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<!DOCTYPE html>
<html>
<head>
<title>NeuroNex+Stanford</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
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</head>
<body>
<textarea id="source">
class: left,
name:opening
# NeuroData
Joshua T. Vogelstein & Vikram Chandrashekhar
<br><br><br><br><br><br><br><br>
<img src="images/funding/jhu_bme_blue.png" STYLE="HEIGHT:95px;"/>
<img src="images/funding/KAVLI.png" STYLE="HEIGHT:95px;"/>
.foot[[[email protected]](mailto:jovo at jhu dot edu)
| <http://neurodata.io/talks/neuronex-stanford.html>]
---
class: center
### <center>What is NeuroData?</center>
<img src="images/neurodata_venn.png" STYLE="width:50%;"/>
### <center>Goal: Build tools that work on .r[your] data</center>
---
### Why is it hard?
- classical statistic theory .r[requires]:
- p dimensions is smaller than n samples
- your data has .r[p >> n]
- recent statistical theory for p >> n,
- but with .r[inaccurate assumptions] for your data
- those methods work poorly on your data
- we develop methods that:
- statistically valid
- computationally efficient
- for your data
---
### Some Examples
1. Hypothesis Testing
2. Dimensionality Reduction
3. Classification
3. Connectome Coding
4. CLARITY & COLM
For 1-3, we have strong theory that I can discuss ad nauseam
---
### Hypothesis Testing
##### Case A: Test whether X is independent of Y
X is CLARITY brain, and Y is condition (eg, control vs. addicted)
--
##### Case B: Test whether population A is the same as population B
Pop A are control CLARITY brains, Pop B are addicted CLARITY brains.
<br>
(this is akin to, and a generalization of, a t-test)
--
#### Main Idea
.r[MGC]: Compare "correlations" between all .r[local] pairs of points
--
<br>
ps - like Marr-Albus Sparse Expansion Theory
--
<br>
pps - can be used for "CCA", eg, behavior vs neural activity
---
### MGC Empirically Dominates
<img src="images/FigHDPower.png" style="width: 100%;"/>
---
### Dimensionality Reduction
Given pairs of high-dimensional X and corresponding class labels Y, find the best low-dimensional representation of X
--
#### Main Idea
.r[LOL]: Use the means and PCA of .r[each class separately]
---
### LOL Empirically Dominates
<img src="images/LOL_real_data.png" style="width: 80%;"/>
---
### Classification
Given pairs of high-dimensional X and corresponding class labels Y, find the best discriminant boundary
--
#### Main Idea
.r[RerF]: Find many good .r[sparse] projections of data
---
### RerF Empirically Dominates
.pull-left[
- random forests (RF) were best
- recent extensions improve
- we are even better
]
.pull-right[
<img src="images/error_histogram_benchmarks.png" style="width: 70%;"/>
]
---
### Connectome Coding
<img src="images/connectome-coding.png" style="width: 100%;"/>
Characterizing the relationship between
the *past environment* and the *present neural connectivity*
--
<br>
(could be relevant for Callaway and Justus stuff?)
---
### CLARITY / COLM
Build comprehensive ecosystem CLARITY/COLM data, including
- storage & management
- visualization
- registration to atlas and one another
- cell detection & counting
- tractography
---
### Storage & Management
<img src="images/nd_pipeline.png" style="width: 100%;"/>
infinitely scalable in cloud
---
### Visualization
.pull-left[
- Google's NeuroGlancer'
- 3D pan, zoom, & rotate
- Multi-channel overlays
- Select individual ROIs
- 30 minutes to load once
]
.pull-right[
<img src="images/ndviz2.jpg" style="width: 120%;"/>
]
---
### Registration
<br>
<img src="images/ndreg.png" style="width: 100%;"/>
- only ~1 hr per brain
- fully automatic (no landmarks)
- works on iDisco and other species too
---
### Cell Detection
<br>
<img src="images/bloby.png" style="width: 100%;"/>
---
### Cell Detection Analysis
<img src="images/regioncounts2.png"/>
---
### Tractography
<br>
<img src="images/ndtract.png" style="width: 100%;"/>
