Category: System effectiveness

Software defined power grid

Posted on by Ray in Data availability, Energy efficiency, Information economy, IoT, Market dynamics, Strategic Inflection Points, System effectiveness, Visionary leadershp

Read an article this past week in IEEE Spectrum (The Software Defined Power Grid is here) about a company that has been implementing software defined power grids throughout USA and the world to better integrate and utilize renewable energy alongside conventional power generation equipment.

Moreover, within the last year or so, Tesla has installed a Virtual Power Plant (VPP) using residential solar and grid scale batteries to better manage the electrical grid of South Australia (see Tesla’s Australian VPP propped up grid during coal outage). VPP use to offset power outages would necessitate something like a software defined power grid.

Software defined power grid

Not sure if there’s a real definition somewhere but from our perspective, a software defined power grid is one where power generation and control is all done through the use of programatic automation. The human operator still exists to monitor and override when something goes wrong but they are not involved in the moment to moment control of which power is saved vs. fed into the grid.

About a decade ago, we wrote a post about smart power meters (Smart metering’s data storage appetite) discussing the implementation of smart meters for home owners that had some capabilities to help monitor and control power use. But although that technology still exists, the software defined power grid has moved on.

The IEEE Spectrum article talks about a phasor measurement units (PMUs) that are already installed throughout most power grids. It turns out that most PMUs are capable of transmitting phasor power status at 60 times a second granularity and each status report is time stamped with high accuracy, GPS synchronized time.

On the other hand, most power grids today use SCADAs (supervisory control and data acquisition) to monitor and manage the power grid. But SCADAs only send data every 2-4 seconds. PMU’s are also installed in most power grids, but their information is not as important as SCADA to the monitoring, management and control of most (non-software defined) power grids.

One software defined power grid

PXiSE, the company in the IEEE Spectrum article, implemented their first demonstration project in Hawaii. That power grid had reached the limit of wind and solar power that it could support with human management. The company took their time and implemented a digital simulation of the power grid. But with the simulation in hand, battery storage and a off the shelf PC, the company was able to manage the grids power generation mix in real time with complete automation.

After that success, the company next turned to a micro-grid (building level power) with electronic vehicles, battery and solar power. Their software defined power grid reduced peak electricity demand within the building, saving significant money. With that success the company took their software defined power grid on the road to South Korea, Chile, Mexico and a number of other locations the world.

Tesla’s VPP

The Tesla VPP in South Australia, is planned to consists of up to 50K houses with solar PV panels and 13.5Kwh of batteries, able to deliver up to 250Mw of power generation and 650Mwh of power storage.

At the present time, the system has ~1000 house systems installed but even with that limited generation and storage capability it has already been called upon at least twice to compensate for coal generation power outage. To manage each and every household, they’d need something akin to the smart meters mentioned above in conjunction with a plethora of PMUs.

Puerto Rico’s power grid problems and solutions

There was an article not so long ago about the disruption to Puerto Rico’s power grid caused by Hurricanes Irma and Maria in IEEE Spectrum (Rebuilding Puerto Rico’s Power Grid: The Inside Story) and a subsequent article on making Puerto Rico’s power grid more resilient to hurricanes and other natural disasters (How to harden Puerto Rico’s power grid). The later article talked about creating micro grids, community PV and battery storage that could be disconnected from the main grid in times of disaster but also used to distribute power generation throughout the island.

Although the researchers didn’t call for the software defined power grid, it is our understanding that something similar would be an outstanding addition to their work there.

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As the use of renewables goes up and the price of batteries decreases while their capabilities go up over time, more and more power grids will need to become software defined. In the end, more software defined power grids with increasing renewables power generation and storage will make any power grid, more resilient and more fault tolerant.

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Silq and QUA vie for Quantum computing language

Posted on by Ray in Quantum Computing, System effectiveness, System quality

Read a couple of articles this past week on new Quantum computing programing languages. Specifically, one in ScienceDaily on Silq, (The 1st intuitive programming language for quantum computers) and another in TechCrunch (Quantum Machines announces QUA, its universal lang. for quantum computing). The Silq discussion is based on an ACM SIGPLAN paper (Silq: A High-Level Quantum Language with Safe Uncomputation and Intuitive Semantics). programing

Up until this point there have been a couple of SDK’s for various quantum computers, most notably QASM for IBM’s, Q# for Microsoft’s and ? for Google’s Quantum Computers. We have discussed QASM in a prior post (see: Quantum Computer Programming post).

But both QUA and Silq are steps up the stack from QASM and Q#, both of which are more realistically likened to machine microcode thanassembly code. For example, with QASM you are talking directly to mechanisms to cohere qubits, electronics needed to connect qubits, electronics to excite qubit states, etc.


QUA and Silqs seem to take different tacks to providing their services.

Silq control flow
  • Silq is trying to abstract itself above the hardware layer and to provide some underlying logical constructs and services that any quantum programmer would want to use. Most notably, Silq mentions that they provide automatic erasure of intermediate calculations results which can impact future quantum calculations if they are not erased. They call this “specific uncomputation“. Silq also offers types, loops, conditionals, superposition (the adding together of two quantum states) and diffusion (spreading of quantum states out).
  • QUA on the other hand is Quantum Machines full stack implementation for quantum computer orchestration. QUA is only a one component of this stack (the highest level) but underneath this is a compiler and a Quantum Machine OPX box, a hardware appliance that interfaces with quantum computers of various types. There’s not much detail about QUA other than it offers conditionals and looping constructs and internal error detection.

