RayOnStorage - Part 4

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.).

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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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.

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.

Picture Credit(s):

• From Wikipedia article, Optical fiber
• From Wikipedia article, Optical fiber
• From IEEE Spectrum Article, Optical set terabit records
• From LightTalk blog, Moore’s law and optical fibre bandwidth

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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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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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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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.

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.

Photo Credit(s):

I’ve used small LIDAR sensors on toy (Arduino based) robots and they operate well within 1m or so. Ultrasonics sensors are another alternative but we found them very susceptible to noise and surface abrasion. With decent LIDAR sensors used in drones and vehicles, they work up to 215m or so.

But research in the lab (ScienceDaily article: Want to catch a photon, start by silencing the sun) has created LIDAR sensors that uses a novel form of analog/optical noise suppression that is capable of using these same LIDAR sensors and using them to map up to 45km of space.

The researchers were able to add a quantum marker to LIDAR beam photon(s) and then filter beam reflections to only honor those reflected photons with the quantum marker. The ScienceDaily article was based on a Nature Communications article, Noise-tolerant single photon sensitive three-dimensional imager.

What’s been changed?

They call the methodology implemented by their device, Quantum Parametric Mode Sorting or QPMS. It’s not intended to compete with software or computational approaches for noise filtering but rather complement those capabilities with a more accurate LIDAR, that can eliminate the vast majority of noise using non-linear optics (see Wikipedia article on Non-linear optics to learn more)..

It turns out the researchers are able to image space with their new augmented LIDAR using a single photon per pixel. They use an FPGA to control the system and programable ODL(optical delay line, delay’s optical signals), with up conversion single photon detector (USPD, that takes one or more photons at one frequency and converts them to another, higher frequency photon) and a silicon avalanche photo diode (SI-APD, which detects a single photon and creates an avalanche [of multiple electrons?] electrical signal from it.

How well does it work?

To measure the resolution capabilities of the circuit they constructed a 50x70mm (~2×2 3/4″) CNC machined aluminums depth resolution calibration device (sort of like an eye chart only for depth perception) see (2c and 2d below) and were able to accurately map the device column topologies.

They were also able to show enhanced perception and noise reduction when obscuring a landscape (Einstein’s head) with an aluminum screen which would be very hard for normal solutions to filter out. The device was able to clearly reconstruct the image even through the aluminum screen.

The result of all this is an all optical fibre noise reduction circuit. I’m sure the FPGA ,SI-APD, USPD, MLL, Transciever, ODL and MEM are electronics or electro-mechanical devices,, but the guts of the enhanced circuit seems all optical.

What does it mean?

What could QPMS mean for optical fibre communications. It’s possible that optical fibres could use significantly less electro-optical amplifiers, if a single photon could travel 45km without noise.

Also LiFi (light fidelity) or open air optical transmission of data could be significantly improved (both in transmission length and noise reduction) using QPMS. And rone could conceivably use LiFi outside of office communications, such as high bandwidth/low-noise, all optical cellular data services for devices. .

And of course boosting LIDAR length, noise reduction and resolution could be a godsend for all LIDAR mapping today. I readi another article (ScienceDaily: Modern technology reveals … secrets of great, white Maya road) about archeologist mapping the (old) Maya road through the jungles of central America using LIDAR equipped planes. I imagine a QPMS equiped LIDAR could map Mayan foot paths.

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Comments?

Read an article the other day which blew me away, Researchers Create ” Intelligent interaction between light and meterial – New form of computing, which discussed the use of a hydrogel (like raspberry jell-o) that could be used both as a photonics switch for optical communications and as modifiable material to create photonics circuits. The research paper on the topic is also available on PNAS, Opto-chemical-mechanical transduction in photeresponsive gel elicits switchable self trapped beams with remote interactions.

Apparently researchers have created this gel (see B in the graphic above)which when exposed to laser light interacts to a) trap the beam within a narrow cylinder and or b) when exposed to parallel beams interact such that it boosts the intensity of one of the beams. They still have some work to show more interactions on laser beam(s) but the trapping of the laser beams is well documented in the PNAS paper.

Jell-o optical fibres

Most laser beams broaden as they travel through space, but when a laser beam ise sent through the new gel it becomes trapped in a narrow volume almost as if sent through a pipe.

