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Viswanath S.,University of Texas at Austin | Ravikant D.V.S.,WalmartLabs | Elber R.,University of Texas at Austin
Proteins: Structure, Function and Bioinformatics

An atomically detailed potential for docking pairs of proteins is derived using mathematical programming. A refinement algorithm that builds atomically detailed models of the complex and combines coarse grained and atomic scoring is introduced. The refinement step consists of remodeling the interface side chains of the top scoring decoys from rigid docking followed by a short energy minimization. The refined models are then re-ranked using a combination of coarse grained and atomic potentials. The docking algorithm including the refinement and re-ranking, is compared favorably to other leading docking packages like ZDOCK, Cluspro, and PATCHDOCK, on the ZLAB 3.0 Benchmark and a test set of 30 novel complexes. A detailed analysis shows that coarse grained potentials perform better than atomic potentials for realistic unbound docking (where the exact structures of the individual bound proteins are unknown), probably because atomic potentials are more sensitive to local errors. Nevertheless, the atomic potential captures a different signal from the residue potential and as a result a combination of the two scores provides a significantly better prediction than each of the approaches alone. © 2012 Wiley Periodicals, Inc. Source

Hu X.,Arizona State University | Tang L.,WalmartLabs | Tang J.,Arizona State University | Liu H.,Arizona State University
WSDM 2013 - Proceedings of the 6th ACM International Conference on Web Search and Data Mining

Microblogging, like Twitter and Sina Weibo, has become a popular platform of human expressions, through which users can easily produce content on breaking news, public events, or products. The massive amount of microblogging data is a useful and timely source that carries mass sentiment and opinions on various topics. Existing sentiment analysis approaches often assume that texts are independent and identically distributed (i.i.d.), usually focusing on building a sophisticated feature space to handle noisy and short texts, without taking advantage of the fact that the microblogs are networked data. Inspired by the social sciences findings that sentiment consistency and emotional contagion are observed in social networks, we investigate whether social relations can help sentiment analysis by proposing a Sociological Approach to handling Noisy and short Texts (SANT) for sentiment classification. In particular, we present a mathematical optimization formulation that incorporates the sentiment consistency and emotional contagion theories into the supervised learning process; and utilize sparse learning to tackle noisy texts in microblogging. An empirical study of two real-world Twitter datasets shows the superior performance of our framework in handling noisy and short tweets. © 2013 ACM. Source

Crawled News Article
Site: gigaom.com

For those skeptics who still think OpenStack isn’t ready for prime time, here’s a tidbit: @WalmartLabs is now running in excess of 100,000 cores of OpenStack on its compute layer. And that’s growing by the day. It’s also the technology that ran parent company Walmart’s prodigious Cyber Monday and holiday season sales operations. If that’s not production, I’m not sure what is. San Bruno, California–based @WalmartLabs, which is the e-commerce innovation and development arm for the Walmart retail colossus, started working with OpenStack about a year and a half ago, at first relying heavily on the usual vendors but increasingly building up its in-house talent pool, Amandeep Singh Juneja, senior director of cloud operations and engineering, said in an interview. @WalmartLabs has about 3,600 employees worldwide, 1,500 of whom are in the Bay Area. Juneja estimated the organization has hired about 1,000 engineers in the last year or so — no mean feat given that there are lots of companies, including the OpenStack vendors, in the market for this expertise. “Traditionally, Walmart is vendor-heavy in its big technology investments — name a vendor and we’ve worked with it and that was also true with OpenStack,” Juneja noted. “We started about one and a half years ago with all the leading distribution vendors involved … we did our first release with Havana and Rackspace. But then we invested internally in building our own engineering muscle. We attended all the meet-ups and summits.” Havana is the code name for the eighth OpenStack code release. Nothing says big like Walmart. It has around $480 billion in annual revenue, more than 2 million employees, and more than 11,000 retail locations worldwide (including Sam’s Club and Walmart International venues). Walmart.com claims more than 140 million weekly visitors. So scale was clearly an issue from the get-go. What @WalmartLabs loved about OpenStack was that it could be molded and modified to fit its specifications, without vendor lock-in. This is a massive private cloud built on a public cloud scale. There are also some macro issues at play here. Since parent company Walmart competes tooth and nail with Amazon.com, the chances of Walmart using Amazon Web Services public cloud are nil. (I asked Juneja whether Walmart would ever use any public cloud capabilities and he politely responded that this question was above his pay grade.) The beauty of open-source projects like OpenStack is that new capabilities continually come on line and there is a community of deeply technical people working on the code. Going forward, Juneja is particularly interested in Ironic, an OpenStack project to enable provisioning of bare metal (as opposed to virtual) machines, and in the Trove database-as-a-service project. Trove, he noted, has matured a bit and Walmart will be using more DbaaS going forward. Another work in progress is the construction of a multi-petabyte object store using the OpenStack Swift technology, but there are also plans to bring more block storage in-house, possibly using OpenStack Cinder. And the team is looking at Neutron for software-defined network projects. One thing Walmart must deal with is its brick-and-mortar roots. The ability to order online and pick up in the store means that what @WalmartLabs builds must interact with inventory and other systems already running the Walmart/Sam’s Club storefronts. Non-e-commerce-related IT projects are run by Walmart’s Information Services Division at the company’s Bentonville, Arkansas headquarters. So the ability of the shiny new OpenStack systems to interface with infrastructure that’s been in place for decades or so — some for as much as 50 years — is critical. It also spells the full employment act for all those @WalmartLabs engineers. Note: this story was updated at 11:30 a.m. PST to reflect that Walmart is running 100K+ cores, not nodes, of OpenStack