From what I see, we are a long ways away from having a true programming language for quantum computers. Quantum Machines sees the problem with today’s quantum computers as the lack of a stack problem.

The Silq group see the problem with today’s quantum computers as a lack of any useful abstraction problem. Silq is trying to provide simpler semantics and control structures that maybe someday could become the foundation of a true quantum computing programming language.

Silq has compared itself to Q#, used in Microsoft’s Quantum Computing solution. So our guess is it works only with Microsoft’s quantum computer.

In contrast, QUA offers an orchestration solution for many different quantum computers but you have to buy into their orchestration hardware and stack.

Who will win out in the end is anyone’s guess. There’s a great need for something that can abstract the quantum hardware from the quantum algorithms being implemented. At the moment I like what I see in Silq just wish it was applied more generically.

At press time there were not many details available on Quantum Machines QUA language. Their stack approach may be better in the long run, but having to use their hardware appliance to run it seems counter productive.

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However, if the programming gods were to ask my opinion as to where a new programming language was really needed, I’d have to say neuromorphic computing (see Our neuromorphic chips a dead end? post). Neuromorphic computing really needs abstraction help. Without some form of suitable abstraction layer, neuromorphic computing seems dead as it stands.

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Thoughts on my first virtual conference

Posted on by Ray in Information economy, Strategic Inflection Points, System effectiveness, System quality, Visionary organizations

I attended a virtual event this week. It was scheduled to last 3 hours. But I only stayed for 2.5 Hours. Below I describe the event from my perspective and after that some notes on how it could be made better.

The virtual event experience

The event home page had a welcome video that you could start when you got there. I didn’t have any idea what to expect so this was nice. It could have spent time discussing the mechanics of the site and how to attend the event but it just was a welcome video, welcoming me to the event and letting me know they appreciated me being able to attend.

Navigation on the site wasn’t that easy to figure out at first. It was at the bottom of the page not at the top or the side. And the navigation home button brought up a list of videos that you could watch (or attend). And that page was in front of the conference page.

I launched the 1st (actually 2nd after the welcome video) which was the CEO keynote session. I thought this was good and the occasional interruption by executives ringing the CEO’s doorbell asking for toilet paper was entertaining. Again he welcomed us to the event and discussed how the pandemic has changed their world and ours. He thanked the customers in attendance and made brief mention of the video (tracks) that one could follow. I don’t recall but the CEO keynote didn’t seem to have any (or many) slides during his session it was just like an informal talk (but) scripted.

It took me a while to figure out how to get back to the main agenda page but once there I proceeded on my chosen track to watch the next video. When I was finished with that I watched the other 3 track videos. The video tracks were not as good as the CEO keynote session and some of them had many more slides than they needed.

They also had a customer interview with an exec which was great and well done. Especially given it seemed to have been recorded over the prior 48 hours.

Somewhere in all of this, I happened to reach the Expo floor. It had a series of technical break out sessions and then the exhibitor buttons which had their own videos, reports, webinars that one could watch/read.

I watched most of the technical breakouts (at least part way through). The tech breakouts were ok, but also had mixed quality as I remember it. That is some having more or less slides and more or less webinar like.

I also watched a few of the exhibitor videos. Some of these auto started when you clicked on their expo buttons, some did not. Some videos were very loud while others were fine.

I’d say the mixed quality of the exhibits were similar to what one might see at any conference with bigger vendors having more polished content while smaller vendors had less polished content.

The conference had a public chat channel but there was one channel for the whole conference and it didn’t appear until much later (maybe when I entered the first breakout sessions or expo “hall”)

How to make our next virtual conference better

Below are my thoughts on ways to improve the virtual conference experience.

• Have real scheduled times to watch the videos/webinars/tech sessions. Yes there all online and can truly be watched at any time you want. But I expected a scheduled agenda with breaks between sessions and to have to pick which one I wanted to go to, meaning that some would have to be unattended. I would suggest that the videos only be available during the event at scheduled time slots and that the event organizers build in breaks between each session. They could always be made available at a later date under a conference media page for further viewing but having them scheduled to run in a conference room would make it more conference like. The tracks could be scheduled in other side rooms of the conference.

• Also, would it be too much to ask that they have some sort of video roll call of participants with headshots and maybe a title. Something akin to a conference badge. Perhaps they could show this during the breaks between sessions. Even if you rolled through the virtual badge shots quickly, during breaks, it would act as sort of an analog of walking from one session to another.

• I don’t know whether there was any interest in social media, but having a twitter, facebook, other social media event hash tag prominently displayed on the bottom 1/3rd or on some early slide deck would have been useful. To generate some social buz

• Also, at conferences, one can typically see a screen which tracks the social media hash tag. I saw none of this at the event. Having some small panel running social media activity might have led to more social media interaction. It could be along the side of the main page, viewable during all videos, breaks and other sessions.

