Artistic AI

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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Photonics + Nonlinear optical crystals = Quantum computing at room temp

Read an article the other day in ScienceDaily (Path to quantum computing at room temp) which was reporting on a Phys.Org article (Researchers see path to quantum computing at room temp). Both articles were discussing recent research documented in a Physical Review Letters (Controlled-Phase Gate Using Dynamically Coupled Cavities and Optical Nonlinearities, behind paywall) being done at the Army Research Laboratory, Army and MIT researchers used photonis circuits and non-linear optical (NLO) crystals to provide quantum entanglement between photon waves. I found a pre-print version of the paper on Arxiv.org, (Controlled-Phase Gate Using Dynamically Coupled Cavities and Optical Nonlinearities).

NLO Crystals

Nonlinear optics (source: Wikipedia Nonlinear Optics article) uses NLO crystals whicht when exposed to high electrical fields and high intensity light can modify or modulate light polarization, frequency, phase and path. For example:

Comparison of a phase-conjugate mirror with a conventional mirror. With the phase-conjugate mirror the image is not deformed when passing through an aberrating element twice.
  • Double or tripling light frequency, where one can double or triple the frequency of light (with two [or three] photons destroyed and a new one created).
  • Cross phase modulation where the wavelength phase of one photon can affect the wavelength phase of another photon.
  • Cross polarization wave generation where the polarization vector of a photon can be changed to be perpendicular to the original photon.
  • Phase conjugation mirror where light beams interact to exactly reverse “the propagation direction and phase variability” of a beam of light.

The Wikipedia article discusses a dozen more affects like this that NLO crystals can have on photons.

Quantum photon traps using NLO

MIT and Army researchers have theorized that there is another NLO crystal affect which can create a quantum photon trap. The researchers believe they can engineer a NLO crystal cavity(s) that act as a photon trap. With such an NLO crystal and photonics circuits, the traps could have the value of either a photon inside or a photon not inside the trap, but as it’s a quantum photon trap, it takes on both values at the same time.

Using photon trap NLO crystals, the researchers believe these devices could serve as room temperature qubits and quantum (photonic) gates.

The researchers state that with recent advances in nano-fabrication and the development of ultra-confined NLO crystals, experimental demonstrations of the photonics qubits and quantum gates appear feasible.

Quantum computing today

As our blog readers mayrecall, quantum computers today can take on many approaches but they all require extremely cold temperatures (a few Kelvin) to work. Even at that temperature quantum computing today is extremely susceptible to noise and other interference.

A quantum computer based on photonics, NLO crystals and operations at room temperature would be much more energy efficient, have many more qubits and much less susceptible to noise. Such a quantum computer could result in quantum computing being as ubiquitous as GPUs, TPU/IPUs or FPGA computational resources today .

Ubiquitous quantum computing would turn over our world. Digital information security today depends on mathematics for key exchanges which are extremely hard to do with digital computers. Quantum computers with sufficient qubits have no difficulty with such mathematics. Block chain relies on similar technology, so that too would also be at risk.

Standards organizations are working on security based on quantum proof algorithms but to date, we have yet to see any descriptions, let alone implementations of any quantum proof security in any information security scheme.

If what the researchers propose, pans out, advances in photonic quantum computing could restart information security of our world.

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OFA DNNs, cutting the carbon out of AI

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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Breaking optical data transmission speed records

Read an article this week about records being made in optical transmission speeds (see IEEE Spectrum, Optical labs set terabit records). Although these are all lab based records, the (data center) single mode optical transmission speed shown below is not far behind the single mode fibre speed commercially available today. But the multi-mode long haul (undersea transmission) speed record below will probably take a while longer until it’s ready for prime time.

First up, data center optical transmission speeds

Not sure what your data center transmission rates are but it seems pretty typical to see 100Gbps these days and inter switch at 200Gbps are commercially available. Last year at their annual Optical Fiber Communications (OFC) conference, the industry was releasing commercial availability of 400Gbps and pushing to achieve 800Gbps soon.

Since then, the researchers at Nokia Bell Labs have been able to transmit 1.52Tbps through a single mode fiber over 80 km distance. (Unclear, why a data center needs an 80km single mode fibre link but maybe this is more for a metro area than just a datacenter.

