"bio" entries

Four short links: 25 February 2015

Four short links: 25 February 2015

Bricking Cars, Mapping Epigenome, Machine Learning from Encrypted Data, and Phone Privacy

  1. Remotely Bricking Cars (BoingBoing) — story from 2010 where an intruder illegally accessed Texas Auto Center’s Web-based remote vehicle immobilization system and one by one began turning off their customers’ cars throughout the city.
  2. Beginning to Map the Human Epigenome (MIT) — Kellis and his colleagues report 111 reference human epigenomes and study their regulatory circuitry, in a bid to understand their role in human traits and diseases. (The paper itself.)
  3. Machine Learning Classification over Encrypted Data (PDF) — It is worth mentioning that our work on privacy-preserving classification is complementary to work on differential privacy in the machine learning community. Our work aims to hide each user’s input data to the classification phase, whereas differential privacy seeks to construct classifiers/models from sensitive user training data that leak a bounded amount of information about each individual in the training data set. See also The Morning Paper’s unpacking of it.
  4. Privacy of Phone Audio (Reddit) — unconfirmed report from Redditor I started a new job today with Walk N’Talk Technologies. I get to listen to sound bites and rate how the text matches up with what is said in an audio clip and give feed back on what should be improved. At first, I though these sound bites were completely random. Then I began to notice a pattern. Soon, I realized that I was hearing peoples commands given to their mobile devices. Guys, I’m telling you, if you’ve said it to your phone, it’s been recorded…and there’s a damn good chance a 3rd party is going to hear it.
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Four short links: 24 February 2015

Four short links: 24 February 2015

Open Data, Packet Dumping, GPU Deep Learning, and Genetic Approval

  1. Wiki New Zealand — open data site, and check out the chart builder behind the scenes for importing the data. It’s magic.
  2. stenographer (Google) — open source packet dumper for capturing data during intrusions.
  3. Which GPU for Deep Learning?a lot of numbers. Overall, I think memory size is overrated. You can nicely gain some speedups if you have very large memory, but these speedups are rather small. I would say that GPU clusters are nice to have, but that they cause more overhead than the accelerate progress; a single 12GB GPU will last you for 3-6 years; a 6GB GPU is plenty for now; a 4GB GPU is good but might be limiting on some problems; and a 3GB GPU will be fine for most research that looks into new architectures.
  4. 23andMe Wins FDA Approval for First Genetic Test — as they re-enter the market after FDA power play around approval (yes, I know: one company’s power play is another company’s flouting of safeguards designed to protect a vulnerable public).
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Four short links: 6 February 2015

Four short links: 6 February 2015

Active Learning, Tongue Sensors, Cybernetic Management, and HTML5 Game Publishing

  1. Real World Active Learningthe point at which algorithms fail is precisely where there’s an opportunity to insert human judgment to actively improve the algorithm’s performance. An O’Reilly report with CrowdFlower.
  2. Hearing With Your Tongue (BoingBoing) — The tongue contains thousands of nerves, and the region of the brain that interprets touch sensations from the tongue is capable of decoding complicated information. “What we are trying to do is another form of sensory substitution,” Williams said.
  3. The Art of Management — cybernetics and management.
  4. kiwi.jsa mobile & desktop browser based HTML5 game framework. It uses CocoonJS for publishing to the AppStore.
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Four short links: 7 January 2015

Four short links: 7 January 2015

Program Synthesis, Data Culture, Metrics, and Information Biology

  1. Program Synthesis ExplainedThe promise of program synthesis is that programmers can stop telling computers how to do things, and focus instead on telling them what they want to do. Inductive program synthesis tackles this problem with fairly vague specifications and, although many of the algorithms seem intractable, in practice they work remarkably well.
  2. Creating a Data-Driven Culture — new (free!) ebook from Hilary Mason and DJ Patil. The editor of that team is the luckiest human being alive.
  3. Ev Williams on Metrics — a master-class in how to think about and measure what matters. If what you care about — or are trying to report on — is impact on the world, it all gets very slippery. You’re not measuring a rectangle, you’re measuring a multi-dimensional space. You have to accept that things are very imperfectly measured and just try to learn as much as you can from multiple metrics and anecdotes.
  4. Nature, the IT Wizard (Nautilus) — a fun walk through the connections between information theory, computation, and biology.
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Four short links: 25 December 2015

Four short links: 25 December 2015

Smart Cities, Blockchain Innovation, Brain Interfaces, and Knowledge Graphs

  1. Smartest Cities Rely on Citizen Cunning and Unglamorous Technology (The Guardian) — vendors like Microsoft, IBM, Siemens, Cisco and Hitachi construct the resident of the smart city as someone without agency; merely a passive consumer of municipal services – at best, perhaps, a generator of data that can later be aggregated, mined for relevant inference, and acted upon. Should he or she attempt to practise democracy in any form that spills on to the public way, the smart city has no way of accounting for this activity other than interpreting it as an untoward disruption to the orderly flow of circulation.
  2. Second Wave of Blockchain Innovation — the economic challenges of innovating on the blockchain.
  3. Introduction to the Modern Brain-Computer Interface Design (UCSD) — The lectures were first given by Christian Kothe (SCCN/UCSD) in 2012 at University of Osnabrueck within the Cognitive Science curriculum and have now been recorded in the form of an open online course. The course includes basics of EEG, BCI, signal processing, machine learning, and also contains tutorials on using BCILAB and the lab streaming layer software.
  4. Machine Learning with Knowledge Graphs (video) — see also extra readings.
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Four short links: 12 December 2014

