This page houses links to papers, research ideas and more. The main goal of this page is to be the gateway to knowledge used to build the end-product of the thesis. The “Paper Database” houses useful information such as the state of the paper (i.e. read/summarized/etc, link to the original paper and properties describing the content of the paper). This allows for easier filtering later on.
Paper Database
Paper
Status
Usefulness
Link
Properties
Notes
Evaluated
⭐⭐⭐
image-processing
alignment
gaussian processes
spatial transcriptomics
Evaluated
⭐⭐
machine-learning
image-processing
alignment
Focuses too much on the assumption that data is available and in an image-ready format (i.e. MRI)
optimal transport
machine-learning
Evaluated
⭐⭐⭐
image-processing
alignment
spatial transcriptomics
⚠️ Requires manual estimation of overlap percentage!
Evaluated
⭐⭐⭐
alignment
spatial transcriptomics
machine-learning
Evaluated
⭐⭐⭐
image-processing
alignment
spatial transcriptomics
Evaluated
⭐⭐⭐
image-processing
alignment
spatial transcriptomics
In progress
⭐
optimal transport
transformer
machine-learning
In progress
dimension-reduction
embedding
spatial transcriptomics
They claim to be very fast due to their closed-form solution, but in reality this method takes quite long…
Links to Papers
Diffeomorphic Image Registration with Neural Velocity Field
Learning single-cell perturbation responses using neural optimal transport
Partial alignment of multislice spatially resolved transcriptomics data (PASTE2)
Wasserstein Wormhole: Scalable Optimal Transport Distance with Transformers
