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An Amoeba-Based Computer Found Solutions To 8-City Traveling Salesman Problem (vice.com)

dmoberhaus shares a report from Motherboard: A team of Japanese researchers from Keio University in Tokyo have demonstrated that an amoeba is capable of generating approximate solutions to a remarkably difficult math problem known as the "traveling salesman problem." The traveling salesman problem goes like this: Given an arbitrary number of cities and the distances between them, what is the shortest route a salesman can take that visits each city and returns to the salesman's city of origin. As these Japanese researchers demonstrated, a certain type of amoeba can be used to calculate nearly optimal solutions to the traveling salesman problem for up to eight cities. Even more remarkably, the amount of time it takes the amoeba to reach these nearly optimal solutions grows linearly, even though the number of possible solutions increases exponentially. The reason this amoeba is considered especially useful in biological computing is because it can extend various regions of its body to find the most efficient way to a food source and hates light.

To turn this natural feeding mechanism into a computer, the Japanese researcher placed the amoeba on a special plate that had 64 channels that it could extend its body into. This plate is then placed on top of a nutrient rich medium. The amoeba tries to extend its body to cover as much of the plate as possible and soak up the nutrients. Yet each channel in the plate can be illuminated, which causes the light-averse amoeba to retract from that channel. To model the traveling salesman problem, each of the 64 channels on the plate was assigned a city code between A and H, in addition to a number from 1 to 8 that indicates the order of the cities. To guide the amoeba toward a solution to the traveling salesman problem, the researchers used a neural network that would incorporate data about the amoeba's current position and distance between the cities to light up certain channels. The neural network was designed such that cities with greater distances between them are more likely to be illuminated than channels that are not. When the algorithm manipulates the chip that the amoeba is on it is basically coaxing it into taking forms that represent approximate solutions to the traveling salesman problem.

87 comments

  1. The true solution, or a usable solution? by ctilsie242 · · Score: 4, Interesting

    With genetic algorithms, you can come up with a solution in linear time (as in 100 seconds for 100 cities, 200 seconds for 200 cities, etc.) that is "good enough". It won't come out with the best one, proven mathematically, but if you are looking for a useful answer rather than _the_ answer, it works.

    This work with the amoeba seems like it can give a passable solution, but it would be interesting if it did give the actual shortest out there.

    1. Re:The true solution, or a usable solution? by alvinrod · · Score: 1

      This probably isn't much different than ant colony solutions, which have been studied for quite a while. The results aren't perfect, so it's not a true solution, but I think the experimental results show that the solutions tend to be close enough to ideal to be useful.

    2. Re:The true solution, or a usable solution? by rtb61 · · Score: 2

      The computational trick is, it is not about going from one city to another, it is all about the journey itself and what route it takes. So you break up the journey from city to city, into smaller segments along that route and test those smaller segments, with the size of the segments defining accuracy or in journey terms, main intersections along that route. Although it sounds like you are creating more elements to analyse, what you are really doing is analysing the actual route rather than the destinations because that is what the problem is about the route and not the destinations.

      --
      Chaos - everything, everywhere, everywhen
    3. Re: The true solution, or a usable solution? by phantomfive · · Score: 2

      The traveling salesman problem doesn't need an estimate, we can find a correct solution, and it is easily parallelizable. If you have many processors (or amoebas acting like processors), you can find it easily. The trick here was training amoebas, not solving the problem.

      --
      "First they came for the slanderers and i said nothing."
    4. Re:The true solution, or a usable solution? by ShanghaiBill · · Score: 3, Informative

      There are tons of simple heuristics for quickly getting "good enough" solutions to optimization problems. So that is not interesting at all, and is not "solving" the TSP. To solve the TSP means to get the absolute shortest path. An amoeba based computer can't do that in polynomial time.

    5. Re: The true solution, or a usable solution? by Anonymous Coward · · Score: 0

      If you have many processors, you can find it easily.

      For routing problems of more than 100 nodes, "many" means more processors than there are quarks in the universe.

    6. Re: The true solution, or a usable solution? by phantomfive · · Score: 1

      This is a problem with 8 nodes.

      --
      "First they came for the slanderers and i said nothing."
    7. Re:The true solution, or a usable solution? by Anonymous Coward · · Score: 0

      If it's the one I saw ~20 years ago, then the answer is: it's a novelty.

      If it's not that one, then WTF aren't these people reading their own literature?

