Sci-Advent – ‘Electronic amoeba’ finds approximate solution to traveling salesman problem in linear time

Researchers at Hokkaido University and Amoeba Energy in Japan have, inspired by the efficient foraging behavior of a single-celled amoeba, developed an analog computer for finding a reliable and swift solution to the traveling salesman problem — a representative combinatorial optimization problem.

Amoeba-inspired analog electronic computing system integrating resistance crossbar for solving the travelling salesman problem. Scientific Reports, 2020; 10 (1) DOI: 10.1038/s41598-020-77617-7

Many real-world application tasks such as planning and scheduling in logistics and automation are mathematically formulated as combinatorial optimization problems. Conventional digital computers, including supercomputers, are inadequate to solve these complex problems in practically permissible time as the number of candidate solutions they need to evaluate increases exponentially with the problem size — also known as combinatorial explosion. Thus new computers called “Ising machines,” including “quantum annealers,” have been actively developed in recent years. These machines, however, require complicated pre-processing to convert each task to the form they can handle and have a risk of presenting illegal solutions that do not meet some constraints and requests, resulting in major obstacles to the practical applications.

These obstacles can be avoided using the newly developed “electronic amoeba,” an analog computer inspired by a single-celled amoeboid organism. The amoeba is known to maximize nutrient acquisition efficiently by deforming its body. It has shown to find an approximate solution to the traveling salesman problem (TSP), i.e., given a map of a certain number of cities, the problem is to find the shortest route for visiting each city exactly once and returning to the starting city. This finding inspired Professor Seiya Kasai at Hokkaido University to mimic the dynamics of the amoeba electronically using an analog circuit, as described in the journal Scientific Reports. “The amoeba core searches for a solution under the electronic environment where resistance values at intersections of crossbars represent constraints and requests of the TSP,” says Kasai. Using the crossbars, the city layout can be easily altered by updating the resistance values without complicated pre-processing.

Kenta Saito, a PhD student in Kasai’s lab, fabricated the circuit on a breadboard and succeeded in finding the shortest route for the 4-city TSP. He evaluated the performance for larger-sized problems using a circuit simulator. Then the circuit reliably found a high-quality legal solution with a significantly shorter route length than the average length obtained by the random sampling. Moreover, the time required to find a high-quality legal solution grew only linearly to the numbers of cities. Comparing the search time with a representative TSP algorithm “2-opt,” the electronic amoeba becomes more advantageous as the number of cities increases. “The analog circuit reproduces well the unique and efficient optimization capability of the amoeba, which the organism has acquired through natural selection,” says Kasai.

“As the analog computer consists of a simple and compact circuit, it can tackle many real-world problems in which inputs, constraints, and requests dynamically change and can be embedded into IoT devices as a power-saving microchip,” says Masashi Aono who leads Amoeba Energy to promote the practical use of the amoeba-inspired computers.

This is a Joint Release between Hokkaido University and Amoeba Energy Co., Ltd. More information

10-10 Celebrate Ada Lovelace day!

It’s Ada Lovelace day, celebrating the work of women in mathematics, science, technology and engineering. To join the celebration +Plus Magazine revisits a collection of interviews with female mathematicians produced earlier this year. The interviews accompany the Women of Mathematics photo exhibition, which celebrates female mathematicians from institutions throughout Europe. It was launched in Berlin in the summer of 2016 and is now touring European institutions.

To watch the interviews with the women or read the transcripts, and to see the portraits that featured in the exhibition, click on the links below. For more content by or about female mathematicians click here.

Raspberry Pi

I am very pleased to have finally received the Raspberry Pi 3 that I ordered the other day. I also got a Sense Hat – an add-on board for Raspberry Pi, made especially for the Astro Pi mission

The Sense HAT has an 8×8 RGB LED matrix, a five-button joystick and includes the following sensors:

  • Gyroscope
  • Accelerometer
  • Magnetometer
  • Temperature
  • Barometric pressure
  • Humidity

There is even a  Python library providing easy access to everything on the board. I can’t wait to start using it with some of the APIs available at Bluemix for example. Any ideas are more than welcome.


Bluemix – a set of tools/tutorials for app development

IBM’s Bluemix provides access to a large set of API’s such as Watson services like AlchemyAPI, Natural Language Classifier, Visual Recognition, Personality Insights and more. I have recently started playing with it a bit more. You can set up a free account (free for 30 days) and see what you think.

