology, the tome that forms the bedrock of biology classes for first-year university and advanced high school students in the US. But behind the scenes is a machine-readable concept map of the 5000 or so ideas covered in the book, along with information on how they are all related.

When a student asks a question - "what does a protein do?", for instance - the system first converts it into a more structured query, such as "what is the function of a protein?", and then uses this to search and find results from the concept map.

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