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[WSG20] Daily Study Group: Biodiversity Explorations with Machine Learning

POSTED BY: Jofre Espigule-Pons
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POSTED BY: Jofre Espigule-Pons
Rohit Namjoshi
Rohit Namjoshi
Posted 5 years ago
POSTED BY: Rohit Namjoshi
POSTED BY: James Kralik

Hi Jofre,

Yes, this presentation is going into the right direction. Is it possible to get access to the notebook?

Thanks in advance.
POSTED BY: Jürgen Kanz
POSTED BY: Jofre Espigule-Pons
POSTED BY: Jofre Espigule-Pons
C Ellis
C Ellis
Posted 5 years ago

Jofre - Great presentation yesterday on audio processing. Couldn't help but reflect upon how the results were somewhat inconclusive (ie end of slide 3) despite both the overall process and coding appearing quite sound. With that said, is it possible the bird you recorded wasn't actually an owl?

Mourning doves can sound like owls ( https://www.audubon.org/news/no-thats-not-owl-outside-your-window ) and would be much more common habitants in the forest of lamp poles populating the UICI stadium parking lots. The initial WL entity search did return "pigeon, dove" as its AudioIdentify result.

A search of inaturalist showed the Rock Dove could serve as another likely suspect for A/B test use.

Just a thought. Again, excellent presentation. Thank you.
POSTED BY: C Ellis

Nice animations! You are right, for a comparative analysis one would need to take into account the rise in number of observers over the last years. Or maybe you could plot their relative abundance over time for these two species. In this article they also point out the change in habitat for the green anole as you mentioned: https://www.anoleannals.org/2015/06/10/are-brown-anoles-in-florida-really-driving-green-anoles-to-extinction/
POSTED BY: Jofre Espigule-Pons

Today (Day-5), we are going to train the "Wolfram ImageIdentify Net V1"- Neural Network with additional images from “INaturalistSearch”.

I would like to do the same with "YOLO V2 Trained on MS-COCO Data" and or "YOLO V3 Trained on Open Images Data". The input shall be an image and the outputs are Label, Probability, and Bounding Box.

How to train such a network? I have not found any documentation. The final objective is to identify all mushrooms on the following image. enter image description here
POSTED BY: Jürgen Kanz
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POSTED BY: James Kralik

@James Kralik , I recommend you to use GBIFImport instead, specially when the number of observations is very large. You can download the occurrences data directly on the GBIF site: https://www.gbif.org/occurrence/search?taxon_key=4287413

Once you have downloaded the dataset for this species, you can then import the local CSV/Text file containing the occurrences using ResourceFunction["GBIFImport"]
POSTED BY: Jofre Espigule-Pons

I'm trying to expand on the anole example, but apparently iNaturalistSearch is limited to a maximum of 200 observations, even though 3046 observations for the brown anole were counted for Houston. I'm unable to use the Page and MaxItems options to automate the extraction (although I can brute force it by manually extracting 200 observations at a time into separate variables and then using Join. I also tried to extract 3 different species using the Or ("|") operator, but that did not work. My goal is to visually show the displacement of the green anole by the brown anole over the last 20 years in Houston.

In Jofre's stink bug example, he used a SemanticImport of a *.csv file, but I'm not sure of its source.

In my meandering around the web, I became aware of another invasive lizard that's beginning to get noticed in Texas, the Argentine tegus - they're the size of a dog and grow to about 4 feet long. Oh, and BTW, they're voracious omnivores!
POSTED BY: James Kralik

Thanks for pointing to this syntax error. I edited the code. Concerning the shortcut for ResourceFunction, I'm not aware of any trick. It would be nice to have one though.
POSTED BY: Jofre Espigule-Pons
Updating Name
Updating Name
Posted 5 years ago

At the end of the Day 2 challenge example Jofre provided, the syntax trained["TrainedNet"][image] would not execute, but if I used c[image] it works as expected. Is there some code missing (i.e., I didn't see trained[] defined)?

Also, is there a shortcut for ResourceFunction["iNaturalistSearch"] that will create the iconized form on the fly like Ctrl + Enter for entities?
POSTED BY: Updating Name

Thank you very much, this is very helpful!! Andrew Skipor
POSTED BY: Andrew Skipor
POSTED BY: Jofre Espigule-Pons

Thanks, Andrew
POSTED BY: Andrew Skipor

Yes, if you change "Month" to "Day" you will get daily observations on DateHistogram.
POSTED BY: Jofre Espigule-Pons

Note: At the "Predict" section from today's session there was an issue for those running 12.1 version or earlier. You will need to change a bit the code. Use to the following:

pm = PredictorMeasurements[p, testing -> "Rings"]

Instead of using the 12.2 version code:

pm = PredictorMeasurements[p, testing]

Thank you, Neil for catching this issue.
POSTED BY: Jofre Espigule-Pons

You showed the histogram data, but during the class you increased the resolution for the month of May. I don' recall how you did that? Did you change "Month" to "Day" in the Histogram plot?

Thanks Andrew
POSTED BY: Andrew Skipor

POSTED BY: Jofre Espigule-Pons
POSTED BY: Andrew Skipor

The following sections are the ones related to tick species. If you are interested in getting tick observations from central Wisconsin only. I recommend you using ResourceFunction["INaturalistSearch"] (see the next last example)
POSTED BY: Jofre Espigule-Pons

Hello , Can you please post the Notebook, you showed in regards to the "Tick" example. I want to try to correlate its population growth with weather such as rainfall... I am interested in the central WI area..

Thanks Andrew
POSTED BY: Andrew Skipor

POSTED BY: James Kralik

Hi @Jay Morreale, the recording link was included in today's email reminder. The link is: https://www.gotostage.com/channel/daily-study-group
POSTED BY: Jamie Peterson
POSTED BY: Abrita Chakravarty

POSTED BY: Jofre Espigule-Pons

Hi Jamie, I wasn't able to attend today. Will you be posting the recording soon? Sincerely, Jay Morreale Member p-brane LLC
POSTED BY: Jay Morreale

Looking forward to it, @Jofre Espigule-Pons!
POSTED BY: Jamie Peterson
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