Kavli

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# NeuroData (Science)

Joshua T. Vogelstein

.foot[[jovo@jhu.edu](mailto:jovo@jhu.edu) | <http://neurodata.io/talks/> | [@neuro_data](https://twitter.com/neuro_data)]

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### What is Neural Data Science?

A field that develops and applies  statistical models, algorithms, and (database / machine learning) systems  to 
- manage
- visualize 
- wrangle
- summarize 
- generalize 
- control

neural data.

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### Why is it hard?

1. volume: terabytes
2. variety: multi-modal (images, atlases, annotations, networks)
4. veracity: noisy

Subject matter expertise is required to mitigate these challenges, including
- computer science
- statistical machine learning 
- brain science

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### NeuroData Approach

1. build computational tools for manage & visualize
2. build statistical tools wrangle, summarize, and control
3. apply them to answer hard & important questions!

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### Manage

Data management systems enable users to create, read, edit, and delete "records"

- stores multiple modalities (e.g., images & annotations) 
- scales to terabytes
- atlases
- annotations
- networks

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#### Example: NeuroData Cloud

- 200+ teravoxels
- 100+ public & private datasets
- 30+ collaborators 
- All 3D+ data & annotations (no ephys, etc.)
- Largest public open neuroscience data repository in the world!

.footnote[https://neurodata.io/ndcloud/]

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### Visualize

Data visualization systems generate maps, charts, and tables to highlight/illustrate insightful perspectives on the data.

- pan
- zoom
- overlay multiple channels
- overlay annotations
- manually annotate

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#### Example: NeuroGlancer

.footnote[https://github.com/neurodata/neuroglancer]

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### Wrangle

Data wrangling consists of any operation one applies to the data that maintains its representation, such as outlier detection, missing value imputation, and deconvolution

- bias field correction
- motion correction
- nonlinear multi-modal registration

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#### Example: COBALT

- Large deformation diffeomorphic metric mapping (LDDMM)
- Fully automatic (no landmarks)
- Modalities: iDisco, CLARITY, MRI, histology, etc.,
- Species: human, rat, mouse, zebrafish...

.footnote[https://neurodata.io/ndreg/]

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### Summarize

Data summaries include point estimates, confidence intervals, clusters, principle components analysis, etc.

- network estimation from MRI
- spike detection from calcium imaging 
- synapse detection
- cell body detection from CLARITY images

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#### Example: COBALT

.footnote[https://neurodata.io/ndreg]

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### Generalize

Infer properties of a "population" (typically very high-dimensional)

- hypothesis testing
- modeling 
- simulation

---

---

.footnote[https://neurodata.io/mgc]

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### Predict

Prediction the something about a future sample given a data corpus

- classify: X is of type A
- regress: given X, Y is expected to be 6
- forecast: X is expected to be 6 tomorrow

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### Example: RerF

- generalization of random forests 
- significantly improve over best machine learning algs on >100 benchmark problems

.footnote[https://neurodata.io/rerf/]

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class: middle

## .center[Applications in Connectomics]

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### Human Connectome Heritability

.footnote[https://neurodata.io/graspy]
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### Modeling Drosophila Mushroom Body

.footnote[https://neurodata.io/graspy]

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class: inverse

### Batch Effects in  Connectomics

- 20 datasets, >3000 scans

.footnote[https://neurodata.io/ndmg]

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class: inverse

### Batch Effects in  Connectomics

- 20 datasets, >3000 scans
- sex effect is smaller than site effect

.footnote[https://neurodata.io/ndmg]

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### Papers

1. Vogelstein et al. *Nature Methods* (2018) [[manage & viz]](https://rdcu.be/banSS)
2. Kutten et al. *MICCAI* (2018) [[wrangle]](https://link.springer.com/chapter/10.1007%2F978-3-319-66182-7_32)
3. Vogelstein et al. *eLife* (2019) [[generalize]](https://elifesciences.org/articles/41690)
4. Tomita et al. *arXiv* (2015) [[predict]](https://arxiv.org/abs/1506.03410)
5. Athreya et al. *JMLR* (2018) [[graphs]](http://jmlr.org/papers/v18/17-448.html)
6. Kiar et al. *bioRxiv* (2018) [[MRI]](https://www.biorxiv.org/content/10.1101/188706v6)