Diagram of a single mode (SM) optical fiber: 1.- Core 8-10 µm; 2.- Cladding 125 µm; 3.- Buffer 250 µm; & 4.- Jacket 400 µm

The key to transmitting data faster across single mode fibre, is how quickly one can encode/decode data (symbols) both on the digital to analog encoding (transmitting) end and the analog to digital decoding (receiving) end.

The team at Nokia used a new generation silicon-germanium chip (55nm CMOS process) able to generate 128 gigabaud symbol transmission (encoding/decoding) with 6.2 bits per symbol across single mode fiber.

Using optical erbium amplifiers, the team at Nokia was able to achieve 1.4Tbps over 240km of single mode fibre.

A wall-mount cabinet containing optical fiber interconnects. The yellow cables are single mode fibers; the orange and aqua cables are multi-mode fibers: 50/125 µm OM2 and 50/125 µm OM3 fibers respectively.

Used to be that transmitting data across single mode fibre was all about how quickly one could turn laser/light on and off. These days, with coherent transmission, data is being encoded/decoded in amplitude modulation, phase modulation and polarization (see Coherent data transmission defined article).

Nokia Lab’s is attempting to double the current 800Gbps data transmission speed or reach 1.6Tbps. At 1.52Tbps, they’re not far off that mark.

It’s somewhat surprising that optical single mode fibre technology is advancing so rapidly and yet, at the same time, commercially available technology is not that far behind.

Long haul optical transmission speed

Undersea or long haul optical transmission uses multi-core/mode fibre to transmit data across continents or an ocean. With multi-core/multi-mode fibre researchers and the Japan National Institute for Communications Technology (NICT) have demonstrated a 3 core, 125 micrometer wide long haul optical fibre transmission system that is able to transmit 172Tbps.

The new technology utilizes close-coupled multi-core fibre where signals in each individual core end up intentionally coupled with one another creating a sort of optical MIMO (Multi-input/Multi-output) transmission mechanism which can be disentangled with less complex electronics.

Although the technology is not ready for prime time, the closest competing technology is a 6-core fiber transmission cable which can transmit 144Tbps. Deployments of that cable are said to be starting soon.

Shouldn’t there be a Moore’s law for optical transmission speeds

Ran across this chart in a LightTalk Blog discussing how Moore’s law and optical transmission speeds are tracking one another. It seems to me that there’s a need for a Moore’s law for optical cable bandwidth. The blog post suggests that there’s a high correlation between Moore’s law and optical fiber bandwidth.

Indeed, any digital to analog optical encoding/decoding would involve TTL, by definition so there’s at least a high correlation between speed of electronic switching/processing and bandwidth. But number of transistors (as the chart shows) and optical bandwidth doesn’t seem to make as much sense probably makes the correlation evident. With the possible exception that processing speed is highly correlated with transistor counts these days.

But seeing the chart above shows that optical bandwidth and transistor counts are following each very closely.

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So, we all thought 100Gbps was great, 200Gbps was extraordinary and anything over that was wishful thinking. With, 400Gbps, 800 Gbps and 1.6Tbps all rolling out soon, data center transmission bottlenecks will become a thing in the past.

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DNA storage using nicks

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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Anti-Gresham’s Law: Good information drives out bad

(Good information is in blue, bad information is in Red)

Read an article the other day in ScienceDaily (Faster way to replace bad info in networks) which discusses research published in a recent IEEE/ACM Transactions on Network journal (behind paywall). Luckily there was a pre-print available (Modeling and analysis of conflicting information propagation in a finite time horizon).

The article discusses information epidemics using the analogy of a virus and its antidote. This is where bad information (the virus) and good information (the antidote) circulate within a network of individuals (systems, friend networks, IOT networks, etc). Such bad information could be malware and its good information counterpart could be a system patch to fix the vulnerability. Another example would be an outright lie about some event and it’s counterpart could be the truth about the event.

The analysis in the paper makes some simplifying assumptions. That in a any single individual (network node), both the virus and the antidote cannot co-exist. That is either an individual (node) is infected by the virus or is cured by the antidote or is yet to be infected or cured.

The network is fully connected and complex. That is once an individual in a network is infected, unless an antidote is developed the infection proceeds to infect all individuals in the network. And once an antidote is created it will cure all individuals in a network over time. Some individuals in the network have more connections to other nodes in the network while different individuals have less connections to other nodes in the network.