• As for the public chat. I think it would have been better to have a separate chat channels for each video, breakout, exhibit, etc. rather than having a single chat room for the whole conference. It would have been great if the separate chat window popped up when you started viewing a video, breakout or entered an exhibit.

• Have lots more technical breakouts. didn’t see a great quantity of these maybe 5-7 tech breakouts and the 4 original tech track videos. Again separate chat channels so one could ask questions pertaining to the session would have been great.

• The exhibits were all other vendors (sponsors) showing there stuff. I didn’t see any show and tell for the conference event organizers that one would see in any conference if you walked out on the show floor. Would it have been to much to ask to have a virtual walk through tour of each of the conference organizers products and a couple of demos of their products/services. Just like one could see at any conference.

• The expo floor exhibitor sessions could be left available to view anytime the event was “open” but the tech breakout sessions would be available multiple times a day but scheduled just like any other event sessions. And it would be nice to have a separate chat channel for each expo exhibitor and tech break out sessions., so we could ask questions of their staff.

• Another thing available at most conference events is a social media booth where bloggers, podcasters, and vloggers could sit around and talk about the event and their products and whatever else came to mind. I didn’t see anything like this and having a separate chat window for these booths would be useful.

• Also, it would be nice if one could obtain vendor certifications or a detailed tutorials on some product/service.

• On a personal note, I am an industry analyst it would be nice to have a separate analyst track. I come to these events to have face time with execs and get a download on what their upcoming strategy is and how they did over the last year or so. Yes these could all be done offline but they could also be accomplished during the event with its own secure chat channel

• I’m also an influencer. So having a separate press track would have been great as well. Often the analyst and press track overlap for a couple of sessions and then go there separate (NDA) ways.

• For both the analysts and the Press/influencers having a live Q&A session with the execs, technical team, and select customers would have been great. But alas there was nothing like this. But with a separate secure chat room this could have also been done.

• I can’t stress enough that the conference event navigation needs to be better and more intuitive.

I know that there’s a lot here and there’s probably a whole bunch more that could be done better. Other people will no doubt have their own opinions. But these are mine.

It was the first virtual conference (I attended) and the vendor sort of played iit by ear and designing it almost in real time. Given all that, they did a great job. Now it’s time to do better.

I’m a conference geek. I go to an average of 10 or more vendor conferences a year so this is a major part of what I do.

IMHO, nothing besides ubiquitous, true virtual reality will ever replace the effectiveness of in real life conferences. That being said, there are ways to make current virtual events come closer to real conferences.

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I thought about sending this to the conference organizers but their conference is over, and hopefully next year it will be back IRL. But there’s plenty more virtual conferences left on my schedule for this year.

I would prefer all of them to be done better, for me, analysts, press/influencers and ultimately customers.

Were all in this together.

Comments.

Artistic AI

Posted on by Ray in Artificial Intelligence, Deep Learning, Machine Learning, Neural network, Strategic Inflection Points, System effectiveness, System quality

Read a couple of articles in the past few weeks on OpenAI’s Jukebox and another one on computer generated art, in Art in America, (artistically) Creative AI poses problems to art criticism. Both of these discuss how AI is starting to have an impact on music and the arts.

I can recall almost back when I was in college (a very long time ago) where we were talking about computer generated art work. The creative AI article talks some about the history of computer art, which in those days used computers to generate random patterns, some of which would be considered art.

AI painting

More recent attempts at AI creating artworks uses AI deep learning neural networks together with generative adversarial network (GANs). These involve essentially two different neural networks.

  • The first is an Art deep neural networks (Art DNN) discriminator (classification neural network) that is trained using an art genre such as classical, medieval, modern art paintings, etc. This Art DNN is used to grade a new piece of art as to how well it conforms to the genre it has been trained on. For example, an Art DNN, could be trained on Monet’s body of work and then it would be able to grade any new art on how well it conforms to Monet’s style of art.
  • The second is a Art GAN which is used to generate random artworks that can then be fed to the Art DNN to determine if it’s any good. This is then used as reinforcement to modify the Art GAN to generate a better match over time.

The use of these two types of networks have proved to be very useful in current AI game playing as well as many other DNNs that don’t start with a classified data set.

However, in this case, a human artist does perform useful additional work during the process. An artist selects the paintings to be used to train the Art DNN. And the artist is active in tweaking/tuning the Art GAN to generate the (random) artwork that approximates the targeted artist.

And it’s in these two roles that that there is a place for an (human) artist in creative art generation activities.

AI music

Using AI to generate songs is a bit more complex and requires at least 3 different DNNs to generate the music and another couple for the lyrics:

  • First a song tokenizer DNN which is a trained DNN used to compress an artist songs into, for lack of a better word musical phrases or tokens. That way they could take raw audio of an artist’s song and split up into tokens, each of which had 0-2047 values. They actually compress (encode) the artist songs using 3 different resolutions which apparently lose some information for each level but retain musical attributes such as pitch, timbre and volume.
  • A second musical token generative DNN, which is trained to generate musical tokens in the same distribution of a selected artist. This is used to generate a sequence of musical tokens that matches an artist’s musical work. They use a technique based on sparse transformers that can generate (long) sequences of tokens based on a training dataset.
  • A third song de-tokenizer DNN which is trained to take the generated musical tokenst (in the three resolutions) convert them to musical compositions.

