Homework

• For next time we meet

– Look at this link • https://en.wikipedia.org/wiki/Research_Experiences_for_Undergraduates

– Look at this link (and watch the video) • http://research.microsoft.com/en-us/um/redmond/projects/projectpremonition/default.aspx

– Review Dr. Keoghs slides • http://www.cs.ucr.edu/~eamonn/public/REU_Day_1.pdf

• Over the life of the program, you need to provide us with 4 photographs, with a

short accompanying paragraph explaining what you are doing “In this photo, we see me, Susan Shu, operating a centrifuge under the mentorship of Dr. Bob Doe. We are using the centrifuge to determine

the…. ”. Please email these to eamonn@cs.ucr.edu with the subject heading “images for blog”. Note that this images may appear online (on Facebook and/or blogs etc)

Eamonn Keogh

Computer Science & Engineering Department University of California - Riverside

Riverside, CA 92521 eamonn@cs.ucr.edu

REU: Welcome

Introductions

Eamonn Keogh Computer Science Data Mining, Artificial Intelligence, Applications of Machine Learning in Medical and Agricultural Domains

Christian R. Shelton Computer Science Machine Learning, Adaptive Decision Making, Computational Statistical Inference, Artificial Intelligence.

Adena Why Entomology

Daniel R. Jeske Statisitics Spatial Analysis, Models for Crop Pests, Life Data Analysis, Sequential Hypothesis Testing.

Your research mentor is not shown

How did we get here?

• The NSF is the National Science Foundation

• The NSF funds REUs

• Two years ago I wrote a grant proposal asking for funding for this program

• In April 15, we won the award ;-)

• The 3 year budget is $389,550

• Almost all that is for the fellows

What is the schedule?

• It is a ten week program

• In the first two weeks, as a group you will have some instruction (about ½ time) and meet your research mentors

• In the remaining eight weeks you will be doing research (independent of each other) in your mentors labs.

• In those eight weeks there will be occasional events and meetings you need to attend, as a group. (I will give you advanced notice by email)

What you need to do • We are paying you! You have a job, a research job. You need to deliver!

• You need to attend all scheduled events.

• You need to respond to emails (check once a day)

• You need to provide a final report/give a talk (details later)

• Over the life of the program, you need to provide us with 4 photographs, with a short accompanying paragraph explaining what you are doing “In this photo, we see me, Susan Shu, operating a centrifuge under the mentorship of Dr. Bob

Doe. We are using the centrifuge to determine the…. ”. Please email these to eamonn@cs.ucr.edu with the subject heading “images for blog”. Note that this images may paper online (on Facebook and/or blogs etc)

• Have fun, learn a lot, and do good research.

Eamonn Keogh

Computer Science & Engineering Department University of California - Riverside

Riverside, CA 92521 eamonn@cs.ucr.edu

Using Computers to Understand (and control) Insects

What is the Deadliest Animal? (not counting humans!)

What is the Deadliest Animal?

500+ per year

200+ per year

10+ per year

300+ per year

2,000,000+ per year

50,000+ per year

What is the Deadliest Animal?

50,000+ per year 500+ per year

200+ per year

10+ per year

300+ per year

2,000,000+ per year

One penny weights about the same as one thousand mosquitoes

How can something so small be so deadly?

What is Malaria?

• Malaria is a disease that involves high fevers, shaking chills, joint pain, flu-like symptoms. In some cases it can produce coma and death.

• There are more than 225 million cases of malaria each year, killing around 1-million people.

Where does Malaria come from? Malaria has been known since ancient times. Many believed it came from “bad air” (Italian: mala aria, “bad air”) 500 years ago, a handful of people believed that insects might be involved in human diseases.

It was Sir Ronald Ross, an British army surgeon working in India, who proved in 1897 that malaria is transmitted by mosquitoes. Sir Ronald Ross received the 1902 Nobel Prize for Physiology or Medicine for his work (This was somewhat controversial, as many others made similar discoveries around the same time )

Malaria Parasites

1st Vector

Initial Human host

Liver infection

Blood infection

2nd Vector

Next Human host

Malaria Transmission Cycle

We get malaria from mosquitoes

We get malaria from

humans

• There are 3,528 kinds of mosquitoes

• Only a handful of species take human blood • Only the females take human blood

• There are 100 trillion mosquitoes alive today

• Mosquitoes have been around for at least 100 million years

• We know this from fossil records/DNA studies

• Mosquitoes have spread malaria for at least 35 million years

• We know this from insects found in amber

The Mosquito

Where does malaria cause problems?

www.worldmapper.org

Given that we have known for over one hundred years how Malaria is spread, where is the magic pill or immunization? For a variety of reasons, a cure or immunization continues to alluded mankind.

However there are some interventions that can help

In the 20th century, smallpox killed 400 million people worldwide, it is now eradicated.

Polio is almost eradicated.

Interventions to Mitigate Malaria

• The use of insecticidal treated mosquito nets

• Spraying of insecticides (including controversial chemicals such as DDT)

• Introduction of fish/turtles/crustaceans to eat mosquito larva

• The introduction of dragonflies which eat adult mosquitoes.

• Habitat reduction by draining ponds and pools

• Use of chemical films to reduce the surface tension of water (drowning the pupa).

• .. and hundreds more proven or tentative ideas

Interventions Cost Money!