The network functions in a bi-directional manner. That is any node, lets say RAY, can infect/cure any node it is connected to and conversely any node it is connected to can infect/cure the RAY node.

Gresham’s law, (see Wikipedia article) is a monetary principle which states bad money in circulation drives out good. Where bad money is money that is worth less than the commodity it is backed with and good money is money that’s worth more than the commodity it is backed with. In essence, good money is hoarded and people will preferentially use bad money.

My anti-Gresham’s law is that good information drives out bad. Where good information is the truth about an event, security patches, antidotes to infections, etc. and bad infrormation is falsehoods, malware, biological viruses., etc

The Susceptible Infected-Cured (SIC) model

The paper describes a SIC model that simulates the (virus and antidote) epidemic propagation process or the process whereby virus and its antidote propagates throughout a network. This assumes that once a network node is infected (at time0), during the next interval (time0+1) it infects it’s nearest neighbors (nodes that are directly connected to it) and they in turn infect their nearest neighbors during the following interval (time0+2), etc, until all nodes are infected. Similarly, once a network node is cured it will cure all it’s neighbor nodes during the next interval and these nodes will cure all of their neighbor nodes during the following interval, etc, until all nodes are cured.

What can the SIC model tell us

The model provides calculations to generate a number of statistics, such as half-life time of bad information and extinction time of bad-information. The paper discusses the SIC model across complex (irregular) network topologies as well as completely connected and star topologies and derives formulas for each type of network

In the discussion portion of the paper, the authors indicate that if you are interested in curing a population with bad information it’s best to map out the networks’ topology and focus your curation efforts on those node(s) that lie along the (most) shortest path(s) within a network.

I wrongly thought that the best way to cure a population of nodes would be to cure the nodes with the highest connectivity. While this may work and such nodes, are no doubt along at least one if not all, shortest paths, it may not be the optimum solution to reduce extinction time, especially If there are other nodes on more shortest paths in a network, target these nodes with a cure.

Applying the SIC model to COVID-19

It seems to me that if we were to model the physical social connectivity of individuals in a population (city, town, state, etc.). And we wanted to infect the highest portion of people in the shortest time we would target shortest path individuals to be infected first.

Conversely, if we wanted to slow down the infection rate of COVID-19, it would be extremely important to reduce the physical connectivity of indivduals on the shortest path in a population. Which is why social distancing, at least when broadly applied, works. It’s also why, when infected, self quarantining is the best policy. But if you wished to not apply social distancing in a broad way, perhaps targeting those individuals on the shortest path to practice social distancing could suffice.

However, there are at least two other approaches to using the SIC model to eradicate (extinguish the disease) the fastest:

  1. Now if we were able to produce an antidote, say a vaccine but one which had the property of being infectious (say a less potent strain of the COVID-19 virus). Then targeting this vaccine to those people on the shortest paths in a network would extinguish the pandemic in the shortest time. Please note, that to my knowledge, any vaccine (course), if successful, will eliminate a disease and provide antibodies for any future infections of that disease. So the time when a person is infected with a vaccine strain, is limited and would likely be much shorter than the time soemone is infected with the original disease. And most vaccines are likely to be a weakened version of an original disease may not be as infectious. So in the wild the vaccine and the original disease would compete to infect people.
  2. Another approach to using the SIC model and is to produce a normal (non-transmissible) vaccine and target vaccination to individuals on the shortest paths in a population network. As once vaccinated, these people would no longer be able to infect others and would block any infections to other individuals down network from them. One problem with this approach is if everyone is already infected. Vaccinating anyone will not slow down future infection rates.

There may be other approaches to using SIC to combat COVID-19 than the above but these seem most reasonable to me.

So, health organizations of the world, figure out your populations physical-social connectivity network (perhaps using mobile phone GPS information) and target any cure/vaccination to those individuals on the highest number of shortest paths through your network.

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  1. Figure 2 from the Modeling and analysis of conflicting information propagation in a finite time horizon article pre-print
  2. Figure 3 from the Modeling and analysis of conflicting information propagation in a finite time horizon article pre-print
  3. COVID-19 virus micrograph, from USA CDC.

A tale of two countries and how they controlled the Coronavirus

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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New science used to combat COVID-19 disease

Read an article last week in Science Magazine (A completely new culture on doing research… ) on how the way science is done to combat disease has changed the last few years.

