First steps in Deep Learning

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# First steps in Deep Learning
## Species identification and camera traps

.large[Olivier Gimenez [<i class="fab  fa-twitter "></i>](https://twitter.com/oaggimenez) [<i class="fab  fa-github "></i>](https://github.com/oliviergimenez) | Imaginecology conference [<i class="fas  fa-home "></i>](https://imaginecology.sciencesconf.org/)]

.footnote[
<i class="fas  fa-camera "></i> Alain Laurent & David Hackel]

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## Predator-prey interactions

.footnote[
<i class="fas  fa-camera "></i>[Sarah Skinner](https://www.comedywildlifephoto.com/gallery/finalists/2019_finalists.php)]

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<li>Coll. A. Chaine, M. Kervellec, V. Mielle, [OFB](https://ofb.gouv.fr/) and Ain/Jura hunting associations
<li>How do environmental factors affect lynx and its preys ?

.footnote[
<i class="fas  fa-camera "></i> [Peter Bucks](https://twitter.com/peterbucks)]

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## Camera traps

.footnote[
<i class="fas  fa-camera "></i> [Tiard Schulz](https://tiard-schulz-fotografie.jimdosite.com/)]

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* Non-invasive monitoring

* Gigas of pix to tag by hand

* Deep learning?

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.footnote[
Source: [Andrew Ng](https://en.wikipedia.org/wiki/Andrew_Ng)]

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## <https://ecostat.gitlab.io/imaginecology/>

#### Kuddos to [Vincent Miele](https://lbbe.univ-lyon1.fr/-Miele-Vincent-.html) and [Gaspard Dussert](https://www.linkedin.com/in/gaspard-dussert/?originalSubdomain=fr) !

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.footnote[
<i class="fas  fa-camera "></i> [Sylvain Gatti](https://www.linkedin.com/in/sylvaingatti/?locale=fr_FR)]

I used the how-to guide on [detection of animals on camera trap images](https://gitlab.com/ecostat/imaginecology/-/tree/master/projects/cameraTrapDetectionWithRetinanet/)

[RetinaNet](https://arxiv.org/pdf/1708.02002.pdf) for detecting and classifying

Check out [my workflow](https://github.com/oliviergimenez/DLcamtrap)

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## Results?

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## Transfer learning on a site (Jura)

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## Automatic tagging in another site (Ain)

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      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">species</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1">trueP</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1">falseP</th>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">badgers</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">535</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">123</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">41</td>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">chamois</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">70</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">456</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">2</td>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">wild cat</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">95</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">45</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">25</td>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">roe deer</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">872</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">65</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">229</td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">hare</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">0</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">129</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">0</td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">lynx</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">193</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">7</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">10</td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">fox</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">786</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">54</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">136</td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">wild boar</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">579</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">170</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">64</td>
    </tr>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">deer</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">3</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">68</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">21</td>
    </tr>
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      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">species</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1">trueP</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1">falseP</th>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">badgers</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">535</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">123</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">41</td>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #4BD9A0; font-weight: bold;">chamois</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #4BD9A0; font-weight: bold;">70</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #4BD9A0; font-weight: bold;">456</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #4BD9A0; font-weight: bold;">2</td>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">wild cat</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">95</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">45</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">25</td>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #4BD9A0; font-weight: bold;">roe deer</td>
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      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #4BD9A0; font-weight: bold;">65</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #4BD9A0; font-weight: bold;">229</td>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">hare</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">0</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">129</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">0</td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #4BD9A0; font-weight: bold;">lynx</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #4BD9A0; font-weight: bold;">193</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #4BD9A0; font-weight: bold;">7</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #4BD9A0; font-weight: bold;">10</td>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">fox</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">786</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">54</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">136</td>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">wild boar</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">579</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">170</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">64</td>
    </tr>
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      <td class="gt_row gt_left" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">deer</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">3</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">68</td>
      <td class="gt_row gt_center" style="border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: white; background-color: #F97B64; font-weight: bold;">21</td>
    </tr>
  </tbody>
  
  
</table></div>

---
class: center, middle
background-image: url(https://media.giphy.com/media/j4rPM934CLIvC/giphy.gif)
background-size: cover

---
class: inverse, center, middle
background-image: url(https://www.tennislegend.fr/gif/zzS0DOD26.gif)
background-size: contain

---
class: left, top
background-image: url(https://media.giphy.com/media/3o7btPCcdNniyf0ArS/giphy.gif)
background-size: cover

### Generalisation to another site is challenging

### Lack of diversity in training dataset

### Pool both sites, and redo

---
class: inverse, center, middle
# Lessons learned

---

.pull-left[

### Terminology is tricky

]

.pull-right[
]

---

.pull-left[

### Terminology is tricky

* [imaginecology](https://ecostat.gitlab.io/imaginecology/basics.html) glossary

]

.pull-right[
![](img/glossary.png)
]

---

.pull-left[

### Terminology is tricky

* [imaginecology](https://ecostat.gitlab.io/imaginecology/basics.html) glossary

* [Statistical view](https://www.stat.colostate.edu/~jah/talks_public_html/isec2020/index.html) by Jennifer Hoeting

]

.pull-right[<br><br><br><br><br>
![](img/hoeting.png)
]

---

.pull-left[

### Terminology is tricky

* [imaginecology](https://ecostat.gitlab.io/imaginecology/basics.html) glossary

* [Statistical view](https://www.stat.colostate.edu/~jah/talks_public_html/isec2020/index.html) by Jennifer Hoeting

### What about

]

.pull-right[
]

---

.pull-left[

### Terminology is tricky

* [imaginecology](https://ecostat.gitlab.io/imaginecology/basics.html) glossary

* [Statistical view](https://www.stat.colostate.edu/~jah/talks_public_html/isec2020/index.html) by Jennifer Hoeting

### What about

* Reproducibility?