---
class: middle
# <center>[demo](https://tinyurl.com/yco8h787)</center>
---
class: top, left
### Acknowledgements
<div class="container">
<img src="faces/cep.png"/>
<div class="centered">Carey Priebe</div>
</div>
<div class="container">
<img src="faces/randal.jpg"/>
<div class="centered">Randal Burns</div>
</div>
<div class="container">
<img src="faces/mim.jpg"/>
<div class="centered">Michael Miller</div>
</div>
<div class="container">
<img src="faces/bcaffo.jpg"/>
<div class="centered">Brian Caffo</div>
</div>
<div class="container">
<img src="faces/milham.jpg"/>
<div class="centered">Michael Milham</div>
</div>
<div class="container">
<img src="faces/dtward.jpg"/>
<div class="centered">Daniel Tward</div>
</div>
<div class="container">
<img src="faces/minh.jpg"/>
<div class="centered">Minh Tang</div>
</div>
<div class="container">
<img src="faces/avanti.jpg"/>
<div class="centered">Avanti Athreya</div>
</div>
<div class="container">
<img src="faces/vince.jpg"/>
<div class="centered">Vince Lyzinski</div>
</div>
<div class="container">
<img src="faces/dpmcsuss.jpg"/>
<div class="centered">Daniel Sussman</div>
</div>
<div class="container">
<img src="faces/yichen.jpg"/>
<div class="centered">Yichen Qin</div>
</div>
<div class="container">
<img src="faces/youngser.jpg"/>
<div class="centered">Youngser Park</div>
</div>
<div class="container">
<img src="faces/cshen.jpg"/>
<div class="centered">Cencheng Shen</div>
</div>
<div class="container">
<img src="faces/shangsi.jpg"/>
<div class="centered">Shangsi Wang</div>
</div>
<div class="container">
<img src="faces/gkiar.jpg"/>
<div class="centered">Greg Kiar</div>
</div>
<div class="container">
<img src="faces/ebridge.jpg"/>
<div class="centered">Eric Bridgeford</div>
</div>
<div class="container">
<img src="faces/vikram.jpg"/>
<div class="centered">Vikram Chandrashekhar</div>
</div>
<div class="container">
<img src="faces/tyler.jpg"/>
<div class="centered">Tyler Tomita</div>
</div>
<div class="container">
<img src="faces/james.jpg"/>
<div class="centered">James Brown</div>
</div>
<div class="container">
<img src="faces/disa.jpg"/>
<div class="centered">Disa Mhembere</div>
</div>
<div class="container">
<img src="faces/drishti.jpg"/>
<div class="centered">Drishti Mannan</div>
</div>
<div class="container">
<img src="faces/jesse.jpg"/>
<div class="centered">Jesse Patsolic</div>
</div>
<div class="container">
<img src="faces/falk_ben.jpg"/>
<div class="centered">Benjamin Falk</div>
</div>
<div class="container">
<img src="faces/kwame.jpg"/>
<div class="centered">Kwame Kutten</div>
</div>
<div class="container">
<img src="faces/perlman.jpg"/>
<div class="centered">Eric Perlman</div>
</div>
<img src="images/funding/nsf_fpo.png" STYLE="HEIGHT:95px;"/>
<img src="images/funding/nih_fpo.png" STYLE="HEIGHT:95px;"/>
<img src="images/funding/darpa_fpo.png" STYLE=" HEIGHT:95px;"/>
<img src="images/funding/iarpa_fpo.jpg" STYLE="HEIGHT:95px;"/>
<img src="images/funding/KAVLI.jpg" STYLE="HEIGHT:95px;"/>
<img src="images/funding/schmidt.jpg" STYLE="HEIGHT:95px;"/>
---
### Questions? Now hiring!
.pull-left[
| task | link |
| --- | --- |
| testing | [MGC](https://github.com/neurodata/mgc) |
| dim red | [LOL](https://github.com/neurodata/LOL) |
| classify | [RerF](https://github.com/neurodata/R-RerF/) |
| conn code | [GraphStats](https://github.com/neurodata/graphstats/)
| CLARITY | [COBALT](https://github.com/neurodata/COBALT) |
| email | [[email protected]](mailto:[email protected]) |
| web | [neurodata.io](http://neurodata.io/) |
| startup | [gigantum.com](http://gigantum.com/) |
<span style="font-size:200%; color:red;">♥, 🦁, 👪, 🌎, 🌌</span>
]
<br>
<img src="images/liono.JPG" STYLE="position:absolute; TOP:110px; LEFT:480px; HEIGHT:500px;"/>
<!-- background-image: url("images/OCPaper.png")
background-size: contain;
-->
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