Crawled News Article
Site: www.cnet.com

Minecraft is one of the most widely used games around these days. So it was notable when the programmer who wrote it, Markus "Notch" Persson, embraced Google's Dart programming language for Web apps. "I love it," Persson tweeted in November, shortly after Google released Dart 1.0. That's music to the ears of Google developers who created Dart to rewrite the rules of Web programming and, as they see it, to overcome shortcomings of the JavaScript language at the foundation of Web apps today. To fully succeed, though, Google will have to persuade a lot of skeptics to see things the way Notch does. Google believes Dart speeds up both developers and the programs they write, but skeptics worry that it fragments Web programming and undermines the industry's focus on better JavaScript. So far, it's been a largely academic debate, but that will change in coming months. That's because Google right now is building Dart technology directly into Chrome. "The next step for us is to get the Dart virtual machine into Chrome," said Lars Bak, the leader of Google's project, adding that he hopes it'll be done within a year. "If everything pans out the way it's predicted, with a factor of two performance boost and a factor of ten in startup-time boost, I'm pretty sure the other browsers will be enticed with what we're doing." Bak is "pretty sure," but Mozilla, Apple, and Microsoft -- which make the other three of the top four browsers in use today -- don't care for Dart. When Google ships a Dart-enabled Chrome, the debate over the language will transform from dueling blog posts to live code on the Web that affects the public. Dart on the Web There are two ways Dart can make its way to the Web. Today, it can get there only with Google software called dart2js that converts a programmer's Dart software into JavaScript that any browser can run. That's not controversial, and indeed many languages including CoffeeScript, Red Hat's Ceylon, and Microsoft's TypeScript take that approach. Second -- and this is the project the Dart team is working on now -- is building the Dart virtual machine (VM) into a browser. A virtual machine is a software layer that acts like self-contained computer on its own, running instructions in its own particular language. So far Dart programs only work directly in an experimental Chrome build called Dartium, but building the Dart VM into Chrome would mean native Dart programs would have a place on the Web. That's the phase that Dart fans such as Mixbook are eager to see. That same step worries some other developers who've seen past problems when the Web was fragmented with software platforms that worked in one browser but not another. "What I find worrying is [Google's] tendency to push for in-house, works-only-on-Chrome solutions instead of trying to work with the wider web standards community," said Henri Bergius, founder of the NoFlo project and co-creator of FlowHub. In this they strongly resemble Microsoft of the bad old IE market dominance and ActiveX era." Dart has some big differences compared to ActiveX, though. For one thing, it's open-source software, which means anyone can adopt it for free and that Google is, at least in principle, open to outside contributions. And last week, Google convinced the Ecma standards group to tackle Dart, an effort that could more formally ensure that others get a say in Dart. Dart's Dash debut One advantage of JavaScript is an informality that encourages a seat-of-the-pants programming style -- you can write and go without too much advance planning. But that informality can become a drawback for big programming projects -- and sophisticated Web apps have hundreds of thousands of lines of code. Dart is geared for larger-scale projects where informality can cause problems. For example, it's got optional "typing," which essentially means that when one part of a program calls upon another, the programmer must lay out what kind of data it sends out and what kinds it expects back. That's the kind of thing that lets programming tools do a better job finding bugs early, and it's something that could make Web-app programming easier for developers coming in from native-app languages like C++ and Java. Google released Dart in testing form two years ago. Before it was publicly announced and was still called Dash, though, Dart got off to an inauspicious start by antagonizing JavaScript fans with us-vs.