• Even cheap solutions have hidden costs

• Insecticidal treated mosquito nets are cheap to make, but…

• To make mosquito nets work, you need educators, incentive programs, maintenance etc

“...aid agencies and non-governmental organizations are quietly grappling with a problem: Data suggest that nearly half of Africans who have access to the nets refuse to sleep under them” (LA Times May-2-2010).

• We need to know where/when the problem is the greatest.

Where are the insects?

Which insects are they?

When did they arrive?

• The classic solution?

Use sticky traps – Inaccurate

– Costly

– Long time lag

Planning interventions requires knowledge

My Work at UCR

• I believe that we can count and classify insects with sensors. – Must be cheap

– Must be low powered

– Must be accurate

0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 x 10 4 -0.2

-0.1

0

0.1

0.2

One second of audio from our sensor. The Common Eastern Bumble Bee (Bombus impatiens) takes about one tenth of a second to pass the laser.

Background noise Bee begins to cross laser Bee has past though the laser

UCR Wingbeat Sensor

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17 Bee count

21 Mosquito count

2134 Housefly count

17 Bee count

21 Mosquito count

2134 Housefly count

Spay the dark red areas at dusk

Using Pesticides Intelligently

If we are not sure where the insects are…

If we know where the insects are…

High cost (fuel/pesticide) Damage to environment

Low cost Little damage to environment

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The holy grail of computational

entomology

With a single click of a button, we can take action on our emails/spam. We can delete, forward, save them etc

17 Bee count

21 Mosquito count

2134 Housefly count

Can we do this with insects? Can we “delete” mosquitoes (Kill them) Can we “forward” bees (Make them go North and pollinate almonds etc)

The holy grail of computational

entomology

The question comes down to, can we control insects. At least in some cases, we already do, implicitly or explicitly. Consider the Jewel Beetle……….

The holy grail of computational

entomology

The males are attached to the female’s slightly iridescence brown color and dimpled texture, and prefer larger females …

Julodimorpha bakewelli (Jewel Beetle) is a species of beetle found in arid regions of Australia.

Controlling Insects with Computers

Insect cyborgs are cool, but not the answer. We need to be able to control insects at a cost of say 1,000,000 insects per penny.

Controlling Insects with Computers

We already control some insects with technology/computers We are exploiting the fact that moths evolved without artificial lights. What else can we exploit?

What else can we exploit?

The more we learn about nature, the more we can improve human the human condition

Capturing or killing individually targeted insects

• Most efforts to capture or kill insects are “shotgun”. Many non-targeted insects (including beneficial ones) are killed/captured.

• In some cases, the ratios are 1,000 to 1 (i.e. 1,000 non-targeted insects are effected for each one that was targeted).

• We believe our sensors allow an ultra precise approach, with a ratio approaching 1 to 1.

• This has obvious implications for SIT/metagenomics

Kill It seems obvious you could kill a mosquito with a powerful enough laser and with enough time.

But we need to do it fast, with as little power as possible.

We have gotten this down to 1/20th of a second, and just 1 watt. (and falling)

The mosquitoes may survive the laser strike, but they cannot fly away (as was the case in photo shown right)

Zoom-in (after removing the wing) Collaboration with UCR mechanical engineers Amir Rose and Dr. Guillermo Aguilar

We are building a SIT Hotel California for female mosquitoes (you can check out anytime you like, but you can never leave)

Culex tarsalis

Capture

We envision building robotic traps that can be left in the field, and programed with different sampling missions. Such traps could be placed and retrieved by drones. Capturing live insects is important if you want to do metagenomics. Some examples of sampling missions…

Capture examples of gravid{Aedes aegypti}

Capture examples of insects that are NOT Anopheles AND have a wingbeat frequency > 400 (to exclude bees, etc.)

Capture examples of any insects with a wingbeat frequency > 500, encountered between 4:00am and 4:10am

Capture examples of fed{Anopheles gambiae} OR fed{Anopheles quadriannulatus} OR fed{Anopheles melas}

Capture About 10% of the insects captured by Venus fly traps are flying insects We believe that we can build inexpensive mechanical traps that can capture sex/species targeted insects.

Capture examples of gravid{Aedes aegypti}

Capture insects marked{ Cripple(left-C|right-S) }

Capture examples of insects that are NOT Anopheles AND have a wingbeat frequency > 400 (to exclude bees, etc.)

Capture examples of any insects with a wingbeat frequency > 500, encountered between 4:00am and 4:10am

Capture examples of fed{Anopheles gambiae} OR fed{Anopheles quadriannulatus} OR fed{Anopheles melas}

12AM 3AM 6AM 9AM 12PM 3PM 6PM 9PM 12AM

dawn dusk nighttime daytime

Culex quinquefasciatus

Daily Activity Plots for a Mosquito Species that Transmit West Nile Virus

West Nile Cases in 2012

Another use for our sensor

This is why Computational Entomology

12AM 3AM 6AM 9AM 12PM 3PM 6PM 9PM 12AM

dawn dusk daytime

Culex quinquefasciatus

*Biology and behavior of male mosquitoes in relation to new approaches to control disease transmitting mosquitoes

A 2014 paper* discusses the circadian rhythm of a species of mosquito. The pattern was learned on dozens of data points

In 2014 we were doing this with tens of thousands of data points. We are currently redoing this with millions of data points

Questions?