    8. Re:The true solution, or a usable solution? by Anonymous Coward · · Score: 0

      Citation needed

    9. Re: The true solution, or a usable solution? by Anonymous Coward · · Score: 0

      Octopus sex isn't my thing. The beak bites!

    10. Re:The true solution, or a usable solution? by ls671 · · Score: 1

      The problem with what you suggest is that there doesn't seem to be any route (or road) in the description of the problem linked in TFA. Imagine you use an airplane. So, it seems like keeping a straight line between cities is optimal.
      https://en.wikipedia.org/wiki/...

      Otherwise, like in real life where there are roads, you would have a point.

      --
      Everything I write is lies, read between the lines.
    11. Re:The true solution, or a usable solution? by Anonymous Coward · · Score: 0

      Does this mean an Amoeba is more intelligent than your average American?

    12. Re: The true solution, or a usable solution? by Anonymous Coward · · Score: 0

      i think this is fantastic. I will get right on it once I get my lab built and permits approved. Happy holidays!

    13. Re: The true solution, or a usable solution? by joao.cordeiro · · Score: 1

      The fact that it is impossible for the Amoeba to vote for Trump makes it incapable of being more retarded then half of the American votes.

    14. Re:The true solution, or a usable solution? by Anonymous Coward · · Score: 0

      To be fair, it said "solutions". This doesn't really indicate the quality. And yes, there are dozens of ways to get good approximations to TSP. Linear programming and simulated annealing come to mind immediately.

    15. Re:The true solution, or a usable solution? by Anonymous Coward · · Score: 0

      Screw all that. Use a Sierpinski curve.

      Done and done. These guys wasted a fuckton of effort building a Rube Goldberg machine.

    16. Re:The true solution, or a usable solution? by Anonymous Coward · · Score: 0

      Also, maybe they should've hired someone with a damn computer science background and a few decades of experience--or just done a damn literature search first.

    17. Re: The true solution, or a usable solution? by Anonymous Coward · · Score: 0

      Most Americans didn't vote for Trump either.

    18. Re: The true solution, or a usable solution? by Anonymous Coward · · Score: 0

      Most Americans didn't vote for Trump either.

      By a lot. But then, technically, no US president ever received the votes of most Americans. Optional voting is a boon to popular nutcases able to rally a large percentage of their minority to actually vote.

    19. Re: The true solution, or a usable solution? by Anonymous Coward · · Score: 0

      No, this is a problem with unlimited nodes. The researchers used at most 8 nodes because the point was to show the technique.

  2. What thuh.. by Anonymous Coward · · Score: 0

    "An Amoeba-Based Computer Found Solutions To 8-City Traveling Salesman Problem" = Nope, Japanes AI still can't write headlines for a damn, dame desu

  3. The Travelling Salesman problem by Anonymous Coward · · Score: 0

    also requires that each city is visited exactly once. So did the amoebae solve a different problem, or was the article not accurate?

    1. Re: The Travelling Salesman problem by Anonymous Coward · · Score: 0

      It visited exactly once as you say but it seems like they just left the lights on those ones to artificially prevent it from coming back so in a way that's sort of cheating.

    2. Re: The Travelling Salesman problem by Anonymous Coward · · Score: 0

      Oh cheating is such an ugly word. I prefer clever

  4. amoeba didn't solve it, system solved it by Anonymous Coward · · Score: 0

    The amoeba didn't solve it did it... the nutrient solved it.

    The nutrient gradient would be the solution, the amoeba simply followed that.

    1. Re: amoeba didn't solve it, system solved it by Anonymous Coward · · Score: 0

      It is good to know these things are out there. If it is super lazy it can bang out a solution, take a nap, bang out another solution, etc. and be home in time for, well, I suppose we can guess what for. Speaking of naps, is this amoeba comfy? Can one sleep on it? Then we can eat snow cones if we want

    2. Re: amoeba didn't solve it, system solved it by Anonymous Coward · · Score: 0

      Was the solution better than a gradient follower would find?

      At the end of the day, its a gradient follower, and this is a system designed to provide that gradient.

      The neural network could have also had the Amoeba part in it.

    3. Re: amoeba didn't solve it, system solved it by Anonymous Coward · · Score: 0

      Sure. A funny computer, using an amoeba as a readout/presentation device.

  5. Ants do the same thing by Anonymous Coward · · Score: 0

    How much money was wasted on this?