Check it out:

 Here is what IBM has to say about it:

Bluemix is the latest cloud offering from IBM. It enables organizations and developers to quickly and easily create, deploy, and manage applications on the cloud. Bluemix is an implementation of IBM’s Open Cloud Architecture based on Cloud Foundry, an open source Platform as a Service (PaaS). Bluemix delivers enterprise-level services that can easily integrate with your cloud applications without you needing to know how to install or configure them.Bluemix

I will be happy to hear what you build and how you use bluemix. Keep in touch.

Installing Spark 1.6.1 on a Mac with Scala 2.11

I have recently gone through the process of installing Spark in my mac for testing and development purposes. I also wanted to make sure I could use the installation not only with Scala, but also with PySpark through a Jupyter notebook.

If you are interested in doing the same, here are the steps I followed. First of all, here are the packages you will need:

  • Python 2.7 or higher
  • Java SE Development Kit
  • Scala and Scala Build Tool
  • Spark 1.6.1 (at the time of writing)
  • Jupyter Notebook


You can chose the best python distribution that suits your needs. I find Anaconda to be fine for my purposes. You can obtain a graphical installer from I am using Python 2.7 at the time of writing.

Java SE Development Kit

You will need to download Oracle Java SE Development Kit 7 or 8 at Oracle JDK downloads page. In my case, at the time of writing I am using 1.7.0_80. You can check the version you have by opening a terminal and typing

java -version

You also have to make sure that the appropriate environment variable is set up. In your


  add the following lines:

export JAVA_HOME=$(/usr/libexec/java_home)

Scala and Scala Build Tool

In this case, I found it much easier to use Homebrew to install and manage the Scala language. I f you have never used Homebrew, I recommend that you take a look. To install it you have to type the following in your terminal:

ruby -e "$(curl -fsSL"

Once you have Hombrew you can install Scala and the Scala Build Tool as follows:

> brew install scala
> brew install bst

You may want to create appropriate environments in your 



export SCALA_HOME=/usr/local/bin/scala

Spark 1.6.1

Obtain Spark from

Note that for building Spark with Scala 2.11 you will need to download the Spark source code and build it appropriately.


Once you have downloaded the tgz file, unzip it into an appropriate location (your home directory for example) and navigate to the unzipped folder (for example



To build Spark with Scala 2.11 you need to type the following commands:

> ./dev/
> build/sbt clean assembly

This may take a while, so sit tight! When finished, you can check that everything is working by launching either the Scala shell:

> ./bin/spark-shell

or the Python shell:

> ./bin/pyspark

Once again there are some environment variables that are recommended:

export SPARK_PATH=~/spark-1.6.1
export PYSPARK_DRIVER_PYTHON="jupyter" 
alias sparknb='$SPARK_PATH/bin/pyspark --master local[2]'

The last line is an alias that will enable us to launch a Jupyter notebook with PySpark. Totally optional!

Jupyter Notebook

If all is working well you are ready to go. Source your


  and  launch a Jupyter notebook:

> sparknb

Et voilà!

How much should we fear the rise of artificial intelligence?

  1. When the arena is something as pure as a board game, where the rules are entirely known and always exactly the same, the results are remarkable. When the arena is something as messy, unrepeatable and ill-defined as actuality, the business of adaptation and translation is a great deal more difficult.

Tom Chatfield

From the opinion article of Tom Chatfiled in The Guardian.

Astronaut Bowman

Artificial Intelligence – Debunking Myths

Exploring around the interwebs, I came across this article by Rupert Goodwins in ArsTechnica about debunking myths about Artificial Intelligence. 

HAL 9000 in the film 2001.

It is a good read and it you have a few minutes to spare, do give it a go.

Rupert addresses the following myths:

  1. AI’s makes machines that can think.
  2. AI will not be bound by human ethics.
  3. AI will get out of control
  4. Breakthroughs in AI will all happen in sudden jumps.

It is true that there are a number of effort to try to replicate (and therefore understand) human thought. Some examples include the Blue Brain project in the École Polytechnique Fédérale de Lausanne (EPFL) in Switzerland. However, this does not imply that they will get immediately a machine such as HAL or C3-PO.

This is because the brain is fat more complex than the current efforts are able to simulate. As a matter of fact, even simpler brains are significantly more complex for simulation. This does not mean that we should not try to understand and learn how brains work.

Part of the problem is that it is difficult to even define what we mean by “thought”— the so called hard problem. So finding a solution to the strong AI problem is not going to be here soon, but we should definitely try.

So, once that myth is out of the way, the idea that a Terminator-like robot is around the corner is put into perspective. Sure, there are attempts at getting some self-driving cars and such but we are not quite there yet. All in all, it is true that a number of technological advances can be used for good or bad causes, and that is surely something that we all should bear in mind.