These three pretty constitute the bulk of the work for AI to generate song music. They use data augmented with information from LyricWiki, which has the lyrics 600K recorded songs in English. LyricWiki also has song metadata which includes the artist, the genre, keywords associated with the song, etc. When training the music generator a they add the artist’s name and genre information so that the musical token generator DNN can construct a song specific to an artist and a genre.

The lyrics take another couple of steps. They have data for the lyrics for every song recorded of an artist from LyricWiki. They use a number of techniques to generate the lyrics for each song and to time the lyrics to the music. lexical text generator trained on the artist lyrics to generate lyrics for a song. Suggest you check out the explanation in OpenAI Jukebox’s website to learn more.

As part of the music generation process, the models learn how to classify songs to a genre. They have taken the body of work for a number of artists and placed them in genre categories which you can see below.

The OpenAI Jukebox website has a number of examples on their home page as well as a complete catalog behind their home page. The catalog has over a 7000 songs under a number of genres, from Acoustic to Rock and everything in between. In the fashion of a number of artists in each genre, both with and without lyrics . For the (100%) blues category they have over 75 songs and songs similar to artists from B.B. King to Taj Mahal including songs similar to Fats Domino, Muddy Water, Johnny Winter and more.

OpenAI Jukebox calls the songs “re-renditions” of the artist. And the process of adding lyrics to the songs as lyric conditioning.

Source code for the song generator DNNs is available on GitHub. You can use the code to train on your own music and have it generate songs in your own musical style.

The songs sound ok but not great. The tokenizer/de-tokenizer process results in noise in the music generated. I suppose more time resolution tokenizing might reduce this somewhat but maybe not.

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The AI song generator is ok but they need more work on the lyrics and to reduce noise. The fact that they have generated so many re-renditions means to me the process at this point is completely automated.

I’m also impressed with the AI painter. Yes there’s human interaction involved (atm) but it does generate some interesting pictures that follow in the style of a targeted artist. I really wanted to see a Picasso generated painting or even a Jackson Pollack generated painting. Now that would be interesting

So now we have AI song generators and AI painting generators but there’s a lot more to artworks than paintings and songs, such as sculpture, photography, videography, etc. It seems that many of the above approaches to painting and music could be applied to some of these as well.

And then there’s plays, fiction and non-fiction works. The songs are ~3 minutes in length and the lyrics are not very long. So anything longer may represent a serious hurdle for any AI generator. So for now these are still safe.

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OFA DNNs, cutting the carbon out of AI

Posted on by Ray in Artificial Intelligence, Data density, Deep Learning, Distributed computing, Energy efficiency, Information economy, Machine Learning, Processing performance, System effectiveness

Read an article (Reducing the carbon footprint of AI… in Science Daily) the other day about a new approach to reducing the energy demands for AI deep neural net (DNN) training and inferencing. The article was reporting on a similar piece in MIT News but both were discussing a technique original outlined in a ICLR 2020 (Int. Conf. on Learning Representations) paper, Once-for-all: Train one network & specialize it for efficient deployment.

The problem stems from the amount of energy it takes to train a DNN and use it for inferencing. In most cases, training and (more importantly) inferencing can take place on many different computational environments, from IOT devices, to cars, to HPC super clusters and everything in between. In order to create DNN inferencing algorithms for use in all these environments, one would have to train a different DNN for each. Moreover, if you’re doing image recognition applications, resolution levels matter. Resolution levels would represent a whole set of more required DNNs that would need to be trained.

The authors of the paper suggest there’s a better approach. Train one large OFA (once-for-all) DNN, that covers the finest resolution and largest neural net required in such a way that smaller, sub-nets could be extracted and deployed for less weighty computational and lower resolution deployments.

The authors contend the OFA approach takes less overall computation (and energy) to create and deploy than training multiple times for each possible resolution and deployment environment. It does take more energy to train than training a few (4-7 judging by the chart) DNNs, but that can be amortized over a vastly larger set of deployments.

OFA DNN explained

Essentially the approach is to train one large (OFA) DNN, with sub-nets that can be used by themselves. The OFA DNN sub-nets have been optimized for different deployment dimensions such as DNN model width, depth and kernel size as well as resolution levels.

While DNN width is purely the number of numeric weights in each layer, and DNN depth is the number of layers, Kernel size is not as well known. Kernels were introduced in convolutional neural networks (CovNets) to identify the number of features that are to be recognized. For example, in human faces these could be mouths, noses, eyes, etc. All these dimensions + resolution levels are used to identify all possible deployment options for an OFA DNN.

OFA secrets

One key to the OFA success is that any model (sub-network) selected actually shares the weights of all of its larger brethren. That way all the (sub-network) models can be represented by the same DNN and just selecting the dimensions of interest for your application. If you were to create each and every DNN, the number would be on the order of 10**19 DNNs for the example cited in the paper with depth using {2,3,4) layers, width using {3,4,6} and kernel sizes over 25 different resolution levels.

In order to do something like OFA, one would need to train for different objectives (once for each different resolution, depth, width and kernel size). But rather than doing that, OFA uses an approach which attempts to shrink all dimensions at the same time and then fine tunes that subsets NN weights for accuracy. They call this approach progressive shrinking.