-them wording: "The goal of the Dash effort is ultimately to replace JavaScript as the lingua franca of Web development on the open Web platform," an early memo about it said. "Things that start out revolutionary and with a 'replace' agenda have failed repeatedly on the Web," said JavaScript founder and Mozilla Chief Technology Officer Brendan Eich. Google doesn't really intend to replace JavaScript -- indeed, such a feat would be impossible given how many sites rely on it -- but more to compete alongside JavaScript. A victory for Dart would mean a gradual shift toward Dart, though, so that new Web sites employ it and programmers use dart2js to handle browsers that only can handle JavaScript. JavaScript performance improvements have been impressive, but Bak thinks "it's harder and harder to get gains. I think if you really want to go to next level, like a factor of two, you have to go to a different technology," he said. Unlocking that performance will free programmers to tackle new classes of Web apps, he argued. Dart resistance Eich is skeptical of Google's performance claims and of the wisdom of adding a Dart virtual machine. "Most browsers have no reason to include Dart because doing so would not only be extremely difficult for engineers to accomplish in each major browser, it would also result in a quality hit," Eich said. Specifically, he pointed to problems with having two separate virtual machines, both trying to clean up computer memory through a process called garbage collection and both trying to control Web page elements through the browser's Document Object Model (DOM) interface. "Two runtimes sharing the DOM adds both bug habitat and a performance tax," Eich said. That's an objection Apple has raised, too. Luke Hoban, Microsoft's TypeScript product manager, believes that speeding up JavaScript will deliver limited returns. "In practice, JavaScript performance is not the bottleneck in real-world performance," Hoban said. More often, it's things like pre-written libraries of JavaScript code and the interaction between JavaScript and the browser pages via the DOM, he said. Dion Almaer, vice president of engineering for WalmartLabs Mobile, agrees. "I think the JavaScript engines are awesome," he said, adding that he'd like to see DOM improvements and better use of graphics-chip acceleration. The practical difficulties of Dart, including the resistance of other browser makers, means that moving to Dart "feels like a big pill to swallow," Almaer said. Microsoft's TypeScript approach Microsoft, which in recent years has re-engaged with the Web standards world and rebuilt Internet Explorer into a much more competitive browser, agrees with Google that JavaScript programming has problems. "The difference is in the approaches to how we solve that. Our belief is that we can build on JavaScript and get it to where it can scale up to large-scale application development," Hoban said. TypeScript is a superset of JavaScript: it'll run JavaScript software unchanged but adds techniques that ordinary JavaScript engines can't handle today. That means TypeScript can take advantage of "one of the most successful programming ecosystems over the last 10 years," Hoban said. "The JavaScript ecosystem is one of the strongest ecosystems around. There's an enormous set of frameworks and libraries and tools. There are millions of programmers who know JavaScript and are comfortable working with it, and it's built into the browser itself," Hoban said. "If you can build on it, you get to leverage all that goodness." Today, TypeScript also relies on a compiler that transforms the code into ordinary JavaScript. It doesn't guarantee a performance boost when that JavaScript runs, but when programmers use TypeScript's more industrial-strength approach, "that tends to be the same code that the JavaScript VMs are very good at optimizing," Hoban said. TypeScript is nice, Bak said, but ultimately too limited. "We are trying to solve a bigger problem," fast program execution and fast program startup, he said. There's only so much that computing industry companies -- Google among them -- can do to improve JavaScript through the Ecma standards group. "Whatever you do in a standards committee, it has to be backwards compatible always," Bak said. "There are things in JavaScript that are just real hard to make really fast." Microsoft is committed, though. About a dozen people are on the TypeScript team, including Anders Hejlsberg, the chief designer of Microsoft's C# programming language, and Steve Lucco, the architect and lead engineer of the Chakra virtual machine at that Internet Explorer uses to execute JavaScript. Microsoft is eating its own dogfood, as the expression goes: it's using TypeScript to power the Bing.com Web site; the Visual Studio Online programming tools, and the Xbox Music app on Windows 8.1, the Web, and the Xbox One game console. Multilingual future Bak is no JavaScript foe. He played a lead role developing V8, the engine in Chrome that executes JavaScript code and that helped push JavaScript performance industrywide to new heights. Now, though, he wants to see many languages flourish on the Web -- not just Dart and JavaScript, but something more like the panoply that you'll find elsewhere in the computing industry. "I hope we get the Web platform to a point where there are different types of technology that can be used, so there is innovation going on," Bak said. "The more the merrier."