Four short links: 12 December 2014

Tech Ethics, Yahoo's KVS, Biology Inside, and Smart Luggage

  1. Do Artifacts Have Ethics? — 41 questions to ask yourself about the technology you create.
  2. MDBM — Yahoo’s fast key-value store, in use for over a decade. Super-fast, using mmap and passing around (gasp) raw pointers.
  3. The Revolution in Biology is Here, Now (Mike Loukides) — I’ve been asked plenty of times (and I’ve asked plenty of times), “what’s the killer product for synthetic biology?” BioFabricate convinced me that that’s the wrong question. We may never have some kind of biological iPod. That isn’t the right way to think. What I saw, instead, was real products that you might never notice. Bricks made from sand that are held together by microbes designed to excrete the binder. Bricks and packing material made from fungus (mycelium). Plastic excreted by bacteria that consume waste methane from sewage plants. You wouldn’t know, or care, whether your plastic Lego blocks are made from petroleum or from bacteria, but there’s a huge ecological difference.
  4. Bluesmart — Indiegogo campaign for a “connected carry-on,” aka a smart suitcase. From the mobile app you can track it, learn when it’s close (or too far away), (un)lock, weigh…and you can plug your devices in and recharge from the built-in battery. Sweet!
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Four short links: 5 December 2014

Four short links: 5 December 2014

Gaming Cancer, Touch Interface, Petal Lampshade, and Biology HLL

  1. Nanodocan online game that allows bioengineers and the general public to design new nanoparticle strategies toward the treatment of cancer. (via The Economist)
  2. Rendering Haptic Volumetric Shapes in Mid-Air Using Ultrasound (PDF) — SIGGRAPH paper on using ultrasound to fool your senses into feeling a 3D shape in the air. (via Slashdot)
  3. Open Up Lamp — genius lampshade that opens with the heat of the lightbulb, like petals opening. (via Matt Webb)
  4. Anthaa high-level language for biology, making it easy to rapidly compose reproducible work flows using individually testable and reusable Antha Elements. (via Mike Loukides)
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Four short links: 18 November 2014

Four short links: 18 November 2014

A Worm Mind Forever LEGO Voyaging, Automatic Caption Generator, ELK Stack, and Amazonian Deployment

  1. A Worm’s Mind in a Lego Body — the c. elegans worm’s 302 neurons has been sequenced, modelled in open source code, and now hooked up to a Lego robot. It is claimed that the robot behaved in ways that are similar to observed C. elegans. Stimulation of the nose stopped forward motion. Touching the anterior and posterior touch sensors made the robot move forward and back accordingly. Stimulating the food sensor made the robot move forward. There is video.
  2. Show and Tell: A Neural Image Caption Generator — Google Research paper on generating captions like “Two pizzas sitting on top of a stove top oven” from a photo. Wow.
  3. Big Data with the ELK Stack — ElasticSearch, logstash, and Kibana. Interesting and powerful combination of tools!
  4. Apollo: Amazon’s Deployment EngineApollo will stripe the rolling update to simultaneously deploy to an equivalent number of hosts in each location. This keeps the fleet balanced and maximizes redundancy in the case of any unexpected events. When the fleet scales up to handle higher load, Apollo automatically installs the latest version of the software on the newly added hosts. Lust.
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Four short links: 10 November 2014

Four short links: 10 November 2014

Metascience, Bio Fab, Real-time Emoji, and Phone Library

  1. Metascience Could Rescue the Replication Crisis (Nature) — Metascience, the science of science, uses rigorous methods to examine how scientific practices influence the validity of scientific conclusions. (via Ed Yong)
  2. OpenTrons (Kickstarter) — 3d-printer style frame for micropipetting, magnetic micro-bead washes, and photography. Open source and kickstarterated. (via Evil Mad Scientist)
  3. Emoji Tracker — real-time emoji use across Twitter. (via Chris Aniszczyk)
  4. libphonenumber — open source Google’s common Java, C++ and Javascript library for parsing, formatting, storing and validating international phone numbers. The Java version is optimized for running on smartphones, and is used by the Android framework since 4.0 (Ice Cream Sandwich).
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Four short links: 29 October 2014

Four short links: 29 October 2014

Tweet Parsing, Focus and Money, Challenging Open Data Beliefs, and Exploring ISP Data

  1. TweetNLP — CMU open source natural language parsing tools for making sense of Tweets.
  2. Interview with Google X Life Science’s Head (Medium) — I will have been here two years this March. In nineteen months we have been able to hire more than a hundred scientists to work on this. We’ve been able to build customized labs and get the equipment to make nanoparticles and decorate them and functionalize them. We’ve been able to strike up collaborations with MIT and Stanford and Duke. We’ve been able to initiate protocols and partnerships with companies like Novartis. We’ve been able to initiate trials like the baseline trial. This would be a good decade somewhere else. The power of focus and money.
  3. Schooloscope Open Data Post-MortemThe case of Schooloscope and the wider question of public access to school data challenges the belief that sunlight is the best disinfectant, that government transparency would always lead to better government, better results. It challenges the sentiments that see data as value-neutral and its representation as devoid of politics. In fact, access to school data exposes a sharp contrast between the private interest of the family (best education for my child) and the public interest of the government (best education for all citizens).
  4. M-Lab Observatory — explorable data on the data experience (RTT, upload speed, etc) across different ISPs in different geographies over time.
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