Progressive shrinking, training for different dimensions

Essentially they train first with the largest value for each dimension (the complete DNN) and then in subsequent training epochs reduce one or more dimensions required for the various deployments and just train that subset. But these subsequent training passes always use the pre-trained larger DNN weights. As they gradually pick off and train for every possible deployment dimension, the process modifies just those weights in that configuration. This way the weights of the largest DNN are optimized for all the smaller dimensions required. And as a result, one can extract a (defined) subnet with the dimensions needed for your inferencing deployments.

They use a couple of tricks when training the subsets. For example, when training for smaller kernel sizes, they use the center most kernels and transform their weights using a transformation matrix to improve accuracy with less kernels. When training for smaller depths, they use the first layers in the DNN and ignore any layers lower in the model. Training for smaller widths, they sort each layer for the highest weights, thus ensuring they retain those parameters that provide the most sensitivity.

It’s sort of like multiple video encodings in a single file. Rather than having a separate file for every video encoding format (Mpeg 2, Mpeg 4, HVEC, etc.), you have one file, with all encoding formats embedded within it. If for example you needed Mpeg-4, one could just extract those elements of the video file representing that encoding level

OFA DNN results

In order to do OFA, one must identify, ahead of time, all the potential inferencing deployments (depth, width, kernel sizes) and resolution levels to support. But in the end, you have a one size fits all trained DNN whose sub-nets can be selected and deployed for any of the pre-specified deployments.

The authors have shown (see table and figure above) that OFA beats (in energy consumed and accuracy level) other State of the Art (SOTA) and Neural (network) Architectural Search (NAS) approaches to training multiple DNNs.

The report goes on to discuss how OFA could be optimized to support different latency (inferencing response time) requirements as well as diverse hardware architectures (CPU, GPU, FPGA, etc.).

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When I first heard of OFA DNN, I thought we were on the road to artificial general intelligence but this is much more specialized than that. It’s unclear to me how many AI DNNs have enough different deployment environments to warrant the use of OFA but with the proliferation of AI DNNs for IoT, automobiles, robots, etc. their will come a time soon where OFA DNNs and its competition will become much more important.

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DNA storage using nicks

Posted on by Ray in Data density, Storage performance, Storage reliability, System effectiveness

Read an article the other day in Scientific American (“Punch card” DNA …) which was reporting on a Nature Magazine Article (DNA punch cards for storing data… ). The articles discussed a new approach to storing (and encoding) data into DNA sequences.

We have talked about DNA storage over the years (most recently, see our Random access DNA object storage post) so it’s been under study for almost a decade.

In prior research on DNA storage, scientists encoded data directly into the nucleotides used to store genetic information. As you may recall, there are two complementary nucleotides A-T (adenine-thymine) and G-C (guanine-cytosine) that constitute the genetic code in a DNA strand. One could use one of these pairs to encode a 1 bit and the other for a 0 bit and just lay them out along a DNA strand.

The main problem with nucleotide encoding of data in DNA is that it’s slow to write and read and very error prone (storing data in DNA separate nucleotides is a lossy data storage). Researchers have now come up with a better way.

Using DNA nicks to store bits

One could encode information in DNA by utilizing the topology of a DNA strand. Each DNA strand is actually made up of a sugar phosphate back bone with a nucleotide (A, C, G or T) hanging off of it, and then a hydrogen bond to its nucleotide complement (T, G, C or A, respectively) which is attached to another sugar phosphate backbone.

It appears that one can deform the sugar phosphate back bone at certain positions and retain an intact DNA strand. It’s in this deformation that the researchers are encoding bits and they call this a “DNA nick”.

Writing DNA nick data

The researchers have taken a standard DNA strand (E-coli), and identified unique sites on it that they can nick to encode data. They have identified multiple (mostly unique) sites for nick data along this DNA, the scientists call “registers” but we would call sectors or segments. Each DNA sector can contain a certain amount of nick data, say 5 to 10 bits. The selected DNA strand has enough unique sectors to record 80 bits (10 bytes) of data. Not quite a punch card (80 bytes of data) but it’s early yet.

Each register or sector is made up of 450 base (nucleotide) pairs. As DNA has two separate strands connected together, the researchers can increase DNA nick storage density by writing both strands creating a sort of two sided punch card. They use this other or alternate (“anti-sense”) side of the DNA strand nicks for the value “2”. We would have thought they would have used the absent of a nick in this alternate strand as being “3” but they seem to just use it as another way to indicate “0” .

The researchers found an enzyme they could use to nick a specific position on a DNA strand called the PfAgo (Pyrococcus furiosus Argonaute) enzyme. The enzyme can de designed to nick distinct locations and register (sectors) along the DNA strand. They designed 1024 (2**10) versions of this enzyme to create all possible 10 bit data patterns for each sector on the DNA strand.

Writing DNA nick data is done via adding the proper enzyme combinations to a solution with the DNA strand. All sector writes are done in parallel and it takes about 40 minutes.

Also the same PfAgo enzyme sequence is able to write (nick) multiple DNA strands without additional effort. So we can replicate the data as many times as there are DNA strands in the solution, or replicating the DNA nick data for disaster recovery.

Reading DNA nick data

Reading the DNA nick data is a bit more complicated.