The beam trading experiment using a hydrogel cube of ~4mm per side. They sent a focused laser beam with a ~20um diameter through an 4mm empty volume and measured the beam’s disbursement to be ~130um diameter. Then the did the same experiment only this time shining the laser beam through the hydrogel cube and over time (>50 seconds) the beam diameter narrows to becomes ~22um. In effect, the gel over time constructs (drills) a self-made optical fibre or cylindrical microscopic waveguide for the laser beam.

A similar process works with multiple laser beam going through the gel. More below on what happens with 2 parallel laser beams.

The PNAS article has a couple of movies showing the effect from the side of the hydrogel. with a single and multiple laser beams.

Apparently as the beam propagates through the hydrogel, it alters the optical-mechanical properties of the material such that the refractive index within the beam diameter is better than outside the beam diameter. Over time, as this material change takes place, the beam diameter narrows back down to almost the size of the incoming beam. They call any material like this that changes its refractive index as chromophores.

It appears that the self-trapping effectiveness is a function of the beam intensity. That is higher intensity incoming laser beams (6.0W in C above) cause the exit beam to narrow while lower (0.37W) intensity incoming laser beams don’t narrow as much.

This self-created optical wave-guide (fibre) through the gel can be reset or reversed (> 45 times) by turning off the laser and leaving the gel in darkness for a time (200 seconds or so). This allows the material to be re-used multiple times to create other optical channels or to create the same one over and over again.

Jell-o optical circuits

It turns out that by illuminating two laser beams in parallel their distances apart can change their interaction even though they don’t cross.

When the two beams are around 200um apart, the two beams self channel to about the size of ~40um (incoming beams at ~20um). But the intensity of the two beams are not the same at the exit as they were at the entrance to the gel. One beam intensity is boosted by a factor of 12 or so and the other is boosted by a factor of 9 providing an asymmetric intensity boost. Unclear how the higher intensity beam is selected but if I read the charts right the more intensely boosted beam is turned on after the the less intensely boosted beam (so 2nd one in gets the higher boost.

When one of the beams is disabled (turned off/blocked), the intensity of the remaining beam is boosted on the order of 20X. This boosting effect can be reversed by illuminating (turning back on/unblocking) the blocked laser. But, oddly the asymmetric boosting, is no longer present after this point. The process seemingly can revert back to the 20X intensity boost, just by disabling the other laser beam again. .

When the two beam are within 25 um of each other, the two beams emerge with the same (or close to similar) intensity (symmetric boosting), and as you block one beam the other increases in intensity but not as much as the farther apart beams (only 9X).

How to use this effect to create an optical circuit is beyond me but they haven’t documented any experiments where the beams collide or are close together but at 90-180 degrees from one another. And what happens when a 3rd beam is introduced? So there’s much room for more discovery.

Just in case you want to try this at home. Here is the description of how to make the gel from the PNAS article: “The polymerizable hydrogel matrix was prepared by dissolving acrylamide:acrylic acid or acrylamide:2-hydroxyethyl methacrylate (HEMA) in a mixture of dimethyl sulfoxide (DMSO):deionized water before addition of the cross-linker. Acrylated SP (for tethered samples) or hydroxyl-substituted SP was then added to the unpolymerized hydrogel matrix followed by an addition of a catalyst. Hydrogel samples were cured in a circular plastic mold (d = 10 mm, h = 4 mm thick).“

How long it will take to get the gel from the lab to your computer is anyones guess. It seems to me they have quite a ways to go to be able to simulate “nor” or “nand” universal logic gates widely used in to create electronic circuits today.

On the other hand, using the gel in optical communications may come earlier. Having a self trapping optical channel seems useful for a number of applications. And the intensity boosting effect would seem to provide an all optical amplifier.

I see two problems:

1. The time it takes to get to a self trapping channel, 50sec is long and it will probably take longer as you increase the size of the material.
2. The size of the material seems large for optical (or electronic) circuitry. 4mm may not be much but it’s astronomical compared to the nm used in electronic circuitry

The size may not be a real concern as the movies don’t seem to show that the beam once trapped changes across the material, so maybe it could be a 1mm, or 1um cube of material that’s used instead. The time is a more significant problem. But then again there may be another gel recipe that acts quicker. But from 50sec down to something like 50nsec is nine orders of magnitude. So there’s a lot of work here.

Comments?

Photo Credit(s): all charts are from thePNAS article, Opto-chemo-mechanical transduction in photo responsive gel…