    1. Re:Ants do the same thing by Anonymous Coward · · Score: 0

      You do not understand the point of basic research

  6. Yeah, that's impressive and all by rsilvergun · · Score: 2

    but can it run Crysis?

    --
    Hi! I make Firefox Plug-ins. Check 'em out @ https://addons.mozilla.org/en-US/firefox/addon/youtube-mp3-podcaster/
    1. Re:Yeah, that's impressive and all by Anonymous Coward · · Score: 0
    2. Re:Yeah, that's impressive and all by quenda · · Score: 2

      Crysis?
      I would have gone with "I, for one, welcome our new Amoeba overlords."

    3. Re:Yeah, that's impressive and all by Anonymous Coward · · Score: 0

      In Soviet Russia, operation overlord is for insensitive clods

    4. Re:Yeah, that's impressive and all by TheGratefulNet · · Score: 3, Funny

      amateurs.

      I have netbsd running on my 'meba cluster.

      (systemd-free, too, mind you)

      --

      --
      "It is now safe to switch off your computer."
    5. Re:Yeah, that's impressive and all by Anonymous Coward · · Score: 0

      How many qubits is that in rubles? Shit is ENTANGLY AF right now, ain't no Magnitskying around it

    6. Re:Yeah, that's impressive and all by Anonymous Coward · · Score: 0

      It should be able to run Amoeba OS one day.

    7. Re:Yeah, that's impressive and all by Anonymous Coward · · Score: 0

      Slashdot is not the place for your stupid memes, we're here for serious discussion.

    8. Re: Yeah, that's impressive and all by Anonymous Coward · · Score: 0

      Ok, seriously discuss your midget boyfriend's butthole experiments.

    9. Re:Yeah, that's impressive and all by dgatwood · · Score: 3, Funny

      but can it run Crysis?

      In general, no. Steam kills Amoebas, because boiling water is too hot for them.

      That said, by lowering the ambient air pressure, you can make water boil at a lower temperature. Amoebas can survive sustained temperatures of 46 C. An online calculator tells me that water boils at 46C at .11 bar, and another one says that .11 bar is the air pressure at about 51,000 feet above sea level.

      Of course, merely being able to survive Steam may still not be sufficient to run Crysis. To determine that with certainty, we need to devise a proper experiment.

      Anybody have an SR-71 handy? We need to test this theory. This important question demands an answer.

      --

      Check out my sci-fi/humor trilogy at PatriotsBooks.

    10. Re:Yeah, that's impressive and all by sheramil · · Score: 1

      Steam kills Amoebas, because boiling water is too hot for them.

      That said, by lowering the ambient air pressure, you can make water boil at a lower temperature. Amoebas can survive sustained temperatures of 46 C.

      They didn't survive Jack Tramiel.

    11. Re:Yeah, that's impressive and all by ITRambo · · Score: 1

      That joke is too last decade to be funny anymore. At least to me.

    12. Re:Yeah, that's impressive and all by dgatwood · · Score: 1

      Dyslexic much?

      --

      Check out my sci-fi/humor trilogy at PatriotsBooks.

    13. Re:Yeah, that's impressive and all by dohzer · · Score: 1

      No, but it can create a one in the hospital system.

    14. Re: Yeah, that's impressive and all by Anonymous Coward · · Score: 0

      Yeah, exactly. Let us measure the IQ of people who jump off a bridge without checking to see if the other person is also going to jump. The real problem here is that there is no primary true licensing model for amoebas, or ancient lobsters

    15. Re:Yeah, that's impressive and all by Anonymous Coward · · Score: 0

      Who would win in a fight, an amoeba or systemd? Well, one is an amorphous blob that reaches out its tentacles to engulf and consume its enemies, and the other is an amoeba. So, tough call.

    16. Re:Yeah, that's impressive and all by dgatwood · · Score: 1

      (Note for anybody who doesn't get the meta-joke, 46 C is C64 backwards, and the (Commodore) Amiga killed the C64/128, not the other way around.)

      --

      Check out my sci-fi/humor trilogy at PatriotsBooks.

  7. Remarkably difficult by Livius · · Score: 1

    The travelling salesman problem is not difficult if you're willing to settle for "approximate solutions".

    1. Re:Remarkably difficult by ShanghaiBill · · Score: 4, Interesting

      The travelling salesman problem is not difficult if you're willing to settle for "approximate solutions".

      As a general rule, solving most problems is not difficult if you don't actually solve them.

