"bio" entries

Four short links: 8 June 2015

Four short links: 8 June 2015

Software Psychology, Virus ID, Mobile Ads, and Complex Coupling

by Nat Torkington | @gnat | +Nat Torkington | June 8, 2015
  1. Psychology of Software Architecture — a wonderful piece of writing, but this stood out: It comes down to behavioral economics and game theory. The license we choose modifies the economics of those who use our work.
  2. Single Blood Test to ID Every Virus You’ve Ever Had — As Elledge notes, “in this paper alone we identified more antibody/peptide interactions to viral proteins than had been identified in the previous history of all viral exploration.”
  3. Internet Users Increasingly Blocking Ads, Including on Mobiles (The Economist) — mobile networks working on ad blockers for their customers, If lots of mobile subscribers did switch it on, it would give European carriers what they have long sought: some way of charging giant American online firms for the strain those firms put on their mobile networks. Google and Facebook, say, might have to pay the likes of Deutsche Telekom and Telefónica to get on to their whitelists.
  4. Connasence (Wikipedia) — a taxonomy of (systems) coupling. Two components are connascent if a change in one would require the other to be modified in order to maintain the overall correctness of the system. (Via Ben Gracewood.)
Four short links: 3 April 2015

Four short links: 3 April 2015

Augmenting Humans, Body-Powered CPUs, Predicting the Future, and Hermit Life

by Nat Torkington | @gnat | +Nat Torkington | April 3, 2015
  1. Unpowered Ankle Exoskeleton — “As we understand human biomechanics better, we’ve begun to see wearable robotic devices that can restore or enhance human motor performance,” says Collins. “This bodes well for a future with devices that are lightweight, energy-efficient, and relatively inexpensive, yet enhance human mobility.”
  2. Body-Powered Processing (Ars Technica) — The new SAM L21 32-bit ARM family of microcontroller (MCUs) consume less than 35 microamps of power per megahertz of processing speed while active, and less than 200 nanoamps of power overall when in deep sleep mode—with varying states in between. The chip is so low power that it can be powered off energy capture from the body. (via Greg Linden)
  3. Temporal Effects in Trend Prediction: Identifying the Most Popular Nodes in the Future (PLOSone) — We find that TBP have high general accuracy in predicting the future most popular nodes. More importantly, it can identify many potential objects with low popularity in the past but high popularity in the future.
  4. The Shut-In Economy — In 1998, Carnegie Mellon researchers warned that the Internet could make us into hermits. They released a study monitoring the social behavior of 169 people making their first forays online. The Web-surfers started talking less with family and friends, and grew more isolated and depressed. “We were surprised to find that what is a social technology has such anti-social consequences,” said one of the researchers at the time. “And these are the same people who, when asked, describe the Internet as a positive thing.”
Four short links: 25 February 2015

Four short links: 25 February 2015

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

by Nat Torkington | @gnat | +Nat Torkington | February 25, 2015
  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.
Four short links: 24 February 2015

Four short links: 24 February 2015

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

by Nat Torkington | @gnat | +Nat Torkington | February 24, 2015
  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).
Four short links: 6 February 2015

Four short links: 6 February 2015

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

by Nat Torkington | @gnat | +Nat Torkington | February 6, 2015
  1. Real World Active Learning — the 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.js — a mobile & desktop browser based HTML5 game framework. It uses CocoonJS for publishing to the AppStore.
Four short links: 7 January 2015

Four short links: 7 January 2015

Program Synthesis, Data Culture, Metrics, and Information Biology

by Nat Torkington | @gnat | +Nat Torkington | January 7, 2015
  1. Program Synthesis Explained — The 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.
Four short links: 25 December 2015

Four short links: 25 December 2015

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

by Nat Torkington | @gnat | +Nat Torkington | December 25, 2014
  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.
Four short links: 12 December 2014

Four short links: 12 December 2014

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

by Nat Torkington | @gnat | +Nat Torkington | December 12, 2014
  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!
Four short links: 5 December 2014

Four short links: 5 December 2014

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

by Nat Torkington | @gnat | +Nat Torkington | December 5, 2014
  1. Nanodoc — an 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. Antha — a high-level language for biology, making it easy to rapidly compose reproducible work flows using individually testable and reusable Antha Elements. (via Mike Loukides)
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

by Nat Torkington | @gnat | +Nat Torkington | November 18, 2014
  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 Engine — Apollo 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.