]

.pull-right[<br><br><br><br><br><br><br><br><br><br><br>
![](img/reproducibility-graphic-online1.jpeg)
]

---

.pull-left[

### Terminology is tricky

* [imaginecology](https://ecostat.gitlab.io/imaginecology/basics.html) glossary

* [Statistical view](https://www.stat.colostate.edu/~jah/talks_public_html/isec2020/index.html) by Jennifer Hoeting

### What about

* Reproducibility?

* Legal and ethical issues?

]

.pull-right[<br><br><br><br><br><br><br><br><br><br><br><br>
![](img/ethics.png)
]

---

.pull-left[

### Terminology is tricky

* [imaginecology](https://ecostat.gitlab.io/imaginecology/basics.html) glossary

* [Statistical view](https://www.stat.colostate.edu/~jah/talks_public_html/isec2020/index.html) by Jennifer Hoeting

### What about

* Reproducibility?

* Legal and ethical issues?

* Carbon footprint?

]

.pull-right[<br><br><br><br><br><br><br><br><br><br><br><br>
![](https://wp.technologyreview.com/wp-content/uploads/2019/06/datacentercolored-10.jpg?fit=1708,1138)
]

---

.pull-left[

### Terminology is tricky

* [imaginecology](https://ecostat.gitlab.io/imaginecology/basics.html) glossary

* [Statistical view](https://www.stat.colostate.edu/~jah/talks_public_html/isec2020/index.html) by Jennifer Hoeting

### What about

* Reproducibility?

* Legal and ethical issues?

* Carbon footprint?

### Ask the experts

]

.pull-right[
]

---

.pull-left[

### Terminology is tricky

* [imaginecology](https://ecostat.gitlab.io/imaginecology/basics.html) glossary

* [Statistical view](https://www.stat.colostate.edu/~jah/talks_public_html/isec2020/index.html) by Jennifer Hoeting

### What about

* Reproducibility?

* Legal and ethical issues?

* Carbon footprint?

### Ask the experts

* [iWildCam](https://www.kaggle.com/c/iwildcam-2020-fgvc7/overview) competition

]

.pull-right[<br><br><br><br><br><br><br><br><br><br><br><br>
![](img/iwildcam.png)
]

---

.pull-left[

### Terminology is tricky

* [imaginecology](https://ecostat.gitlab.io/imaginecology/basics.html) glossary

* [Statistical view](https://www.stat.colostate.edu/~jah/talks_public_html/isec2020/index.html) by Jennifer Hoeting

### What about

* Reproducibility?

* Legal and ethical issues?

* Carbon footprint?

### Ask the experts

* [iWildCam](https://www.kaggle.com/c/iwildcam-2020-fgvc7/overview) competition

* Follow [S. Beery](https://twitter.com/sarameghanbeery) and [M. Tabak](https://twitter.com/Mikey_QSC)

]

.pull-right[![](img/tweet.png)]

---

.pull-left[

### Terminology is tricky

* [imaginecology](https://ecostat.gitlab.io/imaginecology/basics.html) glossary

* [Statistical view](https://www.stat.colostate.edu/~jah/talks_public_html/isec2020/index.html) by Jennifer Hoeting

### What about

* Reproducibility?

* Legal and ethical issues?

* Carbon footprint?

### Ask the experts

* [iWildCam](https://www.kaggle.com/c/iwildcam-2020-fgvc7/overview) competition

* Follow [S. Beery](https://twitter.com/sarameghanbeery) and [M. Tabak](https://twitter.com/Mikey_QSC)

]

.pull-right[
<blockquote class="twitter-tweet" align="right" data-width="360" data-lang="en" data-dnt="true" data-theme="light"><p lang="en" dir="ltr">😇🐍 I am learning <a href="https://twitter.com/hashtag/Python?src=hash&ref_src=twsrc%5Etfw">#Python</a> & for the <a href="https://twitter.com/hashtag/rstats?src=hash&ref_src=twsrc%5Etfw">#rstats</a> user I am, these are 💯👌<br>👉Python for R programmers <a href="https://t.co/OHSNrj9FCm">https://t.co/OHSNrj9FCm</a> <a href="https://twitter.com/kaneplusplus?ref_src=twsrc%5Etfw">@kaneplusplus</a><br>👉Learn R & Python in Parallel <a href="https://t.co/w2iN45ljpE">https://t.co/w2iN45ljpE</a> Nailong Zhang HT <a href="https://twitter.com/rushworth_a?ref_src=twsrc%5Etfw">@rushworth_a</a><a href="https://twitter.com/hashtag/MachineLearning?src=hash&ref_src=twsrc%5Etfw">#MachineLearning</a> <a href="https://twitter.com/hashtag/DeepLearning?src=hash&ref_src=twsrc%5Etfw">#DeepLearning</a> <a href="https://twitter.com/hashtag/DataScience?src=hash&ref_src=twsrc%5Etfw">#DataScience</a> <a href="https://twitter.com/hashtag/CodeNewbie?src=hash&ref_src=twsrc%5Etfw">#CodeNewbie</a> <a href="https://t.co/6q287Kc8pP">pic.twitter.com/6q287Kc8pP</a></p>— Olivier Gimenez 🖖 (@oaggimenez) <a href="https://twitter.com/oaggimenez/status/1325079735500759042?ref_src=twsrc%5Etfw">November 7, 2020</a></blockquote>

]

---
class: center, bottom
background-image: url(img/predictions.jpg)
background-size: cover

.footnote[
Thank you!
]

---
class: right, top
background-image: url(img/the_conversation.png)
background-size: cover 
#### <https://bit.ly/3ezfaIy>