    2. Re:Remarkably difficult by hcs_$reboot · · Score: 1

      The "close to optimal" algorithm is definitely not simple. But of course you could try randomly millions of paths and take the best - which could still be very far from optimal.

      --
      Slashdot, fix the reply notifications... You won't get away with it...
    3. Re:Remarkably difficult by Anonymous Coward · · Score: 0

      As a general rule, solving most problems is not difficult if you don't actually solve them.

      As a general rule, snarky trite know-it-all responses only show the author's ignorance without adding anything of value to the discussion.

    4. Re: Remarkably difficult by anegg · · Score: 1

      My solution to the traveling salesman problem is to just shoot them when they ring the doorbell. Problem solved. Iâ(TM)m US; I suspect the Brits would rather use a knife because gun violence is bad. Iâ(TM)m surprised the Japanese are using amoebas - I thought swords would be more their style. If we all get to work, however, we can solve the traveling salesman problem once and forever, just like polio.

    5. Re:Remarkably difficult by Anonymous Coward · · Score: 0

      As a general rule, Bill has yet to solve any real world problems with his bullshit assertions.

    6. Re: Remarkably difficult by Anonymous Coward · · Score: 0

      If we all get to work, however, we can solve the traveling salesman problem once and forever, just like polio.

      You mean a solution that will be thwarted by some religious nuts?

  8. Amoeba by Anonymous Coward · · Score: 0

    Smarter and more useful than Trump.

    1. Re: Amoeba by Anonymous Coward · · Score: 0

      Three Supreme Court justices.

      Three.

      Be ready.

    2. Re: Amoeba by Anonymous Coward · · Score: 0

      Found the NAZI.

  9. Tesla needs this... by wolfheart111 · · Score: 1

    If u dont mind a little Slime. :)

    --
    [($)]
  10. Right by Dunbal · · Score: 3, Insightful

    So basically - we designed a method to make an amoeba respond in the way we wanted, then lo and behold, the amoeba - when "coaxed" by our model, responded the way we wanted... It's a miracle I tell you.

    --
    Seven puppies were harmed during the making of this post.
    1. Re:Right by 110010001000 · · Score: 1

      Yeah, I don't get it either. Sounds like a complete waste of time. The computer solved the problem and was based on digital electronics not the amoeba. It controlled an amoeba. You could do the same experiment with mice, or ants, or people, or whatever.

    2. Re: Right by Anonymous Coward · · Score: 0

      Amoebas are way more awesome than ants

    3. Re:Right by Anonymous Coward · · Score: 0

      I think the point isn't that the amoeba solved anything, the point was that the amoeba was used to solve something. It was part of the system. If the neural network performs as well without an amoeba it's pointless, if the combination performs better it's not pointless.

    4. Re:Right by eriks · · Score: 1

      Yeah, that was my first though too, since the summary makes it sound that way, but the article explains in depth:

      The challenge for the plasmodium to find the shortest tour is that its branches should not enter the frequently illuminated lanes and should elongate into the optimal combination of the least frequently illuminated lanes. However, the optimal combination cannot be found as long as the branches always obey the control principle; if always the branches shrank when illuminated and expanded when not illuminated, the plasmodium would not avoid falling into a local minimum. To better explore the potential energy landscape and locate the global minimum (the shortest tour), the plasmodium needs to misallocate the resource to its branches and the branches must violate the control principle with a certain small probability, because the lengths of the tours can be compared only when the branches operate contrary to their photoavoidance response

      so the computer is only really defining where the "bounds" of the problem are. The ameoba really is doing the computational work (going *against* the computer's control) to find a nearly-optimal solution.

    5. Re:Right by Dunbal · · Score: 1

      Yeah I could do the same thing with water and valves, with the closed valves "encouraging" the water to flow elsewhere and the open valves "encouraging" the water to flow in that section and look, I just invented the Traveling Salesman Problem solving puddle.

      --
      Seven puppies were harmed during the making of this post.
    6. Re:Right by eriks · · Score: 1

      Not quite... since the water and valves could (I think) only find a "local minimum" or naive solution, not a near-optimal (global minimum) one, like the amoeba does. The lighted areas on the chip don't *prevent* the ameoba from going there, and in fact to find an approximate global minimum solution, the ameoba *has* to sometimes go where it doesn't want to, in order to maximize it's nutrient intake. In other words the water can't "decide" to go through a closed valve, but the ameoba can choose to extend into a lit cell, in order to maximize survival advantage.

