Daniel Haehn PRO
Hi, I am a biomedical imaging and visualization researcher who investigates how computational methods can accelerate biological and medical research.
KIWI Biolab Talk 2023
Visual Computing for Biomedical Applications
MACHINE
PSYCHOLOGY
DANIELHAEHN.COM
I joined UMass Boston in 2019
right after my PhD
Biomedical Imaging
Chart Question Answering
Loraine Franke
Kristin (Yanan) Qi
Mahsa Geshvadi
Jenna Kim
Ryan Zurrin
Kunal Jain
Josh Kotler
Kiran Sandilya Balivada
MACHINE
PSYCHOLOGY
4x PhD Students
2x MS, 2x UGrad Students
We
Computers
GONZO
MONSTER
VAMPIRE
ZOMBIE
GARGOYLE
2x NVIDIA DGX A100
Thank you!
Biomedical Imaging
Chart Question Answering
The Oregon-Massachusetts Mammography Database
OMAMA-DB
Daniel Haehn
Nurit Haspel
Marc Pomplun
Dan Simovici
Bill Lotter
Greg Sorensen
Ryan Zurrin
Pablo Bendiksen
Neha Goyal
Kendrick Khaev
Muskaan Manocha
Jeff Dusenberry
World's Largest Mammography Dataset
publicly available!
with labels!
World's Largest Mammography Dataset
we started with ~1 million images!
2000 x 2000 pixels
100 x 2000 x 2000 voxels
~8 MB
~500 MB
~8 TB
Intelligent Annotation Framework
Two Artificial Neural Networks..
..work together for Quality control
Discriminator finds error pattern of Classifier
Augmented Intelligence
Human + AI
import omama as O
pred = O.DeepSight.run(imgs)
+
=
Drained nodes...
...but it worked in the end!
Browser
Editor
Jupyter Notebook
SSHFS mounted Home Folder
TMUX on head node
SSH Tunnels (hop via head node to compute node)
Real-time Visualization for TMS
Transcranial Magnetic Stimulation
Non-invasive Mental Health Treatment
National Institutes of Health
Lipeng Ning
Steve Pieper
Loraine Franke
Jax Luo
Steve Pieper
Yogesh Rathi
Daniel Haehn
Tae Young Park
Real-time Visualization for TMS
open medical imaging platform
Real-time Visualization for TMS
Real-time Visualization for TMS
with tractography
Real-time Visualization for TMS
HTTPS, WSS, Gyro + 3D Slicer
JavaScript Face Tracking
Real-time Visualization for TMS
CACTAS: Carotid Artery Calcification Computed Tomographic Angiography Scoring
endarterectomy vs. stent
Daniel Haehn
Jae Song
Jenna Kim
CACTAS: Carotid Artery Calcification Computed Tomographic Angiography Scoring
Automatic Plaque Annotations
Single-click Interaction
We need massive manual annotations!
CACTAS-Tool
not surprising: much faster!
similar accuracy!
open medical imaging platform
CACTAS-Tool
vs
CACTAS: Carotid Artery Calcification Computed Tomographic Angiography Scoring
endarterectomy vs. stent
Fly Retina Project
Jens Rister
Barry Stein
Daniel Haehn
Kunal Jain
Looking at the color-sensing photoreceptors
using an Electron Microscope
Kiran Balivada
Jeff Dusenberry
Visualization with Neuroglancer
6144 x 4096 x 862 voxels
10 x 10 x 40 nm^3
How to transfer large datasets across institutions?
260+ GB
curl 'https://eastus1-mediap.svc.ms/transform/zip?cs=fFNQTw' \
-H 'authority: eastus1-mediap.svc.ms' \
-H 'accept: text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.9' \
-H 'accept-language: en-US,en;q=0.9,de;q=0.8' \
-H 'cache-control: max-age=0' \
-H 'content-type: application/x-www-form-urlencoded' \
-H 'origin: https://liveumb-my.sharepoint.com' \
-H 'sec-ch-ua: "Chromium";v="104", " Not A;Brand";v="99", "Google Chrome";v="104"' \
-H 'sec-ch-ua-mobile: ?0' \
-H 'sec-ch-ua-platform: "Linux"' \
-H 'sec-fetch-dest: iframe' \
-H 'sec-fetch-mode: navigate' \
-H 'sec-fetch-site: cross-site' \
-H 'upgrade-insecure-requests: 1' \
-H 'user-agent: Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/104.0.0.0 Safari/537.36' \
--data-raw 'zipFileName=VSDataTileSet2.zip&guid=00c22792-c697-4def-b45e-ec0560018fe4&provider=spo&files=%7B%22items%22%3A%5B%7B%22name%22%3A%22VSDataTileSet2%22%2C%22size%22%3A0%2C%22docId%22%3A%22https%3A%2F%2Fliveumb-my.sharepoint.com%3A443%2F_api%2Fv2.0%2Fdrives%2Fb%21ZHO7Y3eH0EOqfeg_5VdUmSUuEmzqastElTPzN9v8GRKXPTMoP_jwQ44q0Km6lnis%2Fitems%2F01OSC7C5I2RBH7FQHPWFCY7B2FKLTC2YFF%3Fversion%3DPublished%26access_token%3DeyJ0eXAiOiJKV1QiLCJhbGciOiJub25lIn0.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.bTFzRnRSV3RaNE5MU2l2bUI3d3dOdW9tUm5yNmRJUTh3WUQvWUsybjhPaz0%22%2C%22isFolder%22%3Atrue%7D%5D%7D&oAuthToken=' \
--compressed
20 GB Transfer limit
Jeff Dusenberry
Director of Research Computing
at UMass Boston
SFTP
no shell access
work in progress!
automatic segmentation
Biomedical Imaging
Chart Question Answering
Analysis of images and text in visualizations
Computer Vision + Natural Language Processing
Chart Question Answering
Analysis of images and text in visualizations
complex!
identification
estimation
relation
of visual marks to extract information
computational methods might ideally mimic human chart perception
Daniel Haehn
Steve Franconeri
Jessica Hullmann
Narges Mahyar
Niko Kriegeskorte
Hanspeter Pfister
1984
IEEE Vis 2018
Machine Graphical Perception
77°
0.856
[0.2, 0.14, 0.6, 0.8]
2500+ networks
Instance-based Compositional Relation Networks for Machine Graphical Perception
+ Transformers
Yunhai Wang
Mahsa Geshvadi
Daniel Haehn
Culture Change in Computer Science and Engineering at the University of Massachusetts Public University System: A Partnership Between UMass Boston and Amherst
Buju Dasgupta
Shannon C. Roberts
Neena Thota
MACHINE
PSYCHOLOGY
DANIELHAEHN.COM
Thank you!
KIWI Biolab 2023
By Daniel Haehn
KIWI Biolab 2023
Machine Psychology at UMass Boston. See https://mpsych.org!