.pull-left[
##### Tools

- [ndcloud](https://neurodata.io/ndcloud)
- [COBALT](https://neurodata.io/ndreg)
- [MGC](https://neurodata.io/mgc)
- [RerF](https://neurodata.io/rerf)
- [GrasPy](https://neurodata.io/graspy)
- [ndmg](https://neurodata.io/ndmg)
]

.pull-right[
##### Collaborations
- JHU Neuro, CS, AMS, 
- JHSPH Biostats
- Stanford (dlab)
- Child Mind Institute
- Allen Institute
- Janelia Research Campus 
- Applied Physics Lab
- Google 
]

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### Acknowledgements

<div class="small-container">
  <img src="faces/cep.png"/>
  <div class="centered">Carey Priebe</div>
</div>

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  <img src="faces/randal.jpg"/>
  <div class="centered">Randal Burns</div>
</div>

<div class="small-container">
  <img src="faces/mim.jpg"/>
  <div class="centered">Michael Miller</div>
</div>

<div class="small-container">
  <img src="faces/dtward.jpg"/>
  <div class="centered">Daniel Tward</div>
</div>

<div class="small-container">
  <img src="faces/ebridge.jpg"/>
  <div class="centered">Eric Bridgeford</div>
</div>

<div class="small-container">
  <img src="faces/vikram.jpg"/>
  <div class="centered">Vikram Chandrashekhar</div>
</div>

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  <img src="faces/drishti.jpg"/>
  <div class="centered">Drishti Mannan</div>
</div>

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  <img src="faces/jesse.jpg"/>
  <div class="centered">Jesse Patsolic</div>
</div>

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  <img src="faces/falk_ben.jpg"/>
  <div class="centered">Benjamin Falk</div>
</div>

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  <img src="faces/kwame.jpg"/>
  <div class="centered">Kwame Kutten</div>
</div>

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  <img src="faces/perlman.jpg"/>
  <div class="centered">Eric Perlman</div>
</div>

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  <img src="faces/loftus.jpg"/>
  <div class="centered">Alex Loftus</div>
</div>

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  <img src="faces/bcaffo.jpg"/>
  <div class="centered">Brian Caffo</div>
</div>

<div class="small-container">
  <img src="faces/avanti.jpg"/>
  <div class="centered">Avanti Athreya</div>
</div>

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  <img src="faces/vince.jpg"/>
  <div class="centered">Vince Lyzinski</div>
</div>

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  <img src="faces/dpmcsuss.jpg"/>
  <div class="centered">Daniel Sussman</div>
</div>

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  <img src="faces/youngser.jpg"/>
  <div class="centered">Youngser Park</div>
</div>

<div class="small-container">
  <img src="faces/cshen.jpg"/>
  <div class="centered">Cencheng Shen</div>
</div>

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  <img src="faces/shangsi.jpg"/>
  <div class="centered">Shangsi Wang</div>
</div>

<div class="small-container">
  <img src="faces/tyler.jpg"/>
  <div class="centered">Tyler Tomita</div>
</div>

<div class="small-container">
  <img src="faces/james.jpg"/>
  <div class="centered">James Brown</div>
</div>

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  <img src="faces/disa.jpg"/>
  <div class="centered">Disa Mhembere</div>
</div>

<div class="small-container">
  <img src="faces/pedigo.jpg"/>
  <div class="centered">Ben Pedigo</div>
</div>

<div class="small-container">
  <img src="faces/jaewon.jpg"/>
  <div class="centered">Jaewon Chung</div>
</div>

<div class="small-container">
  <img src="faces/jeremias.png"/>
  <div class="centered">Jeremias Sulam</div>
</div><span style="font-size:200%; color:red;">♥, 🦁, 👪, 🌎, 🌌</span>

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