    7. Re:Right by Hognoxious · · Score: 1

      So the amoeba is just a display? I wondered if I'd missed something when I read it.

      Then I asked myself why it was even posted, since it's not really a story, is it?

      And then I remembered where I was.

      --
      Confucius say, "Find worm in apple - bad. Find half a worm - worse."
    8. Re:Right by dudeNumber4 · · Score: 1

      My head hurts. There are 8 "cities" represented by letters A-H. Each city has 8 channels. The amoeba selected channel C1 (C is the first stop) .. B8 (B is the last stop). Since the researchers didn't actually coax that path, how did their relative light pulses work? Did channels B1 through B8 all equally have the most light when compared to the light pulses in C1 through C8? If so, how do they determine that B should be the last stop? If not, if rather all the light impulses across all 64 channels ranged from weakest in C1 through strongest in C8, then that would just show the amoeba's mechanistic response to the light impulses. I'm missing something.

  11. So If You Already Know the Solution .. by Anonymous Coward · · Score: 0

    So if you know the outcome you desire you can coax a biological creature to conform to your desired outcome.

    In other words, Pavlov did this with Dogs.
    I think there are horses that do this as well.

    It is all just a matter of voltage.

  12. Can you imagine... by sacrilicious · · Score: 2

    ...a Beowulf cluster of these?

    --
    - First they ignore you, then they laugh at you, then ???, then profit.
  13. I wouldn't call this amoeba-based. by Anonymous Coward · · Score: 0

    Nowhere does it say the amoeba did the thinking, and if the amoeba does no compooting, it's not amoeba-based.

  14. "Today" on Meta-Slashdot (News for 11-D Nerds) by PseudoThink · · Score: 1

    "4-Dimensional Bags of Mostly Water Evolve Sentience and Create An Amoeba-Based Computer Which Found Solutions To 8-City Traveling Salesman Problem"

  15. Obligatory xkcd quotes by LordHighExecutioner · · Score: 2

    There is an O(1) solution to this NP-complete problem.

    1. Re:Obligatory xkcd quotes by hcs_$reboot · · Score: 1

      There is an O(1) solution

      There will be when q-computing is efficiently working.

      --
      Slashdot, fix the reply notifications... You won't get away with it...
    2. Re:Obligatory xkcd quotes by Anonymous Coward · · Score: 0

      7 Mixed Fruit appetizers coming right up!

  16. The Operating Syatem. by Cmdln+Daco · · Score: 2

    From the title, I thought maybe this was about the Amoeba Operating System . No such luch, alas.

  17. Flawed model by AutumnLeaf · · Score: 1

    The challenge of the Traveling Salesman Problem is the combinations. The amoeba is trying all solutions at once, and the light is telling it where not to go. The real question is, "Given the preconditions, and the behavior of an amoeba, could it not create an approximate solution?" Clearly not.

  18. Amoebas as Salesmen by nukenerd · · Score: 1

    So we can now replace salemen with amoebas? I might even listen to an amoeba.

  19. Since we're talking amoeba by nospam007 · · Score: 1

    A paramecium and an amoeba are walking down the street. The amoeba asks “So, lacking any pseudopodia, how do you manage to get around? The paramecium replies “A cilia question I’ve never heard!”
    -----
    Why did the amoeba flunk the math test?

    Because it multiplied by dividing.

  20. Which is the intelligent part? by nodan · · Score: 1

    Hm, is the intelligent part the amoeba or actually the neural network coaxing them towards the solution?

  21. Commodore's Amoeba was a great computer by Trilobyte · · Score: 1

    ...but it largely shied away from the limelight and never gobbled up much market share.

    I thought Slashdot just posted its annual Amoeba elegy post last week.

    (Sorry.)

  22. An O(1) shot. by Anonymous Coward · · Score: 0

    An octagon of cities is the (global) optimal solution of the 8-city TSP.

    Why? Because the human reasoning believes it until that it is definitively perfect.

  23. Humans are just CPUs of the gods by Anonymous Coward · · Score: 0

    My theory seems to be correct. Humans are just like amoebas for the gods. Solving tough questions with minimal input.

  24. there's an app for that by Anonymous Coward · · Score: 0

    https://play.google.com/store/apps/details?id=amusement.arcade

  25. This sounds familiar. by Anonymous Coward · · Score: 0

    42.