In the olden days (~3-5 years ago), disease outbreaks would generate a slew of research papers to be written, submitted for publication and there they would sit, until peer-reviewed, after which they might get published for the world to see for the first time. Estimates I’ve seen say that the scientific research publishing process takes anywhere from one month (very fast) to 4-8 months, assuming no major revisions are required.

With the emergence of the Zika virus and recent Ebola outbreaks, more and more biological research papers have become available through pre-print servers. These are web-sites which accept any research before publication (pre-print), posting the research for all to see, comment and understand.

Open science via pre-print

Most of these pre-print servers focus on specific areas of science. For example bioRxiv is a pre-print server focused on Biology and medRxiv is for health sciences. On the other hand, arXiv is a pre-print server for “physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering and systems science, and economics.” These are just a sampling of what’s available today.

In the past, scientific journals would not accept research that had been published before. But this slowly change as well. Now most scientific journals have policies gol pre-print publication and will also publish them if they deem it worthwhile, (see wikipedia article List of academic journals by pre-print policies).

As of today (9 March 2020) ,on biorXiv there are 423 papers with keyword=”coronavirus” and 52 papers with the keyword COVID-19, some of these may be the same. The newest (Substrate specificity profiling of SARS-CoV-2 Mpro protease provides basis for anti-COVID-19 drug design) was published on 3/7/2020. The last sentence in their abstract says “The results of our work provide a structural framework for the design of inhibitors as antiviral agents or diagnostic tests.” The oldest on bioRxiv is dated 23 January 2020. Similarly, there are 326 papers on medRxiv with the keyword “coronavirus”, the newest published 5 March 2020.

Pre-print research is getting out in the open much sooner than ever before. But the downside, is that pre-print papers may have serious mistakes or omissions in them as they are not peer-reviewed. So the cost of rapid openness is the possibility that some research may be outright wrong, badly done, or lead researchers down blind alleys.

However, the upside is any bad research can be vetted sooner, if it’s open to the world. We see similar problems with open source software, some of it can be buggy or outright failure prone. But having it be open, and if it’s popular, many people will see the problems (or bugs) and fixes will be rapidly created to solve them. With pre-print research, the comment list associated with a pre-print can be long and often will identify problems in the research.

Open science through open journals

In addition to pre-print servers , we are also starting to see the increasing use of open scientific journals such as PLOS to publish formal research.

PLOS has a number of open journals focused on specific arenas of research, such as PLOS Biology, PLOS Pathogyns, PLOS Medicine, etc.

Researchers or their institutions have to pay a nominal fee to publish in PLOS. But all PLOS publications are fully expert, peer-reviewed. But unlike research from say Nature, IEEE or other scientific journals, PLOS papers are free to anyone, and are widely available. (However, I just saw that SpringerNature is making all their coronavirus research free).

Open science via open data(sets)

Another aspect of scientific research that has undergone change of late is the sharing and publication of data used in the research.

Nature has a list of recommended data repositories. All these data repositories seem to be hosted by FAIRsharing at the University of Oxford and run by their Data Readiness Group. They list 1349 databases of which the vast majority (1250) are for the natural sciences with over 1380 standards used for data to be registered with FAIRsharing.

We’ve discussed similar data repositories in the past (please see Data banks, data deposits and data withdrawals, UK BioBank, Big open data leads to citizen science, etc). Having a place to store data used in research papers makes it easier to understand and replicate science.

Collaboration software

The other change to research activities is the use of collaborative software such as Slack. Researchers at UW Madison were already using Slack to collaborate on research but when Coronavirus went public, they Slack could help here too. So they created a group (or channel) under their Slack site called “Wu-han Clan” and invited 69 researchers from around the world. The day after they created it they held their first teleconference.

Other collaboration software exists today but Slack seems most popular. We use Slack for communications in our robotics club, blogging group, a couple of companies we work with, etc. Each has a number of invite-only channels, where channel members can post text, (data) files, links and just about anything else of interest to the channel.

Although I have not been invited to participate in Wu-han Clan (yet), I assume they usee Slack to discuss and vet (pre-print) research, discuss research needs, and other ways to avert the pandemic.

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So there you have it. Coronavirus scientific research is happening at warp speed compared to diseases of yore. Technologies to support this sped up research have all emerged over the last five to 10 years but are now being put to use more than ever before. Such technological advancement should lead to faster diagnosis, lower worldwide infection/mortality rates and a quicker medical solution.

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