In Figure 1 the read process starts by by denaturing (splitting dual strands into single strands dsDNA) and then splitting the single strands (ssDNA) up based on register or sector length which are then sequenced. The specific register (sector) sequences are identified in the sequence data and can then be read/decoded and placed in the 80 bit string. The current read process is destructive of the DNA strand (read once).

There was no information on the read time but my guess is it takes hours to perform. Another (faster) approach uses a “two-dimensional (2D) solid-state nanopore membrane” that can read the nick information directly from a DNA string without dsDNA-ssDNA steps. Also this approach is non-destructive, so the same DNA strand could be read multiple times.

Other storage characteristics of nicked DNA

Given the register nature of the nicked DNA data organization, it appears that data can be read and written randomly, rather than sequentially. So nicked DNA storage is by definition, a random access device.

Although not discussed in the paper, it appears as if the DNA nicked data can be modified. That is the same DNA string could have its data be modified (written multiple times).

The researcher claim that nicked DNA storage is so reliable that there is no need for error correction. I’m skeptical but it does appear to be more reliable than previous generations of DNA storage encoding. However, there is a possibility that during destructive read out we could lose a register or two. Yes one would know that the register bits are lost which is good. But some level of ECC could be used to reconstruct any lost register bits, with some reduction in data density.

The one significant advantage of DNA storage has always been its exceptional data density or bits stored per volume. Nicked storage reduces this volumetric density significantly, i.e, 10 bits per 450 (+ some additional DNA base pairs required for register spacing) base pairs or so nicked DNA storage reduces DNA storage volumetric density by at least a factor of 45X. Current DNA storage is capable of storing 215M GB per gram or 215 PB/gram. Reducing this by let’s say 100X, would still be a significant storage density at ~2PB/gram.

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A tale of two countries and how they controlled the Coronavirus

Posted on by Ray in Scenario planning, Strategic Inflection Points, Strategic planning, System effectiveness, System quality

Read an article in IEEE Spectrum last week about Taiwan’s response to COVID-19 (see: Big data helps Taiwan fight Coronavirus) which was reporting on an article in JAMA (see Response to COVID-19 in Taiwan) about Taiwan’s success in controlling the COVID-19 outbreak in their country.

I originally intended this post to be solely about Taiwan’s response to the virus but then thought that it more instructive to compare and contrast Taiwan and South Korea responses to the virus, who both seem to have it under control now (18 Mar 2020).

But first a little about the two countries (source wikipedia: South Korea and Taiwan articles):

Taiwan (TWN) and South Korea (ROK) both enjoy close proximity, trade and travel between their two countries and China

  • South Korea (ROK) has a population of ~50.8M, an area of 38.6K SqMi (100.0K SqKm) and extends about 680 Mi (1100 Km) away from the Asian mainland (China).
  • Taiwan (TWN ) has a population of ~23.4M, an area of 13.8K SqMi (35.8K Sq Km) and is about 110 Mi (180 Km) away from the Asian mainland (China).

COVID-19 disease progression & response in TWN and ROK

There’s lots of information about TWN’s response (see articles mentioned above) to the virus but less so on ROK’s response.

Nonetheless, here’s some highlights of the progression of the pandemic and how they each reacted (source for disease/case progression from : wikipedia Coronavirus timeline Nov’19 to Jan’20, and Coronavirus timeline Feb’20; source for TWN response to virus JAMA article supplement and ROK response to virus Timeline: What the world can learn from South Korea’s COVID-19 response ).

