bootcamp

#### Open Access to the Brain: a Computer "Connectome" Links Brain Images in Fine Detail

Joshua T. Vogelstein 
      
      <img src="images/neurodata_purple.png" style="height:450px; float:right;"/>
      
      
      <br><br><br><br><br><br><br><br><br>
      
      
      
      .footnote[[jovo@jhu.edu](mailto:jovo@jhu.edu) | <http://neurodata.io/> | [@neuro_data](https://twitter.com/neuro_data)]
      
      <br>

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      class: middle, inverse

# .center[Motivation]

---
    
      # .center[Brains are Beautiful]

---

# .center[Brains are Ubiquitous]

.footnote[source: [Ethnic Origins of Beauty](http://www.lesoriginesdelabeaute.com/en/accueil.html)]

---

# .center[Brains are Ubiquitous]

.footnote[source: [Earth BioGenome Project](https://www.ucdavis.edu/news/earth-biogenome-project-aims-sequence-dna-all-complex-life)]

---

# .center[Brains are Awesome]

.footnote[source: [hbo](https://www.hbo.com/westworld/season-2/1-journey-into-night/premiere-reactions-roundup)]

---

# .center[Brains are Expensive]

.footnote[source: [nami](https://nami.org/Learn-More/Mental-Health-By-the-Numbers)]

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# .center[Changing the World]

- Democratize intelligences
      - Understand  intelligences
      - Enhance  intelligences

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      class: middle, inverse

# .center[Approach]

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# .center[Gather the Data]

.pull-left[
      - 20+ labs 
      - 30+ datasets
      - 100+ terabytes
      ]

.pull-left[
      - from nano to macro
      - worm, fly, mouse, primate, human
      - largest and most diverse open repository in brain science
      ]

---

# .center[Manage the Data]

.pull-left[
      - too big for your hard drive
      - too big to open in Preview or Photos
      - too big to visualize online
      ]

.pull-right[
      - too many files to keep track of
      - too expensive to download data
      - big data systems
      ]

.footnote[source: [wikimedia](https://commons.wikimedia.org/wiki/File:High_Performance_Computing_Center_Stuttgart_HLRS_2015_07_Cray_XC40_Hazel_Hen_IO.jpg)]

---

# .center[Process the Data]

.pull-left[
      - convert bits to networks
      - distributed pipelines
      - integrated quality assurance
      ]

.footnote[source: [wired](https://www.wired.com/story/the-matrix-code-sushi-recipe/)]

---

# .center[Model the Data]

.pull-left[
      - statistical models of networks
      - incorporate uncertainty
      - address populations
      ]

.pull-right[
      - develop estimators
      - prove theorems
      ]

---

# .center[Analyze the Data]

.pull-left[
      - 4 different populations
      - dots represent brain regions
      - lines represent connections
      ]

.pull-right[
      - each brain is an average over many people
      - averages look similar to one another
      ]

---

### Differences Between Studies

.pull-left[
      - 20 studies of ~100 individuals each
      - each line is the difference between a pair of studies
      - right to left: small to large differences
      ]

<img src="images/inverse_batch.png"  style="height: 400px;"/>
      
      
      
      
      
      ---
      
      ### Differences Between Sexes

.pull-left[
      - 20 studies of ~100 individuals each
      - each line is the difference between a pair of studies
      - right to left: small to large differences
      ]

.pull-right[
      - sex differences are small
      - could be due to demographics
      - could be due to study artifacts
      ]

<img src="images/inverse_batch_sex.png"  style="height: 400px;"/>

---

# .center[Share the Data]

.pull-left[
      - 1000+ unique visitors / week
      - ~100,000 unique visitors
      ]

.pull-left[
      - 200+ cities
      - 130+ countries 
      - all inhabited continents
      ]

---

# .center[Next Steps]

<br>

- Working with Amazon to provide free storage for everyone 
      - Make software "self-serve" to eliminate the bottleneck of us
      - Require more data to pool together
      - New AI to harmonize data
      - Discover more connections across datasets

---

# .center[Summary]

<br>

- Brains are beautiful
      - Brains are ubiquitous
      - Brains are awesome 
      - Brains are circuits
      - We build big data systems and machine learning algorithms to make sense of them 
      - Everyone can access and benefit from this work

---

# .center[References]

<br>

- Open Connectome Project [[1]](https://doi.org/10.1145/2484838.2484870)
      - A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data [[2]](https://www.nature.com/articles/s41592-018-0181-1)
      - A High-Throughput Pipeline Identifies Robust Connectomes But Troublesome Variability [[3]](https://doi.org/10.1101/188706)
      -  Discovering and Deciphering Relationships Across Disparate Data Modalities [[4]](https://elifesciences.org/articles/41690)

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      ## .center[Acknowledgements]

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        <div class="centered">Carey Priebe</div>
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          <div class="centered">Drishti Mannan</div>
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      </div> <span style="font-size:200%; color:red;">♥, 🦁, 👪, 🌎, 🌌</span> 
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