A few decades ago discovering events was difficult and there was no unified platform to search for them. Fast forward to present, technology has made our lives easy and it is now simple for people to discover events around them and also keep up to date with the latest news and developments. But with the sheer volume of content available both online and offline, a new problem has arisen — searching for relevant events among all the clutter. EventsHigh aims to help people with this pain point. What is it? EventsHigh is an event discovery platform that aims to bring all events under one roof and help people find relevant events based on their location, interest and availability. While there are many events discovery platforms in the market, EventsHigh’s USPs include a map and list based UI, recommendations and other personalized features. In a survey they conducted, EventsHigh found that 85% of the participants generally came to know about an event after it had happened and then regretted missing it. So they aim to make event discovery easier and more seamless through their mobile and web based app.The app is functional in Delhi, Mumbai, Bangalore, Pune, Hyderabad, Chennai, Kolkata and two international cities, Singapore and Jakarta. They cover over 20 categories of events some of which include events related to music, technology, comedy, and literature etc. – User Interface: While checking out events under various categories for a particular area, users can opt for either a list or a map-view based on their preference -Users can also keep themselves up to date about events happening ‘today’, ‘tomorrow’ or ‘weekend’ and ‘favourite’ or invite a friend to an event. –Custom feed: Based on the categories users chose and their likes and dislikes they can customize their feeds and see events they may be interested in. –Notifications: Users can set alerts for their interests and the app will send them a notification whenever a relevant event comes up. The event detail page on the app gives users details like venue, time, link to book tickets etc. EventsHigh was started by Nikesh Garera and Arvind Batra, who were part of the Kosmix team in the Bay Area that was later acquired and became WalmartLabs. They developed a strong background in machine learning and big data as a result. Nikesh (CEO) is an alumnus from Carnegie Mellon and Johns Hopkins where he pursued his MS and Ph.D respectively. Arvind (CTO) did his MS from Georgia Tech. Parag Sarda, a ME from Indian Institute of Science, joined them a few months ago. He leads their Android effort and brings his engineering experience from his prior work at Google and WalmartLabs to the table. While Arvind and Nikesh were working at Kosmix, they had a strong yearning to attend the Google I/O event but kept missing out on the announcements and were never able to book tickets for it. So they built a web-based crawler that would notify them when the Google I/O tickets went up for sale. This was how the idea for EventsHigh came about. They realized that there was a need for an event discovery platform and started working on it after moving back to Bangalore recently. They found that most Indian cities had thousands of events happening every week, but as all the information was scattered the onus was on the user to sift through and find what he or she needed. So they developed a product to address this pain point. EventsHigh bagged the second place at Tie Pitchfest San Francisco, first place for their Android app at Startup Launchpad and were among the top 10 startups shortlisted by TiE Bangalore for ‘AnthahPrerna’. They were also selected for the $20K bootstrap track of FBStart mobile app programme. While their mobile app is free to download and use, they have a B2C business model through which they help event organisers get the right leads and reach the right target audience for their events. They have events from over 50,000+ event organizers on their platform and about 100,000+ monthly unique visitors. What we liked? While the content, layout and overall user experience is good, what stands out is the map based UI, which gives users a bird’s eye view of events happening in their area. Users can also pinch and zoom in on events and favourite or invite their friends while still in the map mode. The notifications for various events are a boon for absent minded users. The volume of events and search filters makes event discovery simple and easy. The search bar in the app delivered desired results for different keywords as well. What could be improved? While the app makes event discovery easier, the next step could be to make it more social and let users know if their friends or contacts are attending a particular event or if they have also checked out the details about the same event. Nikesh confirmed that they are working on this and are in the process of adding other new features too. For example, in the future users will be able to see more event attributes such as whether an event is free or ticketed, kid ­friendly or not, parking available at venue etc. With an experienced team and a well-executed product, EventsHigh is a unique app and it is definitely worth trying out if you are interested in discovering and attending events in your city. What do you think about this app, do let us know in the comments. Also do check out other apps under our App Fridays and Pursuit of APPiness series.

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