  • Dec. 31, 2019: China Wuhan municipal health announced “urgent notice on the treatment of pneumonia of unknown cause”. Taiwan immediately tightened inbound screening processes. ==> TWN: officials board and inspect passengers for fever or pneumonia symptoms on direct flights from Wuhan
  • Jan. 8, 2020: ROK identifies 1st possible case of the disease in a women who recently returned from China Wuhan province
  • Jan 20: ROK reports 1st laboratory confirmed case ==> TWN: Central Epidemic Command Center activated, activates Level 2 travel alert for Wuhan; ROK CDC starts daily press briefings on disease progress in the nation
  • Jan. 21: TWN identifies 1st laboratory confirmed case ==> TWN: activates Level 3 travel alert for Wuhan
  • Jan 22: ==> TWN: cancels entry permits for 459 tourists from Wuhan set to arrive later in Jan
  • Jan 23: ==> TWN: bans residents from Wuhan, travelers from China required to make online health declaration before entering
  • Jan. 24 ROK reports 2nd laboratory confirmed case ==> TWN bans export of facemasks; ROK, sometime around now the gov’t started tracking confirmed cases using credit card and CCTV data to understand where patients contacted the disease
  • Jan. 25: ==> TWN: tours to china are suspended until Jan 31, activates level 3 travel alert for Hubei Province and Level 2 for rest of China, enacts export ban on surgical masks until Feb 23
  • Jan 26: ==> TWN: all tour groups from Wuhan have to leave,
  • Jan. 27: TWN reports 1st domestic transmission of the disease ==>TWN NHIA and NIA (National health and immigration authorities) integrate (adds all hospital) patients past 14-day travel history to NHIA database, all tour groups from Hubei Province have to leave
  • Jan 28: ==> TWN: activates Level 3 travel alert for all of China except Hong Kong and Macau; ROK requests inspection of all people who have traveled from Wuhan in the past 14 days
  • Jan 29: ==> TWN: institutes electronic monitoring of all quarantined patients via gov’t issued cell phones; ROK about now requests production of massive numbers of WHO approved test kits for the Coronavirus
  • Jan. 30: ROK reports 2 more (4 total) confirmed cases of the disease ==> TWN: tours to or transiting China suspended until Feb 29;
  • Jan 31: ==> TWN: all remaining tour groups from China asked to leave
  • Feb 2 ==> TWN extended school break from Feb 15 to Feb 25,gov’t facilities available for quarantine, soldiers mobilized to man facemask production lines, 60 additional machines installed daily facemask output to reach 10M facemasks a day.
  • Feb 3: ==> TWN: enacts name based rationing system for facemasks, develops mobile phone app to allow public to see pharmacy mask stocks, Wenzhou city Level 2 travel alert; ROK CDC releases enhanced quarantine guidelines to manage the disease outbreak, as of today ROK CDC starts making 2-3 press releases a day on the progress of the disease
  • Feb 5: ==> TWN: Zheijanp province Level 2 travel alert, all cruise ships with suspected cases in past 28 days banned, any cruise ship with previous dockings in China, Hong Kong, or Macau in past 14 days are banned
  • Feb 6:==> TWN: Tours to Hong Kong & Macau suspended until Feb 29, all Chinese nationals banned, all international cruise ship are banned, all contacts from Diamond Princess cruise ship passengers who disembarked on Jan 31 are traced
  • Feb 7: ==> TWN: All foriegn nationals with travel to China, Hong Kong or Macau in the past 14 days are banned, all Foreigners must see an immigration officer,
  • Feb 14:==> TWN: Entry quarantine system launched fill out electronic health declaration for faster entry
  • Feb 16: ==> TWN: NHIA database expanded to cover 30 day travel history for travelers form or transited through China, Hong Kong, Macau, Singapore and Thailand.
  • Feb 18 ==> TWN: all hospitals, clinics and pharmacies have access to patients travel history; ROK most institutions postpone the re-start of school after spring break
  • Feb 19 ==> TWN establishes gov’t policies to disinfect schools and school areas, school buses, high speed rail, railways, tour busses and taxis
  • Feb 20 ==> ROK Daegu requests all individuals to stay home
  • Feb 21 ==> TWN establishes school suspension guidelines based on cases diagnosed in school; ROK Seoul closes all public gatherings and protests
  • Feb 24 ==> TWN, travelers with history of travel to china, from countries with level 1 or 2 travel alerts, and all foreign nationals subject to 14 day quarantine (By this time many countries are in level 1-2-3 travel alert status in TWN)
  • Feb 26 ==> ROK opens drive-thru testing clinics, patients are informed via text messages (3 days later) the results of their tests
  • Mar 3? ==> ROK starts selling facemasks at post offices
  • Mar 5 ==> ROK bans the export of face masks

As of Mar 16, (as reported in Wikipedia), TWN had 67 cases and 1 death; and ROK had 8,326 cases and 75 deaths. As of Mar 13 (as reported is Our world in data article), TWN had tested 16,089 and ROK had tested 248,647 people.

Summary of TWN and ROK responses to the virus

For starters, both TWN and ROK learned valuable lessons from the last infections from China SARS-H1N1 and used those lessons to deal better with COVID-19. Also neither country had any problem accessing credit information, mobile phone location data, CCTV camera or any other electronic information to trace infected people in their respective countries.

If I had to characterize the responses to the virus from the two countries:

  1. TWN was seemingly focused early on reducing infections from outside, controlling & providing face masks to all, and identifying gov’t policies (ceasing public gathering, quarantine and disinfectant procedure) to reduce transmission of the disease. They augmented and promoted the use of public NHIA databases to track recent travel activity and used any information available to monitor the infected and track down anyone they may have contacted. Although TWN has increased testing over time, they did not seem to have much of an emphasis on broad testing. At this point, TWN seems to have the virus under control.
  2. ROK was all about public communications, policies (quarantine and openness), aggressively testing their population and quarantining those that were infected. ROK also tracked the goings on and contacts of anyone that was infected. ROK started early on broadly testing anyone that wanted to be tested. Using test results, infected individuals were asked to quarantine. A reporter I saw talking about ROK mentions 3 T’s: Target, Test, & Trace At this point, ROK seems to have the virus under control.

In addition, Asian countries in general are more prone to use face masks when traveling, which may be somewhat restrict Coronavirus transmission. Although it seems to primarily reduce transmission, most of the public in these countries (now) routinely wear face masks when out and about. And previously they routinely wore face masks when traveling to reduce disease transmission.

