Posts Tagged ‘clipcacheondisk’
Growing Up Murdoch – The Atlantic
March 13, 2025Consciousness: The Road to Reductionism | American Scientist
March 3, 2025https://www.americanscientist.org/article/consciousness-the-road-to-reductionism
Consciousness: the road to Reductionism. (2025, February 18). American
Scientist. https://www.americanscientist.org/article/consciousness-the-road-to-reductionism By Alan J. McComas
1803.00567 Computational Optimal Transport
March 1, 2025https://arxiv.org/abs/1803.00567
explains the dual problem well
Peyré, G., & Cuturi, M. (2018, March 1). Computational Optimal transport. arXiv.org. https://arxiv.org/abs/1803.00567
tutorial_on_optimal_transport.pdf
Suffix Array and BWT Explaination
February 11, 2025The book with a nice explanation of suffix array and BWT is
Bioinformatics Algorithms: An Active Learning Approach by Phillip Compeau & Pavel Pevzner. https://www.bioinformaticsalgorithms.org/
Scale-free networks – PubMed
February 3, 2025https://pubmed.ncbi.nlm.nih.gov/12701331/
Barabási, A., & Bonabeau, E. (2003). Scale-Free networks. Scientific American, 288(5), 60–69.
https://doi.org/10.1038/scientificamerican0503-60
Diffusion pseudotime robustly reconstructs lineage branching | Nature Methods
February 3, 2025https://www.nature.com/articles/nmeth.3971
Haghverdi, L., Büttner, M., Wolf, F. A., Buettner, F., & Theis, F. J. (2016). Diffusion pseudotime robustly reconstructs lineage branching. Nature Methods, 13(10), 845–848. https://doi.org/10.1038/nmeth.3971
(first page summarizes the Pseudotime algorithm)
Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data | Nature Protocols
February 3, 2025https://www.nature.com/articles/s41596-020-00409-w
(Single Cell overview; goes over every step)
Andrews, T. S., Kiselev, V. Y., McCarthy, D., & Hemberg, M. (2020). Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data. Nature Protocols, 16(1), 1–9.
https://doi.org/10.1038/s41596-020-00409-w
Fast unfolding of communities in large networks – IOPscience
February 3, 20251803.00567 Computational Optimal Transport
January 18, 2025https://arxiv.org/abs/1803.00567
Peyré, G., & Cuturi, M. (2018, March 1). Computational Optimal transport. arXiv.org. https://arxiv.org/abs/1803.00567
tutorial_on_optimal_transport.pdf
Learning single-cell perturbation responses using neural optimal transport | Nature Methods
January 18, 2025https://www.nature.com/articles/s41592-023-01969-x
Bunne, C., Stark, S. G., Gut, G., Del Castillo, J. S., Levesque, M., Lehmann, K., Pelkmans, L., Krause, A., & Rätsch, G. (2023). Learning single-cell perturbation responses using neural optimal transport. Nature Methods, 20(11), 1759–1768.
https://doi.org/10.1038/s41592-023-01969-x
not so useful for learning OT
linkstream2 microblog 