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Include more on sparsity and scalability (#1092)
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Marius1311 committed Jul 19, 2023
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Expand Up @@ -6,7 +6,7 @@ If you find CellRank useful for your research, please check out :doc:`citing Cel

Design principles
-----------------
Our framework is based on three key principles: `Robustness`_, `Modularity`_ and `Sparsity`_.
Our framework is based on three key principles: `Robustness`_, `Modularity`_ and `Scalability`_.

Robustness
~~~~~~~~~~
Expand Down Expand Up @@ -50,10 +50,12 @@ arrange cells in a :func:`circular embedding <cellrank.pl.circular_projection>`
:func:`cascades of gene activation <cellrank.pl.heatmap>` along a trajectory, and
:func:`cluster expression trends <cellrank.pl.cluster_trends>`. See our :doc:`tutorials <../notebooks/tutorials/index>` to learn more.

Sparsity
Scalability
~~~~~~~~
All CellRank kernels yield sparse transition matrices :math:`T`. Further, the :class:`cellrank.estimators.GPCCA`
estimator exploits sparsity in all major computations. Sparsity allows CellRank to scale to large datasets.
estimator exploits sparsity in all major computations. Sparsity allows CellRank to scale to millions of cells.

For example, when computing :meth:`fate probabilities <cellrank.estimators.GPCCA.compute_fate_probabilities>`, we transform the matrix inversion problem into a set of linear systems, which we solve in parallel using the sparsity-optimized `GMRES`_ algorithm, implemented efficiently in `PETSc`_. We use similar tricks to infer macrostates of cellular dyanmics via sparsity-optimized partial real Schur decompositions (implemented under the hood via `pyGPCCA`_ and `SLEPc`_).

Why is it called "CellRank"?
----------------------------
Expand All @@ -64,3 +66,6 @@ website relevance).

.. _PageRank: https://en.wikipedia.org/wiki/PageRank
.. _pyGPCCA: https://github.com/msmdev/pyGPCCA
.. _GMRES: https://en.wikipedia.org/wiki/Generalized_minimal_residual_method
.. _PETSc: https://petsc.org/release/
.. _SLEPc: https://slepc.upv.es/

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