Also both countries took the news out of Wuhan China about the extent of the infections, deaths and ease of disease transmission as truthful and acted on this before any significant infections were detected in their respective countries

What the rest of the world can learn from these two countries

What we need to take from TWN a& ROK is that

  1. Face masks and surgical masks are a critical resource during any pandemic. National production needs to be boosted immediately with pricing and distribution controls so that they are not hoarded, nor subject to price gouging. In the USA we have had nothing on this front other than requests to the public to stop hoarding them and the lack of availability to support healthcare workers).
  2. Test kits are also a critical resource during any pandemic. Selection of the test kit, validation and boosting production of test kits needs to be an early and high priority. The USA seems to have fallen down on this job.
  3. Travel restrictions, control and quarantines need to be instituted early on from infected countries. USA did take action to restrict travel and have instituted quarantines on cruise ship passengers and any repatriated nationals from China.
  4. Limited testing can help control the virus as long as it’s properly targeted. Mass, or rather less, targeted testing can also help control the virus as well. In the USA given the lack of test kits, we are limited to targeted testing.
  5. Open, rapid and constant communications can be an important adjunct to help control virus spread. The USA seems to be still working on this. Many states seem to have set up special communications channels to discuss the latest information. But there doesn’t seem to be any ongoing, every day communications effort on behalf of the USA CDC to communicate pandemic status.
  6. When one country reports infections, death and ease of transmission of a disease start to take serious precautions immediately. Disease transmission in our travel intensive world is much too easy and rapid to stop once it takes hold in a nation. Any nation today that starts to encounter and infectious agent with high death rates and seemingly easy transmission must be taken seriously as the start of something much bigger.

Stay safe, be well.

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Earth globe within a locked cage

Breaking IoT security

Posted on by Ray in Data security, Distributed computing, Internet of Things, System effectiveness, System quality

Read an article the other day (Researchers exploit low entropy of IoT devices to break RSA certificates) about researchers cracking IoT device security and breaking their public key encryption keys. The report focused on PKI and RSA certificates and IoT devices. The article mentioned the research paper describing the attack in more detail.

safe 'n green by Robert S. Donovan (cc) (from flickr)
safe ‘n green by Robert S. Donovan (cc) (from flickr)

RSA certificates publish a public key and the digital signature of the certificate and identify the device that owns the certificate.

What the researchers were able to show was that ~250K keys in IoT device RSA certificates were insecure. They were able to compromise the 250K RSA certificates using a single Microsoft Azure VM and about $3K of computer time.

It turns out that if two RSA certificate public keys share the same factor, it’s much easier to determine the greatest common devisor GCD) of the two public keys than it is to factor any one of them. And once you have the GCD of the two keys, it’s relatively trivial to determine the other factor in a public key. And that’s just what they did.

Public key infrastructure (PKI) encryption depends on asymmetric cryptography using a “public” key to encrypt messages (or to encrypt a one time key to be used in later encryption of messages) and the use of a “private” key to decrypt the message (or keys) and sign digital certificates. There are certificate authorities and a number of other elements used in PKI but the asymmetric cryptography at its heart, rests on the foundation of the difficulty in factoring large numbers but those large numbers need to be random and prime.

True randomness is hard

Just some of the recently donated seeds that are being added to the Reading Food Growing Network seed swap boxes, including some Polish gherkin seeds.

The problem starts with generating truly random numbers in a digital computer. Digital algorithms typically depend on a computer to perform the some set of instructions, in the same way and sequence so as to get the same answer every time we run the algorithm.

But if you want random numbers this predictability of always coming up with the same answer each time results in non-random numbers (or rather random numbers that are the same each time you run the algorithm). So to get around this, most random number generators can make use of a (random) seed which is used as an input to the algorithm to generate random numbers.

However, this seed needs to be a random number. But to create a random number it needs to be generated not with instructions but using something outside the digital computer. One approach noted above is to use a human typing keys to generate a random number to be used as a seed.

The researchers exploited the fact that most IoT devices don’t use a random (enough) seed for their PKI key generation. And they were able to use the GCD trick to figure out the factors to the PKI.

But the lack of true randomness (or entropy) is the real problem. Somehow, these devices need to have a cheap and effective way to generate a random seed. Until this can be found, they will be subject to these sorts of attacks.

… but not impossible to obtain

I remember in times past when tasked to create a public key-private key pair I had to type some random characters. The Public key encryption algorithm used the inter-character time interval of my typing to generate a random seed that was then used to generate the key pair used in the public key. I believe the two keys also need to be prime numbers.

Earth globe within a locked cage

Perhaps a better approach would be to assign them keys from a centralized key distributor. That way the randomness could be controlled by the (key) distributor.

There are other approaches that depend on the sensors available to an IoT device. If the device has a camera or mic, taking raw data from the camera or sound sensor and doing a numerical transform on them may suffice. Strain gauges, liquid levels, temperature, humidity, wind speed, etc. all of these devices have something which senses the world around them and many of these are, at their base, analog sensors. Reading and converting some portion of these analog signals from raw analog to a digital random seed could be very effective way to generate true(r) randomness.

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The paper has much more information about the attack and their results if your interested. They said that ~50% of the compromised devices were from a large network supplier. Such suppliers probably also have a vast majority of devices deployed. Still it’s troubling, nonetheless.

Until changes are made to IoT devices, they will continue to be insecure. Not as much of a problem when they are read only sensors but when the information they sense is used by robots or other automation to make decisions about actions, then having insecure IoT becomes a safety issue.

This is not the first time such an attack was attempted and each time, it’s been very successful. That alone should be cause for alarm. But IoT and similar devices are hard to patch in the field and their continuing insecurity may be more of a result of the difficulty of updating a large install base than anything else.

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